remap every 100000 values

existing written view

doc/.gitignore

@@ -1,3 +1,5 @@
 /build/
 /doxygen/
 /build_dir.txt
+/.DS_Store
+/.gitignore

doc/Makefile

@@ -57,7 +57,7 @@ html:
 	@echo "Generating Doxygen documentation..."
 	doxygen Doxyfile
 	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) -b html -c ./ $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/conf.py

@@ -36,7 +36,7 @@ extensions = [
     'sphinx.ext.pngmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
-    'breathe',
+#    'breathe',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -51,7 +51,7 @@ source_suffix = '.rst'
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = 'source/index'
 
 # General information about the project.
 project = u'OBITools3'
@@ -292,7 +292,7 @@ texinfo_documents = [
 #texinfo_no_detailmenu = False
 
 #Breathe configuration
-sys.path.append( "../breathe/" )
-breathe_projects = { "OBITools3": "../doxygen/xml/" }
+sys.path.append( "breathe/" )
+breathe_projects = { "OBITools3": "doxygen/xml/" }
 breathe_default_project = "OBITools3"
 

doc/doxygen/xml/.gitignore

@@ -1,4 +0,0 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore

doc/source/DMS.rst

@@ -13,7 +13,7 @@ Up to now, each of these categories of data were stored in separate
 files, and nothing made it mandatory to keep them together.
 
 
-The `Data Management System` (DMS) of OBITools3 can be regarded as a basic 
+The `Data Management System` (DMS) of OBITools3 can be viewed like a basic 
 database system.
 
 
@@ -27,9 +27,7 @@ OBIDMS UML
 
 An OBIDMS directory contains :
   * one `OBIDMS history file <#obidms-history-files>`_
-  * Two different kinds of directories :
-     * OBIDMS column directories
-     * OBIDMS column group directories containing OBIDMS column directories
+  * OBIDMS column directories
 
 
 OBIDMS column directories
@@ -39,16 +37,9 @@ OBIDMS column directories contain :
     * all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
     * one `OBIDMS version file <#obidms-version-files>`_
 
-The directory name is the column attribute, or sub-attribute if the column directory is in a column group directory.
+The directory name is the column attribute with the extension ``.obicol``.
 
-
-OBIDMS column group directories
-===============================
-
-OBIDMS column group directories contain OBIDMS column directories. They are used to store dictionary-like data, where 
-each key corresponds to an OBIDMS column.
-
-The directory name is the dictionary attribute. Each key is considered a sub-attribute and is associated to its column.
+Example: ``count.obicol``
 
 
 OBIDMS column files
@@ -57,7 +48,7 @@ OBIDMS column files
 Each OBIDMS column file contains :
 	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
 	  on most systems) containing metadata
-	* one column of data with the same `OBIType <types.html#obitypes>`_
+	* Lines of data with the same `OBIType <types.html#obitypes>`_
 
 
 Header
@@ -79,7 +70,14 @@ The header of an OBIDMS column contains :
 Data
 ----
 
-A column of data with the same `OBIType <types.html#obitypes>`_.
+A line of data corresponds to a vector of elements. Each element is associated with an element name. 
+Elements names are stored in the header. The correspondance between an element and its name is done 
+using their order in the lists of elements and elements names.  This structure allows the storage of 
+dictionary-like data.
+
+Example: In the header, the attribute ``elements_names`` will be associated with the value ``"sample_1;
+sample_2;sample_3"``, and a line of data with the type ``OBInt_t`` will be stored as an ``OBInt_t`` vector 
+of size three e.g. ``5|8|4``.
 
 
 Mandatory columns
@@ -158,3 +156,5 @@ operations ever done in the OBIDMS directory and the views in between them :
 .. image:: ./images/history.png
     :width: 150 px
     :align: center
+
+

doc/source/data.rst

@@ -2,8 +2,8 @@
 Data in OBITools3
 #################
 
-The OBITools3 inaugure a new way to manage DNA metabarcoding data. 
-They rely on a `Data management System` (DMS) that can be considered as
+The OBITools3 introduce a new way to manage DNA metabarcoding data. 
+They rely on a `Data management System` (DMS) that can be viewed like 
 a simplified database system.
 
 

doc/source/guidelines.rst

@@ -70,7 +70,7 @@ Tickets should always be labeled with the branches for which they are relevant.
 Documentation
 *************
 
-C functions are documented in the header files.
+C functions are documented in the header files for public functions, and in the source file for private functions.
 
 
 **************
@@ -92,7 +92,7 @@ C99 :
 	* Object layer
 	* OBITools3 library
 
-`Python 3 <https://www.python.org/>`_ :
+`Python 3.5 <https://www.python.org/>`_ :
 	* Top layer code (scripts)	
 	
 For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original 
@@ -111,6 +111,8 @@ Enum members, macros, constants:                ``ALL_CAPS``
 
 Functions, local variables:                     ``lower_case``
 
+Public functions:                               ``obi_lower_case``
+
 Functions that shouldn't be called directly:    ``_lower_case`` (``_`` prefix)
 
 Global variables:                                ``g_lower_case`` (``g_`` prefix)
@@ -120,9 +122,6 @@ Pointers:                                        ``pointer_ptr`` (``_ptr`` suffi
 .. note::
     Underscores are used to delimit 'words'.
 
-.. todo::
-    ``obi_function`` for public functions names?
-
 
 *****************
 Programming rules

doc/source/index.rst

@@ -11,7 +11,6 @@ OBITools3 documentation
 
    Programming guidelines <guidelines>
    Data structures <data>
-   Pistes de reflexion <pistes>
 
 
 Indices and tables

doc/source/specialvalues.rst

@@ -7,13 +7,16 @@ NA values
 =========
 
 All OBITypes have an associated NA (Not Available) value. 
-NA values are implemented by specifying an explicit NA value for each type, corresponding to the R standards:
+NA values are implemented by specifying an explicit NA value for each type, 
+corresponding to the R standards as much as possible:
 
-* For the types ``OBIInt_t``, ``OBIBool_t``, ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``INT_MIN``.
+* For the type ``OBIInt_t``, the NA value is ``INT_MIN``.
 
-* For the type ``OBIChar_t``: the NA value is ``\0`` (?).
+* For the type ``OBIBool_t``, the NA value is ``2``.
 
-* For the type ``OBIStr_t`` : the NA value is ``\0`` (?).
+* For the type ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``SIZE_MAX``.
+
+* For the type ``OBIChar_t``: the NA value is ``\0``.
 
 * For the type ``OBIFloat_t``::
 
@@ -29,7 +32,7 @@ NA values are implemented by specifying an explicit NA value for each type, corr
         x.word[hw] = 0x7ff00000;
         x.word[lw] = 1954;
         return x.value;
-    }   
+    }
 
 
 Minimum and maximum values for ``OBIInt_t``

doc/source/types.rst

@@ -7,11 +7,14 @@ OBITypes
 :download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
 
 
+.. image:: ./UML/Obicolumn_classes_UML.png
+
+:download:`html version of the OBIDMS classes UML file <UML/Obicolumn_classes_UML.class.violet.html>`
+
+
 .. toctree::
    :maxdepth: 2
 
    The elementary types <elementary>
    The containers <containers>
    Special values <specialvalues>
-
-

doc/sphinx/build_dir.txt

@@ -0,0 +1 @@
+build/lib.macosx-10.6-intel-3.5

doc/sphinx/source/pistes.rst

@@ -1,23 +0,0 @@
-###################
-Pistes de reflexion
-###################
-
-
-******************************
-Ce que l'on veut pouvoir faire
-******************************
-
-    * Gerer les valeurs manquantes
-    * Modifier une colonne en cours d'ecriture (mmap)
-    * Ajouter des valeurs a la fin du fichier d'une colonne en cours d'ecriture (mmap)
-    
-
-******
-Divers
-******
-
-* Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
-* Utilisation de semaphores pour la lecture
-* Utilisation de tas pour l'indexation des chaines de caracteres. Chaque colonne dont 
-  le type est OBIStr_t est stockee dans 3 fichiers : un fichier contenant les chaines, un 
-  fichier contenant les index, et un fichier contenant le tas.

python/obitools3/obicount.py

@@ -1,31 +0,0 @@
-import sys
-import argparse
-
-
-from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
-
-
-if __name__ == '__main__': 
-    
-    parser = argparse.ArgumentParser(description='Computes the sum of a column.')
-    
-    parser.add_argument('-d', '--dms', dest='dms_name', type=str,
-                       help='Name of the OBIDMS containing the column')
-    parser.add_argument('-c', '--column', dest='column_name', type=str, default='count',
-                       help="Name of the OBIDMS column (default: 'count')")
-    parser.add_argument('-v', '--version', dest='version_number', type=int, default=-1,
-                       help='Version number of the column (default: latest version)')
-    
-    args = parser.parse_args()
-   
-    c = OBIDMS_column.open(args.dms_name, args.column_name, version_number=args.version_number)
-    
-    # check that 1 element / line and summable type?
-
-    total = 0    
-    
-    for count in c :
-        total+=count
-    
-    print("Total count = ", total)    
-

python/obitools3/obidms/_obidms.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidms.h
 ../../../src/obidms.c
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -12,3 +14,11 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h

python/obitools3/obidms/_obidms.pxd

@@ -2,37 +2,93 @@
 
 from .capi.obidms       cimport OBIDMS_p
 from .capi.obidmscolumn cimport OBIDMS_column_p
-from .capi.obitypes     cimport obiversion_t, OBIType_t
+from .capi.obiview      cimport Obiview_p
+from .capi.obitypes     cimport obiversion_t, OBIType_t, index_t
+from ._obitaxo          cimport OBI_Taxonomy
+
+cdef class OBIDMS_column:
+
+    cdef  OBIDMS_column_p*   pointer
+    cdef  OBIDMS             dms
+    cdef  Obiview_p          view
+    cdef  str                data_type
+    cdef  str                dms_name
+    cdef  str                column_name
+    cdef  index_t            nb_elements_per_line
+    cdef  list               elements_names
+        
+    cpdef         update_pointer(self)
+    cpdef list    get_elements_names(self)
+    cpdef str     get_data_type(self)
+    cpdef index_t get_nb_lines_used(self)
+    cpdef str     get_creation_date(self)
+    cpdef str     get_comments(self)
+    cpdef         close(self)
+    @staticmethod
+    cdef  object  get_subclass_type(OBIDMS_column_p column_p)
+
+
+cdef class OBIDMS_column_multi_elts(OBIDMS_column):
+    
+    cpdef set_line(self, index_t line_nb, dict values)
+
+
+cdef class OBIDMS_column_line:
+
+    cdef OBIDMS_column column
+    cdef index_t index
+
+
+cdef class OBIView:
+    
+    cdef Obiview_p pointer
+    cdef str       name
+    cdef str       comments
+    cdef dict      columns
+    cdef dict      columns_pp    # TODO this dict might be unnecessary
+    cdef OBIDMS    dms
+    
+    cpdef delete_column(self, str column_name)
+    cpdef add_column(self, 
+                     str column_name, 
+                     obiversion_t version_number=*, 
+                     str type=*,
+                     index_t nb_lines=*, 
+                     index_t nb_elements_per_line=*,
+                     list elements_names=*,
+                     str avl_name=*,
+                     str comments=*,
+                     bint create=*
+                    )
+    cpdef select_line(self, index_t line_nb)
+    cpdef select_lines(self, list line_selection)
+    cpdef save_and_close(self)
+
+
+cdef class OBIView_NUC_SEQS(OBIView):
+
+    cdef OBIDMS_column ids
+    cdef OBIDMS_column sequences
+    cdef OBIDMS_column descriptions
+    
+    cpdef delete_column(self, str column_name)
+    
+
+cdef class OBIView_line :
+
+    cdef index_t index
+    cdef OBIView view
+
 
-cdef class OBIDMS_column
-            
 cdef class OBIDMS:
 
     cdef OBIDMS_p pointer
     cdef str dms_name
     
-    cpdef dict list(self)
-    
-    cpdef OBIDMS_column open_column(self,
-                                    str column_name,
-                                    bint create=*, 
-                                    bint clone=*, bint clone_data=*,
-                                    obiversion_t version_number=*, 
-                                    OBIType_t data_type=*,
-                                    size_t nb_lines=*, 
-                                    size_t nb_elements_per_line=*, 
-                                    str elements_names=*)
+    cpdef close(self)
+    cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
+    cpdef OBIView open_view(self, str view_name)
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
+    cpdef dict read_view_infos(self, str view_name)
+    cpdef dict read_views(self)
 
-
-cdef class OBIDMS_column:
-
-    cdef OBIDMS_column_p pointer
-    cdef OBIDMS dms
-    cdef str data_type   # TODO keep as OBIType_t? both?
-    cdef str dms_name
-    cdef str column_name
-
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef list   get_elements_names(self)
-    cpdef str    get_data_type(self)
-    cpdef size_t get_nb_lines_used(self)

python/obitools3/obidms/_obidms.pyx

@@ -1,40 +1,635 @@
 #cython: language_level=3
 
-from pathlib import Path
-
 from obitools3.utils cimport bytes2str, str2bytes
 
-from .capi.obidms cimport obi_dms
-from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
-                                obi_column_get_latest_version_from_name, \
-                                obi_column_get_line_count_from_name, \
-                                obi_column_get_nb_lines_used, \
-                                obi_column_get_elements_names, \
-                                obi_create_column, \
-                                obi_clone_column, \
-                                obi_open_column, \
-                                obi_close_column
-from .capi.obitypes cimport const_char_p, name_data_type
+from .capi.obidms cimport obi_dms, \
+                          obi_close_dms
+                          
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_format_date, \
+                                OBIDMS_column_p, \
+                                OBIDMS_column_header_p
+                                
+from .capi.obitypes cimport const_char_p, \
+                            OBIType_t, \
+                            OBI_INT, \
+                            OBI_FLOAT, \
+                            OBI_BOOL, \
+                            OBI_CHAR, \
+                            OBI_STR, \
+                            OBI_SEQ, \
+                            name_data_type, \
+                            only_ATGC    # discuss
+                            
+from ._obidms cimport OBIDMS, \
+                      OBIDMS_column, \
+                      OBIView, \
+                      OBIView_line
 
+from ._obitaxo cimport OBI_Taxonomy
 
-from ._obidms cimport OBIDMS
-from ._obidms cimport OBIDMS_column
+from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
 
 from ._obidmscolumn_int cimport OBIDMS_column_int, \
-                                OBIDMS_column_int_writable
-
+                                OBIDMS_column_multi_elts_int
+                                
 from ._obidmscolumn_float cimport OBIDMS_column_float, \
-                                  OBIDMS_column_float_writable
+                                  OBIDMS_column_multi_elts_float
 
 from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
-                                 OBIDMS_column_bool_writable
+                                 OBIDMS_column_multi_elts_bool
 
 from ._obidmscolumn_char cimport OBIDMS_column_char, \
-                                 OBIDMS_column_char_writable
+                                 OBIDMS_column_multi_elts_char
 
-from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
-                                OBIDMS_column_idx_writable
+from ._obidmscolumn_str cimport OBIDMS_column_str, \
+                                OBIDMS_column_multi_elts_str
 
+from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
+                                OBIDMS_column_multi_elts_seq
+
+from .capi.obiview cimport Obiview_p, \
+                           Obiviews_infos_all_p, \
+                           Obiview_infos_p, \
+                           Column_reference_p, \
+                           obi_new_view_nuc_seqs, \
+                           obi_new_view, \
+                           obi_new_view_cloned_from_name, \
+                           obi_new_view_nuc_seqs_cloned_from_name, \
+                           obi_open_view,  \
+                           obi_read_views, \
+                           obi_unmap_read_views, \
+                           obi_view_delete_column, \
+                           obi_view_add_column, \
+                           obi_view_get_column, \
+                           obi_view_get_pointer_on_column_in_view, \
+                           obi_select_line, \
+                           obi_select_lines, \
+                           obi_save_and_close_view, \
+                           VIEW_TYPE_NUC_SEQS, \
+                           NUC_SEQUENCE_COLUMN, \
+                           ID_COLUMN, \
+                           DESCRIPTION_COLUMN
+                           
+from libc.stdlib cimport malloc
+from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+
+
+cdef class OBIDMS_column :
+
+    # Should only be initialized through a subclass
+    def __init__(self, OBIView view, str column_name):
+        
+        cdef OBIDMS_column_p  column_p
+        cdef OBIDMS_column_p* column_pp
+        
+        column_pp = <OBIDMS_column_p*> PyCapsule_GetPointer(((view.columns_pp)[column_name]), NULL) # or use C function
+        column_p = column_pp[0]     # TODO ugly cython dereferencing but can't find better
+        
+        # Fill structure
+        self.pointer = column_pp
+        self.dms = view.dms
+        self.view = view.pointer    # TODO pointer or instance?
+        self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
+        self.column_name = bytes2str((column_p.header).name)
+        self.nb_elements_per_line = (column_p.header).nb_elements_per_line
+        self.elements_names = (bytes2str((column_p.header).elements_names)).split(';')
+
+    def __setitem__(self, index_t line_nb, object value):
+        self.set_line(line_nb, value)
+
+    def __getitem__(self, index_t line_nb):
+        return self.get_line(line_nb)
+
+    def __len__(self):
+        return (self.pointer)[0].header.lines_used
+    
+    def __sizeof__(self):
+        return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size)
+    
+    def __iter__(self):
+    
+        # Declarations
+        cdef index_t lines_used
+        cdef index_t line_nb
+        
+        # Yield each line
+        lines_used = (self.pointer)[0].header.lines_used
+        for line_nb in range(lines_used):
+            yield self.get_line(line_nb)
+    
+    cpdef update_pointer(self):
+        self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
+
+    cpdef list get_elements_names(self):
+        return self.elements_names
+         
+    cpdef str get_data_type(self):
+        return self.data_type
+    
+    cpdef index_t get_nb_lines_used(self):
+        return (self.pointer)[0].header.lines_used
+        
+    cpdef str get_creation_date(self):
+        return bytes2str(obi_column_format_date((self.pointer)[0].header.creation_date))
+    
+    cpdef str get_comments(self):
+        return bytes2str((self.pointer)[0].header.comments)
+    
+    def __repr__(self) :
+        cdef str to_print
+        to_print = ''
+        for line in self :
+            to_print = to_print + str(line) + "\n"
+        return to_print
+        
+    cpdef close(self):
+        if obi_truncate_and_close_column((self.pointer)[0]) < 0 :
+            raise Exception("Problem closing a column")
+
+
+    @staticmethod
+    cdef object get_subclass_type(OBIDMS_column_p column_p) :
+        
+        cdef object subclass
+        cdef OBIDMS_column_header_p header
+        cdef OBIType_t col_type
+        cdef bint col_writable
+        cdef bint col_one_element_per_line
+
+        header = column_p.header        
+        col_type = header.returned_data_type
+        col_writable = column_p.writable
+        col_one_element_per_line = ((header.nb_elements_per_line) == 1)
+        
+        if col_type == OBI_INT :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_int
+            else :
+                subclass = OBIDMS_column_multi_elts_int
+        elif col_type == OBI_FLOAT :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_float
+            else :
+                subclass = OBIDMS_column_multi_elts_float
+        elif col_type == OBI_BOOL :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_bool
+            else :
+                subclass = OBIDMS_column_multi_elts_bool
+        elif col_type == OBI_CHAR :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_char
+            else :
+                subclass = OBIDMS_column_multi_elts_char
+        elif col_type == OBI_STR :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_str
+            else :
+                subclass = OBIDMS_column_multi_elts_str
+        elif col_type == OBI_SEQ :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_seq
+            else :
+                subclass = OBIDMS_column_multi_elts_seq
+        else :
+            raise Exception("Problem with the data type")
+
+        return subclass
+
+    
+######################################################################################################
+
+cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
+    
+    def __getitem__(self, index_t line_nb):
+        return OBIDMS_column_line(self, line_nb)
+
+    cpdef set_line(self, index_t line_nb, dict values):
+        for element_name in values :
+            self.set_item(line_nb, element_name, values[element_name])
+
+######################################################################################################
+
+cdef class OBIDMS_column_line :
+
+    def __init__(self, OBIDMS_column column, index_t line_nb) :
+        self.index = line_nb
+        self.column = column
+        
+    def __getitem__(self, str element_name) :
+        return self.column.get_item(self.index, element_name)
+     
+    def __setitem__(self, str element_name, object value):
+        self.column.set_item(self.index, element_name, value)
+
+    def __contains__(self, str element_name):
+        return (element_name in self.column.elements_names)
+
+    def __repr__(self) :
+        return str(self.column.get_line(self.index))
+
+##########################################
+
+
+cdef class OBIView :
+    
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""): 
+        
+        cdef Obiview_p view = NULL
+        cdef int i
+        cdef list col_list
+        cdef str col_name
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef index_t* line_selection_p
+        cdef object col_capsule
+        
+        self.dms = dms
+        
+        if line_selection is not None :
+            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+            for i in range(len(line_selection)) :
+                line_selection_p[i] = line_selection[i]     # TODO type problem?
+            line_selection_p[len(line_selection)] = -1
+        else :
+            line_selection_p = NULL
+       
+        if new :
+            if view_to_clone is not None :
+                if type(view_to_clone) == str :
+                    view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
+                else :
+                    view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
+            elif view_to_clone is None :
+                view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
+        elif not new :
+            if view_name is not None :
+                view = obi_open_view(dms.pointer, str2bytes(view_name))
+            elif view_name is None :
+                view = obi_open_view(dms.pointer, NULL)
+        
+        if view == NULL :
+            raise Exception("Error creating/opening view")
+
+        self.pointer = view
+        self.name = bytes2str(view.name)
+        
+        # go through columns to build list and open python object (TODO make separate function?)
+        self.columns = {}
+        self.columns_pp = {}
+                
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
+            (self.columns_pp)[col_name] = col_capsule
+            
+            subclass = OBIDMS_column.get_subclass_type(column_p)
+            self.columns[col_name] = subclass(self, col_name)
+            
+            i+=1
+
+
+    def __repr__(self) :
+        
+        cdef str s
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        
+        s = self.name
+        s = s + ", " + self.comments + ", " + str(self.pointer.line_count) + " lines" 
+        for column_name in self.columns :   # TODO make function in OBIDMS_column class
+            column = self.columns[column_name]
+            column_p = (column.pointer)[0]
+            s = s + "\n" + column_name + ", version " + str(column_p.header.version) + ", data type: " + column.data_type
+        return s
+        
+    
+    cpdef delete_column(self, str column_name) :
+        
+        cdef int i
+        cdef Obiview_p view
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef str column_n
+ 
+        view = self.pointer
+ 
+        if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
+            raise Exception("Problem deleting a column from a view")
+        
+        # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
+        (self.columns).pop(column_name)
+        (self.columns_pp).pop(column_name)
+        
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
+            (self.columns_pp)[col_name] = col_capsule
+            i+=1
+
+        for column_n in self.columns :
+            (self.columns[column_n]).update_pointer()
+
+    
+    cpdef add_column(self, 
+                     str column_name, 
+                     obiversion_t version_number=-1, 
+                     str type='',
+                     index_t nb_lines=0, 
+                     index_t nb_elements_per_line=1,    # TODO 1?
+                     list elements_names=None,
+                     str avl_name="default_AVL_tree",
+                     str comments="",
+                     bint create=True   # TODO
+                     ) :
+        
+        cdef bytes column_name_b
+        cdef bytes elements_names_b
+        cdef object subclass
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_p column_p
+        
+        column_name_b = str2bytes(column_name)
+        
+        if nb_elements_per_line > 1 :
+            elements_names_b = str2bytes(';'.join(elements_names))
+        elif nb_elements_per_line == 1 :
+            elements_names_b = column_name_b
+    
+        if type :    
+            if type == 'OBI_INT' :
+                data_type = OBI_INT
+            elif type == 'OBI_FLOAT' :
+                data_type = OBI_FLOAT
+            elif type == 'OBI_BOOL' :
+                data_type = OBI_BOOL
+            elif type == 'OBI_CHAR' :
+                data_type = OBI_CHAR
+            elif type == 'OBI_STR' :
+                data_type = OBI_STR
+            elif type == 'OBI_SEQ' :
+                data_type = OBI_SEQ
+            else :
+                raise Exception("Invalid provided data type")
+        
+        if (obi_view_add_column(self.pointer, column_name_b, version_number,     # should return pointer on column?
+                                data_type, nb_lines, nb_elements_per_line, 
+                                elements_names_b, str2bytes(avl_name), 
+                                str2bytes(comments), create) < 0) :
+            raise Exception("Problem adding a column in a view")
+        
+        # Store the column pointer
+        column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
+        if column_pp == NULL :
+            raise Exception("Problem getting a column in a view")
+        
+        col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO
+        (self.columns_pp)[column_name] = col_capsule
+        
+        # Open and store the subclass
+        column_p = column_pp[0]     # TODO ugly cython dereferencing
+        subclass = OBIDMS_column.get_subclass_type(column_p)
+        (self.columns)[column_name] = subclass(self, column_name)
+                
+    
+    cpdef save_and_close(self) :
+        if (obi_save_and_close_view(self.pointer) < 0) :
+            raise Exception("Problem closing a view")
+    
+
+    def __iter__(self):
+        # iter on each line of all columns
+        
+        # Declarations
+        cdef index_t lines_used
+        cdef index_t line_nb
+        cdef OBIView_line line  # TODO for NUC SEQS View
+        
+        # Yield each line TODO line class
+        lines_used = (self.pointer).line_count
+        
+        for line_nb in range(lines_used) :
+            line = self[line_nb]
+            yield line
+
+
+    def __getitem__(self, object item) :
+        if type(item) == str :
+            return (self.columns)[item]
+        elif type(item) == int :     # TODO int?
+            return OBIView_line(self, item)
+
+
+    cpdef select_line(self, index_t line_nb) :
+        if obi_select_line(self.pointer, line_nb) < 0 :
+            raise Exception("Problem selecting a line")
+
+    
+    cpdef select_lines(self, list line_selection) :
+        cdef index_t* line_selection_p
+        line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+        for i in range(len(line_selection)) :
+            line_selection_p[i] = line_selection[i]     # TODO type problem?
+        line_selection_p[len(line_selection)] = -1
+        if obi_select_lines(self.pointer, line_selection_p) < 0 :
+            raise Exception("Problem selecting a list of lines")
+    
+    
+    def __contains__(self, str column_name):
+        return (column_name in self.columns)
+    
+    
+    def __str__(self) :
+        cdef OBIView_line line
+        cdef str to_print
+        to_print = ""
+        for line in self.__iter__() :
+            to_print = to_print + str(line) + "\n"
+        return to_print
+
+#############################################
+
+cdef class OBIView_NUC_SEQS(OBIView):
+    
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""): 
+        
+        cdef Obiview_p view = NULL
+        cdef int i
+        cdef list col_list
+        cdef str col_name
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef index_t* line_selection_p
+                
+        self.dms = dms
+        
+        if line_selection is not None :
+            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+            for i in range(len(line_selection)) :
+                line_selection_p[i] = line_selection[i]     # TODO type problem?
+            line_selection_p[len(line_selection)] = -1
+        else :
+            line_selection_p = NULL
+       
+        if new :
+            if view_to_clone is not None :
+                if type(view_to_clone) == str :
+                    view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
+                else :
+                    view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
+            elif view_to_clone is None :
+                view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
+        elif not new :
+            if view_name is not None :
+                view = obi_open_view(dms.pointer, str2bytes(view_name))
+            elif view_name is None :
+                view = obi_open_view(dms.pointer, NULL)
+        
+        if view == NULL :
+            raise Exception("Error creating/opening view")
+
+        self.pointer = view
+        self.name = bytes2str(view.name)
+        self.comments = bytes2str(view.comments)
+        
+        # go through columns to build list and open python object (TODO make separate function?)
+        self.columns = {}
+        self.columns_pp = {}
+                
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
+            (self.columns_pp)[col_name] = col_capsule
+            
+            subclass = OBIDMS_column.get_subclass_type(column_p)
+            self.columns[col_name] = subclass(self, col_name)
+            
+            i+=1
+        
+        self.ids = self.columns[bytes2str(ID_COLUMN)]
+        self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
+        self.descriptions = self.columns[bytes2str(DESCRIPTION_COLUMN)]
+
+
+    cpdef delete_column(self, str column_name) :
+        
+        cdef int i
+        cdef Obiview_p view
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef str column_n
+ 
+        if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DESCRIPTION_COLUMN))) :
+            raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
+        
+        view = self.pointer
+ 
+        if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
+            raise Exception("Problem deleting a column from a view")
+        
+        # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
+        (self.columns).pop(column_name)
+        (self.columns_pp).pop(column_name)
+        
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
+            (self.columns_pp)[col_name] = col_capsule
+            i+=1
+
+        for column_n in self.columns :
+            (self.columns[column_n]).update_pointer()
+
+            
+    def __getitem__(self, object item) :
+        if type(item) == str :
+            return (self.columns)[item]
+        elif type(item) == int :     # TODO int?
+            return OBI_Nuc_Seq_Stored(self, item)
+    
+    
+    def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
+        for key in sequence_obj :
+            self[line_idx][key] = sequence_obj[key]
+            
+
+#############################################
+
+cdef class OBIView_line :
+
+    def __init__(self, OBIView view, index_t line_nb) :
+        self.index = line_nb
+        self.view = view
+    
+    def __getitem__(self, str column_name) :
+        return ((self.view).columns)[column_name][self.index]
+    
+    def __setitem__(self, str column_name, object value):
+        # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
+        cdef type value_type
+        cdef str value_obitype
+        if column_name not in self.view :
+            if value == None :
+                raise Exception("Trying to create a column from a None value (can't guess type)")
+            value_type = type(value)
+            if value_type == int :
+                value_obitype = 'OBI_INT'
+            elif value_type == float :
+                value_obitype = 'OBI_FLOAT'
+            elif value_type == bool :
+                value_obitype = 'OBI_BOOL'            
+            elif value_type == str :
+                if only_ATGC(str2bytes(value)) :    # TODO
+                    value_obitype = 'OBI_SEQ'
+                elif len(value) == 1 :
+                    value_obitype = 'OBI_CHAR'
+                elif (len(value) > 1) :
+                    value_obitype = 'OBI_STR'
+            else :
+                raise Exception("Could not guess the type of a value to create a new column")
+            self.view.add_column(column_name, type=value_obitype)
+
+        (((self.view).columns)[column_name]).set_line(self.index, value)
+
+    def __contains__(self, str column_name):
+        return (column_name in self.view)
+        
+    def __repr__(self):
+        cdef dict line
+        cdef str column_name
+        line = {}
+        for column_name in self.view.columns :
+            line[column_name] = self[column_name]
+        return str(line)
+
+##########################################
 
 cdef class OBIDMS :
     
@@ -49,235 +644,97 @@ cdef class OBIDMS :
         # Fill structure and create or open the DMS
         self.dms_name = dms_name
         self.pointer = obi_dms(<const_char_p> dms_name_b)
+        if self.pointer == NULL :
+            raise Exception("Failed opening or creating an OBIDMS")
 
 
-#    def __del__(self) :                        # TODO problem with closing dir breaking everything
-#        obi_close_dms(self.pointer)
+    cpdef close(self) :
+        if (obi_close_dms(self.pointer)) < 0 :
+            raise Exception("Problem closing an OBIDMS")
 
-
-    cpdef dict list(self):
     
-        # Declarations
-        cdef object p
-        cdef dict dms = {}
+    cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) :
+        return OBI_Taxonomy(self, taxo_name)
+    
+
+    cpdef OBIView open_view(self, str view_name) :
+        
+        cdef object view_class
+        cdef dict view_infos
+        
+        view_infos = self.read_view_infos(view_name)
+        
+        if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :
+            view_class = OBIView_NUC_SEQS
+        else :
+            view_class = OBIView
+        
+        return view_class(self, view_name)
+    
+
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None, str comments="") :
+        
+        cdef object view_class
+        
+        if view_type is not None :
+            if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
+                view_class = OBIView_NUC_SEQS
+        else :
+            view_class = OBIView
+        
+        return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments)
+
+
+    cpdef dict read_view_infos(self, str view_name) :
+        all_views = self.read_views()
+        return all_views[view_name]
+
+
+    cpdef dict read_views(self) :    # TODO function that prints the dic nicely and function that prints 1 view. Add column type in col ref
+        
+        cdef Obiviews_infos_all_p all_views_p
+        cdef Obiview_infos_p view_p
+        cdef Column_reference_p column_refs
+        cdef int nb_views
+        cdef int i, j
+        cdef str view_name
         cdef str column_name
-        cdef bytes column_name_b
-        cdef str data_type
-        cdef obiversion_t latest_version
-        cdef size_t line_count
+        cdef dict views
+        cdef bytes name_b
         
-        p = Path(self.dms_name+'.obidms')
-
-        print("{:<25} {:<25} {:<25} {:<25}".format('-Column name-','-Data type-','-Latest version number-', '-Line count of latest version-'))
-        for entry in p.iterdir():
-            if entry.suffix == ".obicol":
-                column_name = entry.stem
-                column_name_b = str2bytes(column_name)
-                dms[column_name] = {}
-                data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
-                latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
-                line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
-                dms[column_name]['data_type'] = data_type
-                dms[column_name]['latest_version'] = latest_version
-                dms[column_name]['line_count'] = line_count
-                print("{:<25} {:<25} {:<25} {:<25}".format(column_name, data_type, latest_version, line_count))
-
-        return dms
-     
-    cpdef OBIDMS_column open_column(self,
-                                    str column_name,
-                                    bint create=False, 
-                                    bint clone=False, bint clone_data=True,
-                                    obiversion_t version_number=-1, 
-                                    OBIType_t data_type= <OBIType_t> 0,
-                                    size_t nb_lines=0, 
-                                    size_t nb_elements_per_line=1, 
-                                    str elements_names=None):
-        
-        # Declarations
-        cdef OBIDMS_column column
-        cdef bytes column_name_b
-        
-        # Format the character string to send to C function
-        column_name_b = str2bytes(column_name)
-        
-        # Get the data type if not provided
-        if not data_type :
-            if create :
-                raise Exception("A data type must be specified")
+        views = {}
+        all_views_p = obi_read_views(self.pointer)
+        if all_views_p == NULL :
+            raise Exception("No views to read")
+        nb_views = <int> (all_views_p.header).view_count
+        for i in range(nb_views) :
+            view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
+            view_name = bytes2str(view_p.name)
+            views[view_name] = {}
+            views[view_name]["comments"] = bytes2str(view_p.comments)
+            views[view_name]["view_type"] = bytes2str(view_p.view_type)
+            views[view_name]["column_count"] = <int> view_p.column_count
+            views[view_name]["line_count"] = <int> view_p.line_count
+            views[view_name]["view_number"] = <int> view_p.view_number
+            views[view_name]["created_from"] = bytes2str(view_p.created_from)
+            views[view_name]["creation_date"] = bytes2str(obi_column_format_date(view_p.creation_date))     # TODO move this function in utils or somethings
+            if (view_p.all_lines) :
+                views[view_name]["line_selection"] = None
             else :
-                data_type = obi_column_get_data_type_from_name(self.pointer, column_name_b)
-
-        # Open the column with the right subclass depending on the data type and the mode (read-only or writable)
-        if data_type == 1 :
-            if (create or clone) :
-                column = OBIDMS_column_int_writable(self, column_name, 
-                                                    create, clone, clone_data, 
-                                                    version_number, data_type, 
-                                                    nb_lines, nb_elements_per_line, 
-                                                    elements_names)
-            else :
-                 column = OBIDMS_column_int(self, column_name, 
-                                                 create, clone, clone_data, 
-                                                 version_number, data_type, 
-                                                 nb_lines, nb_elements_per_line, 
-                                                 elements_names)
-               
-        elif data_type == 2 :
-            if (create or clone) :
-                column = OBIDMS_column_float_writable(self, column_name, 
-                                                      create, clone, clone_data, 
-                                                      version_number, data_type, 
-                                                      nb_lines, nb_elements_per_line, 
-                                                      elements_names)
-            else :
-                 column = OBIDMS_column_float(self, column_name, 
-                                                   create, clone, clone_data, 
-                                                   version_number, data_type, 
-                                                   nb_lines, nb_elements_per_line, 
-                                                   elements_names)
-
-        elif data_type == 3 :
-            if (create or clone) :
-                column = OBIDMS_column_bool_writable(self, column_name, 
-                                                     create, clone, clone_data, 
-                                                     version_number, data_type, 
-                                                     nb_lines, nb_elements_per_line, 
-                                                     elements_names)
-            else :
-                 column = OBIDMS_column_bool(self, column_name, 
-                                                  create, clone, clone_data, 
-                                                  version_number, data_type, 
-                                                  nb_lines, nb_elements_per_line, 
-                                                  elements_names)
-
-        elif data_type == 4 :
-            if (create or clone) :
-                column = OBIDMS_column_char_writable(self, column_name, 
-                                                     create, clone, clone_data, 
-                                                     version_number, data_type, 
-                                                     nb_lines, nb_elements_per_line, 
-                                                     elements_names)
-            else :
-                 column = OBIDMS_column_char(self, column_name, 
-                                                  create, clone, clone_data, 
-                                                  version_number, data_type, 
-                                                  nb_lines, nb_elements_per_line, 
-                                                  elements_names)
-    
-#         elif data_type == 5 :
-#             if (create or clone) :
-#                 column = OBIDMS_column_idx_writable(self, column_name, 
-#                                                     create, clone, clone_data, 
-#                                                     version_number, data_type, 
-#                                                     nb_lines, nb_elements_per_line, 
-#                                                     elements_names)
-#             else :
-#                  column = OBIDMS_column_idx(self, column_name, 
-#                                             create, clone, clone_data, 
-#                                             version_number, data_type, 
-#                                             nb_lines, nb_elements_per_line, 
-#                                             elements_names)
-   
-        else :
-            raise Exception("Problem with the data type")
-            
-        return column
-
-
-
-cdef class OBIDMS_column :
-
-    # Should only be initialized through a subclass
-    def __init__(self, 
-                 OBIDMS dms, 
-                 str column_name,
-                 bint create, 
-                 bint clone, bint clone_data,
-                 obiversion_t version_number, 
-                 OBIType_t type,
-                 size_t nb_lines, 
-                 size_t nb_elements_per_line, 
-                 str elements_names):
+                views[view_name]["line_selection"] = {}
+                views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
+                views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
+            views[view_name]["column_references"] = {}
+            column_refs = view_p.column_references
+            for j in range(views[view_name]["column_count"]) :
+                column_name = bytes2str((column_refs[j]).column_name)
+                views[view_name]["column_references"][column_name] = {}
+                views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
         
-        # Declarations
-        cdef bytes column_name_b
-        cdef bytes dms_name_b
-        cdef bytes elements_names_b
+        obi_unmap_read_views(all_views_p);
         
-        # Fill structure
-        self.dms = dms
-        self.data_type = bytes2str(name_data_type(type))
-        self.column_name = column_name
-        
-        # Format the character strings to send them to C functions
-        column_name_b = str2bytes(column_name)
-        dms_name_b = str2bytes(self.dms.dms_name)
-        
-        # Create, clone or open column
-        if create :
-            if elements_names == None :  
-                elements_names_b = column_name_b
-            else :
-                elements_names_b = str2bytes(elements_names)
-            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
-        else :
-            if clone :
-                self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
-            else :
-                self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
+        return views
     
     
-    def __iter__(self):
     
-        # Declarations
-        cdef list elements_names
-        cdef str element_name
-        cdef bint multiple_elements
-        cdef object line               # TODO
-        cdef size_t lines_used
-        cdef size_t line_nb
-        
-        # Check if there are multiple elements per line anf if yes, get their names
-        elements_names = self.get_elements_names()
-        if len(elements_names) > 1 :
-            multiple_elements = True
-        else :
-            element_name = elements_names[0]
-        
-        # Yield each line
-        lines_used = obi_column_get_nb_lines_used(self.pointer)
-        for line_nb in xrange(lines_used):
-            if multiple_elements :
-                line = []
-                for element_name in elements_names :
-                    line.append(self.get_item(line_nb, element_name))
-            else :
-                line = self.get_item(line_nb, element_name)
-            yield line
-
-
-    def __setitem__(self, size_t line_nb, object value):
-        self.set_item(line_nb, "", value)
-
-        
-    def __getitem__(self, size_t line_nb):
-        return self.get_item(line_nb, "")
-
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        raise NotImplementedError
-    
-    cpdef list get_elements_names(self):
-        cdef bytes elements_names
-        elements_names = obi_column_get_elements_names(self.pointer)
-        return (bytes2str(elements_names)).split(';')
-
-             
-    cpdef str get_data_type(self):
-        return self.data_type
-
-    
-    cpdef size_t get_nb_lines_used(self):
-        return obi_column_get_nb_lines_used(self.pointer)
-        
-   
+    

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_bool.c
 ../../../src/obidmscolumn_bool.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -14,3 +16,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_bool.pxd

@@ -1,17 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obibool_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
-    cpdef close(self)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
 
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -1,11 +1,12 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obibool_with_elt_name, \
-                                obi_column_set_obibool_with_elt_name
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_get_obibool_with_elt_name_in_view, \
+                                obi_column_get_obibool_with_elt_idx_in_view, \
+                                obi_column_set_obibool_with_elt_name_in_view, \
+                                obi_column_set_obibool_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIBool_NA
+from .capi.obitypes     cimport OBIBool_NA, obibool_t
 
 from obitools3.utils cimport str2bytes
 
@@ -13,11 +14,32 @@ from cpython.bool cimport PyBool_FromLong
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
- 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+
+    cpdef object get_line(self, index_t line_nb):
         cdef obibool_t value
         cdef object result
-        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIBool_NA
+        if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef obibool_t value
+        cdef object result
+        value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIBool_NA :
@@ -25,22 +47,32 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
         else :
             result = PyBool_FromLong(value)
         return result
-     
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
-        raise Exception("Column is read-only")
-     
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obibool_t value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIBool_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyBool_FromLong(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
 
-
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
-   
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
-        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0 :
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIBool_NA
+        if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
             raise Exception("Problem setting a value in a column")
- 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-     

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_char.c
 ../../../src/obidmscolumn_char.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -14,3 +16,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -1,17 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obichar_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
-    cpdef close(self)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
 
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -1,44 +1,77 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obichar_with_elt_name, \
-                                obi_column_set_obichar_with_elt_name
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_get_obichar_with_elt_name_in_view, \
+                                obi_column_get_obichar_with_elt_idx_in_view, \
+                                obi_column_set_obichar_with_elt_name_in_view, \
+                                obi_column_set_obichar_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIChar_NA
+from .capi.obitypes     cimport OBIChar_NA, obichar_t
 
-from obitools3.utils cimport str2bytes
+from obitools3.utils cimport str2bytes, bytes2str
 
 
-cdef class OBIDMS_column_char(OBIDMS_column) :
- 
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        cdef char value
+cdef class OBIDMS_column_char(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obichar_t value
         cdef object result
-        value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIChar_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIChar_NA
+        if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef obichar_t value
+        cdef object result
+        value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIChar_NA :
             result = None
         else :
-            result = <bytes> value
+            result = bytes2str(value)
         return result
 
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
-        raise Exception("Column is read-only")
- 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 
-         
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
- 
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
-        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obichar_t value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIChar_NA :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIChar_NA
+        if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
- 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-      
+

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_float.c
 ../../../src/obidmscolumn_float.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -14,3 +16,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -1,16 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obifloat_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
-    cpdef close(self)
-    
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
-    cpdef close(self)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -1,44 +1,77 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obifloat_with_elt_name, \
-                                obi_column_set_obifloat_with_elt_name
+from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
+                                obi_column_get_obifloat_with_elt_name_in_view, \
+                                obi_column_get_obifloat_with_elt_idx_in_view, \
+                                obi_column_set_obifloat_with_elt_name_in_view, \
+                                obi_column_set_obifloat_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIFloat_NA
+from .capi.obitypes     cimport OBIFloat_NA, obifloat_t
 
 from obitools3.utils cimport str2bytes
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+    cpdef object get_line(self, index_t line_nb):
         cdef obifloat_t value
         cdef object result
-        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIFloat_NA :
+            result = None
+        else :
+            result = <double> value
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIFloat_NA
+        if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef obifloat_t value
+        cdef object result
+        value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIFloat_NA :
             result = None
         else :
-            result = <float> value
+            result = <double> value
         return result
-    
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
-        raise Exception("Column is read-only")
 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
-
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
-
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
-        if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obifloat_t value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIFloat_NA :
+                value_in_result = None
+            else :
+                value_in_result = <double> value
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+   
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIFloat_NA
+        if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
             raise Exception("Problem setting a value in a column")
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
  

python/obitools3/obidms/_obidmscolumn_idx.pxd

@@ -1,16 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport obiidx_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
-
-
-cdef class OBIDMS_column_idx(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
-    cpdef close(self)
-    
-cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_idx.pyx

@@ -1,46 +0,0 @@
-#cython: language_level=3
-
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obiidx_with_elt_name, \
-                                obi_column_set_obiidx_with_elt_name
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIIdx_NA
-
-from obitools3.utils cimport str2bytes
-
-from cpython.int cimport PyInt_FromSsize_t
-
-
-cdef class OBIDMS_column_idx(OBIDMS_column):
-
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        cdef obiidx_t value
-        cdef object result
-        value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIIdx_NA :
-            result = None
-        else :
-            result = PyInt_FromSsize_t(value)
-        return result
-    
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
-        raise Exception("Column is read-only")
-
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
-
-cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):     
-
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
-        if obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
-            raise Exception("Problem setting a value in a column")
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_int.c
 ../../../src/obidmscolumn_int.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -14,3 +16,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_int.pxd

@@ -1,16 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obiint_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_int(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
-    cpdef close(self)
-    
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
-    cpdef close(self)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -1,25 +1,45 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obiint_with_elt_name, \
-                                obi_column_set_obiint_with_elt_name
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_get_obiint_with_elt_name_in_view, \
+                                obi_column_get_obiint_with_elt_idx_in_view, \
+                                obi_column_set_obiint_with_elt_name_in_view, \
+                                obi_column_set_obiint_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIInt_NA
+from .capi.obitypes     cimport OBIInt_NA, obiint_t
 
 from obitools3.utils cimport str2bytes
 
 from cpython.int cimport PyInt_FromLong
 
-from ._obidms cimport OBIDMS_column
-
 
 cdef class OBIDMS_column_int(OBIDMS_column):
 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+    cpdef object get_line(self, index_t line_nb):
         cdef obiint_t value
         cdef object result
-        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIInt_NA :
+            result = None
+        else :
+            result = PyInt_FromLong(value)
+        return result
+            
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIInt_NA
+        if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef obiint_t value
+        cdef object result
+        value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIInt_NA :
@@ -28,21 +48,32 @@ cdef class OBIDMS_column_int(OBIDMS_column):
             result = PyInt_FromLong(value)
         return result
     
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
-        raise Exception("Column is read-only")
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obiint_t value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIInt_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyInt_FromLong(value)
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None   # TODO discuss
+        return result
 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
-
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
-
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
-        if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIInt_NA
+        if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -0,0 +1,20 @@
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_seq.pxd

@@ -0,0 +1,14 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
+
+
+cdef class OBIDMS_column_seq(OBIDMS_column):
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -0,0 +1,83 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_get_obiseq_with_elt_name_in_view, \
+                                obi_column_get_obiseq_with_elt_idx_in_view, \
+                                obi_column_set_obiseq_with_elt_name_in_view, \
+                                obi_column_set_obiseq_with_elt_idx_in_view
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBISeq_NA, const_char_p
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+
+cdef class OBIDMS_column_seq(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBISeq_NA :     # TODO
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBISeq_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef object get_line(self, index_t line_nb) :
+        cdef bytes value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBISeq_NA :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+    

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -0,0 +1,20 @@
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_str.pxd

@@ -0,0 +1,14 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
+
+
+cdef class OBIDMS_column_str(OBIDMS_column):
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -0,0 +1,83 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+                                obi_column_get_obistr_with_elt_name_in_view, \
+                                obi_column_get_obistr_with_elt_idx_in_view, \
+                                obi_column_set_obistr_with_elt_name_in_view, \
+                                obi_column_set_obistr_with_elt_idx_in_view
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIStr_NA, const_char_p
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+
+cdef class OBIDMS_column_str(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIStr_NA :     # TODO
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIStr_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef object get_line(self, index_t line_nb) :
+        cdef bytes value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIStr_NA :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+    

python/obitools3/obidms/_obiseq.cfiles

@@ -1,11 +1,11 @@
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_idx.h
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
@@ -14,3 +14,9 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c

python/obitools3/obidms/_obiseq.pxd

@@ -0,0 +1,34 @@
+#cython: language_level=3
+
+from ._obidms cimport OBIView_line
+
+
+cdef class OBI_Seq(dict) :
+    cdef str id
+    cdef str description
+    cdef str sequence
+
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_description(self, str description)
+    cpdef get_description(self)
+    cpdef get_sequence(self)
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    #cpdef str reverse_complement(self)    
+    cpdef set_sequence(self, str sequence)
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+    cdef str id
+    cdef str description
+    cdef str sequence
+
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_description(self, str description)
+    cpdef get_description(self)
+    cpdef set_sequence(self, str sequence)
+    cpdef get_sequence(self)
+   # cpdef str reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -0,0 +1,78 @@
+#cython: language_level=3
+
+from obitools3.utils cimport bytes2str, str2bytes
+
+from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                           ID_COLUMN, \
+                           DESCRIPTION_COLUMN
+
+cdef class OBI_Seq(dict) :
+
+    def __init__(self, str id, str seq, str description=None) :
+        self.set_id(id)
+        self.set_sequence(seq)
+        if description is not None :
+            self.set_description(description)
+        
+    cpdef set_id(self, str id) :
+        self.id = id
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self.id
+            
+    cpdef set_description(self, str description) :
+        self.description = description
+        self[bytes2str(DESCRIPTION_COLUMN)] = description
+        
+    cpdef get_description(self) :
+        return self.description
+        
+    cpdef get_sequence(self) :
+        return self.sequence
+
+    def __str__(self) :
+        return self.sequence    # or not
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    
+    cpdef set_sequence(self, str sequence) :
+        self.sequence = sequence
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+
+    cpdef set_id(self, str id) :
+        self.id = id
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self.id
+            
+    cpdef set_description(self, str description) :
+        self.description = description
+        self[bytes2str(DESCRIPTION_COLUMN)] = description
+
+    cpdef get_description(self) :
+        return self.description
+
+    cpdef set_sequence(self, str sequence) :
+        self.sequence = sequence
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+    cpdef get_sequence(self) :
+        return self.sequence
+    
+    def __str__(self) :
+        return self.sequence    # or not
+    
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+    # TODO static method to import?
+    

python/obitools3/obidms/_obitaxo.cfiles

@@ -0,0 +1,24 @@
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h

python/obitools3/obidms/_obitaxo.pxd

@@ -0,0 +1,31 @@
+#cython: language_level=3
+
+from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
+
+from libc.stdint   cimport int32_t
+
+
+cdef class OBI_Taxonomy :
+
+    cdef str name
+    cdef OBIDMS_taxonomy_p pointer
+    
+    cpdef close(self)
+
+ 
+cdef class OBI_Taxon :
+
+    cdef ecotx_t* pointer
+    cdef int32_t  taxid
+    cdef int32_t  rank
+    cdef int32_t  farest
+    cdef ecotx_t* parent
+    cdef str name
+        
+    cpdef int32_t taxid(self)
+    
+    cpdef int32_t rank(self)
+    
+    cpdef int32_t farest(self)
+    
+    cpdef OBI_Taxon parent(self)

python/obitools3/obidms/_obitaxo.pyx

@@ -0,0 +1,65 @@
+#cython: language_level=3
+
+from obitools3.utils   cimport bytes2str, str2bytes
+
+from .capi.obitaxonomy cimport obi_read_taxonomy, \
+                               obi_close_taxonomy, \
+                               obi_taxo_get_taxon_with_taxid
+
+from ._obidms cimport OBIDMS
+
+from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+
+
+cdef class OBI_Taxonomy :
+
+    def __init__(self, OBIDMS dms, str name) :
+        
+        self.name = name
+        self.pointer = obi_read_taxonomy(dms.pointer, str2bytes(name), True)    # TODO discuss
+    
+    
+    def __getitem__(self, object ref):
+        
+        cdef ecotx_t* taxon_p
+        cdef object taxon_capsule
+        
+        if type(ref) == int :
+            taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer, ref)
+            taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
+            return OBI_Taxon(taxon_capsule)
+    
+         
+    cpdef close(self) :
+        if (obi_close_taxonomy(self.pointer) < 0) :
+            raise Exception("Error closing the taxonomy")
+        
+
+cdef class OBI_Taxon :    # dict subclass?
+
+    def __init__(self, object taxon_capsule) :
+        
+        cdef ecotx_t* taxon
+        
+        taxon = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)   
+        self.pointer = taxon
+        self.taxid = taxon.taxid
+        self.rank = taxon.rank
+        self.farest = taxon.farest
+        self.parent = taxon.parent
+        self.name = bytes2str(taxon.name)
+        
+    cpdef int32_t taxid(self):
+        return self.taxid
+    
+    cpdef int32_t rank(self):
+        return self.rank
+    
+    cpdef int32_t farest(self):
+        return self.farest
+    
+    cpdef OBI_Taxon parent(self):
+        cdef object parent_capsule
+        parent_capsule = PyCapsule_New(self.parent, NULL, NULL)
+        return OBI_Taxon(parent_capsule)
+    

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -8,39 +8,54 @@ from ..capi.obitypes cimport const_char_p, \
                              obibool_t, \
                              obichar_t, \
                              obifloat_t, \
-                             obiidx_t
+                             index_t, \
+                             time_t
+
 
 cdef extern from "obidmscolumn.h" nogil:
-    struct OBIDMS_column_t:
-        pass
+    
+    struct OBIDMS_column_header_t:
+        size_t          header_size
+        size_t          data_size
+        index_t         line_count
+        index_t         lines_used
+        index_t         nb_elements_per_line
+        const_char_p    elements_names
+        OBIType_t       returned_data_type
+        OBIType_t       stored_data_type
+        time_t          creation_date
+        obiversion_t    version
+        obiversion_t    cloned_from
+        const_char_p    name
+        const_char_p    avl_name
+        const_char_p    comments
+    
+    ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
 
+    struct OBIDMS_column_t:
+        OBIDMS_p               dms
+        OBIDMS_column_header_p header
+        bint                   writable
+        
     ctypedef OBIDMS_column_t* OBIDMS_column_p
 
     OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
                                       const_char_p column_name, 
                                       OBIType_t type, 
-                                      size_t nb_lines, 
-                                      size_t nb_elements_per_line, 
-                                      const_char_p elements_names)
-    
-    size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
-    
-    const_char_p obi_column_get_elements_names(OBIDMS_column_p column)
-    
-    void obi_column_make_unwritable(OBIDMS_column_p column)
-    
+                                      index_t nb_lines, 
+                                      index_t nb_elements_per_line, 
+                                      const_char_p elements_names,
+                                      const_char_p avl_name,
+                                      const_char_p comments)
+                
     OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
                                     const_char_p column_name, 
                                     obiversion_t version_number)
-    
-    OBIType_t obi_column_get_type(OBIDMS_column_p column)
-    
+        
     int obi_close_column(OBIDMS_column_p column)
-    
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
-                                                 const_char_p column_name)
-    
+        
     OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
+                                     OBIDMS_column_p line_selection,
                                      const_char_p column_name, 
                                      obiversion_t version_number, 
                                      bint clone_data)
@@ -49,65 +64,268 @@ cdef extern from "obidmscolumn.h" nogil:
     
     obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
                                                          const_char_p column_name)
+        
+    OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, 
+                                                           const_char_p column_name,
+                                                           obiversion_t version_number)
     
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
-                                                 const_char_p column_name)
-    
-    size_t obi_column_get_line_count_from_name(OBIDMS_p dms, 
-                                               const_char_p column_name)
-    
-    
+    int obi_unmap_header(OBIDMS_column_header_p header)
+        
+    char* obi_column_format_date(time_t date)
+
+    int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
+
+
+from ..capi.obiview  cimport Obiview_p  # TODO
+
 cdef extern from "obidmscolumn_int.h" nogil:
+    int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    obiint_t value)
+
+    int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   obiint_t value)
+    
+    obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         const_char_p element_name)
+    
+    obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                        OBIDMS_column_p column, 
+                                                        index_t line_nb, 
+                                                        index_t element_idx)
+
     int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, 
-                                            size_t line_nb, 
+                                            index_t line_nb, 
                                             const_char_p element_name, 
                                             obiint_t value)
+
+    int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                           obiint_t value)
     
     obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, 
-                                                 size_t line_nb, 
+                                                 index_t line_nb, 
                                                  const_char_p element_name)
+    
+    obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, 
+                                                index_t line_nb, 
+                                                index_t element_idx)
 
 cdef extern from "obidmscolumn_bool.h" nogil:
 
+    int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obibool_t value)
+
+    int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obibool_t value)
+    
+    obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
     int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, 
-                                             size_t line_nb, 
+                                             index_t line_nb, 
                                              const_char_p element_name, 
                                              obibool_t value)
+
+    int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obibool_t value)
     
     obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, 
-                                                   size_t line_nb, 
+                                                   index_t line_nb, 
                                                    const_char_p element_name)
+    
+    obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, 
+                                                  index_t line_nb, 
+                                                  index_t element_idx)
 
 cdef extern from "obidmscolumn_char.h" nogil:
 
+    int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obichar_t value)
+
+    int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obichar_t value)
+    
+    obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
     int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, 
-                                             size_t line_nb, 
+                                             index_t line_nb, 
                                              const_char_p element_name, 
                                              obichar_t value)
+
+    int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obichar_t value)
     
     obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, 
-                                                   size_t line_nb, 
+                                                   index_t line_nb, 
                                                    const_char_p element_name)
+    
+    obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, 
+                                                  index_t line_nb, 
+                                                  index_t element_idx)
 
 cdef extern from "obidmscolumn_float.h" nogil:
 
+    int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obifloat_t value)
+
+    int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obifloat_t value)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
     int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                              size_t line_nb, 
-                                              const_char_p element_name, 
-                                              obifloat_t value)
+                                             index_t line_nb, 
+                                             const_char_p element_name, 
+                                             obifloat_t value)
+
+    int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obifloat_t value)
     
     obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                                     size_t line_nb, 
-                                                     const_char_p element_name)
-
-cdef extern from "obidmscolumn_idx.h" nogil:
-
-    int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, 
-                                            size_t line_nb, 
-                                            const_char_p element_name, 
-                                            obiidx_t value)
+                                                   index_t line_nb, 
+                                                   const_char_p element_name)
     
-    obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, 
-                                                 size_t line_nb, 
-                                                 const_char_p element_name)
+    obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, 
+                                                  index_t line_nb, 
+                                                  index_t element_idx)
+
+cdef extern from "obidmscolumn_str.h" nogil:
+
+    int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    char* value)
+
+    int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   char* value)
+    
+    const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
+    int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            const_char_p element_name, 
+                                            char* value)
+
+    int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                           char* value)
+    
+    const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    char* element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx)
+
+cdef extern from "obidmscolumn_seq.h" nogil:
+
+    int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    char* value)
+
+    int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   char* value)
+    
+    const_char_p obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    const_char_p obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
+    int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            const_char_p element_name, 
+                                            char* value)
+
+    int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                           char* value)
+    
+    const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    char* element_name)
+    
+    const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx)
 

python/obitools3/obidms/capi/obitaxonomy.pxd

@@ -0,0 +1,42 @@
+#cython: language_level=3
+
+from .obitypes     cimport const_char_p
+from .obidms       cimport OBIDMS_p
+from libc.stdint   cimport int32_t
+
+
+cdef extern from "obidms_taxonomy.h" nogil:
+
+    struct OBIDMS_taxonomy_t
+    ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
+    
+    struct ecotxnode :
+        int32_t           taxid
+        int32_t           rank
+        int32_t           farest
+        ecotxnode*        parent
+        char*             name
+    
+    ctypedef ecotxnode ecotx_t
+
+
+    OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names)
+    
+    int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
+    
+    ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
+    
+    bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
+    
+    ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    

python/obitools3/obidms/capi/obitypes.pxd

@@ -1,12 +1,16 @@
 #cython: language_level=3
 
 
-from libc.stdint cimport int32_t
+from libc.stdint cimport int32_t, int64_t
+from posix.types cimport time_t
 
 
 cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
+cdef extern from "encode.h" nogil:
+    bint only_ATGC(const_char_p seq)
+
 
 cdef extern from "obidmscolumn.h" nogil:
 
@@ -15,13 +19,16 @@ cdef extern from "obidmscolumn.h" nogil:
 
 cdef extern from "obitypes.h" nogil:
 
-    enum OBIType:       # TODO je sais pas si ça sert de declarer le contenu de l'enum
-        OBI_VOID = 0,
+    enum OBIType:
+        OBI_VOID,
         OBI_INT,
         OBI_FLOAT,
         OBI_BOOL,
         OBI_CHAR,
+        OBI_STR,
+        OBI_SEQ,
         OBI_IDX
+
     
     ctypedef OBIType OBIType_t
     
@@ -32,12 +39,14 @@ cdef extern from "obitypes.h" nogil:
     ctypedef int32_t obiint_t
     ctypedef double obifloat_t
     ctypedef char obichar_t  
-    ctypedef size_t obiidx_t
+    ctypedef int64_t index_t
 
-    extern obiint_t   OBIInt_NA
-    extern obiidx_t   OBIIdx_NA
-    extern obifloat_t OBIFloat_NA
-    extern obichar_t  OBIChar_NA
-    extern obibool_t  OBIBool_NA
+    extern obiint_t      OBIInt_NA
+    extern index_t       OBIIdx_NA
+    extern obifloat_t    OBIFloat_NA
+    extern obichar_t     OBIChar_NA
+    extern obibool_t     OBIBool_NA
+    extern const_char_p  OBISeq_NA
+    extern const_char_p  OBIStr_NA
 
-    char* name_data_type(int data_type)
+    const_char_p name_data_type(int data_type)

python/obitools3/obidms/capi/obiview.pxd

@@ -0,0 +1,114 @@
+#cython: language_level=3
+
+from .obitypes           cimport const_char_p, \
+                                 OBIType_t, \
+                                 obiversion_t, \
+                                 index_t, \
+                                 time_t
+from ..capi.obidms       cimport OBIDMS_p
+from ..capi.obidmscolumn cimport OBIDMS_column_p
+
+
+cdef extern from "obiview.h" nogil:
+
+    extern const_char_p VIEW_TYPE_NUC_SEQS
+    extern const_char_p NUC_SEQUENCE_COLUMN
+    extern const_char_p ID_COLUMN
+    extern const_char_p DESCRIPTION_COLUMN
+
+    struct Column_reference_t :
+        const_char_p  column_name
+        obiversion_t  version
+    
+    ctypedef Column_reference_t* Column_reference_p
+
+
+    struct Obiview_t :
+        OBIDMS_p            dms
+        const_char_p        name
+        OBIDMS_column_p     line_selection
+        OBIDMS_column_p     new_line_selection
+        OBIDMS_column_p     columns
+        bint                read_only
+        Column_reference_t  line_selection_reference
+        index_t             line_count
+        int                 column_count
+        const_char_p        comments
+
+    ctypedef Obiview_t* Obiview_p
+
+
+    struct Obiview_infos_t :
+        int                 view_number
+        int                 column_count
+        index_t             line_count
+        const_char_p        name
+        const_char_p        created_from
+        time_t              creation_date
+        bint                all_lines
+        Column_reference_t  line_selection
+        Column_reference_p  column_references
+        const_char_p        view_type
+        const_char_p        comments
+
+    ctypedef Obiview_infos_t* Obiview_infos_p
+
+
+    struct Obiviews_header_t :
+        size_t header_size
+        size_t views_size
+        int    view_count
+    
+    ctypedef Obiviews_header_t* Obiviews_header_p
+
+
+    struct Obiviews_infos_all_t :
+        Obiviews_header_p    header
+        Obiview_infos_p      view_infos
+
+    ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
+
+
+    Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
+
+    Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
+    
+    Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
+
+    Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
+              
+    Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
+    
+    Obiviews_infos_all_p obi_read_views(OBIDMS_p dms)
+
+    int obi_unmap_read_views(Obiviews_infos_all_p views)
+
+    int obi_view_add_column(Obiview_p view,
+                            const_char_p column_name,
+                            obiversion_t version_number,
+                            OBIType_t data_type,
+                            index_t nb_lines,
+                            index_t nb_elements_per_line,
+                            const_char_p elements_names,
+                            const_char_p avl_name,
+                            const_char_p comments,
+                            bint create)
+
+    int obi_view_delete_column(Obiview_p view, const_char_p column_name)
+    
+    int obi_select_line(Obiview_p view, index_t line_nb)
+
+    int obi_select_lines(Obiview_p view, index_t* line_nbs)
+
+    OBIDMS_column_p obi_view_clone_column(Obiview_p view, const_char_p column_name)
+        
+    OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
+
+    OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
+
+    int obi_save_view(Obiview_p view)
+    
+    int obi_close_view(Obiview_p view)
+    
+    int obi_save_and_close_view(Obiview_p view)
+

python/obitools3/unit_tests.py

@@ -0,0 +1,311 @@
+import os
+import sys
+import shutil
+import unittest
+from random import randint, uniform, choice
+import string
+
+from obitools3.obidms._obidms import OBIDMS
+
+
+LINE_COUNT_FOR_TEST_COLUMN = 10000         # TODO randomize?
+SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000  # TODO randomize?
+NB_ELEMENTS_PER_LINE = 10                  # TODO randomize?
+DMS_NAME = "unit_test_dms"
+
+
+def create_test_obidms():
+    dms_name = DMS_NAME
+    dms_dir_name = dms_name+'.obidms'
+    dms = OBIDMS(dms_name)
+    return (dms, dms_name, dms_dir_name)
+
+
+def create_test_column(dms, data_type, multiple_elements_per_line=False):
+    
+    col_name = "unit_test_"+data_type
+
+    if multiple_elements_per_line :
+        elts_names = elements_names()
+        col = dms.open_column(col_name, 
+                              create=True, 
+                              type=data_type, 
+                              nb_elements_per_line=NB_ELEMENTS_PER_LINE,
+                              elements_names=elts_names)
+        return (col, col_name, elts_names)
+
+    else :
+        col = dms.open_column(col_name, 
+                              create=True, 
+                              type=data_type)
+        return (col, col_name)
+
+
+def elements_names():
+    names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
+    return names
+
+
+def random_obivalue(data_type):
+    r = 1000000
+    if data_type == "OBI_INT" :
+        return randint(-r,r)
+    elif data_type == "OBI_FLOAT" :
+        return uniform(-r,r)
+    elif data_type == "OBI_BOOL" :
+        return randint(0,1)
+    elif data_type == "OBI_CHAR" :
+        return choice(string.ascii_lowercase)
+    elif data_type == "OBI_STR" :
+        length = randint(1,200)
+        randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
+        return randoms
+    elif data_type == "OBI_SEQ" :
+        length = randint(1,200)
+        randoms = ''.join(choice("atgcryswkmdbhvn") for i in range(length))
+        return randoms
+
+class OBIDMS_Column_TestCase(unittest.TestCase):
+    def tearDown(self):
+        self.col.close()
+        self.dms.close()
+        shutil.rmtree(self.dms_dir_name, ignore_errors=True)
+    def test_OBIDMS_column_type(self):
+        assert self.col.get_data_type() == self.data_type, 'Wrong data type associated with column'
+    def test_OBIDMS_column_cloning(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            self.col[i]= random_obivalue(self.data_type)
+        self.col.close()
+        clone = self.dms.open_column(self.col_name, clone=True)
+        self.col = self.dms.open_column(self.col_name)
+        assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
+        i=0
+        for i in range(clone.get_nb_lines_used()) :
+            assert clone[i] == self.col[i], "Different value in original column and cloned column"
+            assert clone[i] is not None, "None value"
+        clone.close()
+    def test_OBIDMS_column_set_and_get(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            v = random_obivalue(self.data_type)
+            self.col[i] = v
+            assert self.col[i] == v, "Different value than the set value"
+            assert self.col[i] is not None, "None value"
+    def test_OBIDMS_referring_column(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            self.col[i] = random_obivalue(self.data_type)
+        ref_col = self.dms.open_column(self.col_name, referring=True)
+        j = 0
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            if i%2 :    # TODO randomize
+                ref_col.grep_line(i)
+                assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
+                assert ref_col[j] is not None, "None value"
+                j+=1
+
+
+class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
+    def test_OBIDMS_column_cloning(self):
+        pass
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type)
+            self.col[i] = v
+        self.col.close()
+        clone = self.dms.open_column(self.col_name, clone=True)
+        self.col = self.dms.open_column(self.col_name)
+        assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
+        i=0
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            assert self.col[i] == clone[i], "Different value in original column and cloned column"
+            assert self.col[i] is not None, "None value"
+        clone.close()
+    def test_OBIDMS_column_set_and_get_with_elements_names(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            for e in range(NB_ELEMENTS_PER_LINE) :
+                v = random_obivalue(self.data_type)
+                self.col.set_item(i, self.elts_names[e], v)
+                assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
+                assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
+    def test_OBIDMS_column_set_and_get(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type)
+            self.col[i] = v
+            assert self.col[i] == v, "Different value than the set value"
+            assert self.col[i] is not None, "None value"
+    def test_OBIDMS_referring_column(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type)
+            self.col[i] = v
+        ref_col = self.dms.open_column(self.col_name, referring=True)
+        j = 0
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            if i%2 :    # TODO randomize
+                ref_col.grep_line(i)
+                assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
+                assert ref_col[j] is not None, "None value"
+                j+=1
+        ref_col.close()
+
+
+class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_INT'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_INT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_INT'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_FLOAT_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_FLOAT'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_FLOAT'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_BOOL_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_BOOL'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_BOOL'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_CHAR_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_CHAR'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                                self.data_type)
+       
+
+class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_CHAR'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_STR'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_STR'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+class OBIDMS_Column_OBI_SEQ_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_SEQ'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_SEQ'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
+
+if __name__ == '__main__': 
+     unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
+                                             "OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_FLOAT_TestCase",
+                                             "OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_BOOL_TestCase",
+                                             "OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_CHAR_TestCase",
+                                             "OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_STR_TestCase",
+                                             "OBIDMS_Column_OBI_STR_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_SEQ_TestCase",
+                                             "OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase"])
+
+

python/obitools3/version.py

@@ -1,5 +1,5 @@
-major = 1
-minor = 1
-serial= '16'
+major = 0
+minor = 0
+serial= '0'
 
-version ="%2d.%02d.%s" % (major,minor,serial)
+version ="%d.%02d.%s" % (major,minor,serial)

src/encode.c

@@ -0,0 +1,345 @@
+/****************************************************************************
+ * Encoding functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file encode.c
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Functions encoding DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <math.h>
+
+#include "encode.h"
+#include "obierrno.h"
+#include "obitypes.h"	// For byte_t type
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO: endianness problem?
+
+
+
+bool only_ATGC(char* seq)
+{
+	char* c = seq;
+
+	while (*c)
+	{
+		if (!((*c == 'A') || \
+			  (*c == 'T') || \
+			  (*c == 'G') || \
+			  (*c == 'C') || \
+			  (*c == 'a') || \
+			  (*c == 't') || \
+			  (*c == 'g') || \
+			  (*c == 'c')))
+		{
+			return 0;
+		}
+		else
+		{
+			c++;
+		}
+	}
+	return 1;
+}
+
+
+byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
+{
+	byte_t*  seq_b;
+	uint8_t  modulo;
+	int32_t  length_b;
+	int32_t  i;
+
+	length_b = ceil((double) length / (double) 4.0);
+
+	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+
+	// Initialize all the bits to 0
+	memset(seq_b, 0, length_b);
+
+	for (i=0; i<length; i++)
+	{
+		// Shift of 2 to make place for new nucleotide
+		seq_b[i/4] <<= 2;
+
+		// Add new nucleotide
+		switch (seq[i])
+		{
+		case 'a':
+		case 'A':
+			seq_b[i/4] |= NUC_A_2b;
+			break;
+		case 'c':
+		case 'C':
+			seq_b[i/4] |= NUC_C_2b;
+			break;
+		case 'g':
+		case 'G':
+			seq_b[i/4] |= NUC_G_2b;
+			break;
+		case 't':
+		case 'T':
+			seq_b[i/4] |= NUC_T_2b;
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
+			return NULL;
+		}
+	}
+
+	// Final shift for the last byte if needed
+	modulo = (length % 4);
+	if (modulo)
+		seq_b[(i-1)/4] <<= (2*(4 - modulo));
+
+	return seq_b;
+}
+
+
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
+{
+	char*   seq;
+	int32_t i;
+	uint8_t shift;
+	uint8_t mask;
+	uint8_t nuc;
+
+	seq = (char*) malloc((length_seq+1) * sizeof(char));
+
+	for (i=0; i<length_seq; i++)
+	{
+		shift = 6 - 2*(i % 4);
+		mask = NUC_MASK_2B << shift;
+		nuc = (seq_b[i/4] & mask) >> shift;
+
+		switch (nuc)
+		{
+		case NUC_A_2b:
+			seq[i] = 'a';
+			break;
+		case NUC_C_2b:
+			seq[i] = 'c';
+			break;
+		case NUC_G_2b:
+			seq[i] = 'g';
+			break;
+		case NUC_T_2b:
+			seq[i] = 't';
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when decoding");
+			return NULL;
+		}
+	}
+
+	seq[length_seq] = '\0';
+
+	return seq;
+}
+
+
+byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
+{
+	byte_t*  seq_b;
+	uint8_t  modulo;
+	int32_t  length_b;
+	int32_t  i;
+
+	length_b = ceil((double) length / (double) 2.0);
+
+	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+
+	// Initialize all the bits to 0
+	memset(seq_b, 0, length_b);
+
+	for (i=0; i<length; i++)
+	{
+		// Shift of 4 to make place for new nucleotide
+		seq_b[i/2] <<= 4;
+
+		// Add new nucleotide
+		switch (seq[i])
+		{
+		case 'a':
+		case 'A':
+			seq_b[i/2] |= NUC_A_4b;
+			break;
+		case 'c':
+		case 'C':
+			seq_b[i/2] |= NUC_C_4b;
+			break;
+		case 'g':
+		case 'G':
+			seq_b[i/2] |= NUC_G_4b;
+			break;
+		case 't':
+		case 'T':
+			seq_b[i/2] |= NUC_T_4b;
+			break;
+		case 'r':
+		case 'R':
+			seq_b[i/2] |= NUC_R_4b;
+			break;
+		case 'y':
+		case 'Y':
+			seq_b[i/2] |= NUC_Y_4b;
+			break;
+		case 's':
+		case 'S':
+			seq_b[i/2] |= NUC_S_4b;
+			break;
+		case 'w':
+		case 'W':
+			seq_b[i/2] |= NUC_W_4b;
+			break;
+		case 'k':
+		case 'K':
+			seq_b[i/2] |= NUC_K_4b;
+			break;
+		case 'm':
+		case 'M':
+			seq_b[i/2] |= NUC_M_4b;
+			break;
+		case 'b':
+		case 'B':
+			seq_b[i/2] |= NUC_B_4b;
+			break;
+		case 'd':
+		case 'D':
+			seq_b[i/2] |= NUC_D_4b;
+			break;
+		case 'h':
+		case 'H':
+			seq_b[i/2] |= NUC_H_4b;
+			break;
+		case 'v':
+		case 'V':
+			seq_b[i/2] |= NUC_V_4b;
+			break;
+		case 'n':
+		case 'N':
+			seq_b[i/2] |= NUC_N_4b;
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
+			return NULL;
+		}
+	}
+
+	// Final shift for the last byte if needed
+	modulo = (length % 2);
+	if (modulo)
+		seq_b[(i-1)/2] <<= (4*modulo);
+
+	return seq_b;
+}
+
+
+char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
+{
+	char*   seq;
+	int32_t i;
+	uint8_t shift;
+	uint8_t mask;
+	uint8_t nuc;
+
+	seq = (char*) malloc((length_seq+1) * sizeof(char));
+
+	for (i=0; i<length_seq; i++)
+	{
+		shift = 4 - 4*(i % 2);
+		mask = NUC_MASK_4B << shift;
+		nuc = (seq_b[i/2] & mask) >> shift;
+
+		switch (nuc)
+		{
+		case NUC_A_4b:
+			seq[i] = 'a';
+			break;
+		case NUC_C_4b:
+			seq[i] = 'c';
+			break;
+		case NUC_G_4b:
+			seq[i] = 'g';
+			break;
+		case NUC_T_4b:
+			seq[i] = 't';
+			break;
+		case NUC_R_4b:
+			seq[i] = 'r';
+			break;
+		case NUC_Y_4b:
+			seq[i] = 'y';
+			break;
+		case NUC_S_4b:
+			seq[i] = 's';
+			break;
+		case NUC_W_4b:
+			seq[i] = 'w';
+			break;
+		case NUC_K_4b:
+			seq[i] = 'k';
+			break;
+		case NUC_M_4b:
+			seq[i] = 'm';
+			break;
+		case NUC_B_4b:
+			seq[i] = 'b';
+			break;
+		case NUC_D_4b:
+			seq[i] = 'd';
+			break;
+		case NUC_H_4b:
+			seq[i] = 'h';
+			break;
+		case NUC_V_4b:
+			seq[i] = 'v';
+			break;
+		case NUC_N_4b:
+			seq[i] = 'n';
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when decoding");
+			return NULL;
+		}
+	}
+
+	seq[length_seq] = '\0';
+
+	return seq;
+}
+
+
+///////////////////// FOR DEBUGGING ///////////////////////////
+//NOTE: The first byte is printed the first (at the left-most).
+
+void print_bits(void* ptr, int32_t size)
+{
+	uint8_t* b = (uint8_t*) ptr;
+	uint8_t byte;
+    int32_t i, j;
+
+    fprintf(stderr, "\n");
+    for (i=0;i<size;i++)
+    {
+        for (j=7;j>=0;j--)
+        {
+            byte = b[i] & (1<<j);
+            byte >>= j;
+            fprintf(stderr, "%u", byte);
+        }
+        fprintf(stderr, " ");
+    }
+    fprintf(stderr, "\n");
+}

src/encode.h

@@ -0,0 +1,181 @@
+/****************************************************************************
+ * Encoding header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file encode.h
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Header file for encoding DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <stdbool.h>
+
+#include "obitypes.h"
+
+
+#define NUC_MASK_2B 0x3   /**< Binary: 11 to use when decoding 2 bits sequences */
+#define NUC_MASK_4B 0xF  /**< Binary: 1111 to use when decoding 4 bits sequences */
+
+
+/**
+ * @brief enum for the 2-bits codes for each of the 4 nucleotides.
+ */
+enum
+{
+    NUC_A_2b = 0x0,   /* binary: 00 */
+    NUC_C_2b = 0x1,   /* binary: 01 */
+    NUC_G_2b = 0x2,   /* binary: 10 */
+    NUC_T_2b = 0x3,   /* binary: 11 */
+};
+
+
+/**
+ * @brief enum for the 4-bits codes for each of the 15 IUPAC nucleotides.
+ */
+enum
+{
+    NUC_A_4b = 0x1,   /* binary: 0001 */
+    NUC_C_4b = 0x2,   /* binary: 0010 */
+    NUC_G_4b = 0x3,   /* binary: 0011 */
+    NUC_T_4b = 0x4,   /* binary: 0100 */
+	NUC_R_4b = 0x5,   /* binary: 0101 */
+	NUC_Y_4b = 0x6,   /* binary: 0110 */
+	NUC_S_4b = 0x7,   /* binary: 0111 */
+	NUC_W_4b = 0x8,   /* binary: 1000 */
+	NUC_K_4b = 0x9,   /* binary: 1001 */
+	NUC_M_4b = 0xA,   /* binary: 1010 */
+	NUC_B_4b = 0xB,   /* binary: 1011 */
+	NUC_D_4b = 0xC,   /* binary: 1100 */
+	NUC_H_4b = 0xD,   /* binary: 1101 */
+	NUC_V_4b = 0xE,   /* binary: 1110 */
+	NUC_N_4b = 0xF,   /* binary: 1111 */
+};
+
+
+/**
+ * @brief Checks if there are only 'atgcATGC' characters in a
+ *        character string.
+ *
+ * @param seq The sequence to check.
+ *
+ * @returns A boolean value indicating if there are only
+ *          'atgcATGC' characters in a character string.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool only_ATGC(char* seq);
+
+
+/**
+ * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
+ *
+ *    A or a : 00
+ *    C or c : 01
+ *    T or t : 10
+ *    G or g : 11
+ *
+ * @warning The DNA sequence must contain only 'atgcATGC' characters.
+ *
+ * @param seq The sequence to encode.
+ * @param length The length of the sequence to encode.
+ *
+ * @returns The encoded sequence.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
+
+
+/**
+ * @brief Decodes a DNA sequence that is coded with each nucleotide on 2 bits.
+ *
+ *    00 -> a
+ *    01 -> c
+ *    10 -> t
+ *    11 -> g
+ *
+ * @param seq The sequence to decode.
+ * @param length_seq The initial length of the sequence before it was encoded.
+ *
+ * @returns The decoded sequence ended with '\0'.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
+
+
+/**
+ * @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
+ *
+ *		A or a : 0001
+ *      C or c : 0010
+ *      G or g : 0011
+ *      T or t : 0100
+ *      R or r : 0101
+ *      Y or y : 0110
+ *      S or s : 0111
+ *      W or w : 1000
+ *      K or k : 1001
+ *      M or m : 1010
+ *      B or b : 1011
+ *      D or d : 1100
+ *      H or h : 1101
+ *      V or v : 1110
+ *      N or n : 1111
+ *
+ * @warning The DNA sequence must contain only IUPAC characters.
+ *
+ * @param seq The sequence to encode.
+ * @param length The length of the sequence to encode.
+ *
+ * @returns The encoded sequence.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* encode_seq_on_4_bits(char* seq, int32_t length);
+
+
+/**
+ * @brief Decodes a DNA sequence that is coded with each nucleotide on 4 bits.
+ *
+ *		A or a : 0001
+ *      C or c : 0010
+ *      G or g : 0011
+ *      T or t : 0100
+ *      R or r : 0101
+ *      Y or y : 0110
+ *      S or s : 0111
+ *      W or w : 1000
+ *      K or k : 1001
+ *      M or m : 1010
+ *      B or b : 1011
+ *      D or d : 1100
+ *      H or h : 1101
+ *      V or v : 1110
+ *      N or n : 1111
+ *
+ * @param seq The sequence to decode.
+ * @param length_seq The initial length of the sequence before it was encoded.
+ *
+ * @returns The decoded sequence ended with '\0'.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
+
+
+////////// FOR DEBUGGING ///////////
+
+// little endian
+void print_bits(void* ptr, int32_t length);
+

src/obiavl.h

@@ -0,0 +1,350 @@
+/****************************************************************************
+ * OBIDMS AVL tree header file	                                            *
+ ****************************************************************************/
+
+/**
+ * @file obiavl.h
+ * @author Celine Mercier
+ * @date December 3rd 2015
+ * @brief Header file for handling AVL trees for storing and retrieving byte arrays (i.e. coding for character strings).
+ */
+
+
+#ifndef OBIAVL_H_
+#define OBIAVL_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <time.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+
+
+#define AVL_MAX_NAME (1024) 								/**< The maximum length of an AVL tree name.
+                              	  	 	 	 	 	 	 	 */
+#define AVL_GROWTH_FACTOR (2)								/**< The growth factor when an AVL tree is enlarged.
+                                	 	 	 	 	 	 	 */
+#define AVL_MAX_DEPTH (1000)								/**< The maximum depth of an AVL tree.
+                                	 	 	 	 	 	 	 */
+#define LEFT_CHILD(node)	(avl->tree)+(node->left_child)  /**< Pointer to the left child of a node in an AVL tree.
+															 */
+#define RIGHT_CHILD(node)	(avl->tree)+(node->right_child) /**< Pointer to the right child of a node in an AVL tree.
+															 */
+#define BYTE_ARRAY_HEADER_SIZE (9)  						/**< The size of the header of a byte array.
+                              	  	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief AVL tree node structure.
+ */
+typedef struct AVL_node {
+	index_t left_child;		/**< Index of left less child node.
+	  	 	 	 	 	 	 */
+	index_t right_child; 	/**< Index of right greater child node.
+	 	 	 	 	 	 	 */
+	int8_t balance_factor; /**< Balance factor of the node.
+							 */
+	index_t value;			/**< Index of the value associated with the node in the data array.
+							 */
+} AVL_node_t, *AVL_node_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data header structure.
+ */
+typedef struct OBIDMS_avl_data_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_used;						/**< Size of the data used in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_max;						/**< Max size of the data in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_avl_data_header_t, *OBIDMS_avl_data_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data structure.
+ */
+typedef struct OBIDMS_avl_data {
+	OBIDMS_avl_data_header_p	header; 		 	/**< A pointer to the header of the AVL tree data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	byte_t*                   	data;   		 	/**< A pointer to the beginning of the data.
+													 */
+} OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
+
+
+/**
+ * @brief OBIDMS AVL tree header structure.
+ */
+typedef struct OBIDMS_avl_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	size_t		avl_size;							/**< Size of the AVL tree in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items in the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items_max;						/**< Maximum number of items in the AVL tree before it has to be enlarged.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		root_idx;							/**< Index of the root of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree structure.
+ */
+typedef struct OBIDMS_avl {
+	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the AVL tree belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_avl_header_p			header; 	 		/**< A pointer to the header of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	struct AVL_node*           	tree;   		 	/**< A pointer to the root of the AVL tree.
+													 */
+	index_t                     path_idx[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of node indices.
+													 	     */
+	int8_t                      path_dir[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of directions
+															 * (0 for left, -1 for right).
+															 */
+	OBIDMS_avl_data_p			data;				/**< A pointer to the structure containing the data
+													 *   that the AVL tree references.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	DIR*						directory;			/**< A directory entry usable to
+										 	 	 	 *    refer and scan the AVL tree directory.
+										 	 	 	 */
+	int							dir_fd;				/**< The file descriptor of the directory entry
+													 *    usable to refer and scan the AVL tree directory.
+													 */
+	int							avl_fd;				/**< The file descriptor of the file
+													 *    to refer and scan the AVL tree.
+													 */
+	int							data_fd;				/**< The file descriptor of the file
+													 *    to refer and scan the data referred to by the AVL tree.
+													 */
+	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the AVL tree is used.
+													 */
+} OBIDMS_avl_t, *OBIDMS_avl_p;
+
+
+/**
+ * @brief Checks if an AVL tree already exists or not.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A value indicating whether the AVL tree exists or not.
+ * @retval 1 if the AVL tree exists.
+ * @retval 0 if the AVL tree does not exist.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_avl_exists(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree and creates it if it does not already exist.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Creates an AVL tree. Fails if it already exists.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the newly created AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree. Fails if it does not already exist.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Closes an AVL tree.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param avl A pointer to the AVL tree structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_avl(OBIDMS_avl_p avl);
+
+
+/**
+ * @brief Adds a value (byte array) in an AVL tree, checking if it is already in it.
+ *
+ * @warning The byte array to add must already be encoded and contain its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The byte array to add in the AVL tree.
+ *
+ * @returns The index of the value, whether it was added or already in the AVL tree.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value);
+
+
+/**
+ * @brief Finds a value (byte array) in an AVL tree, checking first if it is already in it.
+ *
+ * @warning The byte array to add must already be encoded and contain its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The byte array to add in the AVL tree.
+ *
+ * @returns The data index of the value.
+ * @retval -1 if the value is not in the tree.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_find(OBIDMS_avl_p avl, byte_t* value);
+
+
+/**
+ * @brief Recovers a value (byte array) in an AVL tree.
+ *
+ * @warning The byte array recovered is encoded and contains its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param index The index of the value in the data array.
+ *
+ * @returns A pointer to the byte array recovered.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t index);
+
+
+/**
+ * @brief Converts a character string to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_str_to_obibytes(char* value);
+
+
+/**
+ * @brief Converts a byte array to a character string.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the character string contained in the byte array.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_str(byte_t* value_b);
+
+
+/**
+ * @brief Converts a DNA sequence to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_seq_to_obibytes(char* seq);
+
+
+/**
+ * @brief Converts a byte array to a DNA sequence.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the byte array.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_seq(byte_t* value_b);
+
+
+#endif /* OBIAVL_H_ */
+

src/obidebug.h

@@ -1,8 +1,12 @@
-/*
- * obidebug.h
- *
- *  Created on: June 25th 2015
- *      Author: Celine Mercier (celine.mercier@metabarcoding.org)
+/****************************************************************************
+ * Header file for the debugging code                                       *
+ ****************************************************************************/
+
+/**
+ * @file obidebug.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 25 June 2015
+ * @brief Header file for the debugging code.
  */
 
 
@@ -12,7 +16,7 @@
 #include <limits.h>
 
 
-//#ifndef DEBUG_LEVEL
+//#ifndef DEBUG_LEVEL			// TODO
 //#define DEBUG_LEVEL MAXINT
 //#endif
 

src/obidms.c

@@ -1,14 +1,21 @@
-/*
- * obidms.c
- *
- *  @date 23 May 2015
- *  @Author: coissac
+/********************************************************************
+ * OBIDMS functions                                                 *
+ ********************************************************************/
+
+/**
+ * @file obidms.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief OBIDMS functions.
  */
 
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
+#include <stdbool.h>
 #include <sys/stat.h>
+#include <fcntl.h>
 #include <sys/types.h>
 #include <dirent.h>
 
@@ -16,9 +23,11 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obidmscolumn.h"
+#include "private_at_functions.h"
+#include "obilittlebigman.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**************************************************************************
@@ -29,27 +38,60 @@
 
 
 /**
- * Internal function building the directory name from an OBIDMS name.
+ * Internal function building the OBIDMS directory name from an OBIDMS name.
  *
  * The function builds the directory name corresponding to an OBIDMS.
- * It checks also that the name is not too long.
+ * It also checks that the name is not too long.
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param dms_name the name of the OBIDMS
+ * @param dms_name The name of the OBIDMS.
  *
- * @return a pointer to the directory name
- * @retvalue <directory_name> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the directory name.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-static char *build_directory_name(const char *dms_name);
+static char* build_directory_name(const char* dms_name);
+
+
+/**
+ * Internal function building the informations file name from an OBIDMS name.
+ *
+ * The function builds the file name for the informations file of an OBIDMS.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @returns A pointer to the file name.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static char* build_infos_file_name(const char* dms_name);
+
+
+/**
+ * Internal function creating the file containing basic informations on the OBIDMS.
+ *
+ * This file contains:
+ * 		- The endianness of the platform
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_file_descriptor The file descriptor for the OBIDMS directory.
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);
 
 
 /************************************************************************
@@ -58,9 +100,9 @@ static char *build_directory_name(const char *dms_name);
  *
  ************************************************************************/
 
-static char *build_directory_name(const char *dms_name)
+static char* build_directory_name(const char* dms_name)
 {
-	char *directory_name;
+	char* directory_name;
 
 	// Build the database directory name
 	if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)
@@ -83,6 +125,74 @@ static char *build_directory_name(const char *dms_name)
 }
 
 
+static char* build_infos_file_name(const char* dms_name)
+{
+	char* file_name;
+
+	// Build file name
+	if (asprintf(&file_name, "%s_infos", dms_name) < 0)
+	{
+		obi_set_errno(OBIDMS_MEMORY_ERROR);
+		obidebug(1, "\nProblem building an informations file name");
+		return NULL;
+	}
+
+	return file_name;
+}
+
+
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
+{
+	char* 	file_name;
+	int 	infos_file_descriptor;
+	off_t 	file_size;
+	bool	little_endian;
+
+	file_size = sizeof(bool);
+
+	// Create file name
+	file_name = build_infos_file_name(dms_name);
+	if (file_name == NULL)
+		return -1;
+
+    // Create file
+	infos_file_descriptor = openat(dms_file_descriptor, file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
+	if (infos_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError creating an informations file");
+		free(file_name);
+		return -1;
+	}
+
+	free(file_name);
+
+	// Truncate the infos file to the right size
+	if (ftruncate(infos_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError truncating an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Write endianness
+	little_endian = obi_is_little_endian();
+	if (write(infos_file_descriptor, &little_endian, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError writing the endianness in an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Close file
+	close(infos_file_descriptor);
+
+	return 0;
+}
+
+
 /**********************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
@@ -92,8 +202,8 @@ static char *build_directory_name(const char *dms_name)
 int obi_dms_exists(const char* dms_name)
 {
     struct stat buffer;
-	char *directory_name;
-    int check_dir;
+	char*       directory_name;
+    int 		check_dir;
 
 	// Build and check the directory name
     directory_name = build_directory_name(dms_name);
@@ -113,7 +223,9 @@ int obi_dms_exists(const char* dms_name)
 
 OBIDMS_p obi_create_dms(const char* dms_name)
 {
-	char *directory_name;
+	char* directory_name;
+	DIR*  dms_dir;
+	int   dms_file_descriptor;
 
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
@@ -124,7 +236,10 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 	if (mkdir(directory_name, 00777) < 0)
 	{
 		if (errno == EEXIST)
+		{
 			obi_set_errno(OBIDMS_EXIST_ERROR);
+			obidebug(1, "\nAn OBIDMS directory with the same name already exists in this directory.");
+		}
 		else
 			obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		obidebug(1, "\nProblem creating an OBIDMS directory");
@@ -132,8 +247,38 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
+	// Get file descriptor of DMS directory to create the AVL trees directory
+	dms_dir = opendir(directory_name);
+	if (dms_dir == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nProblem opening a newly created OBIDMS directory");
+		free(directory_name);
+		return NULL;
+	}
+
 	free(directory_name);
 
+	dms_file_descriptor = dirfd(dms_dir);
+	if (dms_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nProblem getting the file descriptor of a newly created OBIDMS directory");
+		return NULL;
+	}
+
+	// Create the AVL trees directory
+	if (mkdirat(dms_file_descriptor, AVL_TREES_DIR_NAME, 00777) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nProblem creating an AVL trees directory");
+		return NULL;
+	}
+
+	// Create the informations file
+	if (create_dms_infos_file(dms_file_descriptor, dms_name) < 0)
+		return NULL;
+
 	return obi_open_dms(dms_name);
 }
 
@@ -142,18 +287,36 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 {
 	OBIDMS_p	dms;
 	char*	 	directory_name;
-	DIR*		directory;
+	char* 		infos_file_name;
+	int			infos_file_descriptor;
+	bool		little_endian_dms;
+	bool 		little_endian_platform;
 
 	dms = NULL;
 
+	// Allocate the data structure
+	dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
+	if (dms == NULL)
+	{
+		obi_set_errno(OBIDMS_MEMORY_ERROR);
+		obidebug(1, "\nError allocating the memory for the OBIDMS structure");
+		return NULL;
+	}
+
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
 	if (directory_name == NULL)
+	{
+		free(dms);
 		return NULL;
+	}
+
+	strncpy(dms->directory_name, directory_name, OBIDMS_MAX_NAME);
+	free(directory_name);
 
 	// Try to open the directory
-	directory = opendir(directory_name);
-	if (directory == NULL)
+	dms->directory = opendir(dms->directory_name);
+	if (dms->directory == NULL)
 	{
 		switch (errno)
 		{
@@ -173,25 +336,92 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 				obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		}
 		obidebug(1, "\nCan't open OBIDMS directory");
-		free(directory_name);
+		free(dms);
 		return NULL;
 	}
 
-	// Allocate the data structure
-	dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
-	if (dms == NULL)
+	// Get and store file descriptor of DMS directory to open the informations file
+	dms->dir_fd = dirfd(dms->directory);
+	if (dms->dir_fd < 0)
 	{
-		obi_set_errno(OBIDMS_MEMORY_ERROR);
-		obidebug(1, "\nError allocating the memory for the OBIDMS structure");
-		free(directory_name);
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor for a newly created OBIDMS directory");
+		closedir(dms->directory);
+		free(dms);
 		return NULL;
 	}
 
-	// Initialize the data structure
-	strcpy(dms->directory_name, directory_name);
-	dms->directory = directory;
+	// Open informations file to check endianness
+	infos_file_name = build_infos_file_name(dms_name);
+	infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
+	if (infos_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening an informations file");
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
 
-	free(directory_name);
+	free(infos_file_name);
+
+	// Check endianness of the platform and DMS
+	little_endian_platform = obi_is_little_endian();
+	if (read(infos_file_descriptor, &little_endian_dms, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError reading the endianness in an informations file");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+	if (little_endian_platform != little_endian_dms)
+	{
+		obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
+		obidebug(1, "\nError: The DMS and the platform have different endianness");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	close(infos_file_descriptor);
+
+	dms->little_endian = little_endian_dms;
+
+	// Open the AVL trees directory
+	dms->avl_directory = private_opendirat(dms->dir_fd, AVL_TREES_DIR_NAME);
+	if (dms->avl_directory == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening the AVL trees directory");
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	// Store the AVL trees directory's file descriptor
+	dms->avl_dir_fd = dirfd(dms->avl_directory);
+	if (dms->avl_dir_fd < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor of the AVL trees directory");
+		closedir(dms->avl_directory);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	// Initialize the list of opened columns
+	dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
+	(dms->opened_columns)->columns = (OBIDMS_column_p*) malloc(MAX_NB_OPENED_COLUMNS*sizeof(OBIDMS_column_p));
+	(dms->opened_columns)->nb_opened_columns = 0;
+
+	// Initialize the list of opened AVL trees
+	dms->opened_avls = (Opened_avls_list_p) malloc(sizeof(Opened_avls_list_t));
+	(dms->opened_avls)->avls = (OBIDMS_avl_p*) malloc(MAX_NB_OPENED_AVL_TREES*sizeof(OBIDMS_avl_p));
+	(dms->opened_avls)->nb_opened_avls = 0;
 
 	return dms;
 }
@@ -220,10 +450,22 @@ int obi_close_dms(OBIDMS_p dms)
 {
 	if (dms != NULL)
 	{
+		// Close all columns
+		while ((dms->opened_columns)->nb_opened_columns > 0)
+			obi_close_column(*((dms->opened_columns)->columns));
+
+		// Close dms and AVL trees directories
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
-			obidebug(1, "\nError closing an OBIDSM directory");
+			obidebug(1, "\nError closing an OBIDMS directory");
+			free(dms);
+			return -1;
+		}
+		if (closedir(dms->avl_directory) < 0)
+		{
+			obi_set_errno(OBI_AVL_ERROR);
+			obidebug(1, "\nError closing an AVL trees directory");
 			free(dms);
 			return -1;
 		}

src/obidms.h

@@ -1,54 +1,99 @@
-/*
- * obidms.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/********************************************************************
+ * OBIDMS header file                                               *
+ ********************************************************************/
+
+/**
+ * @file obidmscolumn.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for the OBIDMS functions and structures.
  */
 
+
 #ifndef OBIDMS_H_
 #define OBIDMS_H_
 
+
 #include <stdlib.h>
 #include <sys/stat.h>
 #include <errno.h>
 #include <dirent.h>
 #include <string.h>
 #include <stdio.h>
+#include <stdbool.h>
 
 #include "obierrno.h"
 
-#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name
-                                */
 
-/** @brief A structure describing an OBIDMS instance
+#define OBIDMS_MAX_NAME (2048) 	    		/**< The maximum length of an OBIDMS name.
+                                	 	 	 */
+#define AVL_TREES_DIR_NAME "AVL_trees"    	/**< The name of the AVL trees directory.
+                                	 	 	 */
+#define TAXONOMY_DIR_NAME "TAXONOMY"    	/**< The name of the taxonomy directory.
+                                	 	 	 */
+#define MAX_NB_OPENED_COLUMNS (100) 		/**< The maximum number of columns open at the same time.
+                                	 	 	 */
+#define MAX_NB_OPENED_AVL_TREES (100)  		/**< The maximum number of AVL trees open at the same time.
+                                	 	 	 */
+
+
+struct OBIDMS_column;		// TODO
+
+typedef struct Opened_columns_list {
+	size_t	 		 		nb_opened_columns;
+	struct OBIDMS_column** 	columns;				// TODO allocate array size here
+} Opened_columns_list_t, *Opened_columns_list_p;
+
+
+struct OBIDMS_avl;		// TODO
+
+typedef struct Opened_avls_list {
+	size_t	 		 		nb_opened_avls;
+	struct OBIDMS_avl** 	avls;
+} Opened_avls_list_t, *Opened_avls_list_p;
+
+
+/**
+ * @brief A structure describing an OBIDMS instance
  *
  * A pointer to this structure is returned on creation
  * and opening of an OBITools Data Management System (DMS)
  */
-
 typedef struct OBIDMS {
-	char	directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
-	                                     	 	 *   containing the DMS
-	                                     	 	 */
-	DIR*	directory;							/**< A directory entry usable to
-										 	 	 *   refer and scan the database directory
-										 	 	 */
+	char					directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
+																 *   containing the DMS.
+																 */
+	DIR*					directory;							/**< A directory entry usable to
+																 *   refer and scan the database directory.
+																 */
+	int     				dir_fd;								/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the database directory.
+																 */
+	DIR*					avl_directory;						/**< A directory entry usable to
+																 *   refer and scan the AVL trees directory.
+																 */
+	int						avl_dir_fd;							/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the AVL trees directory.
+																 */
+	bool					little_endian;						/**< Endianness of the database.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Opened_columns_list_p 	opened_columns;						/**< List of opened columns.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Opened_avls_list_p 		opened_avls;						/**< List of opened AVL trees.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_t, *OBIDMS_p;
 
 
-/*@
- * @brief Checks if an OBIDMS exists
+/**
+ * @brief Checks if an OBIDMS exists.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<dms_name>.obidms`.
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return an integer value indicating the status of the database
- * @retvalue 1 the database exist
- * @retvalue 0 the database does not exist
- * @retvalue -1 an error occurred
+ * @returns An integer value indicating the status of the database
+ * @retval 1 if the database exists.
+ * @retval 0 if the database does not exist.
+ * @retval -1 if an error occurred.
  *
- * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
@@ -62,79 +107,64 @@ int obi_dms_exists(const char* dms_name);
  * if a directory with this name does not already exist
  * before creating the new database.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<name>.obidms`
+ * A directory to store AVL trees is also created.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno` variable is set.
+ * @param dms_name A pointer to a C string containing the name of the database.
+ *                 The actual directory name used to store the DMS will be
+ *                 `<dms_name>.obidms`.
  *
- * ###Error values
- * 		- OBIDMS_EXIST_ERROR     : a database with the same name already exists.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the newly created DMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_create_dms(const char *dms_name);
+OBIDMS_p obi_create_dms(const char* dms_name);
 
 
 /**
  * @brief Opens an existing OBITools Data Management instance (OBIDMS).
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<name>.obidms`
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the opened DMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_open_dms(const char *dms_name);
+OBIDMS_p obi_open_dms(const char* dms_name);
 
 
 /**
- * @brief Creates a new OBIDMS instance.
+ * @brief Creates or opens a new OBIDMS instance.
  *
  * If the database already exists, this function opens it, otherwise it
  * creates a new database.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS is
- *             `<name>.obidms`
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the OBIDMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_dms(const char *dms_name);
+OBIDMS_p obi_dms(const char* dms_name);
 
 
 /**
  * @brief Closes an opened OBITools Data Management instance (OBIDMS).
  *
- * @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
+ * @param dms A pointer as returned by obi_create_dms() or obi_open_dms().
  *
- * @return an integer value indicating the success of the operation. Even on
- * 		   error, the `OBIDMS` structure is freed
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation. Even on
+ * 		    error, the `OBIDMS` structure is freed.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred?-.
  *
  * @see obi_create_dms()
  * @see obi_open_dms()

src/obidms_taxonomy.c

@@ -0,0 +1,681 @@
+/********************************************************************
+ * OBIDMS taxonomy functions                                        *
+ ********************************************************************/
+
+/**
+ * @file obidms_taxonomy.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date March 2nd 2016
+ * @brief Functions for reading binary taxonomy files.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdbool.h>
+#include <fcntl.h>
+
+#include "obidms_taxonomy.h"
+#include "obidms.h"
+#include "obidebug.h"
+#include "obierrno.h"
+#include "private_at_functions.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+// TODO : the malloc aren't checked but won't exist for long because mapping instead
+
+
+int compareRankLabel(const void *label1, const void *label2)
+{
+	return strcmp((const char*)label1,*(const char**)label2);
+}
+
+
+int32_t rank_index(const char* label, ecorankidx_t* ranks)
+{
+	char **rep;
+
+	rep = bsearch(label, ranks->label, ranks->count, sizeof(char*), compareRankLabel);
+
+	if (rep)
+		return rep-ranks->label;	// TODO what???
+
+	return -1;
+}
+
+
+void* read_ecorecord(FILE* f, int32_t* record_size)
+{
+	static void* buffer = NULL;
+	int32_t      buffer_size = 0;
+	int32_t      read;
+
+	if (!record_size)
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: record_size can not be NULL");
+ 		return NULL;
+	}
+
+	read = fread(record_size,
+	      		 1,
+	      		 sizeof(int32_t),
+	             f);
+
+	if (feof(f))
+		return NULL;
+
+	if (read != sizeof(int32_t))
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: error reading record size");
+ 		return NULL;
+	}
+
+//	if (is_big_endian())						// TODO
+//		*recordSize=swap_int32_t(*recordSize);
+
+	if (buffer_size < *record_size)
+	{
+		if (buffer)
+			buffer = realloc(buffer, *record_size);
+		else
+			buffer = malloc(*record_size);
+		if (buffer == NULL)
+		{
+	 		obi_set_errno(OBI_TAXONOMY_ERROR);
+	 		obidebug(1, "\nError reading a taxonomy file: error allocating memory");
+	 		return NULL;
+		}
+	}
+
+	read = fread(buffer,
+	             1,
+				 *record_size,
+				 f);
+
+	if (read != *record_size)
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: error reading a record %d, %d", read, *record_size);
+ 		return NULL;
+	}
+
+	return buffer;
+};
+
+
+ecotx_t* readnext_ecotaxon(FILE* f, ecotx_t* taxon)
+{
+	ecotxformat_t* raw;
+	int32_t        record_length;
+
+	raw = read_ecorecord(f, &record_length);
+
+	if (!raw)
+		return NULL;
+
+//	if (is_big_endian())		// TODO
+//	{
+//		raw->namelength = swap_int32_t(raw->namelength);
+//		raw->parent     = swap_int32_t(raw->parent);
+//		raw->rank       = swap_int32_t(raw->rank);
+//		raw->taxid      = swap_int32_t(raw->taxid);
+//	}
+
+	taxon->parent = (ecotx_t*) ((size_t) raw->parent);
+	taxon->taxid  = raw->taxid;
+	taxon->rank   = raw->rank;
+	taxon->farest = -1;
+
+	taxon->name   = malloc((raw->name_length+1) * sizeof(char));
+
+	strncpy(taxon->name, raw->name, raw->name_length);
+
+	return taxon;
+}
+
+
+FILE* open_ecorecorddb(const char* file_name,
+                       int32_t*    count,
+                       int32_t     abort_on_open_error)
+{
+    FILE*		f;
+	int32_t     read;
+
+	fprintf(stderr, "\n%s\n", file_name);
+
+	f = fopen(file_name, "rb");
+
+	if (!f)
+	{
+		if (abort_on_open_error)
+		{
+	 		obi_set_errno(OBI_TAXONOMY_ERROR);
+	 		obidebug(1, "\nCouldn't open a taxonomy file");
+	 		return NULL;
+		}
+	 	else
+	 	{
+	 		*count = 0;
+	 		return NULL;
+	 	}
+	}
+
+	read = fread(count,
+	      		 1,
+	      		 sizeof(int32_t),
+	      		 f);
+
+	if (read != sizeof(int32_t))
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading taxonomy record size");
+ 		return NULL;
+	}
+
+//	if (!obi_is_little_endian())		// TODO
+//		*count = swap_int32_t(*count);
+
+	return f;
+}
+
+
+ecorankidx_t* read_rankidx(const char* ranks_file_name)
+{
+	int32_t      			count;
+	FILE*        			ranks_file;
+	ecorankidx_t*           ranks_index;
+	int32_t      			i;
+	int32_t      			rank_length;
+	char*					buffer;
+
+	ranks_file = open_ecorecorddb(ranks_file_name, &count, 0);
+
+	if (ranks_file==NULL)
+		return NULL;
+
+	ranks_index = (ecorankidx_t*) malloc(sizeof(ecorankidx_t) + sizeof(char*) * (count-1));
+
+	ranks_index->count = count;
+
+	for (i=0; i < count; i++)
+	{
+		buffer = read_ecorecord(ranks_file, &rank_length);
+		ranks_index->label[i] = (char*) malloc(rank_length+1);
+		strncpy(ranks_index->label[i], buffer, rank_length);
+	}
+
+	return ranks_index;
+}
+
+
+ecotxidx_t* read_taxonomyidx(const char* taxa_file_name, const char* local_taxa_file_name)
+{
+	int32_t      	  count_taxa;
+	int32_t      	  count_local_taxa;
+	FILE*			  f_taxa;
+	FILE* 			  f_local_taxa;
+	ecotxidx_t*		  taxa_index;
+	struct ecotxnode* t;
+	int32_t      	  i;
+	int32_t      	  j;
+
+	f_taxa = open_ecorecorddb(taxa_file_name, &count_taxa,0);
+
+	if (f_taxa == NULL)
+	{
+ 		obidebug(1, "\nError reading taxonomy taxa file");
+ 		return NULL;
+	}
+
+	f_local_taxa = open_ecorecorddb(local_taxa_file_name, &count_local_taxa, 0);
+
+	taxa_index = (ecotxidx_t*) malloc(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count_taxa + count_local_taxa - 1));
+
+	taxa_index->count = count_taxa + count_local_taxa;
+	taxa_index->buffer_size = taxa_index->count;
+
+	taxa_index->max_taxid = 0;
+	printf("Reading %d taxa...\n", count_taxa);
+	for (i=0; i<count_taxa; i++)
+	{
+		readnext_ecotaxon(f_taxa, &(taxa_index->taxon[i]));
+		taxa_index->taxon[i].parent = taxa_index->taxon + (size_t) taxa_index->taxon[i].parent;
+		taxa_index->taxon[i].parent->farest = 0;
+		if (taxa_index->taxon[i].taxid > taxa_index->max_taxid)
+			taxa_index->max_taxid = taxa_index->taxon[i].taxid;
+	}
+
+	if (count_local_taxa > 0)
+		printf("Reading %d local taxa...\n", count_local_taxa);
+	else
+		printf("No local taxa\n");
+
+	count_taxa = taxa_index->count;
+
+	for (; i < count_taxa; i++){
+		readnext_ecotaxon(f_local_taxa, &(taxa_index->taxon[i]));
+		taxa_index->taxon[i].parent = taxa_index->taxon + (size_t) taxa_index->taxon[i].parent;
+		taxa_index->taxon[i].parent->farest=0;
+		if (taxa_index->taxon[i].taxid > taxa_index->max_taxid)
+			taxa_index->max_taxid = taxa_index->taxon[i].taxid;
+	}
+
+	printf("Computing longest branches...\n");
+
+	for (i=0; i < count_taxa; i++)
+	{
+		t = taxa_index->taxon+i;
+		if (t->farest == -1)
+		{
+			t->farest=0;
+            while (t->parent != t)
+            {
+            	j = t->farest + 1;
+            	if (j > t->parent->farest)
+            	{
+            		t->parent->farest = j;
+            		t=t->parent;
+            	}
+            	else
+            		t = taxa_index->taxon;
+            }
+		}
+	}
+
+	return taxa_index;
+}
+
+
+econame_t* readnext_econame(FILE* f, econame_t* name, OBIDMS_taxonomy_p taxonomy)
+{
+
+	econameformat_t* raw;
+	int32_t record_length;
+
+	raw = read_ecorecord(f, &record_length);
+
+	if (!raw)
+		return NULL;
+
+//	if (is_big_endian())		// TODO
+//	{
+//		raw->is_scientificname 	= swap_int32_t(raw->is_scientificname);
+//		raw->namelength 	    = swap_int32_t(raw->namelength);
+//		raw->classlength        = swap_int32_t(raw->classlength);
+//		raw->taxid  	        = swap_int32_t(raw->taxid);
+//	}
+
+	name->is_scientific_name = raw->is_scientific_name;
+
+	name->name = malloc((raw->name_length + 1) * sizeof(char));
+	strncpy(name->name, raw->names, raw->name_length);
+	name->name[raw->name_length] = 0;
+
+	name->class_name = malloc((raw->class_length+1) * sizeof(char));
+	strncpy(name->class_name,(raw->names + raw->name_length), raw->class_length);
+	name->class_name[raw->class_length] = 0;
+
+	name->taxon = taxonomy->taxa->taxon + raw->taxid;
+
+	return name;
+}
+
+
+econameidx_t* read_nameidx(const char *file_name, OBIDMS_taxonomy_p taxonomy)
+{
+	int32_t      		count;
+	FILE*				f;
+	econameidx_t*		index_names;
+	int32_t      		i;
+
+	f = open_ecorecorddb(file_name, &count, 0);
+
+	if (f == NULL)
+		return NULL;
+
+	index_names = (econameidx_t*) malloc(sizeof(econameidx_t) + sizeof(econame_t) * (count-1));
+
+	index_names->count = count;
+
+	for (i=0; i < count; i++)
+		readnext_econame(f, (index_names->names)+i, taxonomy);
+
+	return index_names;
+}
+
+
+static int bcomptaxon (const void* ptaxid, const void* ptaxon)
+{
+  ecotx_t* current_taxon = (ecotx_t*) ptaxon;
+  int32_t  taxid = (int32_t) ((size_t) ptaxid);
+  return taxid - current_taxon->taxid;
+}
+
+
+/////// PUBLIC /////////
+
+
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names)
+{
+	OBIDMS_taxonomy_p  tax;
+	char*			   main_taxonomy_dir_path;
+	char*			   taxonomy_path;
+	char*  			   ranks_file_name;
+	char*              taxa_file_name;
+	char*			   local_taxa_file_name;
+	char*			   alter_names_file_name;
+	int                buffer_size;
+
+	tax = (OBIDMS_taxonomy_p) malloc(sizeof(OBIDMS_taxonomy_t));
+
+	tax->ranks = NULL;
+	tax->taxa  = NULL;
+	tax->names = NULL;
+
+	buffer_size = 2048;		// TODO
+
+	main_taxonomy_dir_path = get_full_path(dms->dir_fd, TAXONOMY_DIR_NAME);
+	if (asprintf(&taxonomy_path, "%s/%s/%s", main_taxonomy_dir_path, taxonomy_name, taxonomy_name) < 0)
+	{
+		free(main_taxonomy_dir_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+
+	free(main_taxonomy_dir_path);
+
+	// Read ranks
+	ranks_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (ranks_file_name == NULL)
+	{
+		free(taxonomy_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(ranks_file_name, buffer_size, "%s.rdx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(ranks_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	tax->ranks = read_rankidx(ranks_file_name);
+	if (tax->ranks == NULL)
+	{
+		free(ranks_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	free(ranks_file_name);
+
+	// Read taxa
+	taxa_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (taxa_file_name == NULL)
+	{
+		free(taxonomy_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(taxa_file_name, buffer_size,"%s.tdx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	local_taxa_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (local_taxa_file_name == NULL)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(local_taxa_file_name, buffer_size,"%s.ldx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		free(local_taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	tax->taxa = read_taxonomyidx(taxa_file_name, local_taxa_file_name);
+	if (tax->taxa == NULL)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		free(local_taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	free(taxa_file_name);
+	free(local_taxa_file_name);
+
+	// Read alternative names
+	if (read_alternative_names)
+	{
+		alter_names_file_name = (char*) malloc(buffer_size*sizeof(char));
+		if (alter_names_file_name == NULL)
+		{
+			free(taxonomy_path);
+			obi_close_taxonomy(tax);
+			return NULL;
+		}
+		if (snprintf(alter_names_file_name, buffer_size,"%s.ndx", taxonomy_path) < 0)
+		{
+			free(taxonomy_path);
+			free(alter_names_file_name);
+			obi_close_taxonomy(tax);
+			return NULL;
+		}
+        tax->names = read_nameidx(alter_names_file_name, tax);
+    	if (tax->names == NULL)
+    	{
+    		free(alter_names_file_name);
+    		obi_close_taxonomy(tax);
+    		return NULL;
+    	}
+        free(alter_names_file_name);
+	}
+
+	free(taxonomy_path);
+
+	return tax;
+}
+
+
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
+{
+	if (taxonomy)
+	{
+		if (taxonomy->ranks)
+			free(taxonomy->ranks);	// TODO those don't free everything but mapping will replace anyway
+
+		if (taxonomy->names)
+			free(taxonomy->names);
+
+		if (taxonomy->taxa)
+			free(taxonomy->taxa);
+
+		free(taxonomy);
+
+		return 0;
+	}
+
+	// TODO no closing files?
+
+	return 1;
+}
+
+
+//////////////////////////////////////////////////////////////////////////
+
+
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
+{
+	ecotx_t* current_taxon;
+	ecotx_t* next_taxon;
+
+	current_taxon = taxon;
+	next_taxon    = current_taxon->parent;
+
+	while ((current_taxon != next_taxon) &&  // root node
+		   (current_taxon->rank != rankidx))
+	{
+		current_taxon = next_taxon;
+		next_taxon    = current_taxon->parent;
+	}
+
+	if (current_taxon->rank == rankidx)
+		return current_taxon;
+	else
+		return NULL;
+}
+
+
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
+{
+	ecotx_t    *current_taxon;
+	int32_t     count;
+
+	count = taxonomy->taxa->count;
+
+	current_taxon = (ecotx_t*) bsearch((const void *) ((size_t) taxid),
+                                       (const void *) taxonomy->taxa->taxon,
+                                       count,
+                                       sizeof(ecotx_t),
+                                       bcomptaxon);
+	return current_taxon;
+}
+
+
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
+{
+	ecotx_t* next_parent;
+
+	next_parent = taxon->parent;
+
+	while ((other_taxid != next_parent->taxid) && (strcmp(next_parent->name, "root")))
+		next_parent = next_parent->parent;
+
+	if (other_taxid == next_parent->taxid)
+		return 1;
+	else
+		return 0;
+}
+
+
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("species", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the species associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("genus", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the genus associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("family", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the family associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("kingdom", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the kingdom associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("superkingdom", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the superkingdom associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+

src/obidms_taxonomy.h

@@ -0,0 +1,101 @@
+/********************************************************************
+ * OBIDMS taxonomy headeer file                                     *
+ ********************************************************************/
+
+/**
+ * @file obidms_taxonomy.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date March 2nd 2016
+ * @brief Header file for the functions handling the reading of binary taxonomy files.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+
+
+typedef struct {
+	int32_t  taxid;
+	int32_t  rank;
+	int32_t	 parent;
+	int32_t  name_length;
+	char     name[1];
+} ecotxformat_t;
+
+
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	int32_t  		  farest;
+	struct ecotxnode* parent;
+	char*			  name;
+} ecotx_t;
+
+
+typedef struct {
+	int32_t count;
+	int32_t max_taxid;
+	int32_t buffer_size;
+	ecotx_t taxon[1];
+} ecotxidx_t;
+
+
+typedef struct {
+	int32_t count;
+	char*   label[1];
+} ecorankidx_t;
+
+
+typedef struct {
+ 	int32_t is_scientific_name;
+	int32_t  name_length;
+	int32_t  class_length;
+	int32_t  taxid;
+	char     names[1];
+} econameformat_t;
+
+
+typedef struct {
+	char*   		  name;
+	char*   		  class_name;
+	int32_t 		  is_scientific_name;
+	struct ecotxnode* taxon;
+} econame_t;
+
+
+typedef struct {
+	int32_t 	count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+typedef struct OBIDMS_taxonomy_t {
+	ecorankidx_t* ranks;
+	econameidx_t* names;
+	ecotxidx_t*   taxa;
+} OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
+
+
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names);
+
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
+
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
+
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);
+
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+

src/obidmscolumn.h

@@ -1,14 +1,15 @@
 /****************************************************************************
- * OBIDMS_column header file                                                    *
+ * OBIDMS columns header file                                               *
  ****************************************************************************/
 
 /**
  * @file obidmscolumn.h
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 12 May 2015
- * @brief Header file for the shared elements of all the OBIDMS column structures.
+ * @brief Header file for the functions and structures shared by all the OBIDMS columns.
  */
 
+
 #ifndef OBIDMSCOLUMN_H_
 #define OBIDMSCOLUMN_H_
 
@@ -24,63 +25,85 @@
 #include "obierrno.h"
 #include "obilittlebigman.h"
 #include "obidmscolumndir.h"
+#include "obiavl.h"
 
-#define ELEMENTS_NAMES_MAX (2048)
-#define GROWTH_FACTOR (2)
-#define MAXIMUM_LINE_COUNT (1000000)
 
+#define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
+                                	   	 */
+#define ELEMENTS_NAMES_MAX (2048)     	/**< The maximum length of the list of elements names.
+                                	     */
+#define COLUMN_GROWTH_FACTOR (2)	 	/**< The growth factor when a column is enlarged.
+                                	   	 */
+#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO
+                                	     */
+#define FORMATTED_TIME_LENGTH (1024)    /**< The length allocated for the character string containing a formatted date.
+ 	 	 	 	 	 	 	 	 	     */
+#define COMMENTS_MAX_LENGTH (2048)      /**< The maximum length for comments.
+ 	 	 	 	 	 	 	 	 	     */
 
 typedef int32_t obiversion_t; 	/**< Used to store the column version number
                                  */
 
-/**
- * @brief OBIColumnHeader structure.
- */
 
+/**
+ * @brief OBIDMS column header structure.
+ */
 typedef struct OBIDMS_column_header {
-	bool			little_endian;		        /**< endianness of the column:
-											     *   	- `true`  on little endian platforms
-												 *		- `false` on big endian platforms
-												 *
-												 *   @see obi_is_little_endian()
-	 	 	 	 	 	 	 	 	 	 	     */
-	int				header_size;		        /**< size of the header in bytes */
-	size_t			line_count;				    /**< number of lines of data */
-	size_t			lines_used;				    /**< number of lines of data used */
-	size_t			nb_elements_per_line;       /**< number of elements per line (default : 1) */
-	char			elements_names[ELEMENTS_NAMES_MAX+1];				/**< names of the line elements (default : "["column_name"]") */
-	OBIType_t		data_type;				    /**< type of the data */
-	time_t			creation_date;			    /**< date of creation of the file */
-	obiversion_t	version;				    /**< version of the OBIColumn */
-	obiversion_t	cloned_from;			    /**< version of the OBIColumn from which the column was cloned from (-1 if it does not come from cloning).*/
-	char            name[OBIDMS_MAX_COLNAME+1]; /**< The column name as a NULL
-	                                             *   terminated string.
-	                                             */
-	char 			comments[1];				/**< comments stored as a classical
-												 zero end C string.
-												 The size of the comment is only limited
-												 by the header size
-	 	 	 	 	 	 	 	 	 	 	 */
+	size_t			header_size;		   				    /**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	size_t			data_size;			   				    /**< Size of the data in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			line_count;							    /**< Number of lines of data allocated.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			lines_used;							    /**< Number of lines of data used.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			nb_elements_per_line;   			   	/**< Number of elements per line.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char			elements_names[ELEMENTS_NAMES_MAX+1];	/**< Names of the line elements with ';' as separator
+															 *	 (should be the column name if one element per line).
+															 */
+	OBIType_t		returned_data_type;		    			/**< Type of the data that is returned when getting an
+															 *   element from the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIType_t		stored_data_type;		    			/**< Type of the data that is actually stored in the data
+															 *   part of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	time_t			creation_date;			    			/**< Date of creation of the file.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	obiversion_t	version;				   				/**< Version of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	obiversion_t	cloned_from;			    			/**< Version of the column from which this column
+															 *   was cloned from (-1 if it was not created by cloning
+															 *   another column).
+															 */
+	char            name[OBIDMS_COLUMN_MAX_NAME+1]; 	    /**< The column name as a NULL terminated string.
+	                                             	 	 	 */
+	char            avl_name[AVL_MAX_NAME+1]; 	    		/**< If there is one, the AVL tree name as a NULL terminated string.
+	                                             	 	 	 */
+	char 			comments[COMMENTS_MAX_LENGTH+1];		/**< Comments stored as a classical zero end C string.
+												 	 	 	 */
 } OBIDMS_column_header_t, *OBIDMS_column_header_p;
 
 
 /**
- * @brief Structure describing a Column of the OBITools DMS
+ * @brief OBIDMS column structure.
  *
  * A data structure of this type is returned by the functions
- * creating, opening or cloning an OBIDMS_column.
+ * creating, opening or cloning an OBIDMS column.
  */
 typedef struct OBIDMS_column {
-	OBIDMS_p                	dms;			 	/**< A pointer to a DMS instance */
-	OBIDMS_column_directory_p   column_directory;	/**< A pointer to an OBIDMS column directory instance */
-	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column */
-	void*                   	data;   		 	/**< A `void` pointer to the beginning of the
-	                                 	 	  	  	 *   data.
+	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the column belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_directory_p   column_directory;	/**< A pointer to the OBIDMS column directory structure to which the column belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_avl_p 				avl;				/**< A pointer to the AVL tree associated with the column if there is one.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	void*                   	data;   		 	/**< A `void` pointer to the beginning of the data.
 	                                 	 	         *
-													 *   @warning never use this member directly
-													 *            outside of the code of the
-													 *            low level functions
-													 *            of the OBITools DMS
+													 *   @warning Never use this member directly outside of the code of the
+													 *            low level functions of the OBIDMS.
 													 */
 	bool						writable;	     	/**< Indicates if the column is writable or not.
 													 *       - `true` the column is writable
@@ -89,27 +112,36 @@ typedef struct OBIDMS_column {
 													 * A column is writable only by its creator
 													 * until it closes it.
 													 */
+	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the column is used.
+													 */
 } OBIDMS_column_t, *OBIDMS_column_p;
 
 
 /**
- * @brief Returns the latest version of a column in a column directory
+ * @brief Returns the latest version number of a column in a column directory using the column directory structure.
  *
- * @param column_directory
+ * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
  *
- * @return the latest version number kept in the version file
- * @return -1 if an error occurred
+ * @returns The latest version number kept in the version file.
+ * @retval -1 if an error occurred.
+ *
+ * @since May 2015
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
 
 
 /**
- * @brief Returns the latest version of a column in a column directory
+ * @brief Returns the latest version of a column in a column directory using the column name.
  *
- * @param column_name
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The column name.
  *
- * @return the latest version number kept in the version file
- * @return -1 if an error occurred
+ * @returns The latest version number kept in the version file.
+ * @retval -1 if an error occurred.
+ *
+ * @since May 2015
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
 
@@ -118,9 +150,9 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
  * @brief Returns the header size in bytes of a column on this platform.
  *
  * The header size is defined as a multiple of the memory page size.
- * Up to now the header size is defined as one time the page size.
+ * As of now the header size is defined as one time the page size.
  *
- * @return a `size_t` value corresponding to the header size in bytes
+ * @returns The header size in bytes.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
@@ -131,30 +163,46 @@ size_t obi_get_platform_header_size();
 /**
  * @brief Creates a column.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the new column
- * @param type the OBIType code used to create the column
- * @param nb_lines the number of lines to be stored
+ * The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
+ * If there is an AVL tree associated with the column, it is opened or created if it does not already exist.
+ *
+ * @warning If there is one element per line, elements_names should be equal to column_name.	// TODO change this condition?
+ *
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the new column.
+ * @param data_type The OBIType code of the data.
+ * @param nb_lines The number of lines to be stored.
+ * @param nb_elements_per_line The number of elements per line.								// TODO talk about default values
+ * @param elements_names The names of the elements with ';' as separator.
+ * @param avl_name The name of the AVL tree if there is one associated with the column.
+ * @param comments Optional comments associated with the column.
+ *
+ * @returns A pointer on the newly created column structure.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 OBIDMS_column_p obi_create_column(OBIDMS_p dms,
-								  const char* column_name,
-								  OBIType_t type,
-								  size_t nb_lines,
-								  size_t nb_elements_per_line,
-								  const char*  elements_names);
+		                          const char* column_name,
+								  OBIType_t data_type,
+								  index_t nb_lines,
+								  index_t nb_elements_per_line,
+								  const char* elements_names,
+								  const char* avl_name,
+								  const char* comments
+								 );
 
 
 /**
  * @brief Opens a column in read-only mode.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the column
- * @param version_number the version of the column that should be opened (if -1, the latest version number is retrieved)
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the column.
+ * @param version_number The version of the column that should be opened (if -1, the latest version is retrieved).
  *
- * @return a pointer to the opened column
+ * @returns A pointer on the opened column structure.
+ * @retval NULL if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -165,26 +213,27 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
 /**
  * @brief Clones a column, and returns a pointer to the writable new column.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the column to clone
- * @param version_number the version of the column that should be cloned (if -1, the latest version number is retrieved)
- * @param clone_data whether the data should be copied or not
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the column to clone.
+ * @param version_number The version of the column that should be cloned (if -1, the latest version is retrieved).
+ * @param clone_data Whether the data should be copied or not.
  *
- * @return a pointer to the created column
+ * @returns A pointer to the created column.
+ * @retval NULL if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bool clone_data);
+OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p line_selection, const char* column_name, obiversion_t version_number, bool clone_data);
 
 
 /**
  * @brief Closes a column.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -193,12 +242,13 @@ int obi_close_column(OBIDMS_column_p column);
 
 
 /**
- * @brief Truncates a column file to the number of lines used.
+ * @brief Truncates a column file to the number of lines used rounded to the nearest
+ * 		  greater multiple of the page size.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -209,10 +259,10 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
 /**
  * @brief Enlarges a column file.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -221,12 +271,13 @@ int obi_enlarge_column(OBIDMS_column_p column);
 
 
 /**
- * @brief Truncates a column file to the number of lines used and closes it.
+ * @brief Truncates a column file to the number of lines used rounded to the nearest
+ *        greater multiple of the page size and closes it.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -235,134 +286,83 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
 
 
 /*
- * @brief Sets the data in a column to the NA value of the data type.
+ * @brief Sets the data in a column to the NA value of the data OBIType.
  *
- * @param column a pointer on an OBIDMS column
- * @param start the first line number of the block that should be set
- * @param nb_lines the number of lines that should be set
+ * @param column A pointer on an OBIDMS column.
+ * @param start The first line number of the block that should be set.
+ * @param nb_lines The number of lines that should be set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines);
+void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines);	// TODO make private?
 
 
 /**
- * @brief Sets the 'writable' header attribute of an OBIDMS column to False.
+ * @brief Recovers the header of an OBIDMS column from the column name.
  *
- * @param column a pointer on an OBIDMS column
+ * @warning The header structure has to be munmapped by the caller.
+ *
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of an OBIDMS column.
+ * @param version_number The version of the column from which the header should be
+ *        retrieved (-1: latest version).
+ *
+ * @returns A pointer on the mmapped header of the column.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
+
+
+/**
+ * @brief Munmap a mmapped header as returned by obi_column_get_header_from_name().
+ *
+ * @param header A pointer on the mmapped header structure.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_unmap_header(OBIDMS_column_header_p header);
+
+
+/**
+ * @brief Recovers the index of an element in an OBIDMS column from the element's name.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param element_name The name of the element.
+ *
+ * @returns The index of the element in a line of the column.
+ * @retval OBIIdx_NA if an error occurred.						// TODO not sure if this is "clean".
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void obi_column_make_unwritable(OBIDMS_column_p column);
+index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
 
 
 /**
- * @brief Recovers the line count of an OBIDMS column.
+ * @brief Formats a date in a way that is easy to read.
  *
- * @param column a pointer on an OBIDMS column
+ * @warning The pointer returned must be freed by the caller.
  *
- * @return the line count of the column
+ * @param date A date.
  *
- * @since July 2015
+ * @returns The date formatted in a way that is easy to read.
+ *
+ * @since October 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-size_t obi_column_get_line_count(OBIDMS_column_p column);
+char* obi_column_format_date(time_t date);
 
 
-/**
- * @brief Recovers the number of lines used in an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the number of lines used in the column
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_nb_lines_used(OBIDMS_column_p column);
+int obi_select(OBIDMS_column_p lines_column, index_t line_to_grep);
 
 
-/**
- * @brief Recovers the data type of an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the data type of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIType_t obi_column_get_data_type(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the data type of an OBIDMS column from the column name.
- *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of an OBIDMS column
- *
- * @return the data type of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name);
-
-
-/**
- * @brief Recovers the line count of an OBIDMS column from the column name.
- *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of an OBIDMS column
- *
- * @return the line count of the column
- *
- * @since September 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name);
-
-
-/**
- * @brief Recovers the elements names of an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the elements names
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_column_get_elements_names(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the index of an element in an OBIDMS column from its name.
- *
- * @param column a pointer on an OBIDMS column
- * @param element_name the name of the element
- *
- * @return the index of the element in a line of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
-
-
-/**
- * @brief Recovers the number of elements per line in an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the number of elements per line
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column);
-
 
 #endif /* OBIDMSCOLUMN_H_ */

src/obidmscolumn_bool.c

@@ -1,5 +1,5 @@
 /****************************************************************************
- * OBIDMS_column_bool functions                                              *
+ * OBIDMS_column_bool functions                                             *
  ****************************************************************************/
 
 /**
@@ -14,12 +14,13 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +29,8 @@
  *
  **********************************************************************/
 
-int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
+
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,68 +59,111 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
 {
-	if ((line_nb+1) > (column->header)->lines_used)
+	// Check that the view is not read-only
+	if (view->read_only)
 	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
-		return OBIBool_NA;
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
 	}
-	return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-}
 
-
-int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((view->line_selection != NULL) || (!(column->writable)))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
 		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
 		}
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
 
-	obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
 
 
-obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIBool_NA;
-		}
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBIBool_NA;
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIBool_NA;
-    }
+
+	return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIBool_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
 
 	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIBool_NA;
+	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIBool_NA;
+	return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_bool.h

@@ -10,92 +10,165 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_BOOL_H_
+#define OBIDMSCOLUMN_BOOL_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_BOOL_H_ */
 

src/obidmscolumn_char.c

@@ -14,12 +14,13 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +29,8 @@
  *
  **********************************************************************/
 
-int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value)
+
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,12 +59,49 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
 {
-	if ((line_nb+1) > (column->header)->lines_used)
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+
+	return 0;
+}
+
+
+obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIChar_NA;
 	}
 
@@ -70,56 +109,61 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
 }
 
 
-int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
+obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((line_nb+1) > (view->line_count))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIChar_NA;
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
 
-	obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
-
-	return 0;
-}
-
-
-obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIChar_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIChar_NA;
-    }
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
 
 	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIChar_NA;
+	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIChar_NA;
+	return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_char.h

@@ -10,92 +10,165 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_CHAR_H_
+#define OBIDMSCOLUMN_CHAR_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t* obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value);
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue NULL on failure and the `obi_errno` variable is set. TODO an other value should be chosen maybe
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_CHAR_H_ */
 

src/obidmscolumn_float.c

@@ -14,12 +14,13 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +29,7 @@
  *
  **********************************************************************/
 
-int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,68 +58,111 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
 {
-	if ((line_nb+1) > (column->header)->lines_used)
+	// Check that the view is not read-only
+	if (view->read_only)
 	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
-		return OBIFloat_NA;
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
 	}
-	return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-}
 
-
-int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((view->line_selection != NULL) || (!(column->writable)))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
 		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
 		}
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
 
-	obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
 
 
-obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIFloat_NA;
-		}
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBIFloat_NA;
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIFloat_NA;
-    }
+
+	return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIFloat_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
 
 	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIFloat_NA;
+	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIFloat_NA;
+	return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_float.h

@@ -10,92 +10,165 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_FLOAT_H_
+#define OBIDMSCOLUMN_FLOAT_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_FLOAT_H_ */
 

src/obidmscolumn_idx.c

@@ -5,8 +5,8 @@
 /**
  * @file obidsmcolumn_idx.c
  * @author Celine Mercier
- * @date August 10th 2015
- * @brief Functions handling OBIColumns containing data with the OBIType OBI_IDX.
+ * @date February 14th 2016
+ * @brief Functions handling OBIColumns containing data with the index_t type.
  */
 
 
@@ -19,7 +19,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +28,8 @@
  *
  **********************************************************************/
 
-int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
+
+int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -51,74 +52,21 @@ int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
 		(column->header)->lines_used = line_nb+1;
 
 	// Set the value
-	*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+	*(((index_t*) (column->data)) + line_nb) = value;
 
 	return 0;
 }
 
 
-obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
 {
-	if ((line_nb+1) > (column->header)->lines_used)
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIIdx_NA;
 	}
-	return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-}
-
-
-int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
-	obi_column_set_obiidx_with_elt_idx(column, line_nb, element_idx, value);
-
-	return 0;
-}
-
-
-obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIIdx_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIIdx_NA;
-    }
-
-	return obi_column_get_obiidx_with_elt_idx(column, line_nb, element_idx);
+
+	return *(((index_t*) (column->data)) + line_nb);
 }
 

src/obidmscolumn_idx.h

@@ -5,11 +5,15 @@
 /**
  * @file obidsmcolumn_idx.h
  * @author Celine Mercier
- * @date August 10th 2015
+ * @date February 14th 2016
  * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
  */
 
 
+#ifndef OBIDMSCOLUMN_IDX_H_
+#define OBIDMSCOLUMN_IDX_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -17,85 +21,10 @@
 #include "obitypes.h"
 
 
-/**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the index of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- * @warning Pointers returned by obi_open_column() don't allow writing.
- *
- * @param line_nb the number of the line where the value should be set
- *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
+int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
+
+index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
 
 
-/**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
- *
- * @param column a pointer as returned by obi_create_column()
- *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
-
-
-/**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- * @warning Pointers returned by obi_open_column() don't allow writing.
- *
- * @param line_nb the number of the line where the value should be set
- *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
-
-
-/**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+#endif /* OBIDMSCOLUMN_IDX_H_ */
 

src/obidmscolumn_int.c

@@ -14,12 +14,13 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +29,8 @@
  *
  **********************************************************************/
 
-int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
+
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,68 +59,112 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
 }
 
 
-obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
 {
-	if ((line_nb+1) > (column->header)->lines_used)
+	// Check that the view is not read-only
+	if (view->read_only)
 	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
-		return OBIInt_NA;
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
 	}
-	return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-}
 
-
-int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((view->line_selection != NULL) || (!(column->writable)))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
 		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
 		}
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
 
-	obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
 
 
-obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIInt_NA;
-		}
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBIInt_NA;
 	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIInt_NA;
-    }
+
+	return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIInt_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
 
 	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIInt_NA;
+	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIInt_NA;
+	return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_int.h

@@ -5,97 +5,170 @@
 /**
  * @file obidsmcolumn_int.h
  * @author Celine Mercier
- * @date July 21st 2015
+ * @date August 10th 2015
  * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_INT.
  */
 
 
+#ifndef OBIDMSCOLUMN_INT_H_
+#define OBIDMSCOLUMN_INT_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_INT_H_ */
 

src/obidmscolumn_seq.c

@@ -0,0 +1,196 @@
+/****************************************************************************
+ * OBIDMS_column_seq functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_seq.c
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obiview.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+#include "obiavl.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+
+int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	byte_t* value_b;
+	index_t idx;
+
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
+	// Update lines used
+	if ((line_nb+1) > (column->header)->lines_used)
+		(column->header)->lines_used = line_nb+1;
+
+	// Encode the value on a byte array with a header
+	value_b = obi_seq_to_obibytes(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the AVL tree
+	idx = obi_avl_add(column->avl, value_b);
+	if (idx == -1)
+		return -1;
+
+	// Add the value's index in the column
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
+
+	free(value_b);
+
+	return 0;
+}
+
+
+int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+
+	return 0;
+}
+
+
+const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	index_t idx;
+	byte_t* value_b;
+
+	if ((line_nb+1) > ((column->header)->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBISeq_NA;
+	}
+
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+
+	// Check NA
+	if (idx == OBIIdx_NA)
+		return OBISeq_NA;
+
+	value_b = obi_avl_get(column->avl, idx);
+	return obi_obibytes_to_seq(value_b);
+}
+
+
+const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBISeq_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBISeq_NA;
+	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBISeq_NA;
+	return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_seq.h

@@ -0,0 +1,178 @@
+/****************************************************************************
+ * OBIDMS_column_seq header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_seq.h
+ * @author Celine Mercier
+ * @date Novemeber 18th 2015
+ * @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to DNA sequences.
+ */
+
+
+#ifndef OBIDMSCOLUMN_SEQ_H_
+#define OBIDMSCOLUMN_SEQ_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obiview.h"
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_SEQ_H_ */
+

src/obidmscolumn_str.c

@@ -0,0 +1,220 @@
+/****************************************************************************
+ * OBIDMS_column_str functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_str.c
+ * @author Celine Mercier
+ * @date October 28th 2015
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to character strings.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <sys/mman.h>
+
+#include "obidmscolumn.h"
+#include "obiview.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+#include "obiavl.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	byte_t* value_b;
+	index_t idx;
+
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
+	// Update lines used
+	if ((line_nb+1) > (column->header)->lines_used)
+		(column->header)->lines_used = line_nb+1;
+
+	// Encode the value on a byte array with a header
+	value_b = obi_str_to_obibytes(value);
+	if (value_b == NULL)
+		return -1;
+
+	if (!(line_nb%100000))
+	{
+		//fprintf(stderr, "\nbleeeh");
+		// Unmap and remap the AVL
+		if (munmap((column->avl)->tree, ((((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
+			return -1;
+		if (munmap(((column->avl)->data)->data, (((column->avl)->data)->header)->data_size_max) < 0)
+			return -1;
+		(column->avl)->tree = mmap(NULL,
+							  (((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t),	// TODO store avl_size_max
+							  PROT_READ | PROT_WRITE,
+							  MAP_SHARED,
+							  (column->avl)->avl_fd,
+							  ((column->avl)->header)->header_size
+							  );
+		((column->avl)->data)->data = mmap(NULL,
+									  (((column->avl)->data)->header)->data_size_max,
+									  PROT_READ | PROT_WRITE,
+									  MAP_SHARED,
+									  (column->avl)->data_fd,
+									  (((column->avl)->data)->header)->header_size
+									  );
+	}
+
+	// Add in the AVL tree
+	idx = obi_avl_add(column->avl, value_b);
+	if (idx == -1)
+		return -1;
+
+	// Add the value's index in the column
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
+
+	free(value_b);
+
+	return 0;
+}
+
+
+int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+
+	return 0;
+}
+
+
+const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	index_t idx;
+	byte_t* value_b;
+
+	if ((line_nb+1) > ((column->header)->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBIStr_NA;
+	}
+
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+
+	// Check NA
+	if (idx == OBIIdx_NA)
+		return OBIStr_NA;
+
+	value_b = obi_avl_get(column->avl, idx);
+	return obi_obibytes_to_str(value_b);
+}
+
+
+const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIStr_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIStr_NA;
+	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIStr_NA;
+	return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_str.h

@@ -0,0 +1,178 @@
+/****************************************************************************
+ * OBIDMS_column_str header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_str.h
+ * @author Celine Mercier
+ * @date October 28th 2015
+ * @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to character strings.
+ */
+
+
+#ifndef OBIDMSCOLUMN_STR_H_
+#define OBIDMSCOLUMN_STR_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obiview.h"
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_STR_H_ */
+

src/obidmscolumndir.c

@@ -4,7 +4,7 @@
 
 /**
  * @file obidmscolumndir.c
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 18 June 2015
  * @brief Functions for OBIDMS column directories.
  */
@@ -25,7 +25,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**************************************************************************
@@ -43,15 +43,10 @@
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param column_name the name of the OBIDMS column
+ * @param column_name The name of the OBIDMS column.
  *
- * @return a pointer to the OBIDMS column directory name
- * @retvalue <column_directory_name> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the OBIDMS column directory name.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -78,10 +73,10 @@ static char* build_column_directory_name(const char* column_name)
 	}
 
 	// Test if the database name is not too long
-	if (strlen(column_directory_name) >= OBIDMS_COLUMN_DIR_MAX_NAME)
+	if (strlen(column_directory_name) >= OBIDMS_COLUMN_MAX_NAME)
 	{
 		obi_set_errno(OBICOLDIR_LONG_NAME_ERROR);
-		obidebug(1, "\nError building a column directory name");
+		obidebug(1, "\nError due to column name too long");
 		free(column_directory_name);
 		return NULL;
 	}
@@ -102,25 +97,14 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name)
 	char* 	column_directory_name;
 	char* 	full_path;
     int 	check_dir;
-	int 	dms_file_descriptor;
 
 	// Build and check the directory name
     column_directory_name = build_column_directory_name(column_name);
 	if (column_directory_name == NULL)
 		return -1;
 
-	// Get the file descriptor for the dms
-	dms_file_descriptor = dirfd(dms->directory);
-	if (dms_file_descriptor < 0)
-	{
-		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError getting a file descriptor for an OBIDMS directory");
-		free(column_directory_name);
-		return -1;
-	}
-
 	// Get the full path for the column directory
-	full_path = get_full_path(dms_file_descriptor, column_directory_name);
+	full_path = get_full_path(dms->dir_fd, column_directory_name);
 	if (full_path == NULL)
 	{
 		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
@@ -144,7 +128,6 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name)
 OBIDMS_column_directory_p obi_create_column_directory(OBIDMS_p dms, const char* column_name)
 {
 	char* 	column_directory_name;
-	int 	dms_file_descriptor;
 
 	// Build and check the directory name
 	column_directory_name = build_column_directory_name(column_name);
@@ -154,18 +137,8 @@ OBIDMS_column_directory_p obi_create_column_directory(OBIDMS_p dms, const char*
 		return NULL;
 	}
 
-	// Get the file descriptor for the dms
-	dms_file_descriptor = dirfd(dms->directory);
-	if (dms_file_descriptor < 0)
-	{
-		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError getting a file descriptor for an OBIDMS directory");
-		free(column_directory_name);
-		return NULL;
-	}
-
 	// Try to create the directory
-	if (mkdirat(dms_file_descriptor, column_directory_name, 00777) < 0)
+	if (mkdirat(dms->dir_fd, column_directory_name, 00777) < 0)
 	{
 		if (errno == EEXIST)
 			obi_set_errno(OBICOLDIR_EXIST_ERROR);
@@ -187,7 +160,6 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
 	OBIDMS_column_directory_p	column_directory;
 	char*	 					column_directory_name;
 	DIR*						directory;
-	int 						dms_file_descriptor;
 
 	column_directory = NULL;
 
@@ -196,18 +168,8 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
 	if (column_directory_name == NULL)
 		return NULL;
 
-	// Get the file descriptor for the dms
-	dms_file_descriptor = dirfd(dms->directory);
-	if (dms_file_descriptor < 0)
-	{
-		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError getting a file descriptor for an OBIDMS directory");
-		free(column_directory_name);
-		return NULL;
-	}
-
 	// Try to open the column directory
-	directory = private_opendirat(dms_file_descriptor, column_directory_name);
+	directory = private_opendirat(dms->dir_fd, column_directory_name);
 	if (directory == NULL) {
 		switch (errno)
 		{
@@ -246,6 +208,15 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
 	strcpy(column_directory->column_name, column_name);
 	column_directory->directory = directory;
 
+	column_directory->dir_fd = dirfd(directory);
+	if (column_directory->dir_fd < 0)
+	{
+		obi_set_errno(OBICOLDIR_MEMORY_ERROR);
+		obidebug(1, "\nError allocating the memory for an OBIDMS column directory structure");
+		free(column_directory_name);
+		free(column_directory);
+	}
+
 	free(column_directory_name);
 
 	return column_directory;

src/obidmscolumndir.h

@@ -6,57 +6,59 @@
  * @file obidmscolumndir.h
  * @author Celine Mercier
  * @date 18 June 2015
- * @brief Header file for OBIDMS column directories.
+ * @brief Header file for the OBIDMS column directories structures and functions.
  */
 
+
 #ifndef OBIDMSCOLUMNGROUP_H_
 #define OBIDMSCOLUMNGROUP_H_
 
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <dirent.h>
 
 #include "obidms.h"
 
-#define OBIDMS_MAX_COLNAME (128) /**< The maximum length of an OBIDMS column name
-                                  */
 
-#define OBIDMS_COLUMN_DIR_MAX_NAME (2048) 	/**< The maximum length of an OBIDMS column directory name
-                                		 */
+#define OBIDMS_COLUMN_MAX_NAME (1024) /**< The maximum length of an OBIDMS column name.
+                                       */
 
-/** @brief A structure describing an OBIDMS column directory instance
+
+/**
+ * @brief A structure describing an OBIDMS column directory instance.
  *
  * A pointer to this structure is returned on creation
  * and opening of an OBIDMS column directory.
  */
-
 typedef struct OBIDMS_column_directory {
-	OBIDMS_p	dms;	 										/**< A pointer to a DMS instance.
-     	 	 	 	 	 	 	 	 	 	 	 	 		 	 */
-	char 		column_name[OBIDMS_MAX_COLNAME+1];				/**< The name of the column
-																 *   contained in the directory.
-																 */
-	char		directory_name[OBIDMS_COLUMN_DIR_MAX_NAME+1];	/**< The name of the directory
-	                                     	 	 	 	 	 	 *   containing the column.
-	                                     	 	 	 	 	 	 */
-	DIR*		directory;										/**< A directory entry usable to
-										 	 	 	 	 	 	 *   refer and scan the database directory.
-										 	 	 	 	 	 	 */
+	OBIDMS_p	dms;	 										 /**< A pointer to a DMS instance.
+     	 	 	 	 	 	 	 	 	 	 	 	 		 	  */
+	char 		column_name[OBIDMS_COLUMN_MAX_NAME+1];		     /**< The name of the column
+																  *    contained in the directory.
+																  */
+	char		directory_name[OBIDMS_COLUMN_MAX_NAME+1];	     /**< The name of the directory
+	                                     	 	 	 	 	 	  *    containing the column.
+	                                     	 	 	 	 	 	  */
+	DIR*		directory;										 /**< A directory entry usable to
+										 	 	 	 	 	 	  *    refer and scan the column directory.
+										 	 	 	 	 	 	  */
+	int			dir_fd;											 /**< The file descriptor of the directory entry
+																  *   usable to refer and scan the column directory.
+																  */
 } OBIDMS_column_directory_t, *OBIDMS_column_directory_p;
 
 
-/*@
- * @brief Checks if an OBIDMS column directory exists
+/**
+ * @brief Checks if an OBIDMS column directory exists.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
- *                    The actual directory name used to store the column is
- *                    `<column_name>.obicol`.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *
- * @return an integer value indicating the status of the column directory
- * @retvalue 1 the directory exist
- * @retvalue 0 the directory does not exist
- * @retvalue -1 an error occurred
+ * @returns An integer value indicating the status of the column directory.
+ * @retval 1 if the directory exists.
+ * @retval 0 if the directory does not exist.
+ * @retval -1 if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -72,17 +74,14 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name);
  * if a directory with this name does not already exist
  * before creating the new column directory.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column will be
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to an OBIDMS column directory structure describing the newly created
- * 		   directory
- * @retval NULL on error and the `obi_errno` variable is set.
- *
- * ###Error values
- * 		- OBIDMS_COL_DIR_EXIST_ERROR     : xxxxx a database with the same name already exists.
+ * @returns A pointer to an OBIDMS column directory structure describing the newly created
+ * 		    directory.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -94,16 +93,13 @@ OBIDMS_column_directory_p obi_create_column_directory(OBIDMS_p dms, const char*
 /**
  * @brief Opens an existing OBIDMS column directory instance.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column is
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to the OBIDMS column directory structure describing the directory
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_COL_DIR_ERROR     : xxxxx a database with the same name already exists.
+ * @returns A pointer to the OBIDMS column directory structure describing the directory.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -118,17 +114,13 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
  * If the directory already exists, this function opens it, otherwise it
  * creates a new column directory.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column is
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to the OBIDMS column directory structure describing the directory
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to the OBIDMS column directory structure describing the directory.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -139,13 +131,13 @@ OBIDMS_column_directory_p obi_column_directory(OBIDMS_p dms, const char* column_
 /**
  * @brief Closes an opened OBIDMS column directory instance.
  *
- * @param column_directory a pointer to an OBIDMS column directory as returned by
- * obi_create_column_directory() or obi_open_column_directory()
+ * @param column_directory A pointer to an OBIDMS column directory as returned by
+ *                         obi_create_column_directory() or obi_open_column_directory().
  *
- * @return an integer value indicating the success of the operation. Even on
- * 		   error, the `OBIDMS_column_directory` structure is freed
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation. Even on
+ * 		    error, the `OBIDMS_column_directory` structure is freed.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @see obi_create_column_directory()
  * @see obi_open_column_directory()

src/obierrno.c

@@ -1,10 +1,14 @@
-/*
- * obierrno.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Code for obi errnos                                                      *
+ ****************************************************************************/
+
+/**
+ * @file obierrno.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Code for obi errnos.
  */
 
 
-int obi_errno;
+int obi_errno = 0;
 

src/obierrno.h

@@ -1,20 +1,26 @@
-/*
- * obierrno.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Header file for obi errnos                                               *
+ ****************************************************************************/
+
+/**
+ * @file obierrno.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for obi errnos.
  */
 
+
 #ifndef OBIERRNO_H_
 #define OBIERRNO_H_
 
+
 /**
  * @brief The declaration of the external variable `obi_errno`.
  *
  * `obi_errno` is an equivalent of `errno` for the system level error,
- * but for errors generated by the C layer of the OBITools framework.
+ * but for errors generated by the C layer of the OBITools3 framework.
  *
- * @todo We have to look into defining this variable as thread specific.
+ * @TODO We have to look into defining this variable as thread specific.
  */
 extern int obi_errno;
 
@@ -24,8 +30,8 @@ extern int obi_errno;
  *        the specified `err` code
  *
  * This function is defined as a macro to reduce the risk
- * of increasing the problem generating the error by calling
- * a new function.
+ * of increasing the problem by generating another error by calling
+ * another function.
  *
  * @param err The error code as an integer value.
  *
@@ -41,6 +47,8 @@ extern int obi_errno;
  * Error codes set in errno following an error related
  * to the manipulation of an OBIDMS.
  *
+ * @TODO
+ *
  * @{
  */
 #define OBIDMS_EXIST_ERROR     		(1) 	/**< Trying to create an OBIDMS with a name
@@ -57,25 +65,25 @@ extern int obi_errno;
                                     		 */
 #define OBIDMS_ACCESS_ERROR    		(6) 	/**< Permission error trying to access the database
                                     		 */
-
-#define OBICOLDIR_EXIST_ERROR     	(7) 	/**< Trying to create an OBIDMS column directory with a name
-                                    		 *   that corresponds to an existing one
-                                    		 */
-#define OBICOLDIR_NOT_EXIST_ERROR 	(8) 	/**< Trying to open a non-existing OBIDMS column directory
-                                    		 */
-#define OBICOLDIR_LONG_NAME_ERROR 	(9) 	/**< The specified OBIDMS column directory name is too long
-                                    		 */
-#define OBICOLDIR_MEMORY_ERROR    	(10) 	/**< A memory error occurred during allocation while handling
-											 *	 an OBIDMS column directory
-                                    	 	 */
-#define OBICOLDIR_UNKNOWN_ERROR   	(11) 	/**< Undetermined error while handling an OBIDMS column directory
-                                    	 	 */
-#define OBICOLDIR_ACCESS_ERROR    	(12) 	/**< Permission error trying to access an OBIDSM column directory
-                                    		 */
-
-#define OBICOL_BAD_ENDIAN_ERROR   	(13) 	/**< The opened data structure does not corresponds
+#define OBIDMS_BAD_ENDIAN_ERROR   	(7) 	/**< The opened database does not correspond
                                     		 *   to the endianness of the platform.
                                     		 */
+
+#define OBICOLDIR_EXIST_ERROR     	(8) 	/**< Trying to create an OBIDMS column directory with a name
+                                    		 *   that corresponds to an existing one
+                                    		 */
+#define OBICOLDIR_NOT_EXIST_ERROR 	(9) 	/**< Trying to open a non-existing OBIDMS column directory
+                                    		 */
+#define OBICOLDIR_LONG_NAME_ERROR 	(10) 	/**< The specified OBIDMS column directory name is too long
+                                    		 */
+#define OBICOLDIR_MEMORY_ERROR    	(11) 	/**< A memory error occurred during allocation while handling
+											 *	 an OBIDMS column directory
+                                    	 	 */
+#define OBICOLDIR_UNKNOWN_ERROR   	(12) 	/**< Undetermined error while handling an OBIDMS column directory
+                                    	 	 */
+#define OBICOLDIR_ACCESS_ERROR    	(13) 	/**< Permission error trying to access an OBIDSM column directory
+                                    		 */
+
 #define OBICOL_EXIST_ERROR     		(14) 	/**< Trying to create an OBIDMS column with a name
                                     		 *   that corresponds to an existing one
                                     		 */
@@ -90,6 +98,12 @@ extern int obi_errno;
                                     	 	 */
 #define OBICOL_ACCESS_ERROR    		(19) 	/**< Permission error trying to access an OBIDSM column directory
                                     		 */
+#define OBI_AVL_ERROR				(20)    /** Error while handling an AVL tree
+											 */
+#define OBIVIEW_ERROR				(21)    /** Error while handling an OBIView
+											 */
+#define OBI_TAXONOMY_ERROR			(22)    /** Error while handling binary taxonomy files
+ 	 	 	 	 	 	 	 	 	 	 	 */
 /**@}*/
 
 #endif /* OBIERRNO_H_ */

src/obilittlebigman.c

@@ -1,8 +1,12 @@
-/*
- * littlebigman.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Code for endianness checking                                             *
+ ****************************************************************************/
+
+/**
+ * @file obilittlebigman.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Code endianness checking.
  */
 
 #include "obilittlebigman.h"

src/obilittlebigman.h

@@ -1,15 +1,22 @@
-/*
- * littlebigman.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Header file for endianness checking                                      *
+ ****************************************************************************/
+
+/**
+ * @file obilittlebigman.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for endianness checking.
  */
 
+
 #ifndef OBILITTLEBIGMAN_H_
 #define OBILITTLEBIGMAN_H_
 
+
 #include <stdbool.h>
 
+
 /**
  * Test if the architecture of the processor is little endian.
  *
@@ -41,7 +48,7 @@
  *  In this architecture, the last address is
  *  used to store the byte of lighter weight (LITTLE ENDian)
  *
- * @return a `bool` value:
+ * @returns a `bool` value:
  * 		- `true`  if the architecture is little endian
  * 		- `false` if the architecture is big endian
  *

src/obitypes.c

@@ -1,8 +1,12 @@
-/*
- * obitypes.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * OBITypes functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obitypes.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Functions for the handling of OBITypes.
  */
 
 
@@ -13,7 +17,7 @@
 #include "obierrno.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 size_t obi_sizeof(OBIType_t type)
@@ -36,7 +40,9 @@ size_t obi_sizeof(OBIType_t type)
 	case OBI_CHAR:  size = sizeof(obichar_t);
 					break;
 
-	case OBI_IDX:   size = sizeof(obiidx_t);
+	case OBI_STR:   // fallthrough
+	case OBI_SEQ:   // fallthrough
+	case OBI_IDX:	size = sizeof(index_t);
 					break;
 
 	default:        size = 0;
@@ -46,7 +52,7 @@ size_t obi_sizeof(OBIType_t type)
 }
 
 
-size_t obi_array_sizeof(OBIType_t type, size_t nb_lines, size_t nb_elements_per_line)
+size_t obi_array_sizeof(OBIType_t type, index_t nb_lines, index_t nb_elements_per_line)
 {
 	size_t size;
 	size_t rsize;
@@ -86,6 +92,12 @@ char* name_data_type(int data_type)
 		case OBI_CHAR:  name = strdup("OBI_CHAR");
 						break;
 
+		case OBI_STR:   name = strdup("OBI_STR");
+						break;
+
+		case OBI_SEQ:   name = strdup("OBI_SEQ");
+						break;
+
 		case OBI_IDX:   name = strdup("OBI_IDX");
 						break;
 	}

src/obitypes.h

@@ -1,10 +1,15 @@
+/****************************************************************************
+ * Header file for OBITypes                                                 *
+ ****************************************************************************/
+
 /**
  * @file obitypes.h
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 18 May 2015
- * @brief Header file for the OBITypes.
+ * @brief Header file for the handling of OBITypes.
  */
 
+
 #ifndef OBITYPES_H_
 #define OBITYPES_H_
 
@@ -13,10 +18,13 @@
 #include <stdint.h>
 
 
-#define OBIInt_NA (INT32_MIN)
-#define OBIIdx_NA (SIZE_MAX)
-#define OBIFloat_NA (float_NA())
-#define OBIChar_NA (0)				// TODO not sure about this one as it can be impossible to distinguish from uninitialized values
+#define OBIInt_NA (INT32_MIN)		/**< NA value for the type OBI_INT */
+#define OBIIdx_NA (INT64_MIN)		/**< NA value for indices */
+#define OBIFloat_NA (float_NA())	/**< NA value for the type OBI_FLOAT */
+#define OBIChar_NA (0)				/**< NA value for the type OBI_CHAR */
+										 // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
+#define OBISeq_NA ("\0")			// TODO
+#define OBIStr_NA ("\0")			// TODO
 
 
 /**
@@ -26,7 +34,7 @@ typedef enum OBIBool {
     FALSE      = 0,
     TRUE       = 1,
     OBIBool_NA = 2
-} obibool_t, *obibool_p; 		/**< a boolean true/false value */
+} obibool_t, *obibool_p; 		/**< a boolean true/false value */	// TODO check name convention?
 
 
 /**
@@ -38,16 +46,27 @@ typedef enum OBIType {
 	OBI_FLOAT,					/**< a floating value (C type : double) */
 	OBI_BOOL,					/**< a boolean true/false value, see obibool_t enum */
 	OBI_CHAR,					/**< a character (C type : char) */
-	OBI_IDX					    /**< an index in a data structure (C type : size_t) */
+	OBI_STR,				    /**< an index in a data structure (C type : int64_t) referring to a character string */
+	OBI_SEQ,					/**< an index in a data structure (C type : int64_t) referring to a DNA sequence */
+	OBI_IDX					    /**< an index referring to a line in another column (C type : int64_t) */	// TODO delete?
 } OBIType_t, *OBIType_p;
 
 
+typedef int64_t index_t;
 typedef int32_t obiint_t;
 typedef double obifloat_t;
 typedef char obichar_t;
-typedef size_t obiidx_t;
+// TODO same for obistr_t and obiseq_t ?
 
 
+typedef char byte_t;		/**< Defining byte type since the data referred to by AVL trees is stored in bits
+							 *	 and char (stored on one byte) is the smallest addressable unit.
+ 	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief Union used to compute the NA value of the OBI_FLOAT OBIType.
+ */
 typedef union
 {
     double value;
@@ -55,7 +74,11 @@ typedef union
 } ieee_double;
 
 
-static double float_NA(void)	// as defined in R
+/**
+ * @brief Returns the NA value of the OBI_FLOAT OBIType.
+ * This value corresponds to the float NA value as defined in R.
+ */
+static double float_NA(void)
 {
     volatile ieee_double x;
     x.word[0] = 0x7ff00000;
@@ -65,12 +88,12 @@ static double float_NA(void)	// as defined in R
 
 
 /**
- * @brief returns the memory size in bytes of an OBIType
+ * @brief Returns the memory size in bytes of an OBIType.
  *
- * @param type the OBIType code used as query
+ * @param type The OBIType code used as query.
  *
- * @return the size in bytes of the type
- * @retval 0 on error (unknown type)
+ * @returns The size in bytes of the type.
+ * @retval 0 if an error occurred (unknown type).
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
@@ -79,31 +102,32 @@ size_t obi_sizeof(OBIType_t type);
 
 
 /**
- * @brief returns the size requested to store an array of OBIType
+ * @brief Returns the size required to store an array of elements with an OBIType.
  *
- * The returned size is large enough to store an array of size nbelement
- * but rounded at a multiple of the memory page size.
+ * The returned size is large enough to store an array large enough
+ * to store all the elements but rounded at a multiple of the memory page size.				// TODO this might be redundant but still a good thing
  *
- * @param type the OBIType code used as query
- * @param nbelement the number of elements to be stored
+ * @param data_type The OBIType of the elements.
+ * @param nb_lines The number of lines to be stored.
+ * @param nb_elements_per_line The number of elements per line.
  *
- * @return the size in bytes of the array
- * @retval 0 on error (unknown type)
+ * @returns The size in bytes of the array.
+ * @retval 0 if an error occurred (unknown type).
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-size_t obi_array_sizeof(OBIType_t type, size_t nbelements, size_t nb_elements_per_line);
+size_t obi_array_sizeof(OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line);
 
 
 /**
- * @brief returns the name in the form of a character string of an OBIType
+ * @brief Returns the name in the form of a character string of an OBIType.
  *
  *
- * @param data_type the OBIType code used as query
+ * @param data_type The OBIType code used as query.
  *
- * @return the name of the OBIType
- * @retval NULL on error (unknown type or error allocating the memory for the character string)
+ * @returns The name of the OBIType.
+ * @retval NULL if an error occurred (unknown type or error allocating the memory for the character string).
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)

src/obiview.h

@@ -0,0 +1,189 @@
+/********************************************************************
+ * Obiview header file                                              *
+ ********************************************************************/
+
+/**
+ * @file obiview.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 16 December 2015
+ * @brief Header file for the OBIDMS view functions and structures.
+ */
+
+
+#ifndef OBIVIEW_H_
+#define OBIVIEW_H_
+
+
+#include <stdlib.h>
+#include <errno.h>
+#include <stdio.h>
+#include <stdbool.h>
+#include <time.h>
+#include <math.h>
+
+#include "obidms.h"
+#include "obidmscolumn.h"
+#include "obierrno.h"
+
+
+#define OBIVIEW_NAME_MAX_LENGTH (1000)   /**< The maximum length of an OBIDMS view name.
+                                	 	  */
+#define OBIVIEW_COMMENTS_MAX_LENGTH (10000)
+
+#define OBIVIEW_FILE_NAME "obiviews"
+
+#define VIEW_TYPE_MAX_NAME (1024)
+
+#define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW"
+
+#define NUC_SEQUENCE_COLUMN "NUC_SEQ"
+#define NUC_SEQUENCE_AVL "NUC_SEQ_AVL"
+
+#define ID_COLUMN "ID"
+#define ID_AVL "ID_AVL"
+
+#define DESCRIPTION_COLUMN "DESCRIPTION"
+#define DESCRIPTION_AVL "DESCRIPTION_AVL"
+
+#define LINES_COLUMN_NAME "LINES"
+
+
+/**
+ * @brief .
+ */
+typedef struct Column_reference {
+	char 	   	 column_name[OBIDMS_COLUMN_MAX_NAME+1];    /**< Name of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+	obiversion_t version;				   		    	   /**< Version of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+} Column_reference_t, *Column_reference_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiview {
+
+	OBIDMS_p         	dms;
+
+	bool             	read_only;
+
+	OBIDMS_column_p  	line_selection;
+
+	OBIDMS_column_p  	new_line_selection;
+
+	index_t			 	line_count;
+
+	int    			 	column_count;
+
+	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];
+
+	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	char				created_from[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	int					view_number;
+
+	char				view_type[VIEW_TYPE_MAX_NAME+1];
+
+	char 				comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];
+
+} Obiview_t, *Obiview_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiview_infos {
+	int					view_number;
+
+	int 				column_count;
+
+	index_t             line_count;
+
+	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	char				created_from[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	time_t 		 		creation_date;
+
+	bool				all_lines;
+
+	Column_reference_t	line_selection;
+
+	Column_reference_t	column_references[MAX_NB_OPENED_COLUMNS];
+
+	char				view_type[VIEW_TYPE_MAX_NAME+1];
+
+	char 				comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];
+
+} Obiview_infos_t, *Obiview_infos_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiviews_header {
+	size_t header_size;
+	size_t views_size;
+	int    view_count;
+} Obiviews_header_t, *Obiviews_header_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiviews_infos_all {
+	Obiviews_header_p	header;
+
+	Obiview_infos_p 	view_infos;
+
+} Obiviews_infos_all_t, *Obiviews_infos_all_p;
+
+
+Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments);
+
+Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments);
+
+Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
+
+Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
+
+Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
+
+Obiviews_infos_all_p obi_read_views(OBIDMS_p dms);
+
+int obi_unmap_read_views(Obiviews_infos_all_p views);
+
+int obi_view_add_column(Obiview_p view,
+						const char* column_name,
+						obiversion_t version_number,
+						OBIType_t data_type,
+						index_t nb_lines,
+						index_t nb_elements_per_line,
+						const char* elements_names,
+						const char* avl_name,
+						const char* comments,
+						bool create);
+
+int obi_view_delete_column(Obiview_p view, const char* column_name);
+
+int obi_select_line(Obiview_p view, index_t line_nb);
+
+int obi_select_lines(Obiview_p view, index_t* line_nbs);
+
+int obi_view_update_lines(Obiview_p view, index_t line_count);
+
+OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name);
+
+OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
+
+OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
+
+int obi_save_view(Obiview_p view);
+
+int obi_close_view(Obiview_p view);
+
+int obi_save_and_close_view(Obiview_p view);
+
+#endif /* OBIVIEW_H_ */

src/private_at_functions.c

@@ -3,8 +3,8 @@
  ****************************************************************************/
 
 /**
- * @file private_at_functions.h
- * @author Celine Mercier
+ * @file private_at_functions.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 15 June 2015
  * @brief Private replacement functions for *at functions.
  */
@@ -23,14 +23,7 @@
 #include "obierrno.h"
 
 
-#define DEBUG_LEVEL 0
-
-
-/**********************************************************************
- *
- * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
- *
- **********************************************************************/
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 char* get_full_path(int directory_file_descriptor, const char* path_name)
@@ -50,7 +43,7 @@ char* get_full_path(int directory_file_descriptor, const char* path_name)
 		return NULL;
 	}
 
-	// TODO check errors
+	// TODO check errors?
 	strlcat(full_path, "/", MAX_PATH_LEN);
 	strlcat(full_path, path_name, MAX_PATH_LEN);
 
@@ -77,39 +70,3 @@ DIR* private_opendirat(int directory_file_descriptor, const char* path_name)
 }
 
 
-//int private_openat(int directory_file_descriptor, const char* path_name, int flags)
-//{
-//	char* full_path;
-//	int file_descriptor;
-//
-//	full_path = get_full_path(directory_file_descriptor, path_name);
-//	if (full_path == NULL)
-//		return -1;
-//
-//	file_descriptor = open(full_path, flags);
-//
-//	free(full_path);
-//
-//	return file_descriptor;
-//}
-//
-//
-//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode)
-//{
-//	char* full_path;
-//
-//	full_path = get_full_path(directory_file_descriptor, path_name);
-//	if (full_path == NULL)
-//		return -1;
-//
-//	if (mkdir(full_path, mode) < 0)
-//	{
-//		free(full_path);
-//		return -1;
-//	}
-//
-//	free(full_path);
-//
-//	return 0;
-//}
-

src/private_at_functions.h

@@ -1,10 +1,15 @@
+/****************************************************************************
+ * Header file for private *at functions                                    *
+ ****************************************************************************/
+
 /**
- * @file private_openat.h
- * @author Celine Mercier
+ * @file private_at_functions.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 15 June 2015
- * @brief Header file for the replacement *at function.
+ * @brief Header file for the private replacement functions for *at functions.
  */
 
+
 #ifndef PRIVATE_OPENAT_H_
 #define PRIVATE_OPENAT_H_
 
@@ -12,27 +17,22 @@
 #include <sys/stat.h>
 
 
-#define MAX_PATH_LEN 4096
+#define MAX_PATH_LEN 4096	/**< Maximum length for the character string defining a
+ 	 	 	 	 	 	 	 	 file or directory path */
 
 
 /**
- * Internal function getting the full path of a file or a directory from its
- * path relative to a directory file descriptor.
- *
+ * @brief Internal function getting the full path of a file or a directory from its
+ *        path relative to a directory file descriptor.
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param directory_file_descriptor the file descriptor for the directory to which
- * 									path_name is relative
- * @param path_name the path name for the file or directory, relative to directory_file_descriptor
+ * @param directory_file_descriptor The file descriptor for the directory to which
+ * 									path_name is relative.
+ * @param path_name The path name for the file or directory, relative to directory_file_descriptor.
  *
- * @return a pointer to the full path
- * @retvalue <full_path> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the full path.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -43,10 +43,11 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
 /**
  * @brief Replacement function for opendirat() : open a directory relative to a directory file descriptor.
  *
- * @param directory_file_descriptor the file descriptor for the directory in which the directory should be opened
- * @param path_name the path name for the directory to be opened, relative to directory_file_descriptor
+ * @param directory_file_descriptor The file descriptor for the directory in which the directory should be opened.
+ * @param path_name The path name for the directory to be opened, relative to directory_file_descriptor.
  *
- * @return the file descriptor of the opened directory
+ * @returns The file descriptor of the opened directory.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -54,34 +55,4 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
 DIR* private_opendirat(int directory_file_descriptor, const char* path_name);
 
 
-///**
-// * @brief Replacement function for openat() : open a file relative to a directory file descriptor.
-// *
-// * @param directory_file_descriptor the file descriptor for the directory in which the file should be opened
-// * @param path_name the path name for the file, relative to directory_file_descriptor
-// * @param flags the access modes
-// *
-// * @return the file descriptor of the opened file
-// *
-// * @since June 2015
-// * @author Celine Mercier (celine.mercier@metabarcoding.org)
-// */
-//int private_openat(int directory_file_descriptor, const char* path_name, int flags);
-//
-//
-///**
-// * @brief Replacement function for mkdirat() : create a directory relative to a directory file descriptor.
-// *
-// * @param directory_file_descriptor the file descriptor for the directory in which the directory should be created
-// * @param path_name the path name for the new directory, relative to directory_file_descriptor
-// * @param mode the access mode
-// *
-// * @return the file descriptor of the created directory
-// *
-// * @since June 2015
-// * @author Celine Mercier (celine.mercier@metabarcoding.org)
-// */
-//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode);
-
-
 #endif /* PRIVATEOPENAT_H_ */