The default name of an AVL is now the column name + '_indexer', and when

an AVL is opened (as opposed to created), it is read-only

python/obi.py

@@ -0,0 +1,228 @@
+#!/usr/local/bin/python3.4
+'''
+obi -- shortdesc
+
+obi is a description
+
+It defines classes_and_methods
+
+@author:     user_name
+
+@copyright:  2014 organization_name. All rights reserved.
+
+@license:    license
+
+@contact:    user_email
+@deffield    updated: Updated
+'''
+
+import sys
+import pkgutil
+import argparse
+import logging
+import json
+
+default_config = {
+
+    'obi' :        { 'log'            : True,
+                     'loglevel'       : 'INFO',
+                     'version'        : False,
+                     'progress'       : True
+                   }
+                 
+}
+
+
+
+from obitools3 import command
+from obitools3.version import version
+
+__all__ = []
+__version__ = version
+__date__ = '2014-09-28'
+__updated__ = '2014-09-28'
+
+DEBUG = 1
+TESTRUN = 0
+PROFILE = 0
+
+
+
+def loadCommand(name,loader):
+    '''
+    Load a command module from its name and an ImpLoader
+    
+    This function is for internal use
+    
+    @param name:   name of the module
+    @type name: str 
+    @param loader: the module loader
+    @type loader: ImpLoader
+    
+    @return the loaded module
+    @rtype: module 
+    '''
+    
+    module = loader.find_module(name).load_module(name)
+    return module
+
+def getCommandsList():
+    '''
+    Returns the list of sub-commands available to the main `obi` command
+    
+    @return: a dict instance with key corresponding to each command and
+             value corresponding to the module
+             
+    @rtype: dict
+    '''
+    cmds = dict((x[1],loadCommand(x[1],x[0])) 
+                for x in pkgutil.iter_modules(command.__path__) 
+                if not x[2])
+    return cmds
+
+def getLogger(config):
+    '''
+    Returns the logger as defined by the command line option
+    or by the config file
+    :param config:
+    '''
+ 
+    output = config['obi']['outputfilename'] 
+    level  = config['obi']['loglevel'] 
+    logfile= config['obi']['log'] 
+    
+    rootlogger   = logging.getLogger()
+    logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s]  %(message)s")
+
+    stderrHandler = logging.StreamHandler(sys.stderr)
+    stderrHandler.setFormatter(logFormatter)
+
+    rootlogger.addHandler(stderrHandler)
+    
+    if logfile:
+        fileHandler = logging.FileHandler("%s.log" % output)
+        fileHandler.setFormatter(logFormatter)
+        rootlogger.addHandler(fileHandler)
+    
+    try:
+        loglevel = getattr(logging, level) 
+    except:
+        loglevel = logging.INFO
+        
+    rootlogger.setLevel(loglevel)
+    
+    config['obi']['logger']=rootlogger
+    
+    return rootlogger
+
+
+class ObiParser(argparse.ArgumentParser): 
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+def buildArgumentParser():
+    parser = ObiParser()
+    
+    parser.add_argument('--version',   dest='obi:version', 
+                                       action='store_true', 
+                                       default=False, 
+                        help='Print the version of the OBITools')
+
+    parser.add_argument('--no-log',    dest='obi:log', 
+                                       action='store_false', 
+                                       default=None, 
+                        help='Do not create a logfile for the data analyze')
+
+    parser.add_argument('--no-progress', dest='obi:progress', 
+                                       action='store_false', 
+                                       default=None, 
+                        help='Do not print the progress bar during analyzes')
+
+    subparsers = parser.add_subparsers(title='subcommands',
+                                       description='valid subcommands',
+                                       help='additional help')
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+        
+        if hasattr(module, "run"):
+            if hasattr(module, "__title__"):
+                sub = subparsers.add_parser(c,help=module.__title__)
+            else:
+                sub = subparsers.add_parser(c)
+    
+            if hasattr(module, "addOptions"):
+                module.addOptions(sub)
+            
+            sub.set_defaults(**{'obi:module' : module})
+                        
+    return parser
+
+def buildDefaultConfiguration():
+    global default_config
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+    
+        assert hasattr(module, "run")
+        
+        if hasattr(module, 'default_config'):
+            default_config[c]=module.default_config
+        else:
+            default_config[c]={}
+                        
+    return default_config
+        
+
+def getConfiguration():
+    global default_config
+
+    if '__done__' in default_config:
+        return default_config
+    
+    parser = buildArgumentParser()
+    options = vars(parser.parse_args())
+    
+    config =  buildDefaultConfiguration()
+    
+    
+    for k in options:
+        section,key = k.split(':')
+        s = config[section]
+        if options[k] is not None:
+            s[key]=options[k]
+            
+    if config['obi']['version']:
+        print("The OBITools - Version %s" % __version__)
+        sys.exit(0)
+
+    if not 'module' in config['obi']:
+        print('\nError: No obi command specified',file=sys.stderr)
+        parser.print_help()
+        sys.exit(2)
+        
+            
+    if config['obi']['outputfilename'] is None:
+        config['obi']['outputfilename']=config['obi']['indexfilename']
+        
+    getLogger(config)
+    
+    config['__done__']=True
+            
+    return config
+    
+
+if __name__ =="__main__":
+    
+    config = getConfiguration()    
+                
+    config['obi']['module'].run(config)
+    
+    
+    

python/obitools3/command/count.py

@@ -0,0 +1,36 @@
+'''
+Created on 8 mars 2016
+
+@author: coissac
+'''
+
+__title__="Counts sequences in a sequence set"
+
+
+default_config = {   'countmode'       : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='obi:input',     metavar='obi:input', 
+                                              nargs='?', 
+                                              default=None,
+                        help='input data set' )
+
+    group=parser.add_option_group('Obicount specific options')
+    group.add_option('-s','--sequence',
+                             action="store_true", dest="count:sequence",
+                             default=False,
+                             help="Prints only the number of sequence records."
+                             )
+ 
+    group.add_option('-a','--all',
+                             action="store_true", dest="count:all",
+                             default=False,
+                             help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
+                             )
+
+    
+    
+def run(config):
+    # The code of my command
+    pass

python/obitools3/obidms/_obidms.cfiles

@@ -1,7 +1,28 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
 ../../../src/obidms.h
 ../../../src/obidms.c
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -12,17 +33,19 @@
 ../../../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
-../../../src/bloom.c
-../../../src/bloom.h
-../../../src/MurmurHash2.c
-../../../src/murmurhash2.h
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidms.pxd

@@ -56,7 +56,7 @@ cdef class OBIView:
                      index_t nb_lines=*, 
                      index_t nb_elements_per_line=*,
                      list elements_names=*,
-                     str avl_name=*,
+                     str indexer_name=*,
                      str comments=*,
                      bint create=*
                     )

python/obitools3/obidms/_obidms.pyx

@@ -5,7 +5,7 @@ from obitools3.utils cimport bytes2str, str2bytes
 from .capi.obidms cimport obi_dms, \
                           obi_close_dms
                           
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
+from .capi.obidmscolumn cimport obi_close_column, \
                                 obi_column_format_date, \
                                 OBIDMS_column_p, \
                                 OBIDMS_column_header_p
@@ -144,7 +144,7 @@ cdef class OBIDMS_column :
         return to_print
         
     cpdef close(self):
-        if obi_truncate_and_close_column((self.pointer)[0]) < 0 :
+        if obi_close_column((self.pointer)[0]) < 0 :
             raise Exception("Problem closing a column")
 
 
@@ -352,7 +352,7 @@ cdef class OBIView :
                      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 indexer_name="",
                      str comments="",
                      bint create=True   # TODO
                      ) :
@@ -388,7 +388,7 @@ cdef class OBIView :
         
         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), 
+                                elements_names_b, str2bytes(indexer_name), 
                                 str2bytes(comments), create) < 0) :
             raise Exception("Problem adding a column in a view")
         

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_bool.c
 ../../../src/obidmscolumn_bool.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_obibool_with_elt_name_in_view, \
+from .capi.obiview      cimport 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

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_char.c
 ../../../src/obidmscolumn_char.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_obichar_with_elt_name_in_view, \
+from .capi.obiview      cimport 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

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_float.c
 ../../../src/obidmscolumn_float.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
-                                obi_column_get_obifloat_with_elt_name_in_view, \
+from .capi.obiview      cimport 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

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_int.c
 ../../../src/obidmscolumn_int.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_obiint_with_elt_name_in_view, \
+from .capi.obiview      cimport 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

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_seq.c
 ../../../src/obidmscolumn_seq.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_obiseq_with_elt_name_in_view, \
+from .capi.obiview      cimport 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
@@ -10,19 +9,23 @@ from .capi.obitypes     cimport OBISeq_NA, const_char_p
 
 from obitools3.utils cimport str2bytes, bytes2str
 
+from libc.stdlib cimport free
+from libc.string cimport strcmp
+
 
 cdef class OBIDMS_column_seq(OBIDMS_column):
 
     cpdef object get_line(self, index_t line_nb):
-        cdef bytes value
+        cdef char*  value
         cdef object result
-        value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        value = 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
+        if strcmp(value, OBISeq_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+            free(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
@@ -38,33 +41,35 @@ cdef class OBIDMS_column_seq(OBIDMS_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 char*  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))
+        value = 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 :
+        if strcmp(value, OBISeq_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+            free(value)
         return result
 
     cpdef object get_line(self, index_t line_nb) :
-        cdef bytes value
-        cdef object value_in_result
-        cdef dict result
+        cdef char*   value
+        cdef object  value_in_result
+        cdef dict    result
         cdef index_t i
-        cdef bint all_NA
+        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)
+            value = 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 :
+            if strcmp(value, OBISeq_NA) == 0 :
                 value_in_result = None
             else :
-                value_in_result = bytes2str(value)    
+                value_in_result = bytes2str(value)
+                free(value)    
             result[self.elements_names[i]] = value_in_result
             if all_NA and (value_in_result is not None) :
                 all_NA = False

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -1,20 +1,41 @@
 ../../../src/obidmscolumn_str.c
 ../../../src/obidmscolumn_str.h
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -1,7 +1,6 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_obistr_with_elt_name_in_view, \
+from .capi.obiview      cimport 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
@@ -10,19 +9,22 @@ from .capi.obitypes     cimport OBIStr_NA, const_char_p
 
 from obitools3.utils cimport str2bytes, bytes2str
 
+from libc.string cimport strcmp
+
 
 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)
+        cdef const_char_p value
+        cdef object       result
+        value = 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
+        if strcmp(value, OBIStr_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
@@ -38,33 +40,35 @@ cdef class OBIDMS_column_str(OBIDMS_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))
+        cdef const_char_p value
+        cdef object       result
+        value = 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 :
+        if strcmp(value, OBIStr_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
         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
+        cdef const_char_p 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)
+            value = 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 :
+            if strcmp(value, OBIStr_NA) == 0 :
                 value_in_result = None
             else :
-                value_in_result = bytes2str(value)    
+                value_in_result = bytes2str(value)
+            # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
             result[self.elements_names[i]] = value_in_result
             if all_NA and (value_in_result is not None) :
                 all_NA = False

python/obitools3/obidms/_obiseq.cfiles

@@ -1,7 +1,28 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
 ../../../src/obidms.h
 ../../../src/obidms.c
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -12,11 +33,7 @@
 ../../../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/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/_obiseq.pxd

@@ -21,10 +21,6 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
 
 
 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)

python/obitools3/obidms/_obiseq.pyx

@@ -26,7 +26,7 @@ cdef class OBI_Seq(dict) :
         self[bytes2str(DESCRIPTION_COLUMN)] = description
         
     cpdef get_description(self) :
-        return self.description
+        return self.description     # TODO no
         
     cpdef get_sequence(self) :
         return self.sequence
@@ -48,28 +48,25 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
 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
+        return self[bytes2str(ID_COLUMN)]
             
     cpdef set_description(self, str description) :
-        self.description = description
         self[bytes2str(DESCRIPTION_COLUMN)] = description
 
     cpdef get_description(self) :
-        return self.description
+        return self[bytes2str(DESCRIPTION_COLUMN)]
 
     cpdef set_sequence(self, str sequence) :
-        self.sequence = sequence
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
 
     cpdef get_sequence(self) :
-        return self.sequence
+        return self[bytes2str(NUC_SEQUENCE_COLUMN)]
     
-    def __str__(self) :
-        return self.sequence    # or not
+#    def __str__(self) :
+#        return self[bytes2str(NUC_SEQUENCE_COLUMN)]    # or not
     
 #    cpdef str reverse_complement(self) :    TODO in C ?
 #        pass

python/obitools3/obidms/_obitaxo.cfiles

@@ -1,7 +1,28 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/MurmurHash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
 ../../../src/obidms.h
 ../../../src/obidms.c
-../../../src/obiview.h
-../../../src/obiview.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -12,13 +33,7 @@
 ../../../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
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -27,7 +27,7 @@ cdef extern from "obidmscolumn.h" nogil:
         obiversion_t    version
         obiversion_t    cloned_from
         const_char_p    name
-        const_char_p    avl_name
+        const_char_p    indexer_name
         const_char_p    comments
     
     ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
@@ -45,7 +45,7 @@ cdef extern from "obidmscolumn.h" nogil:
                                       index_t nb_lines, 
                                       index_t nb_elements_per_line, 
                                       const_char_p elements_names,
-                                      const_char_p avl_name,
+                                      const_char_p indexer_name,
                                       const_char_p comments)
                 
     OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
@@ -60,7 +60,7 @@ cdef extern from "obidmscolumn.h" nogil:
                                      obiversion_t version_number, 
                                      bint clone_data)
     
-    int obi_truncate_and_close_column(OBIDMS_column_p column)
+    int obi_close_column(OBIDMS_column_p column)
     
     obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
                                                          const_char_p column_name)
@@ -69,37 +69,14 @@ cdef extern from "obidmscolumn.h" nogil:
                                                            const_char_p column_name,
                                                            obiversion_t version_number)
     
-    int obi_unmap_header(OBIDMS_column_header_p header)
+    int obi_close_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, 
                                             index_t line_nb, 
@@ -121,28 +98,6 @@ cdef extern from "obidmscolumn_int.h" nogil:
 
 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, 
                                              index_t line_nb, 
                                              const_char_p element_name, 
@@ -163,28 +118,6 @@ cdef extern from "obidmscolumn_bool.h" nogil:
 
 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, 
                                              index_t line_nb, 
                                              const_char_p element_name, 
@@ -205,83 +138,39 @@ cdef extern from "obidmscolumn_char.h" nogil:
 
 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, 
-                                             index_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)
+                                             index_t line_nb, 
+                                             index_t element_idx, 
+                                             obifloat_t value)
     
     obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                                   index_t line_nb, 
-                                                   const_char_p element_name)
+                                                     index_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)
+                                                    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)
+                                            const_char_p 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 value)
     
     const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, 
-                                                    index_t line_nb, 
-                                                    char* element_name)
+                                                     index_t line_nb, 
+                                                     const_char_p element_name)
     
     const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
                                                     index_t line_nb, 
@@ -289,43 +178,21 @@ cdef extern from "obidmscolumn_str.h" nogil:
 
 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)
+                                            const_char_p 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 value)
     
-    const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, 
-                                                    index_t line_nb, 
-                                                    char* element_name)
+    char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, 
+                                              index_t line_nb, 
+                                              const_char_p element_name)
     
-    const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, 
-                                                    index_t line_nb, 
-                                                    index_t element_idx)
+    char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, 
+                                             index_t line_nb, 
+                                             index_t element_idx)
 

python/obitools3/obidms/capi/obiview.pxd

@@ -3,6 +3,10 @@
 from .obitypes           cimport const_char_p, \
                                  OBIType_t, \
                                  obiversion_t, \
+                                 obiint_t, \
+                                 obibool_t, \
+                                 obichar_t, \
+                                 obifloat_t, \
                                  index_t, \
                                  time_t
 from ..capi.obidms       cimport OBIDMS_p
@@ -90,7 +94,7 @@ cdef extern from "obiview.h" nogil:
                             index_t nb_lines,
                             index_t nb_elements_per_line,
                             const_char_p elements_names,
-                            const_char_p avl_name,
+                            const_char_p indexer_name,
                             const_char_p comments,
                             bint create)
 
@@ -111,4 +115,136 @@ cdef extern from "obiview.h" nogil:
     int obi_close_view(Obiview_p view)
     
     int obi_save_and_close_view(Obiview_p view)
+    
+    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_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_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_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_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 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, 
+                                                   const_char_p 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_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 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, 
+                                                   const_char_p value)
+    
+    char* 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)
+    
+    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)
 

python/obitools3/obiimport.py

@@ -0,0 +1,199 @@
+import sys
+import argparse
+import time
+
+from obitools3.obidms._obidms import OBIDMS
+
+
+def bufferedRead(fileobj,size=209715200):   ## 200 MB
+   buffer = fileobj.readlines(size)
+   while buffer:
+       for l in buffer:
+           yield l
+       buffer = fileobj.readlines(size)
+
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Convert a fasta file in an OBIDMS.')
+    
+    parser.add_argument('-i', '--input', dest='input_file', type=str,
+                       help='Name of the file containing the sequences')
+
+    args = parser.parse_args()
+
+    d = OBIDMS('tdms')
+    
+    view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
+
+#    for i in range(35000000) :
+#        if (not (i%500000)) :
+#            print(str(time.time())+'\t'+str(i))
+#        id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
+#        view[i].set_id(id)
+#        if id != view[i]["ID"] :
+#            print("nope", id, view[i]["ID"])
+    
+    input_file = open(args.input_file, 'r')
+    input_file_buffered = bufferedRead(input_file)
+    
+#         
+#     if args.input_file[-1:] == "a" :
+#     
+#         i = 0
+#         next = False
+#         first = True
+#         
+#         for line in input_file :
+#             
+#             if line[0] == ">" :
+#                 
+#                 if not first :
+#                     # save seq
+#                     #print(i, id, seq)
+#                     view[i].set_sequence(seq)
+#                     i+=1
+#                 
+#                 first = False
+#                     
+#                 #id = line.split(" ", 1)[0][1:]
+#                 #rest = (line[:-1].split(" ", 1)[1]).split(";")
+#                 #view[i].set_id(id)
+#                 
+# #                 description = ""
+# #                 for j in range(len(rest)) :
+# #                     if "=" in rest[j] :
+# #                         rest[j] = rest[j].strip()
+# #                         rest[j] = rest[j].split("=", 1)
+# #                         column_name = rest[j][0]
+# #                         v = rest[j][1]
+# #                         if ((not v.isalpha()) and (v.isalnum())) :
+# #                             conv_v = int(v)
+# #                         elif (v == "True") or (v == "False") :
+# #                             conv_v = bool(v)
+# #                         else :
+# #                             f = True
+# #                             for letter in v :
+# #                                 if ((not letter.isalnum()) or (letter != ".")) :
+# #                                     f = False
+# #                             if f :
+# #                                 conv_v = float(v)
+# #                             else : 
+# #                                 conv_v = v
+# #                         view[i][column_name] = conv_v
+# #                     else :
+# #                         description+=rest[j]
+# #                 
+# #                 if description != "" :
+# #                     description = description.strip()
+# #                     view[i].set_description(description)
+#                     
+#                 #print(id)
+#                 #print(rest)
+#                 #print(description)
+#                 
+#                 next = True
+#                 
+#             elif next == True :
+#                 
+#      #           if not (i % 1E5) :
+#      #               print(i)
+#                 
+#                 seq = line[:-1]
+#                 next = False
+#             
+#             elif not next :
+#                 
+#                 seq += line[:-1]
+# 
+# 
+#     elif args.input_file[-1:] == "q" :
+#         
+#         i = 0
+#         l = 0
+#         next = False
+#
+    l=0
+    i=0
+#     while (True):
+#         l+=1
+#         line = input_file.readline()
+#         if line=="":
+#             break
+    for line in input_file_buffered :
+# 
+             #if i > 1E7 :
+#             #    print('hmm?')
+#                         
+#        if i == 6000000 :
+#            break
+#             
+        if l%4 == 0 :
+#                
+            if (not (i%500000)) :
+                print(str(time.time())+'\t'+str(i))
+# # 
+# #                 #print("header", line)
+# # 
+            id = line.split(" ", 1)[0][1:]
+#            print(id)
+# #                 #rest = (line[:-1].split(" ", 1)[1]).split(";")
+            view[i].set_id(id)
+#            print(view[i]["ID"])
+# 
+#            i+=1
+        
+#        l+=1
+#                 
+# #                 description = ""
+# #                 for j in range(len(rest)) :
+# #                     if "=" in rest[j] :
+# #                         rest[j] = rest[j].strip()
+# #                         rest[j] = rest[j].split("=", 1)
+# #                         column_name = rest[j][0]
+# #                         #print("COLUMN", column_name)
+# #                         v = rest[j][1]
+# #                         if (v == "") and (column_name in view) and (view[column_name].get_data_type() == "OBI_SEQ") :
+# #                             #print(">>>>>>YUP")
+# #                             conv_v = "aa"
+# #                         else :
+# #                             if ((not v.isalpha()) and (v.isalnum())) :
+# #                                 conv_v = int(v)
+# #                             elif (v == "True") or (v == "False") :
+# #                                 conv_v = bool(v)
+# #                             else :
+# #                                 f = True
+# #                                 for letter in v :
+# #                                     if ((not letter.isalnum()) or (letter != ".")) :
+# #                                         f = False
+# #                                 if f :
+# #                                     conv_v = float(v)
+# #                                 else :
+# #                                     conv_v = v
+# #                         view[i][column_name] = conv_v
+# #                     else :
+# #                         description+=rest[j]
+# #                 
+# #                 if description != "" :
+# #                     description = description.strip()
+# #                     view[i].set_description(description)
+#                 
+        elif l%4 == 1 :
+# #                
+            seq = line[:-1]
+#                 #print("seq", seq)
+            view[i].set_sequence(seq)
+            i+=1
+#                         
+        l+=1
+#     
+#     
+    input_file.close()
+
+    #print(view)
+    print(view.__repr__())
+
+    view.save_and_close()
+    d.close()
+
+    print("Done.")

requirements.txt

@@ -1,5 +1,5 @@
 --extra-index-url https://pypi.python.org/simple/
-Cython>=0.21
+Cython==0.23.5
 Sphinx>=1.2.0
 ipython>=3.0.0
 breathe>=4.0.0

src/bloom.c

@@ -61,7 +61,7 @@ static int bloom_check_add(struct bloom * bloom,
   register unsigned int a = murmurhash2(buffer, len, 0x9747b28c);
   register unsigned int b = murmurhash2(buffer, len, a);
   register unsigned int x;
-  register unsigned int i;
+  register int i;	// TODO why was it unsigned?
 
   unsigned bucket_index = (a % bloom->buckets);
 
@@ -122,6 +122,40 @@ static void setup_buckets(struct bloom * bloom, unsigned int cache_size)
 }
 
 
+// TODO
+int bloom_filter_size(int entries, double error)
+{
+	int bytes;
+	double num;
+	double denom;
+	double bpe;
+	int bits;
+	unsigned bucket_bytes;
+	int not_even_by;
+
+	num = log(error);
+	denom = 0.480453013918201; // ln(2)^2
+	bpe = -(num / denom);
+	bits = (int)(((double)entries) * bpe);
+
+	if (bits % 8) {
+		bytes = (bits / 8) + 1;
+	}
+	else {
+		bytes = bits / 8;
+	}
+
+	bucket_bytes = BLOOM_BUCKET_SIZE_FALLBACK;
+	not_even_by = bytes % bucket_bytes;
+	if (not_even_by) {
+	  // adjust bytes
+		bytes += (bucket_bytes - not_even_by);
+	}
+
+	return bytes;
+}
+
+
 int bloom_init_size(struct bloom * bloom, int entries, double error,
                     unsigned int cache_size)
 {
@@ -151,19 +185,21 @@ int bloom_init_size(struct bloom * bloom, int entries, double error,
 
   setup_buckets(bloom, cache_size);
 
-  bloom->bf = (unsigned char *)calloc(bloom->bytes, sizeof(unsigned char));
-  if (bloom->bf == NULL) {
-    return 1;
-  }
+  // TODO comment
+  memset(bloom->bf, 0, bloom->bytes);
+  //bloom->bf = (unsigned char *)calloc(bloom->bytes, sizeof(unsigned char));
+  //if (bloom->bf == NULL) {
+  //  return 1;
+  //}
 
   bloom->ready = 1;
   return 0;
 }
 
 
-int bloom_init(struct bloom * bloom, int entries, double error)
+int bloom_init(struct bloom * bloom, int entries)  //, double error)
 {
-  return bloom_init_size(bloom, entries, error, 0);
+  return bloom_init_size(bloom, entries, BLOOM_FILTER_ERROR_RATE, 0);
 }
 
 

src/bloom.h

@@ -9,6 +9,10 @@
 #define _BLOOM_H
 
 
+// TODO
+#define BLOOM_FILTER_ERROR_RATE (0.001)
+
+
 /** ***************************************************************************
  * On Linux, the code attempts to compute a bucket size based on CPU cache
  * size info, if available. If that fails for any reason, this fallback size
@@ -60,10 +64,17 @@ struct bloom
   unsigned bucket_bits_fast_mod_operand;
 
   double bpe;
-  unsigned char * bf;
   int ready;
+
+  unsigned char bf[];
 };
 
+typedef struct bloom bloom_t;
+
+
+// TODO
+int bloom_filter_size(int entries, double error);
+
 
 /** ***************************************************************************
  * Initialize the bloom filter for use.
@@ -91,7 +102,7 @@ struct bloom
  *     1 - on failure
  *
  */
-int bloom_init(struct bloom * bloom, int entries, double error);
+int bloom_init(struct bloom * bloom, int entries); //, double error);
 
 
 /** ***************************************************************************

src/char_str_indexer.c

@@ -0,0 +1,80 @@
+/****************************************************************************
+ * Character string indexing functions                                      *
+ ****************************************************************************/
+
+/**
+ * @file char_str_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of character strings.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_str_to_blob(const char* value)
+{
+	Obi_blob_p 		 value_b;
+	int32_t 		 length;
+
+	// Compute the number of bytes on which the value will be encoded
+	length = strlen(value) + 1;		// +1 to store \0 at the end (makes retrieving faster)
+
+	value_b = obi_blob((byte_t*)value, ELEMENT_SIZE_STR, length, length);
+	if (value_b == NULL)
+	{
+		obidebug(1, "\nError encoding a character string in a blob");
+		return NULL;
+	}
+
+	return value_b;
+}
+
+
+char* obi_blob_to_str(Obi_blob_p value_b)
+{
+	return value_b->value;
+}
+
+
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_str_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded character string
+	return obi_blob_to_str(value_b);
+}
+

src/char_str_indexer.h

@@ -0,0 +1,61 @@
+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef CHAR_STR_INDEXER_H_
+#define CHAR_STR_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a character string to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_str_to_blob(char* value);
+
+
+/**
+ * @brief Converts a blob to a character string.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the character string contained in the blob.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_blob_to_str(Obi_blob_p value_b);
+
+
+// TODO doc
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value);
+
+char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* CHAR_STR_INDEXER_H_ */
+

src/crc64.c

@@ -0,0 +1,198 @@
+/* Redis uses the CRC64 variant with "Jones" coefficients and init value of 0.
+ *
+ * Specification of this CRC64 variant follows:
+ * Name: crc-64-jones
+ * Width: 64 bites
+ * Poly: 0xad93d23594c935a9
+ * Reflected In: True
+ * Xor_In: 0xffffffffffffffff
+ * Reflected_Out: True
+ * Xor_Out: 0x0
+ * Check("123456789"): 0xe9c6d914c4b8d9ca
+ *
+ * Copyright (c) 2012, Salvatore Sanfilippo <antirez at gmail dot com>
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *   * Redistributions of source code must retain the above copyright notice,
+ *     this list of conditions and the following disclaimer.
+ *   * Redistributions in binary form must reproduce the above copyright
+ *     notice, this list of conditions and the following disclaimer in the
+ *     documentation and/or other materials provided with the distribution.
+ *   * Neither the name of Redis nor the names of its contributors may be used
+ *     to endorse or promote products derived from this software without
+ *     specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE. */
+
+#include <stdint.h>
+
+static const uint64_t crc64_tab[256] = {
+    UINT64_C(0x0000000000000000), UINT64_C(0x7ad870c830358979),
+    UINT64_C(0xf5b0e190606b12f2), UINT64_C(0x8f689158505e9b8b),
+    UINT64_C(0xc038e5739841b68f), UINT64_C(0xbae095bba8743ff6),
+    UINT64_C(0x358804e3f82aa47d), UINT64_C(0x4f50742bc81f2d04),
+    UINT64_C(0xab28ecb46814fe75), UINT64_C(0xd1f09c7c5821770c),
+    UINT64_C(0x5e980d24087fec87), UINT64_C(0x24407dec384a65fe),
+    UINT64_C(0x6b1009c7f05548fa), UINT64_C(0x11c8790fc060c183),
+    UINT64_C(0x9ea0e857903e5a08), UINT64_C(0xe478989fa00bd371),
+    UINT64_C(0x7d08ff3b88be6f81), UINT64_C(0x07d08ff3b88be6f8),
+    UINT64_C(0x88b81eabe8d57d73), UINT64_C(0xf2606e63d8e0f40a),
+    UINT64_C(0xbd301a4810ffd90e), UINT64_C(0xc7e86a8020ca5077),
+    UINT64_C(0x4880fbd87094cbfc), UINT64_C(0x32588b1040a14285),
+    UINT64_C(0xd620138fe0aa91f4), UINT64_C(0xacf86347d09f188d),
+    UINT64_C(0x2390f21f80c18306), UINT64_C(0x594882d7b0f40a7f),
+    UINT64_C(0x1618f6fc78eb277b), UINT64_C(0x6cc0863448deae02),
+    UINT64_C(0xe3a8176c18803589), UINT64_C(0x997067a428b5bcf0),
+    UINT64_C(0xfa11fe77117cdf02), UINT64_C(0x80c98ebf2149567b),
+    UINT64_C(0x0fa11fe77117cdf0), UINT64_C(0x75796f2f41224489),
+    UINT64_C(0x3a291b04893d698d), UINT64_C(0x40f16bccb908e0f4),
+    UINT64_C(0xcf99fa94e9567b7f), UINT64_C(0xb5418a5cd963f206),
+    UINT64_C(0x513912c379682177), UINT64_C(0x2be1620b495da80e),
+    UINT64_C(0xa489f35319033385), UINT64_C(0xde51839b2936bafc),
+    UINT64_C(0x9101f7b0e12997f8), UINT64_C(0xebd98778d11c1e81),
+    UINT64_C(0x64b116208142850a), UINT64_C(0x1e6966e8b1770c73),
+    UINT64_C(0x8719014c99c2b083), UINT64_C(0xfdc17184a9f739fa),
+    UINT64_C(0x72a9e0dcf9a9a271), UINT64_C(0x08719014c99c2b08),
+    UINT64_C(0x4721e43f0183060c), UINT64_C(0x3df994f731b68f75),
+    UINT64_C(0xb29105af61e814fe), UINT64_C(0xc849756751dd9d87),
+    UINT64_C(0x2c31edf8f1d64ef6), UINT64_C(0x56e99d30c1e3c78f),
+    UINT64_C(0xd9810c6891bd5c04), UINT64_C(0xa3597ca0a188d57d),
+    UINT64_C(0xec09088b6997f879), UINT64_C(0x96d1784359a27100),
+    UINT64_C(0x19b9e91b09fcea8b), UINT64_C(0x636199d339c963f2),
+    UINT64_C(0xdf7adabd7a6e2d6f), UINT64_C(0xa5a2aa754a5ba416),
+    UINT64_C(0x2aca3b2d1a053f9d), UINT64_C(0x50124be52a30b6e4),
+    UINT64_C(0x1f423fcee22f9be0), UINT64_C(0x659a4f06d21a1299),
+    UINT64_C(0xeaf2de5e82448912), UINT64_C(0x902aae96b271006b),
+    UINT64_C(0x74523609127ad31a), UINT64_C(0x0e8a46c1224f5a63),
+    UINT64_C(0x81e2d7997211c1e8), UINT64_C(0xfb3aa75142244891),
+    UINT64_C(0xb46ad37a8a3b6595), UINT64_C(0xceb2a3b2ba0eecec),
+    UINT64_C(0x41da32eaea507767), UINT64_C(0x3b024222da65fe1e),
+    UINT64_C(0xa2722586f2d042ee), UINT64_C(0xd8aa554ec2e5cb97),
+    UINT64_C(0x57c2c41692bb501c), UINT64_C(0x2d1ab4dea28ed965),
+    UINT64_C(0x624ac0f56a91f461), UINT64_C(0x1892b03d5aa47d18),
+    UINT64_C(0x97fa21650afae693), UINT64_C(0xed2251ad3acf6fea),
+    UINT64_C(0x095ac9329ac4bc9b), UINT64_C(0x7382b9faaaf135e2),
+    UINT64_C(0xfcea28a2faafae69), UINT64_C(0x8632586aca9a2710),
+    UINT64_C(0xc9622c4102850a14), UINT64_C(0xb3ba5c8932b0836d),
+    UINT64_C(0x3cd2cdd162ee18e6), UINT64_C(0x460abd1952db919f),
+    UINT64_C(0x256b24ca6b12f26d), UINT64_C(0x5fb354025b277b14),
+    UINT64_C(0xd0dbc55a0b79e09f), UINT64_C(0xaa03b5923b4c69e6),
+    UINT64_C(0xe553c1b9f35344e2), UINT64_C(0x9f8bb171c366cd9b),
+    UINT64_C(0x10e3202993385610), UINT64_C(0x6a3b50e1a30ddf69),
+    UINT64_C(0x8e43c87e03060c18), UINT64_C(0xf49bb8b633338561),
+    UINT64_C(0x7bf329ee636d1eea), UINT64_C(0x012b592653589793),
+    UINT64_C(0x4e7b2d0d9b47ba97), UINT64_C(0x34a35dc5ab7233ee),
+    UINT64_C(0xbbcbcc9dfb2ca865), UINT64_C(0xc113bc55cb19211c),
+    UINT64_C(0x5863dbf1e3ac9dec), UINT64_C(0x22bbab39d3991495),
+    UINT64_C(0xadd33a6183c78f1e), UINT64_C(0xd70b4aa9b3f20667),
+    UINT64_C(0x985b3e827bed2b63), UINT64_C(0xe2834e4a4bd8a21a),
+    UINT64_C(0x6debdf121b863991), UINT64_C(0x1733afda2bb3b0e8),
+    UINT64_C(0xf34b37458bb86399), UINT64_C(0x8993478dbb8deae0),
+    UINT64_C(0x06fbd6d5ebd3716b), UINT64_C(0x7c23a61ddbe6f812),
+    UINT64_C(0x3373d23613f9d516), UINT64_C(0x49aba2fe23cc5c6f),
+    UINT64_C(0xc6c333a67392c7e4), UINT64_C(0xbc1b436e43a74e9d),
+    UINT64_C(0x95ac9329ac4bc9b5), UINT64_C(0xef74e3e19c7e40cc),
+    UINT64_C(0x601c72b9cc20db47), UINT64_C(0x1ac40271fc15523e),
+    UINT64_C(0x5594765a340a7f3a), UINT64_C(0x2f4c0692043ff643),
+    UINT64_C(0xa02497ca54616dc8), UINT64_C(0xdafce7026454e4b1),
+    UINT64_C(0x3e847f9dc45f37c0), UINT64_C(0x445c0f55f46abeb9),
+    UINT64_C(0xcb349e0da4342532), UINT64_C(0xb1eceec59401ac4b),
+    UINT64_C(0xfebc9aee5c1e814f), UINT64_C(0x8464ea266c2b0836),
+    UINT64_C(0x0b0c7b7e3c7593bd), UINT64_C(0x71d40bb60c401ac4),
+    UINT64_C(0xe8a46c1224f5a634), UINT64_C(0x927c1cda14c02f4d),
+    UINT64_C(0x1d148d82449eb4c6), UINT64_C(0x67ccfd4a74ab3dbf),
+    UINT64_C(0x289c8961bcb410bb), UINT64_C(0x5244f9a98c8199c2),
+    UINT64_C(0xdd2c68f1dcdf0249), UINT64_C(0xa7f41839ecea8b30),
+    UINT64_C(0x438c80a64ce15841), UINT64_C(0x3954f06e7cd4d138),
+    UINT64_C(0xb63c61362c8a4ab3), UINT64_C(0xcce411fe1cbfc3ca),
+    UINT64_C(0x83b465d5d4a0eece), UINT64_C(0xf96c151de49567b7),
+    UINT64_C(0x76048445b4cbfc3c), UINT64_C(0x0cdcf48d84fe7545),
+    UINT64_C(0x6fbd6d5ebd3716b7), UINT64_C(0x15651d968d029fce),
+    UINT64_C(0x9a0d8ccedd5c0445), UINT64_C(0xe0d5fc06ed698d3c),
+    UINT64_C(0xaf85882d2576a038), UINT64_C(0xd55df8e515432941),
+    UINT64_C(0x5a3569bd451db2ca), UINT64_C(0x20ed197575283bb3),
+    UINT64_C(0xc49581ead523e8c2), UINT64_C(0xbe4df122e51661bb),
+    UINT64_C(0x3125607ab548fa30), UINT64_C(0x4bfd10b2857d7349),
+    UINT64_C(0x04ad64994d625e4d), UINT64_C(0x7e7514517d57d734),
+    UINT64_C(0xf11d85092d094cbf), UINT64_C(0x8bc5f5c11d3cc5c6),
+    UINT64_C(0x12b5926535897936), UINT64_C(0x686de2ad05bcf04f),
+    UINT64_C(0xe70573f555e26bc4), UINT64_C(0x9ddd033d65d7e2bd),
+    UINT64_C(0xd28d7716adc8cfb9), UINT64_C(0xa85507de9dfd46c0),
+    UINT64_C(0x273d9686cda3dd4b), UINT64_C(0x5de5e64efd965432),
+    UINT64_C(0xb99d7ed15d9d8743), UINT64_C(0xc3450e196da80e3a),
+    UINT64_C(0x4c2d9f413df695b1), UINT64_C(0x36f5ef890dc31cc8),
+    UINT64_C(0x79a59ba2c5dc31cc), UINT64_C(0x037deb6af5e9b8b5),
+    UINT64_C(0x8c157a32a5b7233e), UINT64_C(0xf6cd0afa9582aa47),
+    UINT64_C(0x4ad64994d625e4da), UINT64_C(0x300e395ce6106da3),
+    UINT64_C(0xbf66a804b64ef628), UINT64_C(0xc5bed8cc867b7f51),
+    UINT64_C(0x8aeeace74e645255), UINT64_C(0xf036dc2f7e51db2c),
+    UINT64_C(0x7f5e4d772e0f40a7), UINT64_C(0x05863dbf1e3ac9de),
+    UINT64_C(0xe1fea520be311aaf), UINT64_C(0x9b26d5e88e0493d6),
+    UINT64_C(0x144e44b0de5a085d), UINT64_C(0x6e963478ee6f8124),
+    UINT64_C(0x21c640532670ac20), UINT64_C(0x5b1e309b16452559),
+    UINT64_C(0xd476a1c3461bbed2), UINT64_C(0xaeaed10b762e37ab),
+    UINT64_C(0x37deb6af5e9b8b5b), UINT64_C(0x4d06c6676eae0222),
+    UINT64_C(0xc26e573f3ef099a9), UINT64_C(0xb8b627f70ec510d0),
+    UINT64_C(0xf7e653dcc6da3dd4), UINT64_C(0x8d3e2314f6efb4ad),
+    UINT64_C(0x0256b24ca6b12f26), UINT64_C(0x788ec2849684a65f),
+    UINT64_C(0x9cf65a1b368f752e), UINT64_C(0xe62e2ad306bafc57),
+    UINT64_C(0x6946bb8b56e467dc), UINT64_C(0x139ecb4366d1eea5),
+    UINT64_C(0x5ccebf68aecec3a1), UINT64_C(0x2616cfa09efb4ad8),
+    UINT64_C(0xa97e5ef8cea5d153), UINT64_C(0xd3a62e30fe90582a),
+    UINT64_C(0xb0c7b7e3c7593bd8), UINT64_C(0xca1fc72bf76cb2a1),
+    UINT64_C(0x45775673a732292a), UINT64_C(0x3faf26bb9707a053),
+    UINT64_C(0x70ff52905f188d57), UINT64_C(0x0a2722586f2d042e),
+    UINT64_C(0x854fb3003f739fa5), UINT64_C(0xff97c3c80f4616dc),
+    UINT64_C(0x1bef5b57af4dc5ad), UINT64_C(0x61372b9f9f784cd4),
+    UINT64_C(0xee5fbac7cf26d75f), UINT64_C(0x9487ca0fff135e26),
+    UINT64_C(0xdbd7be24370c7322), UINT64_C(0xa10fceec0739fa5b),
+    UINT64_C(0x2e675fb4576761d0), UINT64_C(0x54bf2f7c6752e8a9),
+    UINT64_C(0xcdcf48d84fe75459), UINT64_C(0xb71738107fd2dd20),
+    UINT64_C(0x387fa9482f8c46ab), UINT64_C(0x42a7d9801fb9cfd2),
+    UINT64_C(0x0df7adabd7a6e2d6), UINT64_C(0x772fdd63e7936baf),
+    UINT64_C(0xf8474c3bb7cdf024), UINT64_C(0x829f3cf387f8795d),
+    UINT64_C(0x66e7a46c27f3aa2c), UINT64_C(0x1c3fd4a417c62355),
+    UINT64_C(0x935745fc4798b8de), UINT64_C(0xe98f353477ad31a7),
+    UINT64_C(0xa6df411fbfb21ca3), UINT64_C(0xdc0731d78f8795da),
+    UINT64_C(0x536fa08fdfd90e51), UINT64_C(0x29b7d047efec8728),
+};
+
+
+uint64_t crc64(const char* s, uint64_t l)
+{
+	uint64_t j;
+    uint64_t crc = 0;
+
+    for (j = 0; j < l; j++)
+    {
+        uint8_t byte = s[j];
+        crc = crc64_tab[(uint8_t)crc ^ byte] ^ (crc >> 8);
+    }
+    return crc;
+}
+
+
+/* Test main */
+//#ifdef TEST_MAIN
+//#include <stdio.h>
+//int main(void) {
+//    printf("e9c6d914c4b8d9ca == %016llx\n",
+//        (unsigned long long) crc64(0,(unsigned char*)"123456789",9));
+//    return 0;
+//}
+//#endif
+
+

src/crc64.h

@@ -0,0 +1,9 @@
+/**
+ * @file crc64.h
+ * @date March 24th 2016
+ * @brief Header file for CRC64 function.
+ */
+
+#include <stdint.h>
+
+uint64_t crc64(const char* s, uint64_t l);

src/dna_seq_indexer.c

@@ -0,0 +1,102 @@
+/****************************************************************************
+ * DNA sequence indexing functions                                          *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_seq_to_blob(const char* seq)
+{
+	Obi_blob_p 		 value_b;
+	int32_t          length_encoded_seq;	// length of the encoded sequence in bytes
+	int32_t          seq_length;
+	byte_t*          encoded_seq;
+
+	seq_length = strlen(seq);
+
+	// Check if just ATGC and encode accordingly
+	if (only_ATGC(seq))
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 4.0);
+		// Encode
+		encoded_seq = encode_seq_on_2_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_2, length_encoded_seq, seq_length);
+	}
+	else
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 2.0);
+		// Encode
+		encoded_seq = encode_seq_on_4_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
+	}
+
+	free(encoded_seq);
+
+	return value_b;
+}
+
+
+char* obi_blob_to_seq(Obi_blob_p value_b)
+{
+	// Decode
+	if (value_b->element_size == 2)
+		return decode_seq_on_2_bits(value_b->value, value_b->length_decoded_value);
+	else
+		return decode_seq_on_4_bits(value_b->value, value_b->length_decoded_value);
+}
+
+
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_seq_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded sequence
+	return obi_blob_to_seq(value_b);
+}
+

src/dna_seq_indexer.h

@@ -0,0 +1,63 @@
+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef DNA_SEQ_INDEXER_H_
+#define DNA_SEQ_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a DNA sequence to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_seq_to_blob(const char* seq);
+
+
+/**
+ * @brief Converts a blob to a DNA sequence.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the blob.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_blob_to_seq(Obi_blob_p value_b);
+
+
+// TODO doc
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value);
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* DNA_SEQ_INDEXER_H_ */
+

src/encode.c

@@ -28,9 +28,9 @@
 
 
 
-bool only_ATGC(char* seq)
+bool only_ATGC(const char* seq)
 {
-	char* c = seq;
+	const char* c = seq;
 
 	while (*c)
 	{
@@ -54,7 +54,7 @@ bool only_ATGC(char* seq)
 }
 
 
-byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 {
 	byte_t*  seq_b;
 	uint8_t  modulo;
@@ -64,6 +64,12 @@ byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
 	length_b = ceil((double) length / (double) 4.0);
 
 	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+	if (seq_b == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
+		return NULL;
+	}
 
 	// Initialize all the bits to 0
 	memset(seq_b, 0, length_b);
@@ -93,6 +99,7 @@ byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
 			seq_b[i/4] |= NUC_T_2b;
 			break;
 		default:
+			obi_set_errno(OBI_ENCODE_ERROR);		// TODO
 			obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
 			return NULL;
 		}
@@ -116,6 +123,12 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 	uint8_t nuc;
 
 	seq = (char*) malloc((length_seq+1) * sizeof(char));
+	if (seq == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
+		return NULL;
+	}
 
 	for (i=0; i<length_seq; i++)
 	{
@@ -138,6 +151,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 			seq[i] = 't';
 			break;
 		default:
+			obi_set_errno(OBI_DECODE_ERROR);		// TODO
 			obidebug(1, "\nInvalid nucleotide base when decoding");
 			return NULL;
 		}
@@ -149,7 +163,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 }
 
 
-byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 {
 	byte_t*  seq_b;
 	uint8_t  modulo;
@@ -159,6 +173,12 @@ byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
 	length_b = ceil((double) length / (double) 2.0);
 
 	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+	if (seq_b == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
+		return NULL;
+	}
 
 	// Initialize all the bits to 0
 	memset(seq_b, 0, length_b);
@@ -232,6 +252,7 @@ byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
 			seq_b[i/2] |= NUC_N_4b;
 			break;
 		default:
+			obi_set_errno(OBI_ENCODE_ERROR);	// TODO
 			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
 			return NULL;
 		}
@@ -255,6 +276,12 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
 	uint8_t nuc;
 
 	seq = (char*) malloc((length_seq+1) * sizeof(char));
+	if (seq == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
+		return NULL;
+	}
 
 	for (i=0; i<length_seq; i++)
 	{
@@ -310,6 +337,7 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
 			seq[i] = 'n';
 			break;
 		default:
+			obi_set_errno(OBI_DECODE_ERROR);	// TODO
 			obidebug(1, "\nInvalid nucleotide base when decoding");
 			return NULL;
 		}

src/encode.h

@@ -10,6 +10,10 @@
  */
 
 
+#ifndef ENCODE_H_
+#define ENCODE_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <stdint.h>
@@ -18,8 +22,10 @@
 #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 */
+#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
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 
 
 /**
@@ -69,7 +75,7 @@ enum
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-bool only_ATGC(char* seq);
+bool only_ATGC(const char* seq);
 
 
 /**
@@ -90,7 +96,7 @@ bool only_ATGC(char* seq);
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
 
 
 /**
@@ -141,7 +147,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-byte_t* encode_seq_on_4_bits(char* seq, int32_t length);
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
 
 
 /**
@@ -179,3 +185,6 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
 // little endian
 void print_bits(void* ptr, int32_t length);
 
+
+#endif /* ENCODE_H_ */
+

src/obiavl.h

@@ -6,7 +6,7 @@
  * @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).
+ * @brief Header file for handling AVL trees for storing and retrieving blobs (i.e. coding for character strings).
  */
 
 
@@ -23,41 +23,49 @@
 #include <stdbool.h>
 
 #include "obidms.h"
+#include "obiblob.h"
 #include "obitypes.h"
-
 #include "bloom.h"
+#include "utils.h"
+#include "encode.h"
 
-#define NB_OF_AVLS (64)
-#define MASK (63)
 
+#define MAX_NB_OF_AVLS_IN_GROUP (100)						/**< The maximum number of AVL trees in a group.	// TODO discuss
+                              	  	 	 	 	 	 	 	 */
+#define MAX_NODE_COUNT_PER_AVL (10000000)					/**< The maximum number of nodes in an AVL tree.
+															 *   Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
+                              	  	 	 	 	 	 	 	 */
+#define MAX_DATA_SIZE_PER_AVL (1073741824)		            /**< The maximum size of the data referred to by an AVL tree in a group.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Only used to decide when to create a new AVL in a group.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Should not be greater than int32_t max (2,147,483,647), as indexes will have to be stored on 32 bits.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Here 1073741824 B = 1 GB
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define AVL_MAX_DEPTH (1024)								/**< The maximum depth of an AVL tree. Used to save paths through the tree.
+                              	  	 	 	 	 	 	 	 */
 #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.
-                              	  	 	 	 	 	 	 	 */
-
-typedef struct bloom bloom_t;
 
 
 /**
  * @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.
-							 */
+	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.
+							   */
+	uint64_t crc64;			  /**< Cyclic Redundancy Check code on 64 bits associated with the value.
+	 	 	 	 	 	 	   */
 } AVL_node_t, *AVL_node_p;
 
 
@@ -86,8 +94,10 @@ typedef struct OBIDMS_avl_data_header {
 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.
+	byte_t*                 	data;   		 	/**< A pointer to the beginning of the data.
 													 */
+	int							data_fd;	        /**< File descriptor of the file containing the data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
 
 
@@ -109,38 +119,39 @@ typedef struct OBIDMS_avl_header {
 													 */
 	time_t		creation_date;			    	    /**< Date of creation of the file.
 												     */
-	bloom_t 	bloom_filter;
+	bloom_t 	bloom_filter;			    	    /**< Bloom filter associated with the AVL tree, enabling to know if a value
+													 *   might already be stored in the data associated with the tree.
+     	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
 
 
 /**
  * @brief OBIDMS AVL tree structure.
+ * 		  TODO doc
  */
 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.
-													 */
+	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).
+															 *   (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.
-													 */
-	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the AVL tree is used.
-													 */
-	int							avl_fd;
-	int							data_fd;
+	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 containing the AVL tree.
+													 	 	 */
 } OBIDMS_avl_t, *OBIDMS_avl_p;
 
 
@@ -148,28 +159,30 @@ typedef struct OBIDMS_avl {
  * @brief OBIDMS AVL tree group structure.
  */
 typedef struct OBIDMS_avl_group {
-	// TODO put each group in a directory later
-	OBIDMS_avl_p 	sub_avls[64];	// TODO macro for max
-	int 			current_avl_idx;
-	char			avl_name[AVL_MAX_NAME+1];
-	OBIDMS_p                	dms;
+	OBIDMS_avl_p 	sub_avls[MAX_NB_OF_AVLS_IN_GROUP];		/**< Array containing the pointers to the AVL trees of the group.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	int 			current_avl_idx;						/**< Index in the sub_avls array of the AVL tree currently being filled.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char			name[AVL_MAX_NAME+1];				 	/**< Base name of the AVL group. The AVL trees in it have names of the form basename_idx.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_p        dms;									/**< Pointer to the OBIDMS structure to which the AVL group belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	bool			writable;								/**< Indicates whether the AVL group is read-only or not.
+															 */
+	size_t			counter;								/**< Indicates by how many threads/programs (TODO) the AVL group is used.
+													 	 	 */
 } OBIDMS_avl_group_t, *OBIDMS_avl_group_p;
 
 
-OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name);
-index_t insert_in_avl_group(OBIDMS_avl_group_p avl_group, byte_t* value);
-
-
-
 /**
- * @brief Checks if an AVL tree already exists or not.
+ * @brief Checks if an AVL tree or AVL tree group already exists or not.
  *
- * @param dms The OBIDMS to which the AVL tree belongs.
- * @param avl_name The name of the AVL tree.
+ * @param dms The OBIDMS to which the AVL tree or AVL tree group belongs.
+ * @param avl_name The name of the AVL treeor the base name of the AVL tree group.
  *
- * @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.
+ * @returns A value indicating whether the AVL tree or AVL tree group exists or not.
+ * @retval 1 if the AVL tree or AVL tree group exists.
+ * @retval 0 if the AVL tree or AVL tree group does not exist.
  * @retval -1 if an error occurred.
  *
  * @since December 2015
@@ -178,36 +191,19 @@ index_t insert_in_avl_group(OBIDMS_avl_group_p avl_group, byte_t* value);
 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.
+ * 		 to via the OBIDMS_avl structure. An AVL tree is stored in a directory
+ * 		 with the same name, or with the base name of the AVL group if it is
+ * 		 part of an AVL group.
  *
  * @param dms The OBIDMS to which the AVL tree belongs.
  * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL tree if it is part of an AVL group.
  *
  * @returns A pointer to the newly created AVL tree structure.
  * @retval NULL if an error occurred.
@@ -215,7 +211,7 @@ OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name);
  * @since December 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
+OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
 
 
 /**
@@ -228,6 +224,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
  *
  * @param dms The OBIDMS to which the AVL tree belongs.
  * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL tree if it is part of an AVL group.
  *
  * @returns A pointer to the AVL tree structure.
  * @retval NULL if an error occurred.
@@ -235,17 +232,66 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
  * @since December 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name);
+OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
+
+
+/**
+ * @brief Opens an AVL tree group and creates it if it does not already exist.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_avl_group(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Creates an AVL tree group.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree group.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_open_avl_group(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.
@@ -258,29 +304,59 @@ 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.
+ * @brief Closes an AVL tree group.
  *
- * @warning The byte array to add must already be encoded and contain its header.
+ * @param avl_group A pointer to the AVL tree group structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_avl_group(OBIDMS_avl_group_p avl_group);
+
+
+/**
+ * @brief Recovers a value (blob) in an AVL tree.
+ *
+ * @warning The blob recovered must be decoded to get the original value.
  *
  * @param avl A pointer to the AVL tree.
- * @param value The byte array to add in the AVL tree.
+ * @param index The index of the value in the data array.
  *
- * @returns The index of the value, whether it was added or already in the AVL tree.
+ * @returns A pointer to the blob recovered.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_avl_get(OBIDMS_avl_p avl, index_t index);
+
+
+/**
+ * @brief Adds a value (blob) in an AVL tree NOT checking first if it is already in it.		// TODO to discuss
+ *
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The blob to add in the AVL tree.
+ *
+ * @returns The index of the value newly added 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);
+index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value);
 
 
 /**
- * @brief Finds a value (byte array) in an AVL tree, checking first if it is already in it.
+ * @brief Finds a value (blob) in an AVL tree.
  *
- * @warning The byte array to add must already be encoded and contain its header.
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
  *
  * @param avl A pointer to the AVL tree.
- * @param value The byte array to add in the AVL tree.
+ * @param value The blob to add in the AVL tree.
  *
  * @returns The data index of the value.
  * @retval -1 if the value is not in the tree.
@@ -288,82 +364,40 @@ index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value);
  * @since December 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-index_t obi_avl_find(OBIDMS_avl_p avl, byte_t* value);
+index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value);
 
 
 /**
- * @brief Recovers a value (byte array) in an AVL tree.
+ * @brief Recovers a value (blob) in an AVL tree.
  *
- * @warning The byte array recovered is encoded and contains its header.
+ * @warning The blob recovered must be decoded to get the original value.
  *
- * @param avl A pointer to the AVL tree.
+ * @param avl_group 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.
+ * @returns A pointer to the blob recovered.
  *
- * @since December 2015
+ * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t index);
+Obi_blob_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx);
 
 
 /**
- * @brief Converts a character string to a byte array with a header.
+ * @brief Adds a value (blob) in an AVL tree group, checking if it is already in it.
  *
- * @warning The byte array must be freed by the caller.
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
  *
- * @param value The character string to convert.
+ * @param avl_group A pointer to the AVL tree group.
+ * @param value The blob to add in the AVL tree group.
  *
- * @returns A pointer to the byte array created.
- * @retval NULL if an error occurred.
+ * @returns The index of the value newly added in the AVL tree group.
+ * @retval -1 if an error occurred.
  *
- * @since October 2015
+ * @since April 2016
  * @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);
+index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value);
 
 
 #endif /* OBIAVL_H_ */

src/obiblob.c

@@ -0,0 +1,57 @@
+/****************************************************************************
+ * Obiblob functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obiblob.c
+ * @author Celine Mercier
+ * @date April 11th 2016
+ * @brief Functions handling Obiblob structures.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <math.h>
+
+#include "obiblob.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?
+
+
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value)
+{
+	Obi_blob_p blob;
+
+	// Allocate the memory for the blob structure
+	blob = (Obi_blob_p) malloc(sizeof(Obi_blob_t) + length_encoded_value);
+	if (blob == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a blob");
+		return NULL;
+	}
+
+	// Store the number of bits on which each element is encoded
+	blob->element_size = element_size;
+
+	// Store the length (in bytes) of the encoded value
+	blob->length_encoded_value = length_encoded_value;
+
+	// Store the initial length (in bytes) of the decoded value
+	blob->length_decoded_value = length_decoded_value;
+
+	// Store the encoded value
+	memcpy(blob->value, encoded_value, length_encoded_value);
+
+	return blob;
+}
+

src/obiblob.h

@@ -0,0 +1,54 @@
+/****************************************************************************
+ * Obiblob header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file obiblob.h
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Header file for handling Obi_blob structures.
+ */
+
+
+#ifndef OBIBLOB_H_
+#define OBIBLOB_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "obitypes.h"
+
+
+#define ELEMENT_SIZE_STR (8)								/**< The size of an element from a value of type character string.
+                              	  	 	 	 	 	 	 	 */
+#define ELEMENT_SIZE_SEQ_2 (2)								/**< The size of an element from a value of type DNA sequence encoded on 2 bits.
+                              	  	 	 	 	 	 	 	 */
+#define ELEMENT_SIZE_SEQ_4 (4)								/**< The size of an element from a value of type DNA sequence encoded on 4 bits.
+                              	  	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief Blob structure.
+ *  TODO
+ */
+typedef struct Obi_blob {
+	uint8_t  element_size;		 	/**< Size in bits of one element from the value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_encoded_value;	/**< Length in bytes of the encoded value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_decoded_value;	/**< Length in bytes of the decoded value.
+	 	 	 	 	 	 	 	 	 */
+	byte_t   value[];				/**< Encoded value.
+	 	 	 	 	 	 	 	 	 */
+} Obi_blob_t, *Obi_blob_p;
+
+
+
+// TODO doc
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value);
+
+
+#endif /* OBIBLOB_H_ */
+

src/obiblob_indexer.c

@@ -0,0 +1,37 @@
+/****************************************************************************
+ * Obiblob functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obiblob_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of blob structures.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obiblob_indexer.h"
+#include "obidms.h"
+#include "obiavl.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+inline int obi_indexer_exists(OBIDMS_p dms, const char* name);
+
+inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name);
+
+inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name);
+
+inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name);
+
+inline int obi_close_indexer(Obi_indexer_p indexer);
+
+inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value);
+
+inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx);
+

src/obiblob_indexer.h

@@ -0,0 +1,80 @@
+/****************************************************************************
+ * Blob indexer header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file obiblob_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of values.
+ */
+
+
+#ifndef OBIBLOB_INDEXER_H_
+#define OBIBLOB_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obiavl.h"
+#include "obitypes.h"
+#include "obiblob.h"
+
+
+#define INDEXER_MAX_NAME AVL_MAX_NAME 			/**< Macro to refer to the maximum size of the name of an indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+typedef struct OBIDMS_avl_group Obi_indexer;	/**< Typedef to refer to the used indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer of the used indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+// TODO doc
+inline int obi_indexer_exists(OBIDMS_p dms, const char* name)
+{
+	return obi_avl_exists(dms, name);
+}
+
+
+inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_avl_group(dms, name);
+}
+
+
+inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_create_avl_group(dms, name);
+}
+
+
+inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_open_avl_group(dms, name);
+}
+
+
+inline int obi_close_indexer(Obi_indexer_p indexer)
+{
+	return obi_close_avl_group(indexer);
+}
+
+
+inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value)
+{
+	return obi_avl_group_add(indexer, value);
+}
+
+
+inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx)
+{
+	return obi_avl_group_get(indexer, idx);
+}
+
+
+#endif /* OBIBLOB_INDEXER_H_ */
+

src/obidms.c

@@ -23,7 +23,8 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obidmscolumn.h"
-#include "private_at_functions.h"
+#include "obiblob_indexer.h"
+#include "utils.h"
 #include "obilittlebigman.h"
 
 
@@ -105,7 +106,8 @@ static char* build_directory_name(const char* dms_name)
 	char* directory_name;
 
 	// Build the database directory name
-	if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)
+	directory_name = (char*) malloc((strlen(dms_name) + 8)*sizeof(char));
+	if (sprintf(directory_name, "%s.obidms", dms_name) < 0)
 	{
 		obi_set_errno(OBIDMS_MEMORY_ERROR);
 		obidebug(1, "\nProblem building an OBIDMS directory name");
@@ -130,7 +132,8 @@ 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)
+	file_name = (char*) malloc((strlen(dms_name) + 7)*sizeof(char));
+	if (sprintf(file_name, "%s_infos", dms_name) < 0)
 	{
 		obi_set_errno(OBIDMS_MEMORY_ERROR);
 		obidebug(1, "\nProblem building an informations file name");
@@ -247,7 +250,7 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Get file descriptor of DMS directory to create the AVL trees directory
+	// Get file descriptor of DMS directory to create the indexer directory
 	dms_dir = opendir(directory_name);
 	if (dms_dir == NULL)
 	{
@@ -267,11 +270,11 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Create the AVL trees directory
-	if (mkdirat(dms_file_descriptor, AVL_TREES_DIR_NAME, 00777) < 0)
+	// Create the indexer directory
+	if (mkdirat(dms_file_descriptor, INDEXER_DIR_NAME, 00777) < 0)
 	{
-		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nProblem creating an AVL trees directory");
+		obi_set_errno(OBI_INDEXER_ERROR);
+		obidebug(1, "\nProblem creating an indexer directory");
 		return NULL;
 	}
 
@@ -390,24 +393,24 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 
 	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)
+	// Open the indexer directory
+	dms->indexer_directory = opendir_in_dms(dms, INDEXER_DIR_NAME);
+	if (dms->indexer_directory == NULL)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError opening the AVL trees directory");
+		obidebug(1, "\nError opening the indexer 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)
+	// Store the indexer directory's file descriptor
+	dms->indexer_dir_fd = dirfd(dms->indexer_directory);
+	if (dms->indexer_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);
+		obidebug(1, "\nError getting the file descriptor of the indexer directory");
+		closedir(dms->indexer_directory);
 		closedir(dms->directory);
 		free(dms);
 		return NULL;
@@ -415,13 +418,11 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 
 	// 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;
+	// Initialize the list of opened indexers	// TODO should be handled somewhere else?
+	dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
+	(dms->opened_indexers)->nb_opened_indexers = 0;
 
 	return dms;
 }
@@ -454,7 +455,7 @@ int obi_close_dms(OBIDMS_p dms)
 		while ((dms->opened_columns)->nb_opened_columns > 0)
 			obi_close_column(*((dms->opened_columns)->columns));
 
-		// Close dms and AVL trees directories
+		// Close dms and indexer directories
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
@@ -462,10 +463,10 @@ int obi_close_dms(OBIDMS_p dms)
 			free(dms);
 			return -1;
 		}
-		if (closedir(dms->avl_directory) < 0)
+		if (closedir(dms->indexer_directory) < 0)		// TODO should be handled somewhere else?
 		{
-			obi_set_errno(OBI_AVL_ERROR);
-			obidebug(1, "\nError closing an AVL trees directory");
+			obi_set_errno(OBI_INDEXER_ERROR);
+			obidebug(1, "\nError closing an indexer directory");
 			free(dms);
 			return -1;
 		}
@@ -475,3 +476,175 @@ int obi_close_dms(OBIDMS_p dms)
 	return 0;
 }
 
+
+int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name)
+{
+	int i;
+	Opened_columns_list_p columns_list;
+
+	columns_list = dms->opened_columns;
+
+	for (i=0; i < (columns_list->nb_opened_columns); i++)
+	{
+		if (!strcmp(((*((columns_list->columns)+i))->header)->name, column_name))
+		{	// Found it
+			return 0;
+		}
+	}
+	return 1;
+}
+
+
+OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version)
+{
+	int i;
+
+	for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
+	{
+		if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
+				&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version))
+		{	// Found the column already opened, return it
+			return *(((dms->opened_columns)->columns)+i);
+		}
+	}
+	// Didn't find the column
+	return NULL;
+}
+
+
+void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column)
+{
+	*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
+	((dms->opened_columns)->nb_opened_columns)++;
+}
+
+
+int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column)
+{
+	int i;
+	Opened_columns_list_p columns_list;
+
+	columns_list = dms->opened_columns;
+
+	for (i=0; i < columns_list->nb_opened_columns; i++)
+	{
+		if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
+				&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
+		{	// Found the column. Rearrange list
+			(columns_list->nb_opened_columns)--;
+			(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
+			return 0;
+		}
+	}
+
+	obidebug(1, "\nCould not find the column to delete from list of open columns");
+	return -1;
+}
+
+
+Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name)
+{
+	int i;
+	Opened_indexers_list_p indexers_list;
+
+	indexers_list = dms->opened_indexers;
+
+	for (i=0; i < (indexers_list->nb_opened_indexers); i++)
+	{
+		if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name))	// TODO it references something in AVL_group struct
+		{	// Found the indexer already opened, return it
+			return (indexers_list->indexers)[i];
+		}
+	}
+	// Didn't find the indexer
+	return NULL;
+}
+
+
+void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
+{
+	*(((dms->opened_indexers)->indexers)+((dms->opened_indexers)->nb_opened_indexers)) = indexer;
+	((dms->opened_indexers)->nb_opened_indexers)++;
+}
+
+
+int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
+{
+	int i;
+	Opened_indexers_list_p indexers_list;
+
+	indexers_list = dms->opened_indexers;
+
+	for (i=0; i < indexers_list->nb_opened_indexers; i++)
+	{
+		if (!strcmp(((indexers_list->indexers)[i])->name, indexer->name))	// TODO it references something in AVL_group struct
+		{	// Found the indexer. Rearrange list
+			(indexers_list->nb_opened_indexers)--;
+			(indexers_list->indexers)[i] = (indexers_list->indexers)[indexers_list->nb_opened_indexers];
+			return 0;
+		}
+	}
+
+	obidebug(1, "\nCould not find the indexer to delete from list of open indexers");
+	return -1;
+}
+
+
+char* obi_dms_get_dms_path(OBIDMS_p dms)
+{
+	char* full_path;
+
+	full_path = (char*) malloc((MAX_PATH_LEN)*sizeof(char));
+	if (full_path == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for the char* path to a file or directory");
+		return NULL;
+	}
+
+	if (getcwd(full_path, MAX_PATH_LEN) == NULL)	// TODO not sure at all about this because the DMS must be in the working directory.
+	{												// Maybe better to store when opening, but opening function seems to assume that too.
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError getting the path to a file or directory");
+		return NULL;
+	}
+
+	strcat(full_path, "/");
+	strcat(full_path, dms->directory_name);
+
+	return full_path;
+}
+
+
+char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name)
+{
+	char* full_path;
+
+	full_path = obi_dms_get_dms_path(dms);
+	strcat(full_path, "/");
+	strcat(full_path, path_name);
+
+	return full_path;
+}
+
+
+DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
+{
+	char* full_path;
+	DIR* directory;
+
+	full_path = obi_dms_get_full_path(dms, path_name);
+	if (full_path == NULL)
+		return NULL;
+
+	directory = opendir(full_path);
+	if (directory == NULL)
+	{
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError opening a directory");
+	}
+
+	free(full_path);
+
+	return directory;
+}

src/obidms.h

@@ -23,34 +23,46 @@
 #include <stdbool.h>
 
 #include "obierrno.h"
+//#include "obidmscolumn.h"
+//#include "obiblob_indexer.h"
 
 
-#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.
-                                	 	 	 */
+#define OBIDMS_MAX_NAME (2048) 	    			/**< The maximum length of an OBIDMS name.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS"  	/**< The name of the Obiblob indexer 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_INDEXERS (1000) 			/**< The maximum number of indexers open at the same time.
+                                	 	 	 	 */
+#define MAX_PATH_LEN 4096						/**< Maximum length for the character string defining a
+ 	 	 	 	 	 	 	 	 	 	 	 	 *	 file or directory path.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+typedef int32_t obiversion_t; 	/**< TODO double
+                                 */
 
 
 struct OBIDMS_column;		// TODO
+typedef struct OBIDMS_column* OBIDMS_column_p;
 
-typedef struct Opened_columns_list {
-	size_t	 		 		nb_opened_columns;
-	struct OBIDMS_column** 	columns;				// TODO allocate array size here
+typedef struct Opened_columns_list {		// TODO Handle the problem linked to columns with the same name + means only one version
+	int	 		 			nb_opened_columns;
+	OBIDMS_column_p		 	columns[MAX_NB_OPENED_COLUMNS];
 } Opened_columns_list_t, *Opened_columns_list_p;
 
 
-struct OBIDMS_avl;		// TODO
+struct OBIDMS_avl_group;		// TODO
+typedef struct OBIDMS_avl_group* OBIDMS_avl_group_p;
+typedef OBIDMS_avl_group_p Obi_indexer_p;
 
-typedef struct Opened_avls_list {
-	size_t	 		 		nb_opened_avls;
-	struct OBIDMS_avl** 	avls;
-} Opened_avls_list_t, *Opened_avls_list_p;
+typedef struct Opened_indexers_list {
+	int		 		 		nb_opened_indexers;
+	Obi_indexer_p		    indexers[MAX_NB_OPENED_INDEXERS];
+} Opened_indexers_list_t, *Opened_indexers_list_p;
 
 
 /**
@@ -69,17 +81,17 @@ typedef struct OBIDMS {
 	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.
+	DIR*					indexer_directory;						/**< A directory entry usable to
+																 *   refer and scan the indexer directory.
 																 */
-	int						avl_dir_fd;							/**< The file descriptor of the directory entry
-																 *   usable to refer and scan the AVL trees directory.
+	int						indexer_dir_fd;							/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the indexer 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.
+	Opened_indexers_list_p 	opened_indexers;					/**< List of opened indexers.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_t, *OBIDMS_p;
 
@@ -107,7 +119,7 @@ int obi_dms_exists(const char* dms_name);
  * if a directory with this name does not already exist
  * before creating the new database.
  *
- * A directory to store AVL trees is also created.
+ * A directory to store Obiblob indexers is also created.
  *
  * @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
@@ -174,4 +186,63 @@ OBIDMS_p obi_dms(const char* dms_name);
 int obi_close_dms(OBIDMS_p dms);
 
 
+// TODO doc
+int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name);
+
+
+OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version);
+
+
+void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column);
+
+
+int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column);
+
+
+Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name);
+
+
+void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
+
+
+int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
+
+
+char* obi_dms_get_path(OBIDMS_p dms);
+
+
+/**	TODO
+ * @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.
+ *
+ * @returns A pointer to the full path.
+ * @retval NULL if an error occurred.
+ *
+ * @since June 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_dms_get_full_path(OBIDMS_p dms, 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.
+ *
+ * @returns The file descriptor of the opened directory.
+ * @retval NULL if an error occurred.
+ *
+ * @since June 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);
+
+
 #endif /* OBIDMS_H_ */

src/obidms_taxonomy.c

@@ -20,7 +20,7 @@
 #include "obidms.h"
 #include "obidebug.h"
 #include "obierrno.h"
-#include "private_at_functions.h"
+#include "utils.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -379,8 +379,9 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
 
 	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)
+	main_taxonomy_dir_path = obi_dms_get_full_path(dms, TAXONOMY_DIR_NAME);
+	taxonomy_path = (char*) malloc((strlen(main_taxonomy_dir_path) + strlen(taxonomy_name) + strlen(taxonomy_name) + 3)*sizeof(char));
+	if (sprintf(taxonomy_path, "%s/%s/%s", main_taxonomy_dir_path, taxonomy_name, taxonomy_name) < 0)
 	{
 		free(main_taxonomy_dir_path);
 		obi_close_taxonomy(tax);

src/obidmscolumn.c

@@ -29,7 +29,8 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obilittlebigman.h"
-#include "obiavl.h"
+#include "obiblob_indexer.h"
+#include "utils.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -156,9 +157,12 @@ static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_
 static char* build_column_file_name(const char* column_name, obiversion_t version_number)
 {
 	char* file_name;
+	int version_number_length;
 
 	// Build the file name
-	if (asprintf(&file_name,"%s@%d.odc", column_name, version_number) < 0)
+	version_number_length = (version_number == 0 ? 1 : (int)(log10(version_number)+1));
+	file_name =	(char*) malloc((strlen(column_name) + version_number_length + 6)*sizeof(char));	// TODO check the mallocs...
+	if (sprintf(file_name,"%s@%d.odc", column_name, version_number) < 0)
 	{
 		obi_set_errno(OBICOL_MEMORY_ERROR);
 		obidebug(1, "\nError building a column file name");
@@ -174,7 +178,8 @@ static char* build_version_file_name(const char* column_name)
 	char* file_name;
 
 	// Build the file name
-	if (asprintf(&file_name,"%s.odv", column_name) < 0)
+	file_name =	(char*) malloc((strlen(column_name) + 5)*sizeof(char));
+	if (sprintf(file_name,"%s.odv", column_name) < 0)
 	{
 		obi_set_errno(OBICOL_MEMORY_ERROR);
 		obidebug(1, "\nError building a version file name");
@@ -514,7 +519,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 								  index_t     nb_lines,
 								  index_t     nb_elements_per_line,
 								  const char* elements_names,
-								  const char* avl_name,
+								  const char* indexer_name,
 								  const char* comments
 								 )
 {
@@ -530,6 +535,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	index_t						minimum_line_count;
 	OBIType_t  					returned_data_type;
 	OBIType_t  					stored_data_type;
+	char						final_indexer_name[INDEXER_MAX_NAME];
 
 	new_column = NULL;
 
@@ -549,11 +555,13 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 		obidebug(1, "\nCan't create column because of invalid data type");
 		return NULL;
 	}
-	if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (avl_name == NULL))
-	{
-		obidebug(1, "\nCan't create column because of empty avl name");
-		return NULL;
+	if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (strcmp(indexer_name, "") == 0))
+	{	// TODO make function in obiblob_indexer.c and discuss the fact that it's here
+		strcpy(final_indexer_name, column_name);
+		strcat(final_indexer_name, "_indexer");
 	}
+	else
+		strcpy(final_indexer_name, indexer_name);
 
 	returned_data_type = data_type;
 	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
@@ -719,19 +727,19 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	if (comments != NULL)
 		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated obi_avl is opened or created
+	// If the data type is OBI_STR or OBI_SEQ, the associated obi_indexer is opened or created
 	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
 	{
-		new_column->avl = obi_create_avl_group(dms, avl_name);
-//		if (avl == NULL) TODO
-//		{
-//			obidebug(1, "\nError opening or creating the aVL tree associated with a column");
-//			munmap(new_column->header, header_size);
-//			close(column_file_descriptor);
-//			free(new_column);
-//			return NULL;
-//		}
-		strncpy(header->avl_name, avl_name, AVL_MAX_NAME);
+		new_column->indexer = obi_indexer(dms, final_indexer_name);
+		if (new_column->indexer == NULL)
+		{
+			obidebug(1, "\nError opening or creating the indexer associated with a column");
+			munmap(new_column->header, header_size);
+			close(column_file_descriptor);
+			free(new_column);
+			return NULL;
+		}
+		strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
 	}
 
 	// Fill the data with NA values
@@ -740,8 +748,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	close(column_file_descriptor);
 
 	// Add in the list of opened columns
-	*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = new_column;
-	((dms->opened_columns)->nb_opened_columns)++;
+	obi_dms_list_column(dms, new_column);
+
+	// Set counter to 1 // TODO Discuss counters
 	new_column->counter = 1;
 
 	return new_column;
@@ -757,8 +766,6 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 	char* 						column_file_name;
 	int 						column_file_descriptor;
 	size_t 						header_size;
-	size_t						i;
-	OBIDMS_avl_p avl;
 
 	column = NULL;
 
@@ -766,7 +773,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 	column_directory = obi_open_column_directory(dms, column_name);
 	if (column_directory == NULL)
 	{
-		//obidebug(1, "\nError opening a column directory structure");
+		//obidebug(1, "\nError opening a column directory structure");	// TODO
 		return NULL;
 	}
 
@@ -782,14 +789,12 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 	}
 
 	// Check if the column is already in the list of opened columns
-	for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
+	column = obi_dms_get_column_from_list(dms, column_name, version_number);
+	// If it's found, increment its counter and return it
+	if (column != NULL)
 	{
-		if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
-				&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version_number))
-		{	// Found the column already opened, increase its counter and return the column
-			((*(((dms->opened_columns)->columns)+i))->counter)++;
-			return *(((dms->opened_columns)->columns)+i);
-		}
+		(column->counter)++;
+		return column;
 	}
 
 	// Get the column file name
@@ -872,26 +877,26 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 
 	column->writable = false;
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is opened
+	// If the data type is OBI_STR or OBI_SEQ, the associated indexer is opened
 	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
 	{
-		avl = obi_avl(dms, (column->header)->avl_name);
-		if (avl == NULL)
+		column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
+		if (column->indexer == NULL)
 		{
-			obidebug(1, "\nError opening the AVL tree associated with a column");
+			obidebug(1, "\nError opening the indexer associated with a column");
 			munmap(column->header, header_size);
 			close(column_file_descriptor);
 			free(column);
 			return NULL;
 		}
-		//column->avl = avl;	TODO
 	}
 
 	close(column_file_descriptor);
 
-	// Add in the list of opened columns and set column counter to 1
-	*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
-	((dms->opened_columns)->nb_opened_columns)++;
+	// Add in the list of opened columns
+	obi_dms_list_column(dms, column);
+
+	// Set counter to 1
 	column->counter = 1;
 
 	return column;
@@ -937,7 +942,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   nb_lines,
 								   nb_elements_per_line,
 								   (column_to_clone->header)->elements_names,
-								   (column_to_clone->header)->avl_name,
+								   (column_to_clone->header)->indexer_name,
 								   (column_to_clone->header)->comments
 								  );
 
@@ -960,18 +965,13 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 	}
 	else if (clone_data && (line_selection != NULL))
 	{
-		obidebug(1, "\nCloning data from line selection\n");
 		line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
-		fprintf(stderr, "\nline size = %ld\n", line_size);
 		for (i=0; i<((line_selection->header)->lines_used); i++)
 		{
 			index = *(((index_t*) (line_selection->data)) + i);
-			fprintf(stderr, "\nindex = %lld, i = %lld\n", index, i);
 			memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
-			fprintf(stderr, "\nmemcpied\n");
 		}
 		(new_column->header)->lines_used = (line_selection->header)->lines_used;
-		obidebug(1, "\nCloned data from line selection\n");
 	}
 
 	// Close column_to_clone
@@ -987,50 +987,35 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 
 int obi_close_column(OBIDMS_column_p column)
 {
-	size_t 				  i;
-	bool   				  close_dir;
-	Opened_columns_list_p columns_list;
+	bool    close_dir;
+	int     ret_val = 0;
 
-	columns_list = (column->dms)->opened_columns;
+	// Truncate the column to the number of lines used if it's not read-only
+	if (column->writable)
+		ret_val = obi_truncate_column(column);
 
 	(column->counter)--;
 
 	if (column->counter == 0)
 	{
 		// Delete from the list of opened columns
-		for (i=0; i < (columns_list)->nb_opened_columns; i++)
-		{
-			if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
-					&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
-			{	// Found the column. Rearrange list
-				(columns_list->nb_opened_columns)--;
-				(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
-			}
-		}
+		if (obi_dms_unlist_column(column->dms, column) < 0)
+			ret_val = -1;
 
 		// Close column directory if it was the last column opened from that directory
-		close_dir = 1;
-		for (i=0; i < (columns_list->nb_opened_columns); i++)
-		{
-			if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name))
-			{	// Not the last column from that directory
-				close_dir = 0;
-			}
-		}
+		close_dir = obi_dms_is_column_name_in_list(column->dms, (column->header)->name);
 
-		// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed	TODO
-//		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
-//		{
-//			if (obi_close_avl(column->avl) < 0)
-//				return -1;
-//		}
+		// If the data type is OBI_STR or OBI_SEQ, the associated indexer is closed
+		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
+			if (obi_close_indexer(column->indexer) < 0)
+				ret_val = -1;
 
 		// Munmap data
 		if (munmap(column->data, (column->header)->data_size) < 0)
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nError munmapping column data");
-			return -1;
+			ret_val = -1;
 		}
 
 		// Munmap header
@@ -1038,20 +1023,22 @@ int obi_close_column(OBIDMS_column_p column)
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nError munmapping a column header");
-			return -1;
+			ret_val = -1;
 		}
 
-		free(column);
-
+		// Close column directory
 		if (close_dir)
-			obi_close_column_directory(column->column_directory);
+			if (obi_close_column_directory(column->column_directory) < 0)
+				ret_val = -1;
+
+		free(column);
 	}
 
-	return 0;
+	return ret_val;
 }
 
 
-int obi_truncate_column_to_lines_used(OBIDMS_column_p column)	// TODO is it necessary to unmap/remap?
+int obi_truncate_column(OBIDMS_column_p column)	// TODO is it necessary to unmap/remap?
 {
 	size_t  file_size;
 	size_t  data_size;
@@ -1226,20 +1213,6 @@ int obi_enlarge_column(OBIDMS_column_p column)
 }
 
 
-int obi_truncate_and_close_column(OBIDMS_column_p column)
-{
-	if (column->writable)	// TODO discuss
-	{
-		if (obi_truncate_column_to_lines_used(column) < 0)
-			return -1;
-	}
-	if (obi_close_column(column) < 0)
-		return -1;
-
-	return 0;
-}
-
-
 void obi_ini_to_NA_values(OBIDMS_column_p column,
 						  index_t first_line_nb,
 						  index_t nb_lines)
@@ -1367,7 +1340,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
 }
 
 
-int obi_unmap_header(OBIDMS_column_header_p header)
+int obi_close_header(OBIDMS_column_header_p header)
 {
 	if (munmap(header, header->header_size) < 0)
 	{
@@ -1395,7 +1368,7 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 
 	element_index = 0;
 
-	name = strtok (elements_names, ";");	// TODO not thread safe, see strtok_r maybe
+	name = strtok(elements_names, ";");	// TODO not thread safe, see strtok_r maybe
 	if (strcmp(element_name, name) == 0)
 	{
 		free(elements_names);
@@ -1405,7 +1378,7 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 
 	while (name != NULL)
 	{
-		name = strtok (NULL, ";");			// TODO not thread safe, see strtok_r maybe
+		name = strtok(NULL, ";");			// TODO not thread safe, see strtok_r maybe
 		if (strcmp(element_name, name) == 0)
 		{
 			free(elements_names);
@@ -1420,7 +1393,53 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 }
 
 
-char* obi_column_format_date(time_t date)
+int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
+{
+	// Check if the column is read-only
+	if (!(column->writable))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value in a read-only column");
+    	return -1;
+	}
+
+	// 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;
+
+	return 0;
+}
+
+
+int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
+{
+	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 -1;
+	}
+	return 0;
+}
+
+
+char* obi_column_format_date(time_t date)	// TODO put in utils.c
 {
 	char*       formatted_time;
 	struct tm*  tmp;

src/obidmscolumn.h

@@ -25,11 +25,9 @@
 #include "obierrno.h"
 #include "obilittlebigman.h"
 #include "obidmscolumndir.h"
-#include "obiavl.h"
+#include "obiblob_indexer.h"
 
 
-#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.
@@ -78,7 +76,7 @@ typedef struct OBIDMS_column_header {
 															 */
 	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            indexer_name[INDEXER_MAX_NAME+1]; 		/**< If there is one, the indexer name as a NULL terminated string.
 	                                             	 	 	 */
 	char 			comments[COMMENTS_MAX_LENGTH+1];		/**< Comments stored as a classical zero end C string.
 												 	 	 	 */
@@ -98,7 +96,7 @@ typedef struct OBIDMS_column {
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_avl_group_p 			avl;			    /**< TODO A pointer to the group of AVL trees associated with the column if there is one.
+	Obi_indexer_p    			indexer;		    /**< A pointer to the blob indexer associated with the column if there is one.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	void*                   	data;   		 	/**< A `void` pointer to the beginning of the data.
 	                                 	 	         *
@@ -164,7 +162,7 @@ size_t obi_get_platform_header_size();
  * @brief Creates a column.
  *
  * 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.
+ * If there is an indexer 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?
  *
@@ -174,7 +172,7 @@ size_t obi_get_platform_header_size();
  * @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 indexer_name The name of the indexer 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.
@@ -189,7 +187,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 								  index_t nb_lines,
 								  index_t nb_elements_per_line,
 								  const char* elements_names,
-								  const char* avl_name,
+								  const char* indexer_name,
 								  const char* comments
 								 );
 
@@ -228,7 +226,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p line_selection, c
 
 
 /**
- * @brief Closes a column.
+ * @brief Truncates a column to the number of lines used if it is not read-only and closes it.
  *
  * @param column A pointer on an OBIDMS column.
  *
@@ -253,7 +251,7 @@ int obi_close_column(OBIDMS_column_p column);
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
+int obi_truncate_column(OBIDMS_column_p column);
 
 
 /**
@@ -270,21 +268,6 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
 int obi_enlarge_column(OBIDMS_column_p column);
 
 
-/**
- * @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.
- *
- * @retval 0 if the operation was successfully completed.
- * @retval -1 if an error occurred.
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_truncate_and_close_column(OBIDMS_column_p column);
-
-
 /*
  * @brief Sets the data in a column to the NA value of the data OBIType.
  *
@@ -328,7 +311,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
  * @since October 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_unmap_header(OBIDMS_column_header_p header);
+int obi_close_header(OBIDMS_column_header_p header);
 
 
 /**
@@ -346,7 +329,15 @@ int obi_unmap_header(OBIDMS_column_header_p header);
 index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
 
 
-/**
+// TODO doc
+int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb);
+
+
+// TODO doc
+int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb);
+
+
+/** TODO put in utils.c
  * @brief Formats a date in a way that is easy to read.
  *
  * @warning The pointer returned must be freed by the caller.
@@ -361,8 +352,4 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_column_format_date(time_t date);
 
 
-int obi_select(OBIDMS_column_p lines_column, index_t line_to_grep);
-
-
-
 #endif /* OBIDMSCOLUMN_H_ */

src/obidmscolumn_bool.c

@@ -14,7 +14,6 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -32,25 +31,8 @@
 
 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)
-	{
-		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;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
 	// Set the value
 	*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@@ -59,111 +41,31 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 }
 
 
-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)
-{
-	// 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_obibool_with_elt_idx(column, line_nb, element_idx, value) < 0)
-		return -1;
-
-	return 0;
-}
-
-
 obibool_t obi_column_get_obibool_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 in the column");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		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);
+	index_t 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;
+	return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
 }
 
 
 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);
+	index_t 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

@@ -19,7 +19,6 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
-#include "obiview.h"
 
 
 /**
@@ -96,79 +95,5 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb
 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

@@ -14,7 +14,6 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -32,25 +31,8 @@
 
 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)
-	{
-		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;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
 	// Set the value
 	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@@ -59,111 +41,30 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 }
 
 
-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)
-{
-	// 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 in the column");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		return OBIChar_NA;
-	}
 
 	return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-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)
-{
-	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 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);
+	index_t 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;
+	return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
 }
 
 
 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);
+	index_t 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

@@ -19,7 +19,6 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
-#include "obiview.h"
 
 
 /**
@@ -96,79 +95,5 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
 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

@@ -14,7 +14,6 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -31,25 +30,8 @@
 
 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)
-	{
-		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;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
 	// Set the value
 	*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@@ -58,111 +40,31 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
 }
 
 
-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)
-{
-	// 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_obifloat_with_elt_idx(column, line_nb, element_idx, value) < 0)
-		return -1;
-
-	return 0;
-}
-
-
 obifloat_t obi_column_get_obifloat_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 in the column");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		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);
+	index_t 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;
+	return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
 }
 
 
 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);
+	index_t 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

@@ -19,7 +19,6 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
-#include "obiview.h"
 
 
 /**
@@ -96,79 +95,5 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
 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

@@ -31,25 +31,8 @@
 
 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)
-	{
-		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;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
 	// Set the value
 	*(((index_t*) (column->data)) + line_nb) = value;
@@ -60,12 +43,8 @@ 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)
 {
-	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");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		return OBIIdx_NA;
-	}
 
 	return *(((index_t*) (column->data)) + line_nb);
 }

src/obidmscolumn_idx.h

@@ -20,6 +20,7 @@
 #include "obidmscolumn.h"
 #include "obitypes.h"
 
+// TODO doc
 
 int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
 

src/obidmscolumn_int.c

@@ -14,7 +14,6 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -29,28 +28,10 @@
  *
  **********************************************************************/
 
-
 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)
-	{
-		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;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
 	// Set the value
 	*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@@ -59,112 +40,31 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 }
 
 
-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)
-{
-	// 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_obiint_with_elt_idx(column, line_nb, element_idx, value) < 0)
-		return -1;
-
-	return 0;
-}
-
-
 obiint_t obi_column_get_obiint_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 in the column");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		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);
+	index_t 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;
+	return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
 }
 
 
 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);
+	index_t 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

@@ -19,7 +19,6 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
-#include "obiview.h"
 
 
 /**
@@ -96,79 +95,5 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 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

@@ -14,11 +14,10 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiavl.h"
+#include "dna_seq_indexer.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -30,104 +29,31 @@
  *
  **********************************************************************/
 
-
-int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const 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)
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
-	//if (strlen(value_b) == 0)
-	//	fprintf(stderr, "\nPOUIC");
-
-	//fprintf(stderr, "\n>%s||%s", value, obi_obibytes_to_seq(value_b));
-
-	// Add in the AVL tree
-	idx = insert_in_avl_group(column->avl, value_b);
+	// Add the value in the indexer
+	idx = obi_index_dna_seq(column->indexer, value);
 	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)
+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");
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
 		return OBISeq_NA;
-	}
 
 	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 
@@ -135,67 +61,26 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBISeq_NA;
 
-	//value_b = obi_avl_get((column->avl)[crc(value)], idx);
-	return obi_obibytes_to_seq(value_b);
+	return obi_retrieve_dna_seq(column->indexer, idx);
 }
 
 
-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)
+int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
 {
-	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;
-	}
+	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
 
-	if (view->line_selection)
-		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+	return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t 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);
 }
 
-
-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

@@ -24,7 +24,7 @@
 
 /**
  * @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.
+ * to DNA sequences handled by an indexer, and using the index of the element in the column's line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -40,12 +40,12 @@
  * @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);
+int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const 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.
+ * to DNA sequences handled by an indexer, and using the index of the element in the column's 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.
@@ -57,12 +57,12 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
  * @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);
+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.
+ * to DNA sequences handled by an indexer, using the name of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -78,12 +78,12 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
  * @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);
+int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const 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.
+ * to DNA sequences handled by an indexer, 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.
@@ -95,83 +95,7 @@ int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb,
  * @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);
+char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
 #endif /* OBIDMSCOLUMN_SEQ_H_ */

src/obidmscolumn_str.c

@@ -14,11 +14,10 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
-#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiavl.h"
+#include "char_str_indexer.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -30,83 +29,21 @@
  *
  **********************************************************************/
 
-int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const 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)
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
-	// Add in the AVL tree
-	idx = insert_in_avl_group(column->avl, value_b);
+	// Add the value in the indexer
+	idx = obi_index_char_str(column->indexer, value);
 	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;
 }
 
@@ -114,14 +51,9 @@ int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
 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;
-	}
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
+		return OBISeq_NA;
 
 	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 
@@ -129,67 +61,26 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBIStr_NA;
 
-	//value_b = obi_avl_get(column->avl, idx);
-	return obi_obibytes_to_str(value_b);
+	return obi_retrieve_char_str(column->indexer, idx);
 }
 
 
-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)
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
 {
-	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);
+	index_t 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;
+	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
 }
 
 
 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);
+	index_t 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

@@ -24,7 +24,7 @@
 
 /**
  * @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.
+ * to character strings handled by an indexer, using the index of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -40,12 +40,12 @@
  * @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);
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const 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.
+ * to character strings handled by an indexer, 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.
@@ -62,7 +62,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 
 /**
  * @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.
+ * to character strings handled by an indexer, using the name of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -78,12 +78,12 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
  * @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);
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const 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.
+ * to character strings handled by an indexer, 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.
@@ -98,81 +98,5 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 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

@@ -20,7 +20,7 @@
 
 #include "obidmscolumndir.h"
 #include "obidms.h"
-#include "private_at_functions.h"
+#include "utils.h"
 #include "obierrno.h"
 #include "obidebug.h"
 
@@ -65,7 +65,8 @@ static char* build_column_directory_name(const char* column_name)
 	char* column_directory_name;
 
 	// Build the database directory name
-	if (asprintf(&column_directory_name, "%s.obicol", column_name) < 0)
+	column_directory_name = (char*) malloc((strlen(column_name) + 8)*sizeof(char));
+	if (sprintf(column_directory_name, "%s.obicol", column_name) < 0)
 	{
 		obi_set_errno(OBICOLDIR_MEMORY_ERROR);
 		obidebug(1, "\nError building a column directory name");
@@ -104,7 +105,7 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name)
 		return -1;
 
 	// Get the full path for the column directory
-	full_path = get_full_path(dms->dir_fd, column_directory_name);
+	full_path = obi_dms_get_full_path(dms, column_directory_name);
 	if (full_path == NULL)
 	{
 		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
@@ -169,7 +170,7 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
 		return NULL;
 
 	// Try to open the column directory
-	directory = private_opendirat(dms->dir_fd, column_directory_name);
+	directory = opendir_in_dms(dms, column_directory_name);
 	if (directory == NULL) {
 		switch (errno)
 		{

src/obierrno.h

@@ -98,12 +98,22 @@ 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 OBI_AVL_ERROR				(20)    /** Error while handling an AVL tree	// TODO delete and just keep OBI_INDEXER_ERROR?
 											 */
 #define OBIVIEW_ERROR				(21)    /** Error while handling an OBIView
 											 */
 #define OBI_TAXONOMY_ERROR			(22)    /** Error while handling binary taxonomy files
  	 	 	 	 	 	 	 	 	 	 	 */
+#define OBI_MALLOC_ERROR			(23)    /** Error while allocating memory
+ 	 	 	 	 	 	 	 	 	 	 	 */
+#define OBI_ENCODE_ERROR			(24)    /** Error while encoding a value
+ 	 	 	 	 	 	 	 	 	 	 	 */
+#define OBI_DECODE_ERROR			(25)    /** Error while decoding a value
+ 	 	 	 	 	 	 	 	 	 	 	 */
+#define OBI_UTILS_ERROR				(26)    /** Error in a utils function
+	 	 	 	 	 	 	 	 	 	 	 */
+#define OBI_INDEXER_ERROR			(27)    /** Error handling a blob indexer
+											 */
 /**@}*/
 
 #endif /* OBIERRNO_H_ */

src/obitypes.h

@@ -59,8 +59,7 @@ typedef char obichar_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.
+typedef char byte_t;		/**< Defining byte type.
  	 	 	 	 	 	 	 */
 
 

src/obiview.c

@@ -22,9 +22,15 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obidmscolumn.h"
-#include "private_at_functions.h"
+#include "utils.h"
 #include "obilittlebigman.h"
 #include "obidmscolumn_idx.h"
+#include "obidmscolumn_bool.h"
+#include "obidmscolumn_char.h"
+#include "obidmscolumn_float.h"
+#include "obidmscolumn_int.h"
+#include "obidmscolumn_seq.h"
+#include "obidmscolumn_str.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -73,6 +79,14 @@ static char* build_obiview_file_name();
 int create_obiview_file(int dms_file_descriptor);
 
 
+// TODO doc
+int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p);
+
+
+// TODO doc
+int prepare_to_get_value_in_column(Obiview_p view, OBIDMS_column_p column, index_t* line_nb_p);
+
+
 /************************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -84,7 +98,8 @@ static char* build_obiview_file_name()
 	char* file_name;
 
 	// Build file name
-	if (asprintf(&file_name, OBIVIEW_FILE_NAME) < 0)
+	file_name = (char*) malloc((strlen(OBIVIEW_FILE_NAME) + 1)*sizeof(char));
+	if (sprintf(file_name, OBIVIEW_FILE_NAME) < 0)
 	{
 		obi_set_errno(OBIVIEW_ERROR);
 		obidebug(1, "\nProblem building an obiview file name");
@@ -202,6 +217,58 @@ int create_obiview_file(int dms_file_descriptor)
 }
 
 
+int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
+{
+	// 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 there is a line selection associated with the view or if the column
+	// is read-only, all columns or this column respectively must be cloned
+	if ((view->line_selection != NULL) || (!((*column_pp)->writable)))
+	{
+		// Get the right line number
+		if (view->line_selection != NULL)
+			(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));
+
+		(*column_pp) = obi_view_clone_column(view, ((*column_pp)->header)->name);
+		if ((*column_pp) == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if (((*line_nb_p)+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, ((*line_nb_p)+1)) < 0)
+			return -1;
+	}
+
+	return 0;
+}
+
+
+int prepare_to_get_value_from_column(Obiview_p view, OBIDMS_column_p column, index_t* line_nb_p)
+{
+	if (((*line_nb_p)+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 -1;
+	}
+
+	if (view->line_selection)
+		(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));
+
+	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
@@ -227,25 +294,24 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	if (view== NULL)
 		return NULL;
 
-	fprintf(stderr, "\nmmmm\n");
 	strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
 
 	if (view_to_clone == NULL)
 	{
 		// Adding sequence column
-		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_AVL, "Nucleotide sequences", true) < 0)
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_INDEXER, "Nucleotide sequences", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding id column
-		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_AVL, "Ids", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_INDEXER, "Ids", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding description column
-		if (obi_view_add_column(view, DESCRIPTION_COLUMN, -1, OBI_STR, 0, 1, DESCRIPTION_COLUMN, DESCRIPTION_AVL, "Descriptions", true) < 0)
+		if (obi_view_add_column(view, DESCRIPTION_COLUMN, -1, OBI_STR, 0, 1, DESCRIPTION_COLUMN, DESCRIPTION_INDEXER, "Descriptions", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -696,7 +762,7 @@ int obi_view_add_column(Obiview_p view,
 						index_t nb_lines,
 						index_t nb_elements_per_line,
 						const char* elements_names,
-						const char* avl_name,
+						const char* indexer_name,
 						const char* comments,
 						bool create)	// all infos for creation or open
 {
@@ -718,7 +784,7 @@ int obi_view_add_column(Obiview_p view,
 	// Open or create the column
 	if (create)
 	{	// Create column
-		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, avl_name, comments);
+		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, comments);
 	}
 	else
 	{ // Open column
@@ -777,18 +843,18 @@ OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name)
 			if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
 				column = (view->columns)[i];
 			else
-				obi_truncate_and_close_column(column_buffer);	// TODO weird closing after cloning but can't think of cleaner yet
+				obi_close_column(column_buffer);	// TODO weird closing after cloning but can't think of cleaner yet
 		}
 	}
 
 	if (view->line_selection != NULL)
 	{
-		obi_truncate_and_close_column(view->line_selection);
+		obi_close_column(view->line_selection);
 		view->line_selection = NULL;
 	}
 	if (view->new_line_selection != NULL)
 	{
-		obi_truncate_and_close_column(view->new_line_selection);
+		obi_close_column(view->new_line_selection);
 		view->new_line_selection = NULL;
 	}
 
@@ -817,7 +883,7 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
 	{
 		if (!strcmp((((view->columns)[i])->header)->name, column_name))
 		{
-			obi_truncate_and_close_column((view->columns)[i]);
+			obi_close_column((view->columns)[i]);
 			found = 1;
 		}
 		if (found)
@@ -985,7 +1051,7 @@ int obi_save_view(Obiview_p view)
 		return -1;
 
 	// Get the full path for the column directory
-	full_path = get_full_path((view->dms)->dir_fd, view_file_name);
+	full_path = obi_dms_get_full_path(view->dms, view_file_name);
 	if (full_path == NULL)
 	{
 		obi_set_errno(OBIVIEW_ERROR);
@@ -1148,3 +1214,231 @@ int obi_save_and_close_view(Obiview_p view)
 	return 0;
 }
 
+
+/*********** FOR BOOL COLUMNS ***********/
+
+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 (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+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 (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBIBool_NA;
+	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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 = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, 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* element_name)
+{
+	index_t 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);
+}
+
+/****************************************/
+
+
+/*********** FOR CHAR COLUMNS ***********/
+
+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 (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, 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)
+{
+	if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBIChar_NA;
+	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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 = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, 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* element_name)
+{
+	index_t 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);
+}
+
+/****************************************/
+
+
+/*********** FOR FLOAT COLUMNS ***********/
+
+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 (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+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 (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBIFloat_NA;
+	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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 = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, 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* element_name)
+{
+	index_t 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);
+}
+
+/****************************************/
+
+
+/*********** FOR INT COLUMNS ***********/
+
+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 (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+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 (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBIInt_NA;
+	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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 = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, 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* element_name)
+{
+	index_t 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);
+}
+
+/****************************************/
+
+
+/*********** FOR SEQ COLUMNS ***********/
+
+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, const char* value)
+{
+	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+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 (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBISeq_NA;
+	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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, const char* value)
+{
+	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+}
+
+
+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 = 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);
+}
+
+/****************************************/
+
+
+/*********** FOR STR COLUMNS ***********/
+
+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, const char* value)
+{
+	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+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 (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
+		return OBIStr_NA;
+	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+}
+
+
+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, const char* value)
+{
+	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	return obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+}
+
+
+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 = 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/obiview.h

@@ -37,13 +37,13 @@
 #define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW"
 
 #define NUC_SEQUENCE_COLUMN "NUC_SEQ"
-#define NUC_SEQUENCE_AVL "NUC_SEQ_AVL"
+#define NUC_SEQUENCE_INDEXER "NUC_SEQ_INDEXER"
 
 #define ID_COLUMN "ID"
-#define ID_AVL "ID_AVL"
+#define ID_INDEXER "ID_INDEXER"
 
 #define DESCRIPTION_COLUMN "DESCRIPTION"
-#define DESCRIPTION_AVL "DESCRIPTION_AVL"
+#define DESCRIPTION_INDEXER "DESCRIPTION_INDEXER"
 
 #define LINES_COLUMN_NAME "LINES"
 
@@ -162,7 +162,7 @@ int obi_view_add_column(Obiview_p view,
 						index_t nb_lines,
 						index_t nb_elements_per_line,
 						const char* elements_names,
-						const char* avl_name,
+						const char* indexer_name,
 						const char* comments,
 						bool create);
 
@@ -186,4 +186,455 @@ int obi_close_view(Obiview_p view);
 
 int obi_save_and_close_view(Obiview_p view);
 
+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 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);
+
+
+/**
+ * @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);
+
+
+/**
+ * @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);
+
+
+/**
+ * @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);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences handled by an indexer, 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, const char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences handled by an indexer, 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)
+ */
+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 handled by an indexer, 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, const char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences handled by an indexer, 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)
+ */
+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);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings handled by an indexer, 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, const char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings handled by an indexer, 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 handled by an indexer, 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, const char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings handled by an indexer, 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 /* OBIVIEW_H_ */

src/private_at_functions.c

@@ -1,72 +0,0 @@
-/****************************************************************************
- * Private *at functions                                                    *
- ****************************************************************************/
-
-/**
- * @file private_at_functions.c
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- * @date 15 June 2015
- * @brief Private replacement functions for *at functions.
- */
-
-
-#include <fcntl.h>
-#include <string.h>
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <dirent.h>
-
-#include "private_at_functions.h"
-#include "obidebug.h"
-#include "obierrno.h"
-
-
-#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)
-{
-	char* full_path;
-
-	full_path = (char*) malloc((MAX_PATH_LEN)*sizeof(char));
-	if (full_path == NULL)
-	{
-		obidebug(1, "\nError allocating memory for the char* path to a file or directory");
-		return NULL;
-	}
-
-	if (fcntl(directory_file_descriptor, F_GETPATH, full_path) < 0)
-	{
-		obidebug(1, "\nError getting the path to a file or directory");
-		return NULL;
-	}
-
-	// TODO check errors?
-	strlcat(full_path, "/", MAX_PATH_LEN);
-	strlcat(full_path, path_name, MAX_PATH_LEN);
-
-	return full_path;
-}
-
-
-DIR* private_opendirat(int directory_file_descriptor, const char* path_name)
-{
-	char* full_path;
-	DIR* directory;
-
-	full_path = get_full_path(directory_file_descriptor, path_name);
-	if (full_path == NULL)
-		return NULL;
-
-	directory = opendir(full_path);
-	if (directory == NULL)
-		obidebug(1, "\nError opening a directory");
-
-	free(full_path);
-
-	return directory;
-}
-
-

src/private_at_functions.h

@@ -1,58 +0,0 @@
-/****************************************************************************
- * Header file for private *at functions                                    *
- ****************************************************************************/
-
-/**
- * @file private_at_functions.h
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- * @date 15 June 2015
- * @brief Header file for the private replacement functions for *at functions.
- */
-
-
-#ifndef PRIVATE_OPENAT_H_
-#define PRIVATE_OPENAT_H_
-
-
-#include <sys/stat.h>
-
-
-#define MAX_PATH_LEN 4096	/**< Maximum length for the character string defining a
- 	 	 	 	 	 	 	 	 file or directory path */
-
-
-/**
- * @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.
- *
- * @returns A pointer to the full path.
- * @retval NULL if an error occurred.
- *
- * @since June 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-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.
- *
- * @returns The file descriptor of the opened directory.
- * @retval NULL if an error occurred.
- *
- * @since June 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-DIR* private_opendirat(int directory_file_descriptor, const char* path_name);
-
-
-#endif /* PRIVATEOPENAT_H_ */

src/utils.c

@@ -0,0 +1,58 @@
+/****************************************************************************
+ * Utility functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file utils.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 29 March 2016
+ * @brief Code for utility functions.
+ */
+
+#include <fcntl.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <dirent.h>
+#include <unistd.h>
+
+#include "utils.h"
+#include "obidebug.h"
+#include "obierrno.h"
+#include "obidms.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 count_dir(char *dir)
+{
+	struct dirent *dp;
+	DIR *fd;
+	int count;
+
+	count = 0;
+	if ((fd = opendir(dir)) == NULL)
+	{
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "Error opening a directory: %s\n", dir);
+		return -1;
+	}
+	while ((dp = readdir(fd)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		count++;
+	}
+	return count;
+}

src/utils.h

@@ -0,0 +1,32 @@
+/****************************************************************************
+ * Header file for utility functions                                        *
+ ****************************************************************************/
+
+/**
+ * @file utils.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 29 March 2016
+ * @brief Header file for utility functions.
+ */
+
+
+#ifndef UTILS_H_
+#define UTILS_H_
+
+#include <stdio.h>
+#include <sys/stat.h>
+
+#include "obidms.h"
+
+
+#define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
+                                	   	 */
+
+
+/*
+ * TODO
+ */
+int count_dir(char *dir);
+
+
+#endif /* UTILS_H_ */