diff --git a/python/obitools3/dms/view.pxd b/python/obitools3/dms/view.pxd deleted file mode 100644 index 59dcff3..0000000 --- a/python/obitools3/dms/view.pxd +++ /dev/null @@ -1,60 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport Obiview_p -from .capi.obitypes cimport index_t, \ - obitype_t - -from .dms cimport DMS -from .column cimport Column - - - -cdef class View: - - cdef DMS _dms - cdef Obiview_p _pointer - - cpdef View clone(self, - object view_name, - object comments=*) - - @staticmethod - cdef View _new(DMS dms, - bytes view_name, - bytes comments=*) - - @staticmethod - cdef View _open(DMS dms, - bytes view_name) - - cpdef close(self) - - cpdef get_column(self, - object column_name) - - cpdef delete_column(self, - object column_name) - - cpdef rename_column(self, - object current_name, - object new_name) - - cpdef View_line_selection new_selection(self, - list lines=*) - -cdef class View_line_selection(list): - - cdef View _view - - cdef index_t* __build_binary_list__(self) - - cpdef View materialize(self, - object view_name, - object comments=*) - -cdef class View_line : - - cdef index_t _index - cdef View _view - - diff --git a/python/obitools3/dms/view.pyx b/python/obitools3/dms/view.pyx deleted file mode 100644 index aa860d8..0000000 --- a/python/obitools3/dms/view.pyx +++ /dev/null @@ -1,417 +0,0 @@ -#cython: language_level=3 - -from libc.stdlib cimport malloc - -from .capi.obiview cimport obi_new_view, \ - obi_open_view, \ - obi_save_and_close_view, \ - obi_view_get_pointer_on_column_in_view, \ - obi_view_delete_column, \ - obi_view_create_column_alias - -from .capi.obidmscolumn cimport OBIDMS_column_p - -from obitools3.utils cimport tobytes, \ - bytes2str - - -cdef class View : - - - def __init__(self,dms,int __internalCall__): - - if __internalCall__!=987654: - raise RuntimeError('OBIView constructor cannot be called directly') - - self._dms = dms - self._pointer = NULL - - cpdef View clone(self, - object view_name, - object comments=None): - - - cdef bytes view_name_b = tobytes(view_name) - cdef bytes comments_b - cdef View view = View(self._dms, - 987654) - - if comments is not None: - comments_b = tobytes(comments) - else: - comments_b = b'' - - view._pointer = obi_new_view(self._pointer.dms, - view_name_b, - self._pointer, - NULL, - comments_b) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - bytes2str(view_name_b)) - ) - - return view - - @staticmethod - cdef View _new(DMS dms, - bytes view_name, - bytes comments=b""): - - cdef View view = View(dms, - 987654) # @DuplicatedSignature - - view._pointer = obi_new_view(dms._pointer, - view_name, - NULL, - NULL, - comments) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot create view %s" % view_name) - - return view - - @staticmethod - def new(DMS dms, - object view_name, - object comments=None): - - cdef bytes view_name_b = tobytes(view_name) - cdef bytes comments_b - - if comments is not None: - comments_b = tobytes(comments) - else: - comments_b = b'' - - - return View._new(dms, - view_name_b, - comments_b) - - - @staticmethod - cdef View _open(DMS dms, - bytes view_name): - - cdef View view = View(dms, - 987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - view_name) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name)) - - return view - - @staticmethod - def open(DMS dms, # @ReservedAssignment - object view_name): - - cdef bytes view_name_b = tobytes(view_name) - - return View._open(dms,view_name_b) - - cpdef close(self): - if (obi_save_and_close_view(self._pointer) < 0) : - raise Exception("Problem closing view %s" % - bytes2str(self.name)) - - def __dealloc__(self): - self.close() - - def __repr__(self) : - cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name), - comments = str(self.comments), - line_count = self.line_count) - - #for column_name in self._columns : - # s = s + repr(self._columns[column_name]) + '\n' - - return s - - cpdef get_column(self, - object column_name): - cdef bytes column_name_b = tobytes(column_name) - cdef OBIDMS_column_p* column_pp - cdef OBIDMS_column_p column_p - cdef Column column - cdef obitype_t column_type - - column_pp = obi_view_get_pointer_on_column_in_view(self._pointer, - column_name_b) - - if column_pp == NULL: - raise KeyError("Cannot access to column %s in view %s" % ( - bytes2str(column_name_b), - bytes2str(self.name) - )) - - column_p = column_pp[0] - column_type = column_p.header.returned_data_type - - column = DMS.get_column_class(column_type)(self) - column._pointer = column_pp - - return column - - cpdef delete_column(self, - object column_name) : - - cdef bytes column_name_b = tobytes(column_name) - - if obi_view_delete_column(self._pointer, column_name_b) < 0 : - raise Exception("Problem deleting column %s from a view", - bytes2str(column_name_b)) - - - - cpdef rename_column(self, - object current_name, - object new_name): - - cdef Column column - cdef bytes current_name_b = tobytes(current_name) - cdef bytes new_name_b = tobytes(new_name) - - if (obi_view_create_column_alias(self._pointer, - tobytes(current_name_b), - tobytes(new_name_b)) < 0) : - raise Exception("Problem in renaming column %s to %s" % ( - bytes2str(current_name_b), - bytes2str(new_name_b))) - - - cpdef View_line_selection new_selection(self,list lines=None): - return View_line_selection(self,lines) - - def __iter__(self): - # Iteration on each line of all columns - - # Declarations - cdef index_t line_nb - cdef View_line line - - # Yield each line - for line_nb in range(self.line_count) : - line = self[line_nb] - yield line - - - def __getitem__(self, object item) : - if type(item) == str : - return (self._columns)[item] - elif type(item) == int : - return View_line(self, item) - - - def __contains__(self, str column_name): - return (column_name in self._columns) - - - def __len__(self): - return(self.line_count) - - - def __str__(self) : - cdef View_line line - cdef str to_print - to_print = "" - for line in self : - to_print = to_print + str(line) + "\n" - return to_print - - - @property - def dms(self): - return self._dms - - # line_count property getter - @property - def line_count(self): - return self._pointer.infos.line_count - - # name property getter - @property - def name(self): - return self._pointer.infos.name - - # view type property getter - @property - def type(self): # @ReservedAssignment - return bytes2str(self._pointer.infos.view_type) - - # comments property getter - @property - def comments(self): - return self._pointer.infos.comments - # TODO setter that concatenates new comments? - - -cdef class View_line_selection(list): - - def __init__(self, View view, lines=None) : - if view._pointer == NULL: - raise Exception("Error: trying to create a line selection with an invalidated view") - self._view = view - self._view_name = view.name - - if lines is not None: - self.extend(lines) - - def extend(self, iterable): - cdef index_t i - cdef index_t max_i = self._view.line_count - - for i in iterable: - if i > max_i: - raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" % - (i, - max_i, - self._view_name) - ) - list.append(self,i) - - def append(self, index_t idx) : - if idx >= self._view.line_count : - raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" % - (idx, - self._view.line_count, - bytes2str(self.name)) - ) - list.append(self,idx) - - cdef index_t* __build_binary_list__(self): - cdef index_t* line_selection_p = NULL - cdef int i - cdef size_t l_selection = len(self) - - line_selection_p = malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array - for i in range(l_selection) : - line_selection_p[i] = self[i] - line_selection_p[l_selection] = -1 # flagging the end of the array - - return line_selection_p - - cpdef View materialize(self, - object view_name, - object comments=""): - - cdef View view = View(987654) - cdef bytes view_name_b=tobytes(view_name) - - view._pointer = obi_new_view(self._view._pointer.dms, - view_name_b, - self._view._pointer, - self.__build_binary_list__(), - tobytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - return view - - -cdef class View_line : - - def __init__(self, View view, index_t line_nb) : - self._index = line_nb - self._view = view - - def __getitem__(self, str column_name) : - return ((self._view)._columns)[column_name][self._index] - -# def __setitem__(self, str column_name, object value): -# # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get) -# # TODO OBI_QUAL ? -# cdef type value_type -# cdef str value_obitype -# cdef bytes value_b -# -# if column_name not in self._view : -# if value == None : -# raise Exception("Trying to create a column from a None value (can't guess type)") -# value_type = type(value) -# if value_type == int : -# value_obitype = 'OBI_INT' -# elif value_type == float : -# value_obitype = 'OBI_FLOAT' -# elif value_type == bool : -# value_obitype = 'OBI_BOOL' -# elif value_type == str or value_type == bytes : -# if value_type == str : -# value_b = str2bytes(value) -# else : -# value_b = value -# if only_ATGC(value_b) : # TODO detect IUPAC -# value_obitype = 'OBI_SEQ' -# elif len(value) == 1 : -# value_obitype = 'OBI_CHAR' -# elif (len(value) > 1) : -# value_obitype = 'OBI_STR' -# else : -# raise Exception("Could not guess the type of a value to create a new column") -# self._view.add_column(column_name, type=value_obitype) -# -# (((self._view)._columns)[column_name]).set_line(self._index, value) -# -# def __iter__(self): -# for column_name in ((self._view)._columns) : -# yield column_name -# -# def __contains__(self, str column_name): -# return (column_name in self._view._columns) - - def __repr__(self): - cdef dict line - cdef str column_name - line = {} -# for column_name in self._view._columns : -# line[column_name] = self[column_name] - return str(line) - - -# cpdef dict get_view_infos(self, str view_name) : -# -# cdef Obiview_infos_p view_infos_p -# cdef dict view_infos_d -# cdef Alias_column_pair_p column_refs -# cdef int i, j -# cdef str column_name -# -# view_infos_p = obi_view_map_file(self._pointer, -# tobytes(view_name)) -# view_infos_d = {} -# view_infos_d["name"] = bytes2str(view_infos_p.name) -# view_infos_d["comments"] = bytes2str(view_infos_p.comments) -# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type) -# view_infos_d["column_count"] = view_infos_p.column_count -# view_infos_d["line_count"] = view_infos_p.line_count -# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from) -# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date)) -# if (view_infos_p.all_lines) : -# view_infos_d["line_selection"] = None -# else : -# view_infos_d["line_selection"] = {} -# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name) -# view_infos_d["line_selection"]["version"] = (view_infos_p.line_selection).version -# view_infos_d["column_references"] = {} -# column_references = view_infos_p.column_references -# for j in range(view_infos_d["column_count"]) : -# column_name = bytes2str((column_references[j]).alias) -# view_infos_d["column_references"][column_name] = {} -# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name) -# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version -# -# obi_view_unmap_file(self._pointer, view_infos_p) -# -# return view_infos_d - - diff --git a/python/obitools3/obidms/__init__.py b/python/obitools3/obidms/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/python/obitools3/obidms/_obidms.cfiles b/python/obitools3/obidms/_obidms.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidms.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidms.pxd b/python/obitools3/obidms/_obidms.pxd deleted file mode 100644 index 87f56a5..0000000 --- a/python/obitools3/obidms/_obidms.pxd +++ /dev/null @@ -1,38 +0,0 @@ -#cython: language_level=3 - -from .capi.obidms cimport OBIDMS_p -from .capi.obidmscolumn cimport OBIDMS_column_p -from .capi.obitypes cimport index_t -from ._obitaxo cimport OBI_Taxonomy -from ._obiview cimport OBIView, OBIView_line_selection - - -cdef class OBIDMS_column: - - cdef str _alias # associated property: alias - cdef OBIDMS_column_p* _pointer - cdef OBIView _view - - cpdef close(self) - - @staticmethod - cdef object get_subclass_type(OBIDMS_column_p column_p) - - -cdef class OBIDMS_column_multi_elts(OBIDMS_column): - - cpdef set_line(self, index_t line_nb, dict values) - - -cdef class OBIDMS_column_line: - - cdef OBIDMS_column _column - cdef index_t _index - - -cdef class OBIDMS: - - cdef OBIDMS_p _pointer - - cpdef close(self) - cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) diff --git a/python/obitools3/obidms/_obidms.pyx b/python/obitools3/obidms/_obidms.pyx deleted file mode 100644 index 4c11741..0000000 --- a/python/obitools3/obidms/_obidms.pyx +++ /dev/null @@ -1,271 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obidms cimport obi_dms, \ - obi_close_dms - -from .capi.obidmscolumn cimport obi_close_column, \ - OBIDMS_column_header_p, \ - obi_get_elements_names - -from .capi.obiutils cimport obi_format_date - -from .capi.obitypes cimport const_char_p, \ - OBIType_t, \ - OBI_INT, \ - OBI_FLOAT, \ - OBI_BOOL, \ - OBI_CHAR, \ - OBI_QUAL, \ - OBI_STR, \ - OBI_SEQ, \ - name_data_type - -from .capi.obiview cimport Obiview_p, \ - obi_view_get_pointer_on_column_in_view - -from ._obidmscolumn_int cimport OBIDMS_column_int, \ - OBIDMS_column_multi_elts_int - -from ._obidmscolumn_float cimport OBIDMS_column_float, \ - OBIDMS_column_multi_elts_float - -from ._obidmscolumn_bool cimport OBIDMS_column_bool, \ - OBIDMS_column_multi_elts_bool - -from ._obidmscolumn_char cimport OBIDMS_column_char, \ - OBIDMS_column_multi_elts_char - -from ._obidmscolumn_qual cimport OBIDMS_column_qual, \ - OBIDMS_column_multi_elts_qual - -from ._obidmscolumn_str cimport OBIDMS_column_str, \ - OBIDMS_column_multi_elts_str - -from ._obidmscolumn_seq cimport OBIDMS_column_seq, \ - OBIDMS_column_multi_elts_seq - -from libc.stdlib cimport free - - -cdef class OBIDMS_column : - - # Note: should only be initialized through a subclass - def __init__(self, OBIView view, str column_alias): - - cdef OBIDMS_column_p column_p - cdef OBIDMS_column_p* column_pp - - column_pp = obi_view_get_pointer_on_column_in_view(view._pointer, str2bytes(column_alias)) - column_p = column_pp[0] # TODO ugly cython dereferencing but can't find better - - # Fill structure - self._alias = column_alias - self._pointer = column_pp - self._view = view - - def __setitem__(self, index_t line_nb, object value): - self.set_line(line_nb, value) - - def __getitem__(self, index_t line_nb): - return self.get_line(line_nb) - - def __len__(self): # TODO discuss - return self._view.line_count - - def __sizeof__(self): - return ((self._pointer)[0].header.header_size + (self._pointer)[0].header.data_size) - - def __iter__(self): # TODO discuss - # Declarations - cdef index_t line_nb - # Yield each line - for line_nb in range(self._view.line_count): - yield self.get_line(line_nb) - - def __str__(self) : - cdef str to_print - to_print = '' - for line in self : - to_print = to_print + str(line) + "\n" - return to_print - - def __repr__(self) : - return (self._alias + ", original name: " + self.original_name + ", version " + str(self.version) + ", data type: " + self.data_type) - - cpdef close(self): - if obi_close_column((self._pointer)[0]) < 0 : - raise Exception("Problem closing a column") - - # Column alias property getter and setter - @property - def alias(self): - return self._alias - @alias.setter - def alias(self, new_alias): # @DuplicatedSignature - self._view.change_column_alias(self._alias, new_alias) - - # elements_names property getter - @property - def elements_names(self): - cdef char* elts_names_b - cdef str elts_names - elts_names_b = obi_get_elements_names((self._pointer)[0]) - elts_names = bytes2str(elts_names_b) - free(elts_names_b) - return elts_names.split(';') - - # nb_elements_per_line property getter - @property - def nb_elements_per_line(self): - return ((self._pointer)[0].header).nb_elements_per_line - - # data_type property getter - @property - def data_type(self): - return bytes2str(name_data_type(((self._pointer)[0].header).returned_data_type)) - - # original_name property getter - @property - def original_name(self): - return bytes2str(((self._pointer)[0].header).name) - - # version property getter - @property - def version(self): - return ((self._pointer)[0].header).version - - # comments property getter - @property - def comments(self): - return bytes2str((self._pointer)[0].header.comments) - - # creation_date property getter - @property - def creation_date(self): - return bytes2str(obi_format_date((self._pointer)[0].header.creation_date)) - - @staticmethod - cdef object get_subclass_type(OBIDMS_column_p column_p) : - - cdef object subclass - cdef OBIDMS_column_header_p header - cdef OBIType_t col_type - cdef bint col_writable - cdef bint col_one_element_per_line - - header = column_p.header - col_type = header.returned_data_type - col_writable = column_p.writable - col_one_element_per_line = ((header.nb_elements_per_line) == 1) - - if col_type == OBI_INT : - if col_one_element_per_line : - subclass = OBIDMS_column_int - else : - subclass = OBIDMS_column_multi_elts_int - elif col_type == OBI_FLOAT : - if col_one_element_per_line : - subclass = OBIDMS_column_float - else : - subclass = OBIDMS_column_multi_elts_float - elif col_type == OBI_BOOL : - if col_one_element_per_line : - subclass = OBIDMS_column_bool - else : - subclass = OBIDMS_column_multi_elts_bool - elif col_type == OBI_CHAR : - if col_one_element_per_line : - subclass = OBIDMS_column_char - else : - subclass = OBIDMS_column_multi_elts_char - elif col_type == OBI_QUAL : - if col_one_element_per_line : - subclass = OBIDMS_column_qual - else : - subclass = OBIDMS_column_multi_elts_qual - elif col_type == OBI_STR : - if col_one_element_per_line : - subclass = OBIDMS_column_str - else : - subclass = OBIDMS_column_multi_elts_str - elif col_type == OBI_SEQ : - if col_one_element_per_line : - subclass = OBIDMS_column_seq - else : - subclass = OBIDMS_column_multi_elts_seq - else : - raise Exception("Problem with the data type") - - return subclass - - -###################################################################################################### - - -cdef class OBIDMS_column_multi_elts(OBIDMS_column) : - - def __getitem__(self, index_t line_nb): - return OBIDMS_column_line(self, line_nb) - - cpdef set_line(self, index_t line_nb, dict values): - for element_name in values : - self.set_item(line_nb, element_name, values[element_name]) - - -###################################################################################################### - - -cdef class OBIDMS_column_line : - - def __init__(self, OBIDMS_column column, index_t line_nb) : - self._index = line_nb - self._column = column - - def __getitem__(self, str element_name) : - return self._column.get_item(self._index, element_name) - - def __setitem__(self, str element_name, object value): - self._column.set_item(self._index, element_name, value) - - def __contains__(self, str element_name): - return (element_name in self._column.elements_names) - - def __repr__(self) : - return str(self._column.get_line(self._index)) - - -###################################################################################################### - - -cdef class OBIDMS : - - def __init__(self, str dms_name) : - - # Declarations - cdef bytes dms_name_b - - # Format the character string to send to C function - dms_name_b = str2bytes(dms_name) - - # Fill structure and create or open the DMS - self._pointer = obi_dms( dms_name_b) - if self._pointer == NULL : - raise Exception("Failed opening or creating an OBIDMS") - - - # name property getter - @property - def name(self): - return bytes2str(self._pointer.dms_name) - - - cpdef close(self) : - if (obi_close_dms(self._pointer)) < 0 : - raise Exception("Problem closing an OBIDMS") - - - cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) : - return OBI_Taxonomy(self, taxo_name) - diff --git a/python/obitools3/obidms/_obidmscolumn_bool.cfiles b/python/obitools3/obidms/_obidmscolumn_bool.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_bool.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_bool.pxd b/python/obitools3/obidms/_obidmscolumn_bool.pxd deleted file mode 100644 index 7fd3985..0000000 --- a/python/obitools3/obidms/_obidmscolumn_bool.pxd +++ /dev/null @@ -1,14 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_bool(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - -cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_bool.pyx b/python/obitools3/obidms/_obidmscolumn_bool.pyx deleted file mode 100644 index 2325cb6..0000000 --- a/python/obitools3/obidms/_obidmscolumn_bool.pyx +++ /dev/null @@ -1,78 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \ - obi_get_bool_with_elt_idx_and_col_p_in_view, \ - obi_set_bool_with_elt_name_and_col_p_in_view, \ - obi_set_bool_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIBool_NA, obibool_t - -from obitools3.utils cimport str2bytes - -from cpython.bool cimport PyBool_FromLong - - -cdef class OBIDMS_column_bool(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef obibool_t value - cdef object result - value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIBool_NA : - result = None - else : - result = PyBool_FromLong(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - value = OBIBool_NA - if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef obibool_t value - cdef object result - value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIBool_NA : - result = None - else : - result = PyBool_FromLong(value) - return result - - cpdef object get_line(self, index_t line_nb) : - cdef obibool_t value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIBool_NA : - value_in_result = None - else : - value_in_result = PyBool_FromLong(value) - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - if value is None : - value = OBIBool_NA - if obi_set_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value) < 0: - raise Exception("Problem setting a value in a column") - diff --git a/python/obitools3/obidms/_obidmscolumn_char.cfiles b/python/obitools3/obidms/_obidmscolumn_char.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_char.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_char.pxd b/python/obitools3/obidms/_obidmscolumn_char.pxd deleted file mode 100644 index 515100f..0000000 --- a/python/obitools3/obidms/_obidmscolumn_char.pxd +++ /dev/null @@ -1,14 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_char(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - -cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_char.pyx b/python/obitools3/obidms/_obidmscolumn_char.pyx deleted file mode 100644 index 9c80f11..0000000 --- a/python/obitools3/obidms/_obidmscolumn_char.pyx +++ /dev/null @@ -1,76 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \ - obi_get_char_with_elt_idx_and_col_p_in_view, \ - obi_set_char_with_elt_name_and_col_p_in_view, \ - obi_set_char_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIChar_NA, obichar_t - -from obitools3.utils cimport str2bytes, bytes2str - - -cdef class OBIDMS_column_char(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef obichar_t value - cdef object result - value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIChar_NA : - result = None - else : - result = bytes2str(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - value = OBIChar_NA - if obi_set_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef obichar_t value - cdef object result - value = obi_get_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIChar_NA : - result = None - else : - result = bytes2str(value) - return result - - cpdef object get_line(self, index_t line_nb) : - cdef obichar_t value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIChar_NA : - value_in_result = None - else : - value_in_result = bytes2str(value) - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - if value is None : - value = OBIChar_NA - if obi_set_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0: - raise Exception("Problem setting a value in a column") - diff --git a/python/obitools3/obidms/_obidmscolumn_float.cfiles b/python/obitools3/obidms/_obidmscolumn_float.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_float.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_float.pxd b/python/obitools3/obidms/_obidmscolumn_float.pxd deleted file mode 100644 index 2121ccd..0000000 --- a/python/obitools3/obidms/_obidmscolumn_float.pxd +++ /dev/null @@ -1,14 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_float(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - -cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_float.pyx b/python/obitools3/obidms/_obidmscolumn_float.pyx deleted file mode 100644 index 52602e2..0000000 --- a/python/obitools3/obidms/_obidmscolumn_float.pyx +++ /dev/null @@ -1,76 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \ - obi_get_float_with_elt_idx_and_col_p_in_view, \ - obi_set_float_with_elt_name_and_col_p_in_view, \ - obi_set_float_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIFloat_NA, obifloat_t - -from obitools3.utils cimport str2bytes - - -cdef class OBIDMS_column_float(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef obifloat_t value - cdef object result - value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIFloat_NA : - result = None - else : - result = value - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - value = OBIFloat_NA - if obi_set_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef obifloat_t value - cdef object result - value = obi_get_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIFloat_NA : - result = None - else : - result = value - return result - - cpdef object get_line(self, index_t line_nb) : - cdef obifloat_t value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIFloat_NA : - value_in_result = None - else : - value_in_result = value - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - if value is None : - value = OBIFloat_NA - if obi_set_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value) < 0: - raise Exception("Problem setting a value in a column") - \ No newline at end of file diff --git a/python/obitools3/obidms/_obidmscolumn_int.cfiles b/python/obitools3/obidms/_obidmscolumn_int.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_int.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_int.pxd b/python/obitools3/obidms/_obidmscolumn_int.pxd deleted file mode 100644 index 4bc6711..0000000 --- a/python/obitools3/obidms/_obidmscolumn_int.pxd +++ /dev/null @@ -1,14 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_int(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - -cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_int.pyx b/python/obitools3/obidms/_obidmscolumn_int.pyx deleted file mode 100644 index bccf6b7..0000000 --- a/python/obitools3/obidms/_obidmscolumn_int.pyx +++ /dev/null @@ -1,78 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \ - obi_get_int_with_elt_idx_and_col_p_in_view, \ - obi_set_int_with_elt_name_and_col_p_in_view, \ - obi_set_int_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIInt_NA, obiint_t - -from obitools3.utils cimport str2bytes - -from cpython.int cimport PyInt_FromLong - - -cdef class OBIDMS_column_int(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef obiint_t value - cdef object result - value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIInt_NA : - result = None - else : - result = PyInt_FromLong(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - value = OBIInt_NA - if obi_set_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef obiint_t value - cdef object result - value = obi_get_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIInt_NA : - result = None - else : - result = PyInt_FromLong(value) - return result - - cpdef object get_line(self, index_t line_nb) : - cdef obiint_t value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIInt_NA : - value_in_result = None - else : - value_in_result = PyInt_FromLong(value) - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None # TODO discuss - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - if value is None : - value = OBIInt_NA - if obi_set_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value) < 0: - raise Exception("Problem setting a value in a column") - diff --git a/python/obitools3/obidms/_obidmscolumn_qual.cfiles b/python/obitools3/obidms/_obidmscolumn_qual.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_qual.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_qual.pxd b/python/obitools3/obidms/_obidmscolumn_qual.pxd deleted file mode 100644 index 5015a52..0000000 --- a/python/obitools3/obidms/_obidmscolumn_qual.pxd +++ /dev/null @@ -1,20 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column , OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_qual(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef object get_str_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - cpdef set_str_line(self, index_t line_nb, object value) - - -cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_str_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef object get_str_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) - cpdef set_str_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_qual.pyx b/python/obitools3/obidms/_obidmscolumn_qual.pyx deleted file mode 100644 index bf22a53..0000000 --- a/python/obitools3/obidms/_obidmscolumn_qual.pyx +++ /dev/null @@ -1,189 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \ - obi_get_qual_char_with_elt_idx_and_col_p_in_view, \ - obi_set_qual_char_with_elt_name_and_col_p_in_view, \ - obi_set_qual_char_with_elt_idx_and_col_p_in_view, \ - obi_get_qual_int_with_elt_name_and_col_p_in_view, \ - obi_get_qual_int_with_elt_idx_and_col_p_in_view, \ - obi_set_qual_int_with_elt_name_and_col_p_in_view, \ - obi_set_qual_int_with_elt_idx_and_col_p_in_view - -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIQual_char_NA, OBIQual_int_NA, const_char_p - -from ._obidms cimport OBIView - -from obitools3.utils cimport str2bytes, bytes2str - -from libc.stdlib cimport free -from libc.string cimport strcmp -from libc.stdint cimport uint8_t -from libc.stdlib cimport malloc - - -cdef class OBIDMS_column_qual(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef const uint8_t* value - cdef int value_length - cdef object result - cdef int i - value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, &value_length) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIQual_int_NA : - result = None - else : - result = [] - for i in range(value_length) : - result.append(value[i]) - return result - - cpdef object get_str_line(self, index_t line_nb): - cdef char* value - cdef object result - cdef int i - value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIQual_char_NA : - result = None - else : - result = bytes2str(value) - free(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - cdef uint8_t* value_b - cdef int value_length - if value is None : - if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0: - raise Exception("Problem setting a value in a column") - else : - value_length = len(value) - value_b = malloc(value_length * sizeof(uint8_t)) - for i in range(value_length) : - value_b[i] = value[i] - if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b, value_length) < 0: - raise Exception("Problem setting a value in a column") - free(value_b) - - cpdef set_str_line(self, index_t line_nb, object value): - cdef bytes value_b - if value is None : - if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_char_NA) < 0: - raise Exception("Problem setting a value in a column") - else : - if type(value) == str: - value_b = str2bytes(value) - else : - value_b = value - if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef const uint8_t* value - cdef int value_length - cdef object result - cdef int i - value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), &value_length) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIQual_int_NA : - result = None - else : - result = [] - for i in range(value_length) : - result.append(value[i]) - return result - - cpdef object get_str_item(self, index_t line_nb, str element_name): - cdef char* value - cdef object result - value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIQual_char_NA : - result = None - else : - result = bytes2str(value) - free(value) - return result - - cpdef object get_line(self, index_t line_nb) : - cdef const uint8_t* value - cdef int value_length - cdef object value_in_result - cdef dict result - cdef index_t i - cdef int j - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i, &value_length) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIQual_int_NA : - value_in_result = None - else : - value_in_result = [] - for j in range(value_length) : - value_in_result.append(value[j]) - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef object get_str_line(self, index_t line_nb) : - cdef char* value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIQual_char_NA : - value_in_result = None - else : - 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 - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - cdef uint8_t* value_b - cdef int value_length - if value is None : - if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0: - raise Exception("Problem setting a value in a column") - else : - value_length = len(value) - value_b = malloc(value_length * sizeof(uint8_t)) - for i in range(value_length) : - value_b[i] = value[i] - if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0: - raise Exception("Problem setting a value in a column") - free(value_b) - - cpdef set_str_item(self, index_t line_nb, str element_name, object value): - if value is None : - if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0: - raise Exception("Problem setting a value in a column") - else : - if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0: - raise Exception("Problem setting a value in a column") diff --git a/python/obitools3/obidms/_obidmscolumn_seq.cfiles b/python/obitools3/obidms/_obidmscolumn_seq.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_seq.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_seq.pxd b/python/obitools3/obidms/_obidmscolumn_seq.pxd deleted file mode 100644 index 5319b38..0000000 --- a/python/obitools3/obidms/_obidmscolumn_seq.pxd +++ /dev/null @@ -1,15 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIView, OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_seq(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - - -cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_seq.pyx b/python/obitools3/obidms/_obidmscolumn_seq.pyx deleted file mode 100644 index 77c8335..0000000 --- a/python/obitools3/obidms/_obidmscolumn_seq.pyx +++ /dev/null @@ -1,108 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \ - obi_get_seq_with_elt_idx_and_col_p_in_view, \ - obi_set_seq_with_elt_name_and_col_p_in_view, \ - obi_set_seq_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBISeq_NA, const_char_p - -from ._obidms cimport OBIView - -from obitools3.utils cimport str2bytes, bytes2str - -from libc.stdlib cimport free - - -cdef class OBIDMS_column_seq(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef char* value - cdef object result - value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBISeq_NA : - result = None - else : - try: - result = value - finally: - free(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - cdef bytes value_b - - if value is None : - value_b = OBISeq_NA - elif isinstance(value, bytes) : - value_b = value - elif isinstance(value, str) : - value_b = str2bytes(value) - else: - raise TypeError('Sequence value must be of type Bytes, Str or None') - - if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef char* value - cdef object result - value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBISeq_NA : - result = None - else : - try: - result = value - finally: - free(value) - return result - - - cpdef object get_line(self, index_t line_nb) : - cdef char* value - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBISeq_NA : - value_in_result = None - else : - try: - value_in_result = value - finally: - free(value) - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - cdef bytes value_b - - if value is None : - value_b = OBISeq_NA - elif isinstance(value, bytes) : - value_b = value - elif isinstance(value, str) : - value_b = str2bytes(value) - else: - raise TypeError('Sequence value must be of type Bytes, Str or None') - - if obi_set_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0: - raise Exception("Problem setting a value in a column") - diff --git a/python/obitools3/obidms/_obidmscolumn_str.cfiles b/python/obitools3/obidms/_obidmscolumn_str.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obidmscolumn_str.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obidmscolumn_str.pxd b/python/obitools3/obidms/_obidmscolumn_str.pxd deleted file mode 100644 index 7c813d0..0000000 --- a/python/obitools3/obidms/_obidmscolumn_str.pxd +++ /dev/null @@ -1,14 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t -from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts - - -cdef class OBIDMS_column_str(OBIDMS_column): - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - -cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts): - cpdef object get_item(self, index_t line_nb, str element_name) - cpdef object get_line(self, index_t line_nb) - cpdef set_item(self, index_t line_nb, str element_name, object value) diff --git a/python/obitools3/obidms/_obidmscolumn_str.pyx b/python/obitools3/obidms/_obidmscolumn_str.pyx deleted file mode 100644 index 1b93ff9..0000000 --- a/python/obitools3/obidms/_obidmscolumn_str.pyx +++ /dev/null @@ -1,84 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \ - obi_get_str_with_elt_idx_and_col_p_in_view, \ - obi_set_str_with_elt_name_and_col_p_in_view, \ - obi_set_str_with_elt_idx_and_col_p_in_view -from .capi.obierrno cimport obi_errno -from .capi.obitypes cimport OBIStr_NA, const_char_p - -from obitools3.utils cimport str2bytes, bytes2str - - -cdef class OBIDMS_column_str(OBIDMS_column): - - cpdef object get_line(self, index_t line_nb): - cdef const_char_p value - cdef object result - value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIStr_NA : - result = None - else : - result = bytes2str(value) - # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIStr_NA) < 0: - raise Exception("Problem setting a value in a column") - else : - if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)) < 0: - raise Exception("Problem setting a value in a column") - - -cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts): - - cpdef object get_item(self, index_t line_nb, str element_name): - cdef const_char_p value - cdef object result - value = obi_get_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name)) - if obi_errno > 0 : - raise IndexError(line_nb, element_name) - if value == OBIStr_NA : - result = None - else : - result = bytes2str(value) - # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. - return result - - cpdef object get_line(self, index_t line_nb) : - cdef const_char_p value # @DuplicatedSignature - cdef object value_in_result - cdef dict result - cdef index_t i - cdef bint all_NA - result = {} - all_NA = True - for i in range(self.nb_elements_per_line) : - value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIStr_NA : - value_in_result = None - else : - value_in_result = bytes2str(value) - # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. - result[self.elements_names[i]] = value_in_result - if all_NA and (value_in_result is not None) : - all_NA = False - if all_NA : - result = None - return result - - cpdef set_item(self, index_t line_nb, str element_name, object value): - cdef bytes value_b - if value is None : - value_b = OBIStr_NA - else : - value_b = str2bytes(value) - if obi_set_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0: - raise Exception("Problem setting a value in a column") - diff --git a/python/obitools3/obidms/_obiseq.cfiles b/python/obitools3/obidms/_obiseq.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obiseq.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obiseq.pxd b/python/obitools3/obidms/_obiseq.pxd deleted file mode 100644 index 62ecc5e..0000000 --- a/python/obitools3/obidms/_obiseq.pxd +++ /dev/null @@ -1,21 +0,0 @@ -#cython: language_level=3 - -from ._obiview cimport OBIView_line - - -cdef class OBI_Seq(dict) : - cdef str _id - cdef object _seq - cdef str _definition - - -cdef class OBI_Nuc_Seq(OBI_Seq) : - cdef object _quality - cpdef object get_str_quality(self) - - #cpdef object reverse_complement(self) - -cdef class OBI_Nuc_Seq_Stored(OBIView_line) : - cpdef object get_str_quality(self) - - #cpdef object reverse_complement(self) diff --git a/python/obitools3/obidms/_obiseq.pyx b/python/obitools3/obidms/_obiseq.pyx deleted file mode 100644 index 6be66e4..0000000 --- a/python/obitools3/obidms/_obiseq.pyx +++ /dev/null @@ -1,187 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \ - ID_COLUMN, \ - DEFINITION_COLUMN, \ - QUALITY_COLUMN - - -cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN) -cdef str __str__DEFINITION_COLUMN__ = bytes2str(DEFINITION_COLUMN) -cdef str __str__QUALITY_COLUMN__ = bytes2str(QUALITY_COLUMN) -cdef str __str__NUC_SEQUENCE_COLUMN__ = bytes2str(NUC_SEQUENCE_COLUMN) - - -cdef class OBI_Seq(dict) : - - def __init__(self, str id, - object seq, - str definition=None, - dict tags=None) : - - if tags is not None: - self.update(tags) - - self._id = id - self._seq = seq - - if definition is not None : - self._definition = definition - else: - self._definition = None - - - - def __getitem__(self,str key): - if key == __str__ID_COLUMN__: - return self._id - elif key == __str__DEFINITION_COLUMN__: - return self._definition - else: - return dict.__getitem__(self,key) - - def __setitem__(self,str key,object value): - if key == __str__ID_COLUMN__: - self._id=value - elif key == __str__DEFINITION_COLUMN__: - self._definition=value - else: - dict.__setitem__(self,key,value) - - # sequence id property getter and setter - @property - def id(self): # @ReservedAssignment - return self._id - @id.setter - def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature - self._id = new_id - - # sequence property getter and setter - @property - def seq(self): - return self._seq - @seq.setter - def seq(self, object new_seq): # @DuplicatedSignature - self._seq = new_seq - # self["SEQ"] = new_seq # TODO discuss - - # sequence definition property getter and setter - @property - def definition(self): - return self._definition - @definition.setter - def definition(self, object new_definition): # @DuplicatedSignature - self._definition = new_definition - - -cdef class OBI_Nuc_Seq(OBI_Seq) : - - def __init__(self, str id, - object seq, - str quality=None, - str definition=None, - dict tags=None) : - OBI_Seq.__init__(self,id,seq,tags) - if quality is not None: - self._quality=quality - else: - self._quality=None - - - - def __getitem__(self,str key): - if key == __str__NUC_SEQUENCE_COLUMN__: - return self._seq - elif key == __str__QUALITY_COLUMN__: - return self._quality - else: - return OBI_Seq.__getitem__(self,key) - - def __setitem__(self,str key, object value): - if key == __str__NUC_SEQUENCE_COLUMN__: - self._seq = value - elif key == __str__QUALITY_COLUMN__: - self._quality=value - else: - OBI_Seq.__setitem__(self,key,value) - - - - cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties - return self._quality - - # nuc sequence property getter and setter - @property - def seq(self): - return self._seq - @seq.setter - def seq(self, object new_seq): # @DuplicatedSignature - self._seq = new_seq -# self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq - - # sequence quality property getter and setter - @property - def quality(self): - return self._quality - @quality.setter - def quality(self, object new_quality): # @DuplicatedSignature - self._quality = new_quality -# self[bytes2str(QUALITY_COLUMN)] = new_quality - -# cpdef str reverse_complement(self) : TODO in C ? -# pass - - -cdef class OBI_Nuc_Seq_Stored(OBIView_line) : - - # TODO store the str version of column name macros? - - # sequence id property getter and setter - @property - def id(self): # @ReservedAssignment @DuplicatedSignature - return self[__str__ID_COLUMN__] - - @id.setter - def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature - self[__str__ID_COLUMN__] = new_id - - # sequence definition property getter and setter - @property - def definition(self): - return self[__str__DEFINITION_COLUMN__] - - @definition.setter - def definition(self, str new_def): # @DuplicatedSignature - self[__str__DEFINITION_COLUMN__] = new_def - - # nuc_seq property getter and setter - @property - def nuc_seq(self): - return self[__str__NUC_SEQUENCE_COLUMN__] - - @nuc_seq.setter - def nuc_seq(self, object new_seq): # @DuplicatedSignature - self[__str__NUC_SEQUENCE_COLUMN__] = new_seq - - # quality property getter and setter - @property - def quality(self): - return self[__str__QUALITY_COLUMN__] - - @quality.setter - def quality(self, object new_qual): # @DuplicatedSignature - if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists - self[__str__QUALITY_COLUMN__] = new_qual - else : # Quality is in str form - (((self._view).columns)[__str__QUALITY_COLUMN__]).set_str_line(self._index, new_qual) - - cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties - return ((self._view).columns)[__str__QUALITY_COLUMN__].get_str_line(self._index) - -# cpdef str reverse_complement(self) : TODO in C ? -# pass - - # TODO static method to import OBI_Nuc_Seq to OBI_Nuc_Seq_Stored ? - diff --git a/python/obitools3/obidms/_obitaxo.cfiles b/python/obitools3/obidms/_obitaxo.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/obidms/_obitaxo.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../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/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.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_blob.c -../../../src/obidmscolumn_blob.h -../../../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_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/obidms/_obitaxo.pxd b/python/obitools3/obidms/_obitaxo.pxd deleted file mode 100644 index 671d5e1..0000000 --- a/python/obitools3/obidms/_obitaxo.pxd +++ /dev/null @@ -1,21 +0,0 @@ -#cython: language_level=3 - -from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p -from ._obidms cimport OBIDMS - - -cdef class OBI_Taxonomy : - - cdef str _name - cdef OBIDMS_taxonomy_p _pointer - cdef OBIDMS _dms - - cpdef write(self, str prefix) - cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*) - cpdef close(self) - - -cdef class OBI_Taxon : - - cdef ecotx_t* _pointer - cdef OBI_Taxonomy _tax diff --git a/python/obitools3/obidms/_obitaxo.pyx b/python/obitools3/obidms/_obitaxo.pyx deleted file mode 100644 index 3aae515..0000000 --- a/python/obitools3/obidms/_obitaxo.pyx +++ /dev/null @@ -1,141 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obitaxonomy cimport obi_read_taxonomy, \ - obi_read_taxdump, \ - obi_write_taxonomy, \ - obi_close_taxonomy, \ - obi_taxo_get_taxon_with_taxid, \ - obi_taxo_add_local_taxon, \ - obi_taxo_add_preferred_name_with_taxon, \ - ecotx_t - -from ._obidms cimport OBIDMS - -from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer -from logging import raiseExceptions - - -cdef class OBI_Taxonomy : - - # TODO function to import taxonomy? - - def __init__(self, OBIDMS dms, str name, bint taxdump=False) : - - self._dms = dms - self._name = name - if taxdump : - self._pointer = obi_read_taxdump(str2bytes(name)) - else : - self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True) # TODO discuss - # TODO if not found in DMS, try to import? - - - def __getitem__(self, object ref): - - cdef ecotx_t* taxon_p - cdef object taxon_capsule - - if type(ref) == int : - taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref) - if taxon_p == NULL : - raise Exception("Taxon not found") - taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL) - return OBI_Taxon(taxon_capsule, self) - else : - raise Exception("Not implemented") - - - def __iter__(self): - - cdef ecotx_t* taxa - cdef ecotx_t* taxon_p - cdef object taxon_capsule - cdef int t - - taxa = self._pointer.taxa.taxon - - # Yield each taxid - for t in range(self._pointer.taxa.count): - taxon_p = (taxa+t) - taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL) - yield OBI_Taxon(taxon_capsule, self) - - - cpdef write(self, str prefix) : - if obi_write_taxonomy(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0 : - raise Exception("Error writing the taxonomy to binary files") - - - cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) : - cdef int taxid - taxid = obi_taxo_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid) - if taxid < 0 : - raise Exception("Error adding a new taxon to the taxonomy") - else : - return taxid - - - cpdef close(self) : - if (obi_close_taxonomy(self._pointer) < 0) : - raise Exception("Error closing the taxonomy") - - - -cdef class OBI_Taxon : # TODO dict subclass? - - def __init__(self, object taxon_capsule, OBI_Taxonomy tax) : - self._pointer = PyCapsule_GetPointer(taxon_capsule, NULL) - if self._pointer == NULL : - raise Exception("Error reading a taxon (NULL pointer)") - self._tax = tax - - # name property getter - @property - def name(self): - return bytes2str(self._pointer.name) - - # taxid property getter - @property - def taxid(self): - return self._pointer.taxid - - # rank property getter - @property - def rank(self): - return self._pointer.rank - - # farest property getter - @property - def farest(self): - return self._pointer.farest - - # parent property getter - @property - def parent(self): - cdef object parent_capsule - parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL) - return OBI_Taxon(parent_capsule, self._tax) - - # preferred name property getter and setter - @property - def preferred_name(self): - if self._pointer.preferred_name != NULL : - return bytes2str(self._pointer.preferred_name) - @preferred_name.setter - def preferred_name(self, str new_preferred_name) : # @DuplicatedSignature - if (obi_taxo_add_preferred_name_with_taxon(self._tax._pointer, self._pointer, str2bytes(new_preferred_name)) < 0) : - raise Exception("Error adding a new preferred name to a taxon") - - def __repr__(self): - d = {} - d['taxid'] = self.taxid - d['name'] = self.name - d['preferred name'] = self.preferred_name - d['parent'] = self.parent.taxid - d['farest'] = self.farest - return str(d) - - - diff --git a/python/obitools3/obidms/_obiview.pxd b/python/obitools3/obidms/_obiview.pxd deleted file mode 100644 index 76f3969..0000000 --- a/python/obitools3/obidms/_obiview.pxd +++ /dev/null @@ -1,70 +0,0 @@ -#cython: language_level=3 - -from ._obidms cimport OBIDMS - -from .capi.obiview cimport Obiview_p -from .capi.obitypes cimport obiversion_t, index_t - - -cdef class OBIView: - - cdef Obiview_p _pointer - cdef dict _columns - - cdef __init_columns__(self) - - cpdef OBIView clone(self, - str view_name, - str comments=*) - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=*) - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name) - - cpdef delete_column(self, str column_name) - - cpdef add_column(self, - str column_name, - obiversion_t version_number=*, - str alias=*, - str type=*, - index_t nb_lines=*, - index_t nb_elements_per_line=*, - list elements_names=*, - str indexer_name=*, - str associated_column_name=*, - obiversion_t associated_column_version=*, - str comments=*, - bint create=* - ) - - cpdef change_column_alias(self, str current_alias, str new_alias) - - cpdef update_column_pointers(self) - - cpdef OBIView_line_selection new_selection(self, - list lines=*) - - -cdef class OBIView_line : - - cdef index_t _index - cdef OBIView _view - - -cdef class OBIView_line_selection(list): - - cdef OBIView _view - cdef str _view_name - - cdef index_t* __build_binary_list__(self) - - cpdef OBIView materialize(self, - str view_name, - str comments=*) - diff --git a/python/obitools3/obidms/_obiview.pyx b/python/obitools3/obidms/_obiview.pyx deleted file mode 100644 index 8976ea9..0000000 --- a/python/obitools3/obidms/_obiview.pyx +++ /dev/null @@ -1,426 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obitypes cimport OBI_INT, \ - OBI_FLOAT, \ - OBI_BOOL, \ - OBI_CHAR, \ - OBI_QUAL, \ - OBI_STR, \ - OBI_SEQ, \ - only_ATGC - -from .capi.obiview cimport Obiview_p, \ - obi_new_view, \ - obi_open_view, \ - obi_view_delete_column, \ - obi_view_add_column, \ - obi_view_create_column_alias, \ - obi_view_get_column, \ - obi_view_get_pointer_on_column_in_view, \ - obi_save_and_close_view - -from .capi.obidmscolumn cimport OBIDMS_column_p - -from ._obidms cimport OBIDMS, \ - OBIDMS_column - -from libc.stdlib cimport malloc - - -cdef class OBIView : - - def __init__(self,int __internalCall__): - if __internalCall__!=987654: - raise RuntimeError('OBIView constructor cannot be called directly') - self._pointer = NULL - self._columns = {} - - - cdef __init_columns__(self): - cdef size_t i - cdef str col_alias - cdef OBIDMS_column_p column_p - cdef Obiview_p pointer = self._pointer - - self._columns = {} - - for i in range(pointer.infos.column_count) : - col_alias = bytes2str(pointer.infos.column_references[i].alias) - column_p = (pointer.columns)[i] - subclass = OBIDMS_column.get_subclass_type(column_p) - self._columns[col_alias] = subclass(self, col_alias) - - - cpdef OBIView clone(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView(987654) - - view._pointer = obi_new_view(self._pointer.dms, - str2bytes(view_name), - self._pointer, - NULL, - str2bytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=""): - - cdef OBIView view = OBIView(987654) # @DuplicatedSignature - - view._pointer = obi_new_view(dms._pointer, - str2bytes(view_name), - NULL, - NULL, - str2bytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot create view %s" % view_name) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name): - - cdef OBIView view = OBIView(987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - str2bytes(view_name)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot open view %s" % view_name) - - view.__init_columns__() - - return view - - - def __dealloc__(self): - if (obi_save_and_close_view(self._pointer) < 0) : - raise Exception("Problem closing a view") - - - def __repr__(self) : - cdef str s - s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n" - for column_name in self._columns : - s = s + repr(self._columns[column_name]) + '\n' - return s - - - cpdef delete_column(self, str column_name) : - cdef str column_n - if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 : - raise Exception("Problem deleting a column from a view") - # Update the dictionary of column objects: - (self._columns).pop(column_name) - self.update_column_pointers() - - - cpdef add_column(self, - str column_name, - obiversion_t version_number=-1, - str alias='', - str type='', - index_t nb_lines=0, - index_t nb_elements_per_line=1, - list elements_names=None, - str indexer_name="", - str associated_column_name="", - obiversion_t associated_column_version=-1, - str comments="", - bint create=True - ) : - - cdef bytes column_name_b - cdef bytes elements_names_b - cdef object subclass - cdef OBIDMS_column_p column_p - - column_name_b = str2bytes(column_name) - if alias == '' : - alias = column_name - alias_b = column_name_b - else : - alias_b = str2bytes(alias) - - if elements_names is None : - elements_names_b = str2bytes("") - else : - elements_names_b = str2bytes(';'.join(elements_names)) - - if type : # TODO make C function that does that - if type == 'OBI_INT' : - data_type = OBI_INT - elif type == 'OBI_FLOAT' : - data_type = OBI_FLOAT - elif type == 'OBI_BOOL' : - data_type = OBI_BOOL - elif type == 'OBI_CHAR' : - data_type = OBI_CHAR - elif type == 'OBI_QUAL' : - data_type = OBI_QUAL - elif type == 'OBI_STR' : - data_type = OBI_STR - elif type == 'OBI_SEQ' : - data_type = OBI_SEQ - else : - raise Exception("Invalid provided data type") - - if (obi_view_add_column(self._pointer, column_name_b, version_number, alias_b, - data_type, nb_lines, nb_elements_per_line, - elements_names_b, str2bytes(indexer_name), - str2bytes(associated_column_name), associated_column_version, - str2bytes(comments), create) < 0) : - raise Exception("Problem adding a column in a view") - - # Get the column pointer - column_p = obi_view_get_column(self._pointer, alias_b) - - # Open and store the subclass - subclass = OBIDMS_column.get_subclass_type(column_p) - (self._columns)[alias] = subclass(self, alias) - - - cpdef change_column_alias(self, str current_alias, str new_alias): - cdef OBIDMS_column column - if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) : - raise Exception("Problem changing a column alias") - # Update the dictionaries of column objects - self._columns[new_alias] = self._columns[current_alias] - column = self._columns[new_alias] - column._alias = new_alias - (self._columns).pop(current_alias) - - - cpdef update_column_pointers(self): - cdef str column_n - cdef OBIDMS_column column - for column_n in self._columns : - column = self._columns[column_n] - column._pointer = obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n)) - - - cpdef OBIView_line_selection new_selection(self,list lines=None): - return OBIView_line_selection(self,lines) - - - def __iter__(self): - # Iteration on each line of all columns - - # Declarations - cdef index_t line_nb - cdef OBIView_line line - - # Yield each line - for line_nb in range(self.line_count) : - line = self[line_nb] - yield line - - - def __getitem__(self, object item) : - if type(item) == str : - return (self._columns)[item] - elif type(item) == int : - return OBIView_line(self, item) - - - def __contains__(self, str column_name): - return (column_name in self._columns) - - - def __len__(self): - return(self.line_count) - - - def __str__(self) : - cdef OBIView_line line - cdef str to_print - to_print = "" - for line in self : - to_print = to_print + str(line) + "\n" - return to_print - - - # line_count property getter - @property - def line_count(self): - return self._pointer.infos.line_count - - # name property getter - @property - def name(self): - return bytes2str(self._pointer.infos.name) - - # view type property getter - @property - def type(self): # @ReservedAssignment - return bytes2str(self._pointer.infos.view_type) - - # columns property getter - @property - def columns(self): - return self._columns - - # comments property getter - @property - def comments(self): - return bytes2str(self._pointer.infos.comments) - # TODO setter that concatenates new comments? - - -cdef class OBIView_line : - - def __init__(self, OBIView view, index_t line_nb) : - self._index = line_nb - self._view = view - - - def __getitem__(self, str column_name) : - return ((self._view)._columns)[column_name][self._index] - - - def __setitem__(self, str column_name, object value): - # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get) - # TODO OBI_QUAL ? - cdef type value_type - cdef str value_obitype - cdef bytes value_b - - if column_name not in self._view : - if value == None : - raise Exception("Trying to create a column from a None value (can't guess type)") - value_type = type(value) - if value_type == int : - value_obitype = 'OBI_INT' - elif value_type == float : - value_obitype = 'OBI_FLOAT' - elif value_type == bool : - value_obitype = 'OBI_BOOL' - elif value_type == str or value_type == bytes : - if value_type == str : - value_b = str2bytes(value) - else : - value_b = value - if only_ATGC(value_b) : # TODO detect IUPAC - value_obitype = 'OBI_SEQ' - elif len(value) == 1 : - value_obitype = 'OBI_CHAR' - elif (len(value) > 1) : - value_obitype = 'OBI_STR' - else : - raise Exception("Could not guess the type of a value to create a new column") - self._view.add_column(column_name, type=value_obitype) - - (((self._view)._columns)[column_name]).set_line(self._index, value) - - - def __iter__(self): - for column_name in ((self._view)._columns) : - yield column_name - - - def __contains__(self, str column_name): - return (column_name in self._view._columns) - - - def __repr__(self): - cdef dict line - cdef str column_name - line = {} - for column_name in self._view._columns : - line[column_name] = self[column_name] - return str(line) - - -cdef class OBIView_line_selection(list): - - def __init__(self, OBIView view, lines=None) : - if view._pointer == NULL: - raise Exception("Error: trying to create a line selection with an invalidated view") - self._view = view - self._view_name = view.name - - if lines is not None: - self.extend(lines) - - - def extend(self, iterable): - cdef index_t i - cdef index_t max_i = self._view.line_count - - for i in iterable: - if i > max_i: - raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" % - (i, - max_i, - self._view_name) - ) - list.append(self,i) - - - def append(self, index_t idx) : - if idx >= self._view.line_count : - raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" % - (idx, - self._view.line_count, - self._view_name) - ) - list.append(self,idx) - - - cdef index_t* __build_binary_list__(self): - cdef index_t* line_selection_p = NULL - cdef int i - cdef size_t len_selection = len(self) - - line_selection_p = malloc((len_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array - for i in range(len_selection) : - line_selection_p[i] = self[i] - line_selection_p[len_selection] = -1 # flagging the end of the array - - return line_selection_p - - - cpdef OBIView materialize(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView(987654) - - view._pointer = obi_new_view(self._view._pointer.dms, - str2bytes(view_name), - self._view._pointer, - self.__build_binary_list__(), - str2bytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error: Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__() - - return view - - diff --git a/python/obitools3/obidms/_obiview_nuc_seq.pxd b/python/obitools3/obidms/_obiview_nuc_seq.pxd deleted file mode 100644 index 658827c..0000000 --- a/python/obitools3/obidms/_obiview_nuc_seq.pxd +++ /dev/null @@ -1,29 +0,0 @@ -#cython: language_level=3 - -from ._obidms cimport OBIDMS -from ._obiview cimport OBIView, OBIView_line_selection - - -cdef class OBIView_NUC_SEQS(OBIView): - - cpdef OBIView clone(self, - str new_view_name, - str comments=*) - - cpdef OBIView_line_selection new_selection(self, list lines=*) - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=*) - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name) - - -cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection): - - cpdef OBIView materialize(self, - str view_name, - str comments=*) diff --git a/python/obitools3/obidms/_obiview_nuc_seq.pyx b/python/obitools3/obidms/_obiview_nuc_seq.pyx deleted file mode 100644 index ccef2f4..0000000 --- a/python/obitools3/obidms/_obiview_nuc_seq.pyx +++ /dev/null @@ -1,113 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t - -from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored - -from .capi.obiview cimport obi_new_view_nuc_seqs, \ - obi_open_view - -from obitools3.utils cimport str2bytes - - -cdef class OBIView_NUC_SEQS(OBIView): - - cpdef OBIView clone(self, - str new_view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) - - view._pointer = obi_new_view_nuc_seqs(self._pointer.dms, - str2bytes(new_view_name), - self._pointer, - NULL, - str2bytes(comments), - False) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), new_view_name)) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature - - view._pointer = obi_new_view_nuc_seqs(dms._pointer, - str2bytes(view_name), - NULL, - NULL, - str2bytes(comments), - False) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot create view %s" % view_name) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name): - - cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - str2bytes(view_name)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot open view %s" % view_name) - - view.__init_columns__() - - return view - - - cpdef OBIView_line_selection new_selection(self, list lines=None): - return OBIView_NUC_SEQS_line_selection(self, lines) - - - def __getitem__(self, object item) : - if type(item) == str : - return (self._columns)[item] - elif type(item) == int : - return OBI_Nuc_Seq_Stored(self, item) - - - def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) : - for key in sequence_obj : - self[line_idx][key] = sequence_obj[key] - - -cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection): - - cpdef OBIView materialize(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) - - view._pointer = obi_new_view_nuc_seqs(self._view._pointer.dms, - str2bytes(view_name), - self._view._pointer, - self.__build_binary_list__(), - str2bytes(comments), - False) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), view_name)) - - view.__init_columns__() - - return view diff --git a/python/obitools3/obidms/_obiview_nuc_seq_qual.pxd b/python/obitools3/obidms/_obiview_nuc_seq_qual.pxd deleted file mode 100644 index 69be520..0000000 --- a/python/obitools3/obidms/_obiview_nuc_seq_qual.pxd +++ /dev/null @@ -1,28 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t - -from ._obidms cimport OBIDMS -from ._obiview cimport OBIView -from ._obiview_nuc_seq cimport OBIView_NUC_SEQS, OBIView_NUC_SEQS_line_selection - - -cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): - cpdef OBIView clone(self, - str view_name, - str comments=*) - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=*) - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name) - - -cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): - cpdef OBIView materialize(self, - str view_name, - str comments=*) diff --git a/python/obitools3/obidms/_obiview_nuc_seq_qual.pyx b/python/obitools3/obidms/_obiview_nuc_seq_qual.pyx deleted file mode 100644 index fbe7ef4..0000000 --- a/python/obitools3/obidms/_obiview_nuc_seq_qual.pyx +++ /dev/null @@ -1,97 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t - -from .capi.obiview cimport obi_new_view_nuc_seqs, \ - obi_open_view - -from obitools3.utils cimport bytes2str, str2bytes - - -cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): - - cpdef OBIView clone(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) - - view._pointer = obi_new_view_nuc_seqs(self._pointer.dms, - str2bytes(view_name), - self._pointer, - NULL, - str2bytes(comments), - True) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), view_name)) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView new(OBIDMS dms, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature - - view._pointer = obi_new_view_nuc_seqs(dms._pointer, - str2bytes(view_name), - NULL, - NULL, - str2bytes(comments), - True) - - if view._pointer == NULL : - raise RuntimeError("Error: Cannot create view %s" % view_name) - - view.__init_columns__() - - return view - - - @staticmethod - cdef OBIView open(OBIDMS dms, - str view_name): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - str2bytes(view_name)) - - if view._pointer == NULL : - raise RuntimeError("Error: Cannot open view %s" % view_name) - - view.__init_columns__() - - return view - - -cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): - - cpdef OBIView materialize(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) - - view._pointer = obi_new_view_nuc_seqs(self._view._pointer.dms, - str2bytes(view_name), - self._view._pointer, - self.__build_binary_list__(), - str2bytes(comments), - True) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__() - - return view diff --git a/python/obitools3/obidms/capi/__init__.py b/python/obitools3/obidms/capi/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/python/obitools3/obidms/capi/obialign.cfiles b/python/obitools3/obidms/capi/obialign.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obialign.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obialign.pxd b/python/obitools3/obidms/capi/obialign.pxd deleted file mode 100644 index c2280b9..0000000 --- a/python/obitools3/obidms/capi/obialign.pxd +++ /dev/null @@ -1,41 +0,0 @@ -#cython: language_level=3 - -from obitools3.obidms.capi.obidms cimport OBIDMS_p -from obitools3.obidms.capi.obitypes cimport const_char_p - - -cdef extern from "obi_align.h" nogil: - - int obi_lcs_align_one_column(OBIDMS_p dms, - const_char_p seq_view_name, - const_char_p seq_column_name, - const_char_p seq_elt_name, - const_char_p id_column_name, - const_char_p output_view_name, - const_char_p output_view_comments, - bint print_seq, - bint print_count, - double threshold, - bint normalize, - int reference, - bint similarity_mode, - int thread_count) - - - int obi_lcs_align_two_columns(OBIDMS_p dms, - const_char_p seq1_view_name, - const_char_p seq2_view_name, - const_char_p seq1_column_name, - const_char_p seq2_column_name, - const_char_p seq1_elt_name, - const_char_p seq2_elt_name, - const_char_p id1_column_name, - const_char_p id2_column_name, - const_char_p output_view_name, - const_char_p output_view_comments, - bint print_seq, - bint print_count, - double threshold, - bint normalize, - int reference, - bint similarity_mode); diff --git a/python/obitools3/obidms/capi/obidms.cfiles b/python/obitools3/obidms/capi/obidms.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obidms.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obidms.pxd b/python/obitools3/obidms/capi/obidms.pxd deleted file mode 100644 index 9bb116f..0000000 --- a/python/obitools3/obidms/capi/obidms.pxd +++ /dev/null @@ -1,12 +0,0 @@ -#cython: language_level=3 - -from .obitypes cimport const_char_p - -cdef extern from "obidms.h" nogil: - struct OBIDMS_t: - const_char_p dms_name - - ctypedef OBIDMS_t* OBIDMS_p - - OBIDMS_p obi_dms(const_char_p dms_name) - int obi_close_dms(OBIDMS_p dms) diff --git a/python/obitools3/obidms/capi/obidmscolumn.cfiles b/python/obitools3/obidms/capi/obidmscolumn.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obidmscolumn.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obidmscolumn.pxd b/python/obitools3/obidms/capi/obidmscolumn.pxd deleted file mode 100644 index 9589421..0000000 --- a/python/obitools3/obidms/capi/obidmscolumn.pxd +++ /dev/null @@ -1,227 +0,0 @@ -#cython: language_level=3 - -from ..capi.obidms cimport OBIDMS_p -from ..capi.obitypes cimport const_char_p, \ - OBIType_t, \ - obiversion_t, \ - obiint_t, \ - obibool_t, \ - obichar_t, \ - obifloat_t, \ - index_t, \ - time_t - -from libc.stdint cimport uint8_t - - -cdef extern from "obidmscolumn.h" nogil: - - struct Column_reference_t : - const_char_p column_name - obiversion_t version - - ctypedef Column_reference_t* Column_reference_p - - struct OBIDMS_column_header_t: - size_t header_size - size_t data_size - index_t line_count - index_t lines_used - index_t nb_elements_per_line - const_char_p elements_names - OBIType_t returned_data_type - OBIType_t stored_data_type - time_t creation_date - obiversion_t version - obiversion_t cloned_from - const_char_p name - const_char_p indexer_name - Column_reference_t associated_column - const_char_p comments - - ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p - - struct OBIDMS_column_t: - OBIDMS_p dms - OBIDMS_column_header_p header - bint writable - - ctypedef OBIDMS_column_t* OBIDMS_column_p - - 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) - - OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, - const_char_p column_name, - obiversion_t version_number) - - int obi_close_header(OBIDMS_column_header_p header) - - char* obi_get_elements_names(OBIDMS_column_p column) - - -cdef extern from "obidmscolumn_int.h" nogil: - - int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - obiint_t value) - - int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - obiint_t value) - - obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name) - - obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx) - -cdef extern from "obidmscolumn_bool.h" nogil: - - int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - obibool_t value) - - int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - obibool_t value) - - obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name) - - obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx) - -cdef extern from "obidmscolumn_char.h" nogil: - - int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - obichar_t value) - - int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - obichar_t value) - - obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name) - - obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx) - -cdef extern from "obidmscolumn_float.h" nogil: - - int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - obifloat_t value) - - int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - obifloat_t value) - - obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, - 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) - -cdef extern from "obidmscolumn_str.h" nogil: - - int obi_column_set_obistr_with_elt_name(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(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(OBIDMS_column_p column, - 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, - index_t element_idx) - -cdef extern from "obidmscolumn_seq.h" nogil: - - int obi_column_set_obiseq_with_elt_name(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(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - const_char_p value) - - char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name) - - char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx) - - -cdef extern from "obidmscolumn_qual.h" nogil: - - int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - const_char_p value) - - int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - const_char_p value) - - int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - const uint8_t* value, - int value_length) - - int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - const uint8_t* value, - int value_length) - - char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name) - - char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx) - - const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, - index_t line_nb, - const_char_p element_name, - int* value_length) - - const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, - index_t line_nb, - index_t element_idx, - int* value_length) - diff --git a/python/obitools3/obidms/capi/obierrno.cfiles b/python/obitools3/obidms/capi/obierrno.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obierrno.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obierrno.pxd b/python/obitools3/obidms/capi/obierrno.pxd deleted file mode 100644 index eb8c4bb..0000000 --- a/python/obitools3/obidms/capi/obierrno.pxd +++ /dev/null @@ -1,5 +0,0 @@ -#cython: language_level=3 - - -cdef extern from "obierrno.h" nogil: - extern int obi_errno diff --git a/python/obitools3/obidms/capi/obitaxonomy.cfiles b/python/obitools3/obidms/capi/obitaxonomy.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obitaxonomy.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obitaxonomy.pxd b/python/obitools3/obidms/capi/obitaxonomy.pxd deleted file mode 100644 index d90693c..0000000 --- a/python/obitools3/obidms/capi/obitaxonomy.pxd +++ /dev/null @@ -1,65 +0,0 @@ -#cython: language_level=3 - -from .obitypes cimport const_char_p -from .obidms cimport OBIDMS_p -from libc.stdint cimport int32_t - - -cdef extern from "obidms_taxonomy.h" nogil: - - struct ecotxnode : - int32_t taxid - int32_t rank - int32_t farest - ecotxnode* parent - char* name - char* preferred_name - - ctypedef ecotxnode ecotx_t - - - struct ecotxidx_t : - int32_t count - int32_t max_taxid - int32_t buffer_size - ecotx_t* taxon - - - struct OBIDMS_taxonomy_t : -# ecorankidx_t* ranks -# econameidx_t* names - ecotxidx_t* taxa - - ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p - - - OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names) - - OBIDMS_taxonomy_p obi_read_taxdump(const_char_p taxdump) - - int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p tax_name) - - int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy) - - ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx) - - ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid) - - bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid) - - ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy) - - ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy) - - ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy) - - ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy) - - ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy) - - int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid) - - int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name) - - int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name) - diff --git a/python/obitools3/obidms/capi/obitypes.cfiles b/python/obitools3/obidms/capi/obitypes.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obitypes.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obitypes.pxd b/python/obitools3/obidms/capi/obitypes.pxd deleted file mode 100644 index d765629..0000000 --- a/python/obitools3/obidms/capi/obitypes.pxd +++ /dev/null @@ -1,55 +0,0 @@ -#cython: language_level=3 - - -from libc.stdint cimport int32_t, int64_t, uint8_t - -from posix.types cimport time_t - - -cdef extern from *: - ctypedef char* const_char_p "const char*" - - -cdef extern from "encode.h" nogil: - bint only_ATGC(const_char_p seq) - - -cdef extern from "obitypes.h" nogil: - - enum OBIType: - OBI_VOID, - OBI_INT, - OBI_FLOAT, - OBI_BOOL, - OBI_CHAR, - OBI_QUAL, - OBI_STR, - OBI_SEQ, - OBI_IDX - - - ctypedef OBIType OBIType_t - - enum OBIBool: - pass - - ctypedef OBIBool obibool_t - ctypedef int32_t obiint_t - ctypedef double obifloat_t - ctypedef char obichar_t - ctypedef int64_t index_t - - ctypedef int32_t obiversion_t - - extern obiint_t OBIInt_NA - extern index_t OBIIdx_NA - extern obifloat_t OBIFloat_NA - extern obichar_t OBIChar_NA - extern obibool_t OBIBool_NA - extern const_char_p OBISeq_NA - extern const_char_p OBIStr_NA - extern const_char_p OBIQual_char_NA - extern uint8_t* OBIQual_int_NA - - const_char_p name_data_type(int data_type) - diff --git a/python/obitools3/obidms/capi/obiutils.cfiles b/python/obitools3/obidms/capi/obiutils.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obiutils.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obiutils.pxd b/python/obitools3/obidms/capi/obiutils.pxd deleted file mode 100644 index 726ad0e..0000000 --- a/python/obitools3/obidms/capi/obiutils.pxd +++ /dev/null @@ -1,12 +0,0 @@ -#cython: language_level=3 - - -from posix.types cimport time_t - -from ..capi.obitypes cimport const_char_p - - -cdef extern from "utils.h" nogil: - - const_char_p obi_format_date(time_t date) - diff --git a/python/obitools3/obidms/capi/obiview.cfiles b/python/obitools3/obidms/capi/obiview.cfiles deleted file mode 100644 index 3bbdbcb..0000000 --- a/python/obitools3/obidms/capi/obiview.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../../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/hashtable.h -../../../../src/hashtable.c -../../../../src/murmurhash2.h -../../../../src/murmurhash2.c -../../../../src/obi_align.h -../../../../src/obi_align.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_blob.c -../../../../src/obidmscolumn_blob.h -../../../../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_idx.h -../../../../src/obidmscolumn_idx.c -../../../../src/obidmscolumn_int.c -../../../../src/obidmscolumn_int.h -../../../../src/obidmscolumn_qual.h -../../../../src/obidmscolumn_qual.c -../../../../src/obidmscolumn_seq.c -../../../../src/obidmscolumn_seq.h -../../../../src/obidmscolumn_str.c -../../../../src/obidmscolumn_str.h -../../../../src/obidmscolumn.h -../../../../src/obidmscolumn.c -../../../../src/obidmscolumndir.h -../../../../src/obidmscolumndir.c -../../../../src/obierrno.h -../../../../src/obierrno.c -../../../../src/obilittlebigman.h -../../../../src/obilittlebigman.c -../../../../src/obitypes.h -../../../../src/obitypes.c -../../../../src/obiview.h -../../../../src/obiview.c -../../../../src/sse_banded_LCS_alignment.h -../../../../src/sse_banded_LCS_alignment.c -../../../../src/uint8_indexer.h -../../../../src/uint8_indexer.c -../../../../src/upperband.h -../../../../src/upperband.c -../../../../src/utils.h -../../../../src/utils.c diff --git a/python/obitools3/obidms/capi/obiview.pxd b/python/obitools3/obidms/capi/obiview.pxd deleted file mode 100644 index 792441b..0000000 --- a/python/obitools3/obidms/capi/obiview.pxd +++ /dev/null @@ -1,294 +0,0 @@ -#cython: language_level=3 - -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 -from ..capi.obidmscolumn cimport OBIDMS_column_p, \ - Column_reference_t, \ - Column_reference_p - -from libc.stdint cimport uint8_t - - -cdef extern from "obiview.h" nogil: - - extern const_char_p VIEW_TYPE_NUC_SEQS - extern const_char_p NUC_SEQUENCE_COLUMN - extern const_char_p ID_COLUMN - extern const_char_p DEFINITION_COLUMN - extern const_char_p QUALITY_COLUMN - - - struct Alias_column_pair_t : - Column_reference_t column_refs - const_char_p alias - - ctypedef Alias_column_pair_t* Alias_column_pair_p - - - struct Obiview_infos_t : - time_t creation_date - const_char_p name - const_char_p created_from - const_char_p view_type - bint all_lines - Column_reference_t line_selection - index_t line_count - int column_count - Alias_column_pair_p column_references - const_char_p comments - - ctypedef Obiview_infos_t* Obiview_infos_p - - - struct Obiview_t : - Obiview_infos_p infos - OBIDMS_p dms - bint read_only - OBIDMS_column_p line_selection - OBIDMS_column_p columns - int nb_predicates - # TODO declarations for column dictionary and predicate function array? - - ctypedef Obiview_t* Obiview_p - - - Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments, bint quality_column) - - Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments) - - Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments) - - Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments, bint quality_column) - - Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished) - - int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos) - - Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name) - - int obi_view_add_column(Obiview_p view, - const_char_p column_name, - obiversion_t version_number, - const_char_p alias, - OBIType_t data_type, - index_t nb_lines, - index_t nb_elements_per_line, - char* elements_names, - const_char_p indexer_name, - const_char_p associated_column_name, - obiversion_t associated_column_version, - const_char_p comments, - bint create) - - int obi_view_delete_column(Obiview_p view, const_char_p column_name) - - OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name) - - OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name) - - int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias) - - int obi_save_and_close_view(Obiview_p view) - - - # OBI_INT - int obi_set_int_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - obiint_t value) - - int obi_set_int_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - obiint_t value) - - obiint_t obi_get_int_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - obiint_t obi_get_int_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - - # OBI_BOOL - int obi_set_bool_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - obibool_t value) - - int obi_set_bool_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - obibool_t value) - - obibool_t obi_get_bool_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - obibool_t obi_get_bool_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - - # OBI_CHAR - int obi_set_char_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - obichar_t value) - - int obi_set_char_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - obichar_t value) - - obichar_t obi_get_char_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - obichar_t obi_get_char_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - - # OBI_FLOAT - int obi_set_float_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - obifloat_t value) - - int obi_set_float_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - obifloat_t value) - - obifloat_t obi_get_float_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - obifloat_t obi_get_float_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - - # OBI_QUAL - int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - const char* value) - - int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - const uint8_t* value, - int value_length) - - char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - int* value_length) - - int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const char* element_name, - const char* value) - - int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const char* element_name, - const uint8_t* value, - int value_length) - - char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const char* element_name) - - const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const char* element_name, - int* value_length) - - - # OBI_STR - int obi_set_str_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - const_char_p value) - - int obi_set_str_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - const_char_p value) - - const_char_p obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - const_char_p obi_get_str_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) - - - # OBI_SEQ - int obi_set_seq_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name, - const_char_p value) - - int obi_set_seq_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx, - const_char_p value) - - char* obi_get_seq_with_elt_name_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - const_char_p element_name) - - char* obi_get_seq_with_elt_idx_and_col_p_in_view(Obiview_p view, - OBIDMS_column_p column_p, - index_t line_nb, - index_t element_idx) -