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Closes #34

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This commit is contained in:
Celine Mercier
2016-02-29 17:56:55 +01:00
parent e323d8e702
commit fc5a12bad7
6 changed files with 48 additions and 30 deletions
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3
python/obitools3/obidms/_obidms.pxd
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@ -43,6 +43,7 @@ cdef class OBIView:
cdef Obiview_p pointer cdef Obiview_p pointer
cdef str name cdef str name
cdef str comments
cdef dict columns cdef dict columns
cdef dict columns_pp # TODO this dict might be unnecessary cdef dict columns_pp # TODO this dict might be unnecessary
cdef OBIDMS dms cdef OBIDMS dms
@ -86,7 +87,7 @@ cdef class OBIDMS:
cpdef close(self) cpdef close(self)
cpdef OBIView open_view(self, str view_name) cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*) cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
cpdef dict read_view_infos(self, str view_name) cpdef dict read_view_infos(self, str view_name)
cpdef dict read_views(self) cpdef dict read_views(self)

24
python/obitools3/obidms/_obidms.pyx
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@ -231,7 +231,7 @@ cdef class OBIDMS_column_line :
cdef class OBIView : cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None): def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""):
cdef Obiview_p view = NULL cdef Obiview_p view = NULL
cdef int i cdef int i
@ -256,11 +256,11 @@ cdef class OBIView :
if new : if new :
if view_to_clone is not None : if view_to_clone is not None :
if type(view_to_clone) == str : if type(view_to_clone) == str :
view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p) view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else : else :
view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p) view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None : elif view_to_clone is None :
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p) view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif not new : elif not new :
if view_name is not None : if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name)) view = obi_open_view(dms.pointer, str2bytes(view_name))
@ -300,7 +300,7 @@ cdef class OBIView :
cdef OBIDMS_column_p column_p cdef OBIDMS_column_p column_p
s = self.name s = self.name
s = s + ", " + str(self.pointer.line_count) + " lines" s = s + ", " + self.comments + ", " + str(self.pointer.line_count) + " lines"
for column_name in self.columns : # TODO make function in OBIDMS_column class for column_name in self.columns : # TODO make function in OBIDMS_column class
column = self.columns[column_name] column = self.columns[column_name]
column_p = (column.pointer)[0] column_p = (column.pointer)[0]
@ -461,7 +461,7 @@ cdef class OBIView :
cdef class OBIView_NUC_SEQS(OBIView): cdef class OBIView_NUC_SEQS(OBIView):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None): def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""):
cdef Obiview_p view = NULL cdef Obiview_p view = NULL
cdef int i cdef int i
@ -486,11 +486,11 @@ cdef class OBIView_NUC_SEQS(OBIView):
if new : if new :
if view_to_clone is not None : if view_to_clone is not None :
if type(view_to_clone) == str : if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p) view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else : else :
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p) view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None : elif view_to_clone is None :
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p) view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif not new : elif not new :
if view_name is not None : if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name)) view = obi_open_view(dms.pointer, str2bytes(view_name))
@ -502,6 +502,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
self.pointer = view self.pointer = view
self.name = bytes2str(view.name) self.name = bytes2str(view.name)
self.comments = bytes2str(view.comments)
# go through columns to build list and open python object (TODO make separate function?) # go through columns to build list and open python object (TODO make separate function?)
self.columns = {} self.columns = {}
@ -663,7 +664,7 @@ cdef class OBIDMS :
return view_class(self, view_name) return view_class(self, view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None) : cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None, str comments="") :
cdef object view_class cdef object view_class
@ -673,7 +674,7 @@ cdef class OBIDMS :
else : else :
view_class = OBIView view_class = OBIView
return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection) return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments)
cpdef dict read_view_infos(self, str view_name) : cpdef dict read_view_infos(self, str view_name) :
@ -700,6 +701,7 @@ cdef class OBIDMS :
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
view_name = bytes2str(view_p.name) view_name = bytes2str(view_p.name)
views[view_name] = {} views[view_name] = {}
views[view_name]["comments"] = bytes2str(view_p.comments)
views[view_name]["view_type"] = bytes2str(view_p.view_type) views[view_name]["view_type"] = bytes2str(view_p.view_type)
views[view_name]["column_count"] = <int> view_p.column_count views[view_name]["column_count"] = <int> view_p.column_count
views[view_name]["line_count"] = <int> view_p.line_count views[view_name]["line_count"] = <int> view_p.line_count

4
python/obitools3/obidms/_obiseq.cfiles
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@ -16,3 +16,7 @@
../../../src/private_at_functions.c ../../../src/private_at_functions.c
../../../src/obiavl.h ../../../src/obiavl.h
../../../src/obiavl.c ../../../src/obiavl.c
../../../src/encode.h
../../../src/encode.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c

10
python/obitools3/obidms/capi/obiview.pxd
View File

@ -33,6 +33,7 @@ cdef extern from "obiview.h" nogil:
Column_reference_t line_selection_reference Column_reference_t line_selection_reference
index_t line_count index_t line_count
int column_count int column_count
const_char_p comments
ctypedef Obiview_t* Obiview_p ctypedef Obiview_t* Obiview_p
@ -48,6 +49,7 @@ cdef extern from "obiview.h" nogil:
Column_reference_t line_selection Column_reference_t line_selection
Column_reference_p column_references Column_reference_p column_references
const_char_p view_type const_char_p view_type
const_char_p comments
ctypedef Obiview_infos_t* Obiview_infos_p ctypedef Obiview_infos_t* Obiview_infos_p
@ -67,13 +69,13 @@ cdef extern from "obiview.h" nogil:
ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection) Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection) 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) 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) Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name) Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)

19
src/obiview.c
View File

@ -209,7 +209,7 @@ int create_obiview_file(int dms_file_descriptor)
**********************************************************************/ **********************************************************************/
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection) Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{ {
Obiview_p view; Obiview_p view;
@ -223,7 +223,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
} }
} }
view = obi_new_view(dms, view_name, view_to_clone, line_selection); view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
strcpy(view->view_type, VIEW_TYPE_NUC_SEQS); strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
@ -253,7 +253,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
} }
Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection) Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{ {
Obiview_p view; Obiview_p view;
int i; int i;
@ -278,7 +278,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
return NULL; return NULL;
} }
view->dms = dms; view->dms = dms;
view->column_count = view_to_clone->column_count; view->column_count = view_to_clone->column_count;
if ((view_to_clone->line_selection != NULL) && (line_selection == NULL)) // reorder conditions if ((view_to_clone->line_selection != NULL) && (line_selection == NULL)) // reorder conditions
{ {
@ -359,13 +359,14 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
} }
strcpy(view->name, view_name); strcpy(view->name, view_name);
strcpy(view->comments, comments);
view->read_only = 0; view->read_only = 0;
return view; return view;
} }
Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection) Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
{ {
Obiview_p view; Obiview_p view;
Obiview_p view_to_clone; Obiview_p view_to_clone;
@ -373,7 +374,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
view_to_clone = obi_open_view(dms, view_to_clone_name); view_to_clone = obi_open_view(dms, view_to_clone_name);
if (view_to_clone == NULL) if (view_to_clone == NULL)
return NULL; return NULL;
view = obi_new_view(dms, view_name, view_to_clone, line_selection); view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
obi_close_view(view_to_clone); obi_close_view(view_to_clone);
@ -381,7 +382,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
} }
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection) Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
{ {
Obiview_p view; Obiview_p view;
Obiview_p view_to_clone; Obiview_p view_to_clone;
@ -389,7 +390,7 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
view_to_clone = obi_open_view(dms, view_to_clone_name); view_to_clone = obi_open_view(dms, view_to_clone_name);
if (view_to_clone == NULL) if (view_to_clone == NULL)
return NULL; return NULL;
view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection); view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments);
obi_close_view(view_to_clone); obi_close_view(view_to_clone);
@ -532,6 +533,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
strcpy(view->created_from, view_infos->created_from); strcpy(view->created_from, view_infos->created_from);
strcpy(view->name, view_infos->name); strcpy(view->name, view_infos->name);
strcpy(view->view_type, view_infos->view_type); strcpy(view->view_type, view_infos->view_type);
strcpy(view->comments, view_infos->comments);
// Open the columns to read // Open the columns to read
for (i=0; i<(view_infos->column_count); i++) for (i=0; i<(view_infos->column_count); i++)
@ -1033,6 +1035,7 @@ int obi_save_view(Obiview_p view)
strcpy(view_infos->created_from, view->created_from); strcpy(view_infos->created_from, view->created_from);
strcpy(view_infos->name, view->name); strcpy(view_infos->name, view->name);
strcpy(view_infos->view_type, view->view_type); strcpy(view_infos->view_type, view->view_type);
strcpy(view_infos->comments, view->comments);
// Store reference for the line selection associated with that view // Store reference for the line selection associated with that view
if (view->new_line_selection != NULL) if (view->new_line_selection != NULL)

18
src/obiview.h
View File

@ -26,8 +26,10 @@
#include "obierrno.h" #include "obierrno.h"
#define OBIVIEW_NAME_MAX_LENGTH (10239) /**< The maximum length of an OBIDMS view name. #define OBIVIEW_NAME_MAX_LENGTH (1000) /**< The maximum length of an OBIDMS view name.
*/ */
#define OBIVIEW_COMMENTS_MAX_LENGTH (10000)
#define OBIVIEW_FILE_NAME "obiviews" #define OBIVIEW_FILE_NAME "obiviews"
#define VIEW_TYPE_MAX_NAME (1024) #define VIEW_TYPE_MAX_NAME (1024)
@ -84,6 +86,8 @@ typedef struct Obiview {
char view_type[VIEW_TYPE_MAX_NAME+1]; char view_type[VIEW_TYPE_MAX_NAME+1];
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];
} Obiview_t, *Obiview_p; } Obiview_t, *Obiview_p;
@ -111,6 +115,8 @@ typedef struct Obiview_infos {
char view_type[VIEW_TYPE_MAX_NAME+1]; char view_type[VIEW_TYPE_MAX_NAME+1];
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];
} Obiview_infos_t, *Obiview_infos_p; } Obiview_infos_t, *Obiview_infos_p;
@ -135,13 +141,13 @@ typedef struct Obiviews_infos_all {
} Obiviews_infos_all_t, *Obiviews_infos_all_p; } Obiviews_infos_all_t, *Obiviews_infos_all_p;
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection); Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments);
Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection); Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments);
Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection); Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection); Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name); Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);