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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
View File

@ -43,6 +43,7 @@ cdef class OBIView:
cdef Obiview_p pointer
cdef str name
cdef str comments
cdef dict columns
cdef dict columns_pp # TODO this dict might be unnecessary
cdef OBIDMS dms
@ -86,7 +87,7 @@ cdef class OBIDMS:
cpdef close(self)
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_views(self)

24
python/obitools3/obidms/_obidms.pyx
View File

@ -231,7 +231,7 @@ cdef class OBIDMS_column_line :
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 int i
@ -256,11 +256,11 @@ cdef class OBIView :
if new :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p)
view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else :
view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p)
view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None :
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p)
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif not new :
if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name))
@ -300,7 +300,7 @@ cdef class OBIView :
cdef OBIDMS_column_p column_p
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
column = self.columns[column_name]
column_p = (column.pointer)[0]
@ -461,7 +461,7 @@ cdef class 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 int i
@ -486,11 +486,11 @@ cdef class OBIView_NUC_SEQS(OBIView):
if new :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p)
view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else :
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p)
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None :
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p)
view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif not new :
if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name))
@ -502,6 +502,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
self.pointer = view
self.name = bytes2str(view.name)
self.comments = bytes2str(view.comments)
# go through columns to build list and open python object (TODO make separate function?)
self.columns = {}
@ -663,7 +664,7 @@ cdef class OBIDMS :
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
@ -673,7 +674,7 @@ cdef class OBIDMS :
else :
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) :
@ -700,6 +701,7 @@ cdef class OBIDMS :
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
view_name = bytes2str(view_p.name)
views[view_name] = {}
views[view_name]["comments"] = bytes2str(view_p.comments)
views[view_name]["view_type"] = bytes2str(view_p.view_type)
views[view_name]["column_count"] = <int> view_p.column_count
views[view_name]["line_count"] = <int> view_p.line_count

4
python/obitools3/obidms/_obiseq.cfiles
View File

@ -16,3 +16,7 @@
../../../src/private_at_functions.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/encode.h
../../../src/encode.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c

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
index_t line_count
int column_count
const_char_p comments
ctypedef Obiview_t* Obiview_p
@ -48,6 +49,7 @@ cdef extern from "obiview.h" nogil:
Column_reference_t line_selection
Column_reference_p column_references
const_char_p view_type
const_char_p comments
ctypedef Obiview_infos_t* Obiview_infos_p
@ -67,13 +69,13 @@ cdef extern from "obiview.h" nogil:
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)