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The default element names for columns with multiple elements per line

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are now "O;1;2;...;n"
This commit is contained in:
Celine Mercier
2016-12-02 17:54:51 +01:00
parent e60497651c
commit 852e5488c8
5 changed files with 116 additions and 87 deletions
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99
python/obitools3/obidms/_obidms.pyx
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@ -379,10 +379,10 @@ cdef class OBIView :
else :
alias_b = str2bytes(alias)
if nb_elements_per_line > 1 :
if elements_names is None :
elements_names_b = str2bytes("")
else :
elements_names_b = str2bytes(';'.join(elements_names))
elif nb_elements_per_line == 1 :
elements_names_b = column_name_b
if type : # TODO make C function that does that
if type == 'OBI_INT' :
@ -528,61 +528,44 @@ cdef class OBIView_NUC_SEQS(OBIView):
# TODO discuss
cpdef align(self, OBIView oview, OBIView iview2=None,
double threshold=0.0, bint normalize=True, int reference=0, bint similarity_mode=True) :
cdef OBIView iview1
cdef Obiview_p iview1_p
cdef Obiview_p iview2_p
cdef Obiview_p oview_p
cdef OBIDMS_column icol1
cdef OBIDMS_column_p icol1_p
cdef OBIDMS_column_p* icol1_pp
cdef OBIDMS_column id1_col
cdef OBIDMS_column_p id1_col_p
cdef OBIDMS_column_p* id1_col_pp
cdef OBIDMS_column id2_col
cdef OBIDMS_column_p id2_col_p
cdef OBIDMS_column_p* id2_col_pp
cdef OBIDMS_column ocol
cdef OBIDMS_column_p ocol_p
cdef OBIDMS_column_p* ocol_pp
cdef str id1_col_name
cdef str id2_col_name
cdef str score_col_name
id1_col_name = "ID1" # TODO discuss names, aliases
id2_col_name = "ID2"
score_col_name = "score"
iview1= self
iview1_p = iview1._pointer
icol1 = iview1[bytes2str(NUC_SEQUENCE_COLUMN)]
icol1_pp = icol1._pointer
icol1_p = icol1_pp[0]
oview.add_column(id1_col_name, type='OBI_STR', create=True)
oview.add_column(id2_col_name, type='OBI_STR', create=True)
oview.add_column(score_col_name, type='OBI_FLOAT', create=True)
oview_p = oview._pointer
ocol = oview[score_col_name]
ocol_pp = ocol._pointer
ocol_p = ocol_pp[0]
id1_col = oview[id1_col_name]
id2_col = oview[id2_col_name]
id1_col_pp = id1_col._pointer
id2_col_pp = id2_col._pointer
id1_col_p = id1_col_pp[0]
id2_col_p = id2_col_pp[0]
if obi_align_one_column(iview1_p, icol1_p, NULL, oview_p, id1_col_p, id2_col_p, ocol_p, threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")
pass
#
# cdef OBIView iview1
#
# cdef Obiview_p iview1_p
# cdef Obiview_p iview2_p
# cdef Obiview_p oview_p
#
# cdef OBIDMS_column icol1
# cdef OBIDMS_column_p icol1_p
# cdef OBIDMS_column_p* icol1_pp
#
# cdef OBIDMS_column id1_col
# cdef OBIDMS_column_p id1_col_p
# cdef OBIDMS_column_p* id1_col_pp
#
# cdef OBIDMS_column id2_col
# cdef OBIDMS_column_p id2_col_p
# cdef OBIDMS_column_p* id2_col_pp
#
# cdef OBIDMS_column ocol
# cdef OBIDMS_column_p ocol_p
# cdef OBIDMS_column_p* ocol_pp
#
# cdef str id1_col_name
# cdef str id2_col_name
# cdef str score_col_name
#
# score_col_name = "score"
#
# iview1= self
# iview1_p = iview1._pointer
# icol1 = iview1[bytes2str(NUC_SEQUENCE_COLUMN)]
# icol1_pp = icol1._pointer
# icol1_p = icol1_pp[0]
#
# if obi_align_one_column(iview1_p, icol1_p, threshold, normalize, reference, similarity_mode) < 0 :
# raise Exception("Error aligning sequences")
######################################################################################################