Commit 75a28929 authored by Celine Mercier's avatar Celine Mercier

Renamed Cython alignment library in an attempt to limit some compilation

bugs potentially involving name conflicts
parent d076ea99
......@@ -11,9 +11,9 @@ from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.align._qsassemble import QSolexaReverseAssemble
from obitools3.align._qsrassemble import QSolexaRightReverseAssemble
from obitools3.align._solexapairend import buildConsensus, buildJoinedSequence
from obitools3.libalign._qsassemble import QSolexaReverseAssemble
from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
from obitools3.dms.obiseq cimport Nuc_Seq_Stored, Nuc_Seq
import sys
......
......@@ -8,7 +8,7 @@ from obitools3.dms.column.column cimport Column, Column_line
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.align._freeendgapfm import FreeEndGapFullMatch
from obitools3.libalign._freeendgapfm import FreeEndGapFullMatch
from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
......
......@@ -6,8 +6,8 @@ Created on 14 sept. 2009
@author: coissac
'''
from obitools3.align import AlignedSequence
from obitools3.align import Alignment
from obitools3.libalign import AlignedSequence
from obitools3.libalign import Alignment
from copy import deepcopy
......
......@@ -6,7 +6,7 @@ Created on 17 mai 2010
@author: coissac
'''
from obitools3.align import columnIterator
from obitools3.libalign import columnIterator
def iterOnAligment(ali):
......
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