Renamed Cython alignment library in an attempt to limit some compilation

bugs potentially involving name conflicts

python/obitools3/commands/alignpairedend.pyx

@@ -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

python/obitools3/commands/ngsfilter.pyx

@@ -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
 

python/obitools3/libalign/_dynamic.pyx

@@ -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
 
 

python/obitools3/libalign/solexapairend.py

@@ -6,7 +6,7 @@ Created on 17 mai 2010
 @author: coissac
 '''
 
-from obitools3.align import columnIterator
+from obitools3.libalign import columnIterator
 
 
 def iterOnAligment(ali):