Commit da92eca1 by Eric Coissac

Pacth a bug in LCS upperbond

parent 921eff27
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -17,6 +17,7 @@ cdef class BioSequence(object):
cdef public bint _hasTaxid
cdef public object _wrappers
cdef public object word4table
cdef public object word4over
cpdef bytes get_seq(self)
cpdef set_seq(self, object value)
......@@ -105,4 +106,4 @@ cdef object _bioSeqGenerator(bytes id,
\ No newline at end of file
......@@ -90,6 +90,7 @@ cdef class BioSequence(object):
self._hasTaxid=True
self.__quality=None
self.word4table=None
self.word4over=None
cpdef bytes get_seq(self):
return self.__seq
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:31 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:27 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:32 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:28 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:32 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:28 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:28 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:28 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:29 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:29 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -790,7 +790,7 @@ static int __pyx_pf_8obitools_5align_5array_5array___getbuffer__(arrayobject *__
static void __pyx_pf_8obitools_5align_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static char __pyx_k_2[] = "\nCreated on 6 Nov. 2009\n\n@author: coissac\n";
static char __pyx_k_3[] = "*";
static char __pyx_k_6[] = "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx";
static char __pyx_k_6[] = "/usr/local/src/OBITools-trunk/src/obitools/align/_lcs.pyx";
static char __pyx_k_7[] = "obitools.align._lcs";
static char __pyx_k__l1[] = "l1";
static char __pyx_k__l2[] = "l2";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:29 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:33 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:29 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:34 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:30 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:34 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:30 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:34 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:30 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:34 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:30 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Mon May 7 11:13:25 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:30 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -759,7 +759,7 @@ static PyObject *__pyx_pf_8obitools_5align_10_upperbond_4isLCSReachable(CYTHON_U
static int __pyx_pf_8obitools_5align_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags); /* proto */
static void __pyx_pf_8obitools_5align_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static char __pyx_k_1[] = "\nCreated on 6 Nov. 2009\n\n@author: coissac\n";
static char __pyx_k_4[] = "/Users/coissac/encours/OBITools/src/obitools/align/_upperbond.pyx";
static char __pyx_k_4[] = "/usr/local/src/OBITools-trunk/src/obitools/align/_upperbond.pyx";
static char __pyx_k_5[] = "obitools.align._upperbond";
static char __pyx_k__B[] = "B";
static char __pyx_k__op[] = "op";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:35 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:31 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:35 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:31 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -752,7 +752,7 @@ static PyObject *__pyx_pf_8obitools_6format_13genericparser_14_genericparser_13G
static PyObject *__pyx_pf_8obitools_6format_13genericparser_14_genericparser_13GenericParser_6__call__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_file); /* proto */
static char __pyx_k_1[] = "";
static char __pyx_k_4[] = "transparentIteratorEntry";
static char __pyx_k_5[] = "/Users/coissac/encours/OBITools/src/obitools/format/genericparser/_genericparser.pyx";
static char __pyx_k_5[] = "/usr/local/src/OBITools-trunk/src/obitools/format/genericparser/_genericparser.pyx";
static char __pyx_k_6[] = "obitools.format.genericparser._genericparser";
static char __pyx_k_9[] = "genericEntryIterator";
static char __pyx_k_10[] = "genericEntryIteratorGenerator";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:35 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:31 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -825,7 +825,7 @@ static PyObject *__pyx_pf_8obitools_7options_13_bioseqfilter_31sequenceFilterIte
static PyObject *__pyx_pf_8obitools_7options_13_bioseqfilter_2sequenceFilterIteratorGenerator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_options); /* proto */
static char __pyx_k_1[] = "obitools.options._bioseqfilter";
static char __pyx_k_2[] = "taxonomyFilterGenerator";
static char __pyx_k_5[] = "/Users/coissac/encours/OBITools/src/obitools/options/_bioseqfilter.pyx";
static char __pyx_k_5[] = "/usr/local/src/OBITools-trunk/src/obitools/options/_bioseqfilter.pyx";
static char __pyx_k_8[] = "sequenceFilterIterator";
static char __pyx_k_9[] = "obitools.options.taxonomyfilter";
static char __pyx_k_14[] = "sequenceFilterIteratorGenerator";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:35 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:31 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -806,7 +806,7 @@ static PyObject *__pyx_pf_8obitools_7options_8_options_8fileWithProgressBar(CYTH
static PyObject *__pyx_pf_8obitools_7options_8_options_10allEntryIterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_files, PyObject *__pyx_v_entryIterator, PyObject *__pyx_v_with_progress, PyObject *__pyx_v_histo_step); /* proto */
static char __pyx_k_1[] = "currentInputFileName";
static char __pyx_k_2[] = "";
static char __pyx_k_5[] = "/Users/coissac/encours/OBITools/src/obitools/options/_options.pyx";
static char __pyx_k_5[] = "/usr/local/src/OBITools-trunk/src/obitools/options/_options.pyx";
static char __pyx_k_6[] = "obitools.options._options";
static char __pyx_k_8[] = "obitools.utils";
static char __pyx_k__f[] = "f";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:36 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:32 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 14:13:13 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:32 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -710,7 +710,7 @@ static char __pyx_k_11[] = "insertdirect's docstring";
static char __pyx_k_12[] = "insertreverse's docstring";
static char __pyx_k_13[] = "deletedirect's docstring";
static char __pyx_k_14[] = "deletereverse's docstring";
static char __pyx_k_17[] = "/Users/coissac/encours/OBITools/src/obitools/tools/_solexapairend.pyx";
static char __pyx_k_17[] = "/usr/local/src/OBITools-trunk/src/obitools/tools/_solexapairend.pyx";
static char __pyx_k_18[] = "obitools.tools._solexapairend";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:36 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:32 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......
/* Generated by Cython 0.16 on Wed Apr 25 13:44:36 2012 */
/* Generated by Cython 0.16 on Mon May 7 11:20:32 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
......@@ -604,7 +604,7 @@ static char __pyx_k_3[] = "Word length should be less or equal to 32";
static char __pyx_k_4[] = "word should only contain a, c, g or t (%s)";
static char __pyx_k_5[] = "pos %d/%d moved";
static char __pyx_k_6[] = "\nCreated on 2 juil. 2009\n\n@author: coissac\n";
static char __pyx_k_9[] = "/Users/coissac/encours/OBITools/src/obitools/word/_binary.pyx";
static char __pyx_k_9[] = "/usr/local/src/OBITools-trunk/src/obitools/word/_binary.pyx";
static char __pyx_k_10[] = "obitools.word._binary";
static char __pyx_k__0[] = "0";
static char __pyx_k__1[] = "1";
......
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