dscience:dscience.git
5 years agoDDoc isntall works on unix at least master
Jonathan MERCIER [Wed, 21 Mar 2012 19:08:58 +0000 (20:08 +0100)]
DDoc isntall works on unix at least

5 years agoadd IUPAC
Jonathan MERCIER [Wed, 21 Mar 2012 13:09:43 +0000 (14:09 +0100)]
add IUPAC

5 years agoAble to build doc as a cute doc
Jonathan MERCIER [Tue, 20 Mar 2012 23:36:00 +0000 (00:36 +0100)]
Able to build doc as a cute doc

5 years agoSome enhancement on gff gtf side
Jonathan MERCIER [Tue, 20 Mar 2012 14:27:13 +0000 (15:27 +0100)]
Some enhancement on gff gtf side

5 years agoAdd both GFF / GTF format, reader + writer
Jonathan MERCIER [Tue, 20 Mar 2012 02:20:26 +0000 (03:20 +0100)]
Add both GFF / GTF format, reader + writer

5 years agoAdd gff parser
Jonathan MERCIER [Sun, 18 Mar 2012 02:08:49 +0000 (03:08 +0100)]
Add gff parser

5 years agoAdd gff parser
Jonathan MERCIER [Sun, 18 Mar 2012 01:55:10 +0000 (02:55 +0100)]
Add gff parser

5 years agoAble to parse bed file who contain multiple track
Jonathan MERCIER [Thu, 8 Mar 2012 19:39:29 +0000 (20:39 +0100)]
Able to parse bed file who contain multiple track

5 years agoAble to append some bed data ton an existing bed file
Jonathan MERCIER [Wed, 7 Mar 2012 01:48:04 +0000 (02:48 +0100)]
Able to append some bed data ton an existing bed file

5 years agoFix ucsc module for parsing bed file
Jonathan MERCIER [Wed, 7 Mar 2012 00:27:06 +0000 (01:27 +0100)]
Fix ucsc module for parsing bed file

5 years agoFix fasta reader/ writer
Jonathan MERCIER [Tue, 6 Mar 2012 16:05:33 +0000 (17:05 +0100)]
Fix fasta reader/ writer

5 years agoUpdate fasta example to work around
Jonathan MERCIER [Sat, 3 Mar 2012 13:45:30 +0000 (14:45 +0100)]
Update fasta example to work around

5 years agoMove dscience.sequence to dscience.molecules.sequence
Jonathan MERCIER [Sat, 3 Mar 2012 11:38:00 +0000 (12:38 +0100)]
Move dscience.sequence to dscience.molecules.sequence

5 years agoClean tree project
Jonathan MERCIER [Sat, 3 Mar 2012 02:50:10 +0000 (03:50 +0100)]
Clean tree project

5 years agoSet license to LGPLv3+ into makefile
Jonathan MERCIER [Fri, 2 Mar 2012 23:07:01 +0000 (00:07 +0100)]
Set license to LGPLv3+ into makefile

5 years agoUpdate PAM matrix and add corresponding documentation
Jonathan MERCIER [Fri, 2 Mar 2012 22:42:09 +0000 (23:42 +0100)]
Update PAM matrix and add corresponding documentation

5 years agoAdd nuc matrix
Jonathan MERCIER [Fri, 2 Mar 2012 19:27:01 +0000 (20:27 +0100)]
Add nuc matrix

5 years agoAdd match matrix
Jonathan MERCIER [Fri, 2 Mar 2012 18:27:09 +0000 (19:27 +0100)]
Add match matrix

5 years agoUpdate identity matrix
Jonathan MERCIER [Fri, 2 Mar 2012 18:25:22 +0000 (19:25 +0100)]
Update identity matrix

5 years agoUpdate gonnet matrix
Jonathan MERCIER [Fri, 2 Mar 2012 18:23:22 +0000 (19:23 +0100)]
Update gonnet matrix

5 years agoUpdate dayhoff matrix
Jonathan MERCIER [Fri, 2 Mar 2012 18:22:12 +0000 (19:22 +0100)]
Update dayhoff matrix

5 years agoupdate blosum matrix
Jonathan MERCIER [Fri, 2 Mar 2012 18:20:54 +0000 (19:20 +0100)]
update blosum matrix

5 years agoRemove old package dscience.biology.parser
Jonathan MERCIER [Fri, 2 Mar 2012 17:34:57 +0000 (18:34 +0100)]
Remove old package dscience.biology.parser

5 years agofix doc
Jonathan MERCIER [Fri, 2 Mar 2012 02:48:23 +0000 (03:48 +0100)]
fix doc

5 years agoSome ddoc for module dscience.parser.ucsc
Jonathan MERCIER [Fri, 2 Mar 2012 02:40:09 +0000 (03:40 +0100)]
Some ddoc for module dscience.parser.ucsc

5 years agoSome ddoc for module dscience.parser.ucsc
Jonathan MERCIER [Fri, 2 Mar 2012 02:17:24 +0000 (03:17 +0100)]
Some ddoc for module dscience.parser.ucsc

5 years agocomment BedDetailData struct
Jonathan MERCIER [Fri, 2 Mar 2012 01:46:20 +0000 (02:46 +0100)]
comment BedDetailData struct

5 years agoFix formating BedData struct, add BedDetailData struct for allow to parse file format...
Jonathan MERCIER [Fri, 2 Mar 2012 01:36:49 +0000 (02:36 +0100)]
Fix formating BedData struct, add BedDetailData struct for allow to parse file format BED detail

5 years agoRename module bed to ucsc with some enhancment for this module
Jonathan MERCIER [Thu, 1 Mar 2012 23:38:16 +0000 (00:38 +0100)]
Rename module bed to ucsc with some enhancment for this module

5 years agoAdd bed parser
Jonathan MERCIER [Thu, 1 Mar 2012 13:49:48 +0000 (14:49 +0100)]
Add bed parser

5 years agoadd ini parser
Jonathan MERCIER [Wed, 29 Feb 2012 11:09:19 +0000 (12:09 +0100)]
add ini parser

5 years agomove files
Jonathan MERCIER [Wed, 29 Feb 2012 02:43:22 +0000 (03:43 +0100)]
move files

5 years agoend D2 port
Jonathan MERCIER [Wed, 29 Feb 2012 02:43:00 +0000 (03:43 +0100)]
end D2 port

5 years agocontinue port to D v2
Jonathan MERCIER [Tue, 28 Feb 2012 17:24:07 +0000 (18:24 +0100)]
continue port to D v2

5 years agostart port to D v2, add into dscience.math some tool as for doing motif scanning
Jonathan MERCIER [Tue, 28 Feb 2012 00:03:54 +0000 (01:03 +0100)]
start port to D v2, add into dscience.math some tool as for doing motif scanning

5 years agostart port to D v2, add into dscience.math some tool as for doing motif scanning
Jonathan MERCIER [Mon, 27 Feb 2012 23:54:48 +0000 (00:54 +0100)]
start port to D v2, add into dscience.math some tool as for doing motif scanning

6 years agosome fix
bioinfornatics [Sat, 15 Jan 2011 00:48:07 +0000 (01:48 +0100)]
some fix

6 years agomerge
bioinfornatics [Tue, 11 Jan 2011 00:51:08 +0000 (01:51 +0100)]
merge

6 years agoPDB XMl parser works experimental
bioinfornatics [Mon, 10 Jan 2011 03:11:50 +0000 (04:11 +0100)]
PDB XMl parser works

6 years agoAdd compund in AminoFactory
bioinfornatics [Sat, 8 Jan 2011 02:13:48 +0000 (03:13 +0100)]
Add compund in AminoFactory

6 years agoPDB XML parser done
bioinfornatics [Fri, 7 Jan 2011 22:47:51 +0000 (23:47 +0100)]
PDB XML parser done

6 years agoUse double instead real for coordinate x,y,z and save bug #450 in ldc
bioinfornatics [Thu, 6 Jan 2011 16:08:24 +0000 (17:08 +0100)]
Use double instead real for coordinate x,y,z and save bug #450 in ldc

6 years agovariant test
bioinfornatics [Thu, 6 Jan 2011 11:32:25 +0000 (12:32 +0100)]
variant test

6 years agoMerge branch 'experimental'
bioinfornatics [Thu, 6 Jan 2011 10:45:43 +0000 (11:45 +0100)]
Merge branch 'experimental'

6 years agominor change
bioinfornatics [Thu, 6 Jan 2011 10:45:09 +0000 (11:45 +0100)]
minor change

6 years agoremove unecessary import Stdout
bioinfornatics [Thu, 6 Jan 2011 02:56:22 +0000 (03:56 +0100)]
remove unecessary import Stdout

6 years agoremove unecessary import Stdout
bioinfornatics [Thu, 6 Jan 2011 02:53:17 +0000 (03:53 +0100)]
remove unecessary import Stdout

6 years agominor change
bioinfornatics [Thu, 6 Jan 2011 02:50:55 +0000 (03:50 +0100)]
minor change

6 years agosearch were is the bug
bioinfornatics [Wed, 5 Jan 2011 22:43:10 +0000 (23:43 +0100)]
search were is the bug

6 years agoremove ref keyword recursively
bioinfornatics [Wed, 5 Jan 2011 20:55:14 +0000 (21:55 +0100)]
remove ref keyword recursively

6 years agoRemove old file
bioinfornatics [Wed, 5 Jan 2011 11:24:17 +0000 (12:24 +0100)]
Remove old file

6 years agofix needleman and wunsh
bioinfornatics [Wed, 5 Jan 2011 11:17:57 +0000 (12:17 +0100)]
fix needleman and wunsh

6 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
bioinfornatics [Sun, 2 Jan 2011 15:39:56 +0000 (16:39 +0100)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

6 years agoPerform needleman & Wunsh \
bioinfornatics [Sun, 2 Jan 2011 15:39:20 +0000 (16:39 +0100)]
Perform needleman & Wunsh \
Remove temporary Smith & waterman \
Add compound to molecule for biological function

7 years agorepack git repesitory
HadiM [Wed, 3 Nov 2010 23:46:07 +0000 (00:46 +0100)]
repack git repesitory

7 years agoMerge
bioinfornatics [Fri, 29 Oct 2010 20:59:29 +0000 (22:59 +0200)]
Merge

7 years agosome works on algorithm
bioinfornatics [Fri, 29 Oct 2010 20:54:55 +0000 (22:54 +0200)]
some works on algorithm

7 years agosmall modif
HadiM [Fri, 29 Oct 2010 18:00:03 +0000 (20:00 +0200)]
small modif

7 years agoBegin Fasta class : a class to parse fasta file (not workinf for now, just reading...
HadiM [Fri, 29 Oct 2010 17:55:31 +0000 (19:55 +0200)]
Begin Fasta class : a class to parse fasta file (not workinf for now, just reading the file)

7 years agoAdd some doc to Sequence class
HadiM [Fri, 29 Oct 2010 17:01:40 +0000 (19:01 +0200)]
Add some doc to Sequence class

7 years agoAdd Sequence class to biology/sequence/. See examples/alignement to how it works
HadiM [Fri, 29 Oct 2010 16:51:02 +0000 (18:51 +0200)]
Add Sequence class to biology/sequence/. See examples/alignement to how it works

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
bioinfornatics [Fri, 29 Oct 2010 00:10:47 +0000 (02:10 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoPerform needleman & wunsh
bioinfornatics [Fri, 29 Oct 2010 00:10:08 +0000 (02:10 +0200)]
Perform needleman & wunsh

7 years agotest got done
HadiM [Thu, 28 Oct 2010 14:04:16 +0000 (16:04 +0200)]
test got done

7 years agotest git
HadiM [Thu, 28 Oct 2010 14:03:23 +0000 (16:03 +0200)]
test git

7 years agofix compil bug
HadiM [Thu, 28 Oct 2010 13:06:27 +0000 (15:06 +0200)]
fix compil bug

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Thu, 28 Oct 2010 12:38:32 +0000 (14:38 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agojj
HadiM [Thu, 28 Oct 2010 12:38:28 +0000 (14:38 +0200)]
jj

7 years agoFix merge
bioinfornatics [Thu, 28 Oct 2010 12:35:11 +0000 (14:35 +0200)]
Fix merge

7 years agofix needleman & wunsh Algo
bioinfornatics [Thu, 28 Oct 2010 12:18:47 +0000 (14:18 +0200)]
fix needleman & wunsh Algo

7 years agoFactorise some code in alignement module
HadiM [Thu, 28 Oct 2010 02:10:21 +0000 (04:10 +0200)]
Factorise some code in alignement module

7 years agoAll matrice are in the place git stgit stgit st
HadiM [Thu, 28 Oct 2010 01:35:37 +0000 (03:35 +0200)]
All matrice are in the place git stgit stgit st

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Thu, 28 Oct 2010 00:18:01 +0000 (02:18 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agowork on tools to get matrix
HadiM [Thu, 28 Oct 2010 00:17:52 +0000 (02:17 +0200)]
work on tools to get matrix

7 years agoFix needleman and wunsh algo
bioinfornatics [Thu, 28 Oct 2010 00:13:01 +0000 (02:13 +0200)]
Fix needleman and wunsh algo

7 years agoadd matrix files
HadiM [Wed, 27 Oct 2010 22:35:19 +0000 (00:35 +0200)]
add matrix files

7 years agotools.getMatrix.py
HadiM [Wed, 27 Oct 2010 22:33:58 +0000 (00:33 +0200)]
tools.getMatrix.py

7 years agoFix MatrixFactory.d
bioinfornatics [Wed, 27 Oct 2010 22:29:50 +0000 (00:29 +0200)]
Fix MatrixFactory.d

7 years agoadd tools to get matrix
HadiM [Wed, 27 Oct 2010 22:10:38 +0000 (00:10 +0200)]
add tools to get matrix

7 years agorien
HadiM [Wed, 27 Oct 2010 22:01:59 +0000 (00:01 +0200)]
rien

7 years agoadd blosum62
HadiM [Wed, 27 Oct 2010 21:50:57 +0000 (23:50 +0200)]
add blosum62

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
bioinfornatics [Wed, 27 Oct 2010 21:32:59 +0000 (23:32 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoallow lowercase as sequence
HadiM [Wed, 27 Oct 2010 21:30:37 +0000 (23:30 +0200)]
allow lowercase as sequence

7 years agoAdd Blosum30
bioinfornatics [Wed, 27 Oct 2010 20:47:13 +0000 (22:47 +0200)]
Add Blosum30

7 years agofucking SWmake-debug make-debug
HadiM [Wed, 27 Oct 2010 20:22:07 +0000 (22:22 +0200)]
fucking SWmake-debug make-debug

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Wed, 27 Oct 2010 19:44:16 +0000 (21:44 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoFix Makefile
bioinfornatics [Wed, 27 Oct 2010 19:43:52 +0000 (21:43 +0200)]
Fix Makefile

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Wed, 27 Oct 2010 19:13:08 +0000 (21:13 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoFix Makefile
bioinfornatics [Wed, 27 Oct 2010 19:12:26 +0000 (21:12 +0200)]
Fix Makefile

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Wed, 27 Oct 2010 19:05:08 +0000 (21:05 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
bioinfornatics [Wed, 27 Oct 2010 18:52:15 +0000 (20:52 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agoAdd Makefile for parser and matrix module
bioinfornatics [Wed, 27 Oct 2010 18:52:00 +0000 (20:52 +0200)]
Add Makefile for parser and matrix module

7 years agowork on SW
HadiM [Wed, 27 Oct 2010 18:47:53 +0000 (20:47 +0200)]
work on SW

7 years agoMerge branch 'experimental' of gitorious.org:dscience/dscience into experimental
HadiM [Wed, 27 Oct 2010 18:38:29 +0000 (20:38 +0200)]
Merge branch 'experimental' of gitorious.org:dscience/dscience into experimental

7 years agowork SW
HadiM [Wed, 27 Oct 2010 18:38:16 +0000 (20:38 +0200)]
work SW

7 years agoAdd blast matrix for nucleic alignement
bioinfornatics [Wed, 27 Oct 2010 18:37:20 +0000 (20:37 +0200)]
Add blast matrix for nucleic alignement

7 years agoAdd matrix Factory and one more exception class
bioinfornatics [Wed, 27 Oct 2010 17:28:32 +0000 (19:28 +0200)]
Add matrix Factory and one more exception class

7 years agowork on needleman and wunsh done
bioinfornatics [Wed, 27 Oct 2010 13:50:09 +0000 (15:50 +0200)]
work on needleman and wunsh done

7 years agooptimize memory cost from needleman and wunsh algo
bioinfornatics [Wed, 27 Oct 2010 13:30:58 +0000 (15:30 +0200)]
optimize memory cost from needleman and wunsh algo

7 years agoles matrice ca pue du cul
HadiM [Wed, 27 Oct 2010 01:15:31 +0000 (03:15 +0200)]
les matrice ca pue du cul