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Sticky Revision:

Revision 2090 - Directory Listing
Modified Sat Feb 24 11:11:36 2018 UTC (11 months, 4 weeks ago) by jeanlobry
 

Revision 2049 - Directory Listing
Modified Tue Jul 4 10:25:33 2017 UTC (19 months, 3 weeks ago) by jeanlobry
read.alignment can now handle legacy fasta format

Revision 2046 - Directory Listing
Modified Mon Jul 3 17:36:07 2017 UTC (19 months, 3 weeks ago) by jeanlobry
adding the new argument rmgap to kaks

Revision 2036 - Directory Listing
Modified Mon Apr 24 13:35:30 2017 UTC (22 months ago) by simonpenel
Removing carriage returns in alignments according to Matthias Doering suggestion 

Revision 2024 - Directory Listing
Modified Fri Oct 14 16:12:35 2016 UTC (2 years, 4 months ago) by jeanlobry
fixing a bug in dotchart.uco

Revision 2003 - Directory Listing
Modified Wed Oct 5 19:38:53 2016 UTC (2 years, 4 months ago) by jeanlobry
pour suivre les good practices

Revision 1998 - Directory Listing
Modified Wed Oct 5 18:05:45 2016 UTC (2 years, 4 months ago) by jeanlobry
 

Revision 1991 - Directory Listing
Modified Thu Sep 1 13:02:59 2016 UTC (2 years, 5 months ago) by simonpenel
improved read.alignment function thanks  to Matthew Krause

Revision 1979 - Directory Listing
Modified Tue Jul 12 17:08:12 2016 UTC (2 years, 7 months ago) by jeanlobry
adding a zlib argument to extractseqs

Revision 1957 - Directory Listing
Modified Tue Jun 21 12:40:42 2016 UTC (2 years, 8 months ago) by jeanlobry
gb2fasta now uses a local file example

Revision 1956 - Directory Listing
Modified Tue Jun 21 12:26:42 2016 UTC (2 years, 8 months ago) by jeanlobry
typo

Revision 1949 - Directory Listing
Modified Fri Jun 17 19:41:39 2016 UTC (2 years, 8 months ago) by jeanlobry
adding a suppressWarning to fix Haruo Susuki request

Revision 1922 - Directory Listing
Modified Fri Jun 3 13:37:54 2016 UTC (2 years, 8 months ago) by jeanlobry
Fix the wrning about segmented

Revision 1916 - Directory Listing
Modified Fri Jun 3 12:41:50 2016 UTC (2 years, 8 months ago) by jeanlobry
One UTF-8 warning corrected

Revision 1893 - Directory Listing
Modified Thu Jun 2 11:36:34 2016 UTC (2 years, 8 months ago) by jeanlobry
using the gzipped ct.fasta.gz

Revision 1888 - Directory Listing
Modified Thu Jun 2 10:40:10 2016 UTC (2 years, 8 months ago) by jeanlobry
to fix the getLength(ec999) bug repported by Haruo Suzuki

Revision 1885 - Directory Listing
Modified Thu Jun 2 09:18:04 2016 UTC (2 years, 8 months ago) by jeanlobry
updating file names

Revision 1837 - Directory Listing
Modified Wed Apr 27 13:41:12 2016 UTC (2 years, 9 months ago) by simonpenel
 ambigous bases bug fixed in comp function (r->y, y->r) 

Revision 1833 - Directory Listing
Modified Tue Dec 2 17:01:03 2014 UTC (4 years, 2 months ago) by simonpenel
Adding little endian setting to pass Solaris tests

Revision 1828 - Directory Listing
Modified Thu Nov 27 14:50:55 2014 UTC (4 years, 2 months ago) by simonpenel
Now goldtable15Dec07 is available on the ftp of pbil

Revision 1825 - Directory Listing
Modified Thu Nov 27 11:04:53 2014 UTC (4 years, 2 months ago) by simonpenel
Now acces to voluminous data is done via ftp, changing R code 

Revision 1822 - Directory Listing
Modified Wed Nov 26 13:14:40 2014 UTC (4 years, 2 months ago) by simonpenel
Replace gloalEnv by seqinrEnv in  plot.SeqAcnucWeb.R

Revision 1817 - Directory Listing
Modified Thu Nov 6 17:09:25 2014 UTC (4 years, 3 months ago) by simonpenel
Modification of wrong url, setting example in dotchart.uco to dontrun

Revision 1816 - Directory Listing
Modified Wed Nov 5 16:53:58 2014 UTC (4 years, 3 months ago) by simonpenel
Start fusion with the 3.0-9 version from CRAN which is ok for  R-3.1.2

Revision 1815 - Directory Listing
Modified Fri Oct 10 12:35:58 2014 UTC (4 years, 4 months ago) by simonpenel
adding "row.names(matali)<-NULL "  due to the change

      \item \code{apply(m, 2, identity)} is now the same as the matrix
      \code{m} when it has \emph{named} row names.


Revision 1796 - Directory Listing
Modified Fri Jun 6 17:16:14 2014 UTC (4 years, 8 months ago) by jeanlobry
link source not available in dia.db.growth

Revision 1780 - Directory Listing
Modified Fri Jun 6 10:26:15 2014 UTC (4 years, 8 months ago) by jeanlobry
add an as.string argument so that write.fasta can handle sequences when provided as strings

Revision 1778 - Directory Listing
Modified Wed May 21 15:38:04 2014 UTC (4 years, 9 months ago) by simonpenel
Now the mase format is checked, thanks to Jan-Hendrik Troesemeier

Revision 1777 - Directory Listing
Modified Thu Jan 30 14:39:20 2014 UTC (5 years ago) by simonpenel
In function dist.alignment with nucleotides sequences, if gap option is set to 1, gaps will be counted in the identity measure (thanks to Peter Hraber)

Revision 1775 - Directory Listing
Modified Fri Oct 4 11:44:41 2013 UTC (5 years, 4 months ago) by simonpenel
Checking for N in the sequence, thanks to Jeremy Shearman

Revision 1772 - Directory Listing
Modified Tue Dec 11 14:26:19 2012 UTC (6 years, 2 months ago) by simonpenel
Removing lib.R

Revision 1770 - Directory Listing
Modified Mon Aug 13 09:06:59 2012 UTC (6 years, 6 months ago) by simonpenel
The pipe caracter is now correctly processed thanks to Grabor Grothendieck

Revision 1769 - Directory Listing
Modified Wed Feb 22 10:15:53 2012 UTC (7 years ago) by simonpenel
Small modifications :  supression of stderr C stuff, and partial match problems

Revision 1767 - Directory Listing
Modified Fri Feb 17 14:29:26 2012 UTC (7 years ago) by simonpenel
Modification of kaks: option verbose display  values of L0,L2,L4,A0,A2,A4,B0,B2,B4 

Revision 1765 - Directory Listing
Modified Tue Feb 7 12:34:34 2012 UTC (7 years ago) by simonpenel
Changing  'superior' into 'superior or equal' in the consenus function with thershold option. Thanks to Dave Gerrard for signaling this bug

Revision 1764 - Directory Listing
Modified Wed Dec 7 16:21:05 2011 UTC (7 years, 2 months ago) by simonpenel
read.alignment now return an error message is return when the format is not correct. Thanks to Dave Gerrard for signaling this bug.

Revision 1762 - Directory Listing
Modified Wed Oct 12 09:15:53 2011 UTC (7 years, 4 months ago) by simonpenel
Changing the grep to "Release(.+)Month" in db.growth function. Thanks to John Davey for detecting this bug.

Revision 1761 - Directory Listing
Modified Tue Sep 20 12:59:55 2011 UTC (7 years, 5 months ago) by simonpenel
Addition of the "recstat" function (Prediction of coding DNA sequences through the use of a  Correspondence Analysis). Guy Perriere is now part of the seqinr project.

Revision 1760 - Directory Listing
Modified Mon May 30 14:37:05 2011 UTC (7 years, 8 months ago) by simonpenel
The [ is not anymore translated into \[ but into \lbrack{} ( idem for ]).
Thanks to Gabor Grothendieck for signaling this bug


Revision 1752 - Directory Listing
Modified Thu Oct 14 09:12:04 2010 UTC (8 years, 4 months ago) by simonpenel
The error generated by the rawToChar function is now detected, fixed and signaled.

Revision 1751 - Directory Listing
Modified Fri Sep 10 09:23:48 2010 UTC (8 years, 5 months ago) by simonpenel
Adding y and r in the list of bases in  the comp function - Thanks to Darren Obbard

Revision 1746 - Directory Listing
Modified Mon May 24 09:28:04 2010 UTC (8 years, 9 months ago) by lobry
 

Revision 1742 - Directory Listing
Modified Wed Mar 17 18:46:56 2010 UTC (8 years, 11 months ago) by lobry
fixing the sapply/lapply bug

Revision 1741 - Directory Listing
Modified Sun Mar 7 11:15:09 2010 UTC (8 years, 11 months ago) by lobry
rho has its own file now

Revision 1738 - Directory Listing
Modified Sun Mar 7 11:13:18 2010 UTC (8 years, 11 months ago) by lobry
word -> wordsize

Revision 1737 - Directory Listing
Modified Sun Mar 7 11:12:45 2010 UTC (8 years, 11 months ago) by lobry
rho() has gained a wordsize argument as suggested by Avril Coghlan

Revision 1736 - Directory Listing
Modified Sun Mar 7 10:04:07 2010 UTC (8 years, 11 months ago) by lobry
word -> wordsize

Revision 1729 - Directory Listing
Modified Sat Mar 6 17:33:12 2010 UTC (8 years, 11 months ago) by lobry
No more File argument

Revision 1722 - Directory Listing
Modified Sat Feb 20 17:48:35 2010 UTC (9 years ago) by lobry
fixing Oliver Clay bug

Revision 1720 - Directory Listing
Modified Fri Nov 27 14:44:26 2009 UTC (9 years, 2 months ago) by lobry
new message when an acc is not found

Revision 1717 - Directory Listing
Modified Wed Nov 18 19:41:45 2009 UTC (9 years, 3 months ago) by lobry
doc more explicit

Revision 1707 - Directory Listing
Modified Sun Nov 15 10:04:05 2009 UTC (9 years, 3 months ago) by lobry
stopAtFirst argument suggested by Avril Coghlan

Revision 1704 - Directory Listing
Modified Thu Nov 12 18:10:24 2009 UTC (9 years, 3 months ago) by lobry
looking for an accession number utility

Revision 1701 - Directory Listing
Modified Sat Nov 7 08:09:55 2009 UTC (9 years, 3 months ago) by lobry
fix the bug reported by Darren Obbard

Revision 1673 - Directory Listing
Modified Wed Nov 4 17:02:48 2009 UTC (9 years, 3 months ago) by lobry
extended deleted

Revision 1672 - Directory Listing
Modified Wed Nov 4 17:01:14 2009 UTC (9 years, 3 months ago) by lobry
extended deleted

Revision 1667 - Directory Listing
Modified Mon Oct 12 16:50:32 2009 UTC (9 years, 4 months ago) by lobry
no more File argument

Revision 1664 - Directory Listing
Modified Mon Oct 12 16:30:15 2009 UTC (9 years, 4 months ago) by lobry
new function for stutter ratio

Revision 1662 - Directory Listing
Modified Mon Oct 12 08:54:51 2009 UTC (9 years, 4 months ago) by lobry
 

Revision 1659 - Directory Listing
Modified Mon Oct 12 08:33:55 2009 UTC (9 years, 4 months ago) by lobry
new utility

Revision 1655 - Directory Listing
Modified Fri Oct 9 06:23:09 2009 UTC (9 years, 4 months ago) by lobry
new ylim

Revision 1653 - Directory Listing
Modified Fri Oct 9 06:11:48 2009 UTC (9 years, 4 months ago) by lobry
baseline and +1 shift corrected

Revision 1650 - Directory Listing
Modified Tue Sep 22 13:10:18 2009 UTC (9 years, 5 months ago) by lobry
 

Revision 1642 - Directory Listing
Modified Sat Sep 5 19:08:20 2009 UTC (9 years, 5 months ago) by lobry
 

Revision 1636 - Directory Listing
Modified Thu Sep 3 12:22:25 2009 UTC (9 years, 5 months ago) by lobry
 

Revision 1633 - Directory Listing
Modified Thu Sep 3 08:49:37 2009 UTC (9 years, 5 months ago) by lobry
 

Revision 1621 - Directory Listing
Modified Fri Jul 17 21:45:06 2009 UTC (9 years, 7 months ago) by lobry
new function

Revision 1620 - Directory Listing
Modified Fri Jul 17 21:44:21 2009 UTC (9 years, 7 months ago) by lobry
new function

Revision 1615 - Directory Listing
Modified Wed Jun 24 09:04:46 2009 UTC (9 years, 8 months ago) by lobry
fixing a bug with trailling tabulations

Revision 1612 - Directory Listing
Modified Wed Jun 17 14:56:16 2009 UTC (9 years, 8 months ago) by lobry
deletion of runs of tabulations

Revision 1571 - Directory Listing
Modified Tue Mar 31 15:51:08 2009 UTC (9 years, 10 months ago) by lobry
more tolerance to extra columns in data

Revision 1568 - Directory Listing
Modified Mon Mar 30 18:38:43 2009 UTC (9 years, 10 months ago) by lobry
Yann LESECQUE bug fix

Revision 1565 - Directory Listing
Modified Wed Mar 11 10:01:12 2009 UTC (9 years, 11 months ago) by lobry
new utility functions

Revision 1561 - Directory Listing
Modified Mon Mar 9 18:46:28 2009 UTC (9 years, 11 months ago) by lobry
peakabif now returns more info

Revision 1557 - Directory Listing
Modified Thu Feb 12 15:19:27 2009 UTC (10 years ago) by lobry
new split argument

Revision 1553 - Directory Listing
Modified Thu Feb 12 12:05:59 2009 UTC (10 years ago) by lobry
new utility function al2bp

Revision 1550 - Directory Listing
Modified Wed Feb 4 15:31:10 2009 UTC (10 years ago) by lobry
now plotabif returns its local graphical parameter settings

Revision 1547 - Directory Listing
Modified Wed Feb 4 13:57:48 2009 UTC (10 years ago) by lobry
New function to plot allelic ladder in ABIF data

Revision 1545 - Directory Listing
Modified Wed Feb 4 13:55:38 2009 UTC (10 years ago) by lobry
Function to locate peaks in ABIF data

Revision 1543 - Directory Listing
Modified Wed Feb 4 13:53:31 2009 UTC (10 years ago) by lobry
new plot function for ABIF data

Revision 1528 - Directory Listing
Modified Wed Jan 21 09:22:27 2009 UTC (10 years, 1 month ago) by lobry
file name changed to fit fct name

Revision 1527 - Directory Listing
Modified Wed Jan 21 07:12:32 2009 UTC (10 years, 1 month ago) by lobry
warnings gerated when reading string with internal null character are now suppressed

Revision 1506 - Directory Listing
Modified Fri Dec 12 10:26:33 2008 UTC (10 years, 2 months ago) by lobry
change default for extended argument to avoid warnings

Revision 1501 - Directory Listing
Modified Mon Nov 3 10:37:37 2008 UTC (10 years, 3 months ago) by lobry
new function read.abif

Revision 1495 - Directory Listing
Modified Sun Oct 26 18:25:43 2008 UTC (10 years, 4 months ago) by lobry
generic print for qaw

Revision 1471 - Directory Listing
Modified Sat Oct 11 16:52:56 2008 UTC (10 years, 4 months ago) by lobry
class qaw has gained a generic print method

Revision 1467 - Directory Listing
Modified Sat Oct 11 12:58:49 2008 UTC (10 years, 4 months ago) by lobry
query now allows a missing listname argument

Revision 1463 - Directory Listing
Modified Wed Oct 8 18:42:59 2008 UTC (10 years, 4 months ago) by lobry
backward compatibility patch for outdated R version

Revision 1447 - Directory Listing
Modified Fri Aug 1 08:38:07 2008 UTC (10 years, 6 months ago) by simonpenel


Revision 1444 - Directory Listing
Modified Tue Jul 29 15:56:28 2008 UTC (10 years, 6 months ago) by penel
Original Path: branches/seqinr_cran/pkg/R
renome seqinr en pkg

Revision 1437 - Directory Listing
Modified Thu Jul 17 12:24:14 2008 UTC (10 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
socket -> sockconn

Revision 1433 - Directory Listing
Modified Tue Jul 8 13:31:54 2008 UTC (10 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1431 - Directory Listing
Modified Sun Jun 29 14:40:10 2008 UTC (10 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more arguments

Revision 1428 - Directory Listing
Modified Sat Jun 7 15:55:31 2008 UTC (10 years, 8 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1425 - Directory Listing
Modified Fri Jun 6 14:41:46 2008 UTC (10 years, 8 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1424 - Directory Listing
Modified Fri Jun 6 13:37:06 2008 UTC (10 years, 8 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1420 - Directory Listing
Modified Wed Jun 4 17:09:39 2008 UTC (10 years, 8 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1405 - Directory Listing
Modified Mon May 12 14:35:44 2008 UTC (10 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
do not close all connections

Revision 1399 - Directory Listing
Modified Mon May 12 10:37:56 2008 UTC (10 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
| -> ||

Revision 1396 - Directory Listing
Modified Mon May 12 09:24:47 2008 UTC (10 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
fix bug Indranuj Mukherjee

Revision 1394 - Directory Listing
Modified Sat Mar 15 11:02:40 2008 UTC (10 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
patch bckwd comp

Revision 1391 - Directory Listing
Modified Sat Mar 15 10:02:43 2008 UTC (10 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
modif suggestion CG

Revision 1390 - Directory Listing
Modified Sat Mar 15 08:39:55 2008 UTC (10 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
simplification for freq TRUE

Revision 1382 - Directory Listing
Modified Sat Mar 1 10:25:20 2008 UTC (10 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
two new args

Revision 1371 - Directory Listing
Modified Sun Feb 24 08:13:33 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
use native encoding

Revision 1369 - Directory Listing
Modified Sat Feb 23 13:30:01 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
add init

Revision 1367 - Directory Listing
Modified Sat Feb 23 13:10:06 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
verbose argument

Revision 1365 - Directory Listing
Modified Sat Feb 16 12:48:06 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more arguments

Revision 1364 - Directory Listing
Modified Fri Feb 15 16:47:18 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new verbose argument

Revision 1363 - Directory Listing
Modified Fri Feb 15 16:46:44 2008 UTC (11 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
verbose argument is now forwarded to clientid

Revision 1361 - Directory Listing
Modified Thu Jan 17 10:49:31 2008 UTC (11 years, 1 month ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
phase -> start

Revision 1360 - Directory Listing
Modified Thu Jan 17 09:11:48 2008 UTC (11 years, 1 month ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
frame -> phase

Revision 1358 - Directory Listing
Modified Tue Jan 15 17:28:34 2008 UTC (11 years, 1 month ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more code documentation

Revision 1352 - Directory Listing
Modified Sun Dec 16 14:26:24 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
to avoid codetools warning

Revision 1349 - Directory Listing
Modified Sun Dec 16 14:01:08 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
using a local file for demo

Revision 1342 - Directory Listing
Modified Sat Dec 15 18:09:15 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new argument source

Revision 1341 - Directory Listing
Modified Sat Dec 15 11:40:28 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
maxgensize in dia.bactgensize()

Revision 1321 - Directory Listing
Modified Sun Dec 2 16:27:24 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
initial addition

Revision 1320 - Directory Listing
Modified Sun Dec 2 16:25:27 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
most functions have their own file now

Revision 1319 - Directory Listing
Modified Sun Dec 2 16:24:23 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
readAnnots.socket no more exists

Revision 1318 - Directory Listing
Modified Sun Dec 2 16:22:57 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
using gfrag() instead of getSequenceSocket()

Revision 1317 - Directory Listing
Modified Sun Dec 2 16:22:12 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getKeywordsocket encapsulated

Revision 1316 - Directory Listing
Modified Sun Dec 2 16:21:37 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getLocationSocket encapsulated

Revision 1315 - Directory Listing
Modified Sun Dec 2 16:21:03 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getSequenceSocket encapsulated

Revision 1314 - Directory Listing
Modified Sun Dec 2 16:20:17 2007 UTC (11 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
deprecated functions redundant with isenum

Revision 1307 - Directory Listing
Modified Mon Nov 26 23:46:46 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new generic/methods scheme

Revision 1304 - Directory Listing
Modified Sun Nov 25 23:54:17 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
strip.desc

Revision 1303 - Directory Listing
Modified Sun Nov 25 23:23:38 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getAnnot rewriting

Revision 1301 - Directory Listing
Modified Sun Nov 25 21:11:18 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
bug fix: tolower does not return a list

Revision 1298 - Directory Listing
Modified Sun Nov 25 18:45:20 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
perf optimization

Revision 1297 - Directory Listing
Modified Sun Nov 25 17:20:58 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
R_fasta.R -> read.fasta.R

Revision 1296 - Directory Listing
Modified Sun Nov 25 17:18:49 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
stop if no > found

Revision 1281 - Directory Listing
Modified Wed Nov 21 21:13:30 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
comment lines in FASTA files now supported

Revision 1272 - Directory Listing
Modified Fri Nov 9 10:50:54 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Paste -> paste

Revision 1271 - Directory Listing
Modified Wed Nov 7 21:26:06 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
GCpos() and frame

Revision 1270 - Directory Listing
Modified Wed Nov 7 15:09:45 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
NA.GC

Revision 1269 - Directory Listing
Modified Wed Nov 7 14:36:57 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
GC has now its own file

Revision 1268 - Directory Listing
Modified Wed Nov 7 14:36:09 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
forceToLower

Revision 1267 - Directory Listing
Modified Wed Nov 7 14:35:17 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
return error code

Revision 1251 - Directory Listing
Modified Wed Oct 31 14:53:41 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no more duplicated lists on server

Revision 1247 - Directory Listing
Modified Tue Oct 30 11:09:51 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
socket closed iff error

Revision 1246 - Directory Listing
Modified Tue Oct 30 10:15:16 2007 UTC (11 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
socket connection now closed when just infos are retrieved

Revision 1224 - Directory Listing
Modified Wed Oct 24 07:50:23 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1223 - Directory Listing
Modified Wed Oct 24 07:18:31 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
modlistname = listname

Revision 1220 - Directory Listing
Modified Tue Oct 23 22:25:48 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1219 - Directory Listing
Modified Tue Oct 23 22:25:11 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
closebank() has now its own file

Revision 1216 - Directory Listing
Modified Tue Oct 23 22:12:06 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1215 - Directory Listing
Modified Tue Oct 23 22:00:16 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no more call to prep_requete

Revision 1212 - Directory Listing
Modified Tue Oct 23 21:48:10 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
now uses clientid()

Revision 1209 - Directory Listing
Modified Tue Oct 23 21:26:17 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
release number line fixed

Revision 1208 - Directory Listing
Modified Tue Oct 23 21:22:23 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
now uses acnucopen()

Revision 1204 - Directory Listing
Modified Tue Oct 23 20:41:09 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1194 - Directory Listing
Modified Sun Oct 21 16:40:43 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
gls -> getliststate

Revision 1189 - Directory Listing
Modified Sun Oct 21 15:40:16 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
do not print results from ghelp

Revision 1188 - Directory Listing
Modified Sun Oct 21 15:39:36 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
option to cat results

Revision 1187 - Directory Listing
Modified Sun Oct 21 15:24:46 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
need explicit socket for ghelp() call

Revision 1186 - Directory Listing
Modified Sun Oct 21 10:05:22 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
polish

Revision 1185 - Directory Listing
Modified Sun Oct 21 10:02:00 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Code factorization using function autosocket()

Revision 1183 - Directory Listing
Modified Sat Oct 20 22:50:45 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
now uses ghelp() and kdb()

Revision 1182 - Directory Listing
Modified Sat Oct 20 22:20:13 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
choosebank() has now its own file

Revision 1181 - Directory Listing
Modified Sat Oct 20 22:11:27 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1179 - Directory Listing
Modified Sat Oct 20 21:17:55 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
utility

Revision 1176 - Directory Listing
Modified Sat Oct 20 17:16:48 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1173 - Directory Listing
Modified Sat Oct 20 16:38:42 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1171 - Directory Listing
Modified Sat Oct 20 15:24:43 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1169 - Directory Listing
Modified Sat Oct 20 14:18:12 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1167 - Directory Listing
Modified Sat Oct 20 13:50:27 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1166 - Directory Listing
Modified Sat Oct 20 12:36:06 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no more result returned

Revision 1163 - Directory Listing
Modified Sat Oct 20 10:20:41 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1161 - Directory Listing
Modified Sat Oct 20 09:41:52 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1159 - Directory Listing
Modified Sat Oct 20 09:01:18 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1154 - Directory Listing
Modified Thu Oct 18 13:55:50 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1151 - Directory Listing
Modified Thu Oct 18 12:56:57 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1148 - Directory Listing
Modified Thu Oct 18 08:35:01 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no more subsequence special case

Revision 1146 - Directory Listing
Modified Thu Oct 18 08:03:11 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
socket = auto

Revision 1133 - Directory Listing
Modified Tue Oct 9 17:32:03 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
formatC in getSequenceSocket

Revision 1132 - Directory Listing
Modified Tue Oct 9 17:17:13 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
as.numeric() in as.SeqAcnucWeb()

Revision 1125 - Directory Listing
Modified Sun Oct 7 10:00:54 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
DEV is now an allowed value tagbank parameter in choosebank()

Revision 1120 - Directory Listing
Modified Sat Oct 6 13:31:13 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
modifs for the deletion of the socket slot in objects from class seqAcnucWeb

Revision 1118 - Directory Listing
Modified Sat Oct 6 12:42:43 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no need for the class slot in as.seqAcnucWeb()

Revision 1116 - Directory Listing
Modified Sat Oct 6 12:22:43 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no need for the class slot in as.seqAcnucWeb()

Revision 1115 - Directory Listing
Modified Sat Oct 6 12:17:12 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new method print for objects from class seqAcnucWeb

Revision 1114 - Directory Listing
Modified Sat Oct 6 10:34:37 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
substring() -> substr()

Revision 1112 - Directory Listing
Modified Sat Oct 6 08:57:34 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
function simon() no more usefull

Revision 1111 - Directory Listing
Modified Sat Oct 6 08:56:47 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
parser.socket() is four times faster now

Revision 1110 - Directory Listing
Modified Sat Oct 6 06:10:37 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
query() has now its own file

Revision 1109 - Directory Listing
Modified Mon Oct 1 19:32:54 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
avoiding warnings in GC()

Revision 1108 - Directory Listing
Modified Mon Oct 1 19:29:13 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
... was not forwarded by  GC3()

Revision 1107 - Directory Listing
Modified Mon Oct 1 19:24:23 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
NA propagation in GC()

Revision 1104 - Directory Listing
Modified Mon Oct 1 19:12:16 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
better argument checking in s2c()

Revision 1103 - Directory Listing
Modified Mon Oct 1 18:22:46 2007 UTC (11 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more server answer analysis in getSequenceSocket

Revision 1096 - Directory Listing
Modified Wed Sep 26 09:01:11 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
T -> TRUE

Revision 1093 - Directory Listing
Modified Mon Sep 24 11:07:51 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
removeTrailingSpaces -> trimSpace

Revision 1091 - Directory Listing
Modified Mon Sep 24 11:06:10 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new utility

Revision 1089 - Directory Listing
Modified Sun Sep 23 15:34:14 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
utility function simon() moved to query() where it is used

Revision 1088 - Directory Listing
Modified Sun Sep 23 15:22:07 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
variable nbkw was not used in getKeywordsocket

Revision 1083 - Directory Listing
Modified Sun Sep 23 13:17:20 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no more substring() used

Revision 1080 - Directory Listing
Modified Sun Sep 23 12:31:54 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetools fix and code polish

Revision 1079 - Directory Listing
Modified Thu Sep 20 08:25:44 2007 UTC (11 years, 5 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 1077 - Directory Listing
Modified Wed Sep 19 12:46:14 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetool fix

Revision 1076 - Directory Listing
Modified Tue Sep 18 12:08:08 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
variable onlyparents wasn't used

Revision 1073 - Directory Listing
Modified Tue Sep 18 11:06:01 2007 UTC (11 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
bug fix

Revision 1057 - Directory Listing
Modified Tue Aug 21 11:53:46 2007 UTC (11 years, 6 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Sys.putenv() -> Sys.setenv()

Revision 1056 - Directory Listing
Modified Tue Jul 24 11:28:35 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Bug found by Michael Kube now fixed

Revision 1055 - Directory Listing
Modified Mon Jul 23 13:12:55 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetools warnings fixed

Revision 1054 - Directory Listing
Modified Mon Jul 23 13:04:21 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetolls warning fixed

Revision 1053 - Directory Listing
Modified Mon Jul 23 13:02:27 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetolls warning fixed

Revision 1052 - Directory Listing
Modified Mon Jul 23 13:00:29 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetolls warning fixed

Revision 1051 - Directory Listing
Modified Mon Jul 23 11:08:10 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetools warnings fixed

Revision 1050 - Directory Listing
Modified Mon Jul 23 10:38:36 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
codetools warnings fixed

Revision 1044 - Directory Listing
Modified Sat Jul 21 16:28:11 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
global variable bankname was no more in use, its deletion is now ...  deleted

Revision 1040 - Directory Listing
Modified Fri Jul 20 09:48:11 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
plot.SeqAcnucWeb has now its own file

Revision 1038 - Directory Listing
Modified Fri Jul 20 07:54:28 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
T -> TRUE & F -> FALSE

Revision 1037 - Directory Listing
Modified Fri Jul 20 07:51:49 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
T -> TRUE

Revision 1036 - Directory Listing
Modified Fri Jul 20 07:47:41 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
F -> FALSE

Revision 1031 - Directory Listing
Modified Sat Jul 14 14:57:08 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
local variable charge in computeCharge now clearly used

Revision 1030 - Directory Listing
Modified Sat Jul 14 14:21:42 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
variable m was not used, deleted now

Revision 1029 - Directory Listing
Modified Sat Jul 14 12:46:57 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
error() -> stop()

Revision 1028 - Directory Listing
Modified Sat Jul 14 12:20:55 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
no visible binding problem for variable estimate now fixed

Revision 1027 - Directory Listing
Modified Sat Jul 14 11:41:01 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
partial matching and toupper

Revision 1026 - Directory Listing
Modified Sat Jul 14 10:23:11 2007 UTC (11 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
read.alignment and dist.alignment are now in two different files

Revision 1024 - Directory Listing
Modified Mon Jul 9 14:46:18 2007 UTC (11 years, 7 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
zscore -base- avec formule exacte (Schbath)

Revision 993 - Directory Listing
Modified Tue Apr 24 10:21:56 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
division par zero

Revision 992 - Directory Listing
Modified Sat Apr 21 16:44:20 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
oldGC argument and div/0 check

Revision 991 - Directory Listing
Modified Sat Apr 21 16:44:00 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
utility function

Revision 984 - Directory Listing
Modified Wed Apr 18 10:48:38 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 983 - Directory Listing
Modified Wed Apr 18 09:29:19 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 980 - Directory Listing
Modified Wed Apr 18 05:05:15 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 978 - Directory Listing
Modified Tue Apr 17 12:49:54 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
s2n() has its own file

Revision 976 - Directory Listing
Modified Tue Apr 17 11:27:54 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
alphabet argument added

Revision 974 - Directory Listing
Modified Tue Apr 17 09:07:07 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Gabriel Valiente suggestion

Revision 973 - Directory Listing
Modified Tue Apr 17 08:48:08 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
tolower

Revision 972 - Directory Listing
Modified Tue Apr 17 08:41:24 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
tolower

Revision 968 - Directory Listing
Modified Sun Apr 15 09:29:20 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
ambiguous argument in call to function comp()

Revision 967 - Directory Listing
Modified Sun Apr 15 08:49:55 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
function comp moved in its own file

Revision 966 - Directory Listing
Modified Sun Apr 15 08:48:37 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
ambiguous bases

Revision 965 - Directory Listing
Modified Sat Apr 14 16:25:26 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
function invers() deleted

Revision 964 - Directory Listing
Modified Sat Apr 14 16:00:19 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
handling ambiguous bases

Revision 961 - Directory Listing
Modified Sat Apr 14 15:40:16 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
handling ambiguous bases

Revision 960 - Directory Listing
Modified Sat Apr 14 11:10:08 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 958 - Directory Listing
Modified Fri Apr 13 16:57:57 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more user options

Revision 957 - Directory Listing
Modified Fri Apr 13 16:57:04 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
F -> FALSE

Revision 950 - Directory Listing
Modified Thu Apr 12 21:06:58 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
code polishing

Revision 949 - Directory Listing
Modified Thu Apr 12 09:23:41 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
NAstring argument

Revision 948 - Directory Listing
Modified Wed Apr 11 14:21:03 2007 UTC (11 years, 10 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Stope si la plateforme est windows

Revision 943 - Directory Listing
Modified Thu Apr 5 08:31:40 2007 UTC (11 years, 10 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
linux

Revision 942 - Directory Listing
Modified Thu Mar 29 15:45:27 2007 UTC (11 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
forceToLower

Revision 941 - Directory Listing
Modified Wed Mar 28 20:31:26 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 938 - Directory Listing
Modified Wed Mar 28 13:57:13 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 937 - Directory Listing
Modified Wed Mar 28 10:12:13 2007 UTC (11 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
ambiguous base case

Revision 934 - Directory Listing
Modified Tue Mar 27 16:16:37 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 933 - Directory Listing
Modified Tue Mar 27 15:56:39 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 926 - Directory Listing
Modified Mon Mar 26 12:39:50 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
is.null dans oriloc

Revision 923 - Directory Listing
Modified Sun Mar 25 14:24:59 2007 UTC (11 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
1:length(n) -> seq_len(n)

Revision 922 - Directory Listing
Modified Sun Mar 25 13:57:54 2007 UTC (11 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
1:length(n) -> seq_len(n)

Revision 921 - Directory Listing
Modified Sun Mar 25 13:47:47 2007 UTC (11 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
code polish

Revision 915 - Directory Listing
Modified Sun Mar 11 14:07:12 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
undef type for get.ncbi

Revision 913 - Directory Listing
Modified Sun Mar 11 14:03:28 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
gbk2g2 eukaryotic version

Revision 909 - Directory Listing
Modified Sat Mar 10 15:49:03 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 908 - Directory Listing
Modified Sat Mar 10 15:36:30 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 901 - Directory Listing
Modified Sat Mar 10 14:05:25 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 900 - Directory Listing
Modified Sat Mar 10 13:39:30 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 897 - Directory Listing
Modified Thu Mar 8 16:49:51 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 896 - Directory Listing
Modified Thu Mar 8 16:49:25 2007 UTC (11 years, 11 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
rearranged

Revision 895 - Directory Listing
Modified Thu Mar 8 12:28:09 2007 UTC (11 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
remove empty lines from lastres

Revision 878 - Directory Listing
Modified Fri Mar 2 18:14:51 2007 UTC (11 years, 11 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 876 - Directory Listing
Modified Thu Mar 1 15:41:30 2007 UTC (11 years, 11 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 875 - Directory Listing
Modified Thu Mar 1 15:33:17 2007 UTC (11 years, 11 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 873 - Directory Listing
Modified Thu Mar 1 12:17:00 2007 UTC (11 years, 11 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 871 - Directory Listing
Modified Wed Feb 21 17:15:36 2007 UTC (12 years ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 866 - Directory Listing
Modified Tue Jan 30 13:47:54 2007 UTC (12 years ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 861 - Directory Listing
Modified Tue Jan 9 11:06:04 2007 UTC (12 years, 1 month ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
check is.null in parser.socket

Revision 859 - Directory Listing
Modified Mon Jan 8 17:35:24 2007 UTC (12 years, 1 month ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
vectorization

Revision 856 - Directory Listing
Modified Fri Jan 5 16:54:30 2007 UTC (12 years, 1 month ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Mofif pour la vesrion compressee

Revision 854 - Directory Listing
Modified Mon Dec 18 09:51:59 2006 UTC (12 years, 2 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Defaut de  zlib mis a FALSE

Revision 846 - Directory Listing
Modified Mon Nov 20 16:37:53 2006 UTC (12 years, 3 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Utilsiation de la source C pour les donnes compressees.

Revision 844 - Directory Listing
Modified Sun Nov 19 13:16:46 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
tmp2

Revision 843 - Directory Listing
Modified Sun Nov 19 13:14:02 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
nopss

Revision 842 - Directory Listing
Modified Sun Nov 19 13:13:24 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
tmp

Revision 841 - Directory Listing
Modified Sun Nov 19 13:06:32 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
tmp

Revision 840 - Directory Listing
Modified Sun Nov 19 13:02:21 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 839 - Directory Listing
Modified Sun Nov 19 13:00:24 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 837 - Directory Listing
Modified Fri Nov 17 14:20:40 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
url

Revision 834 - Directory Listing
Modified Fri Nov 17 10:51:57 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
glimmer3

Revision 830 - Directory Listing
Modified Sun Oct 29 11:28:55 2006 UTC (12 years, 3 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
as.string default

Revision 828 - Directory Listing
Modified Wed Oct 25 11:08:06 2006 UTC (12 years, 4 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
utilistaion d'une fonction c pour la recuperation par socket en mode compression zlib

Revision 824 - Directory Listing
Modified Thu Oct 19 12:01:41 2006 UTC (12 years, 4 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 823 - Directory Listing
Modified Thu Oct 19 11:59:32 2006 UTC (12 years, 4 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Ajour de la fonction extractseqs

Revision 822 - Directory Listing
Modified Tue Oct 17 16:58:11 2006 UTC (12 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
glr

Revision 821 - Directory Listing
Modified Tue Oct 17 10:14:01 2006 UTC (12 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 817 - Directory Listing
Modified Sun Oct 15 16:28:37 2006 UTC (12 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
clfcd()

Revision 814 - Directory Listing
Modified Sat Oct 14 10:17:09 2006 UTC (12 years, 4 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
xxxxx in SMJ

Revision 812 - Directory Listing
Modified Sun Sep 10 12:26:19 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
[ and ]

Revision 811 - Directory Listing
Modified Sun Sep 10 12:13:42 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
is.na

Revision 810 - Directory Listing
Modified Sun Sep 10 10:40:27 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
hide fromchar and tochar

Revision 809 - Directory Listing
Modified Sun Sep 10 10:14:09 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
stresc

Revision 807 - Directory Listing
Modified Sun Sep 10 09:48:02 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getType in its own file

Revision 806 - Directory Listing
Modified Sun Sep 10 09:28:22 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
sname option

Revision 803 - Directory Listing
Modified Fri Sep 8 20:18:20 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
readsmj as a single file is better

Revision 802 - Directory Listing
Modified Fri Sep 8 10:16:53 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
new function readfirstrec()

Revision 801 - Directory Listing
Modified Fri Sep 8 09:02:08 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
getType(socket = auto)

Revision 800 - Directory Listing
Modified Fri Sep 8 08:02:23 2006 UTC (12 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
File -> file in read.alignment()

Revision 764 - Directory Listing
Modified Sat Aug 26 10:53:41 2006 UTC (12 years, 6 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more typo options in LaTeX tables

Revision 763 - Directory Listing
Modified Fri Aug 25 20:43:48 2006 UTC (12 years, 6 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
char ctrl size

Revision 754 - Directory Listing
Modified Wed Aug 23 15:42:02 2006 UTC (12 years, 6 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
improved consistancy between a() and aaa()

Revision 749 - Directory Listing
Modified Wed Jul 26 08:16:43 2006 UTC (12 years, 7 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
added some lines to the human curated part

Revision 747 - Directory Listing
Modified Sun Jul 23 10:07:48 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
dia=F

Revision 737 - Directory Listing
Modified Sun Jul 9 13:28:47 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
dotPlot

Revision 736 - Directory Listing
Modified Fri Jul 7 15:49:07 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
comments on readAnnots.socket

Revision 735 - Directory Listing
Modified Thu Jul 6 13:55:40 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
nbl =10000

Revision 731 - Directory Listing
Modified Mon Jul 3 13:48:47 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
crelistfromclientdata

Revision 728 - Directory Listing
Modified Sun Jul 2 13:55:50 2006 UTC (12 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 718 - Directory Listing
Modified Wed May 17 16:04:33 2006 UTC (12 years, 9 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
reverse.align

Revision 716 - Directory Listing
Modified Tue May 16 08:43:40 2006 UTC (12 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
open mode agrument added

Revision 702 - Directory Listing
Modified Sat May 13 06:32:50 2006 UTC (12 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
NA.rscu argument

Revision 697 - Directory Listing
Modified Fri May 12 12:39:26 2006 UTC (12 years, 9 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
write.fasta

Revision 695 - Directory Listing
Modified Fri May 12 09:28:37 2006 UTC (12 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more arguments

Revision 692 - Directory Listing
Modified Tue May 2 07:17:34 2006 UTC (12 years, 9 months ago) by necsulea
Original Path: branches/seqinr_cran/seqinr/R
 nomseq[[i]] au lieu de nomseq

Revision 684 - Directory Listing
Modified Mon May 1 10:18:40 2006 UTC (12 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
modif getTrans.SeqAcnucWeb seq->object

Revision 680 - Directory Listing
Modified Fri Apr 28 09:14:34 2006 UTC (12 years, 9 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
test acgt

Revision 678 - Directory Listing
Modified Thu Apr 27 07:28:15 2006 UTC (12 years, 10 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
upper case option

Revision 677 - Directory Listing
Modified Mon Apr 3 07:59:15 2006 UTC (12 years, 10 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Modification pour homogeneite avec GetFromSequence.Rd

Revision 667 - Directory Listing
Modified Thu Mar 23 10:11:45 2006 UTC (12 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
patch timeout prep_requete

Revision 656 - Directory Listing
Modified Fri Mar 10 13:43:51 2006 UTC (12 years, 11 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
as.string en plus

Revision 652 - Directory Listing
Modified Wed Mar 8 15:05:20 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Rajout d'une fonction GC1, modif de la doc correspondante

Revision 649 - Directory Listing
Modified Wed Mar 8 11:03:00 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Calcul du rho de Karlin, et du zscore qui en d�ve

Revision 647 - Directory Listing
Modified Fri Mar 3 16:35:35 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
J'ai �min�a possibilit�auto" de l'option 'numcode'

Revision 645 - Directory Listing
Modified Thu Mar 2 13:51:23 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Rajout de l'option 'freq' pour les fr�ences de mots

Revision 641 - Directory Listing
Modified Wed Mar 1 09:22:19 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Nettoyage du code pour �e conforme aux directives du CRAN

Revision 640 - Directory Listing
Modified Wed Mar 1 09:11:47 2006 UTC (12 years, 11 months ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Nettoyage du code pour �e conforme aux directives du CRAN

Revision 626 - Directory Listing
Modified Mon Feb 13 19:57:58 2006 UTC (13 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
more conformity tests on input

Revision 623 - Directory Listing
Modified Mon Feb 13 15:06:49 2006 UTC (13 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
factorisation du code de mkresult

Revision 622 - Directory Listing
Modified Mon Feb 13 14:53:49 2006 UTC (13 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
ajout warning si moins de deux sequences et retour NA

Revision 621 - Directory Listing
Modified Mon Feb 13 14:31:57 2006 UTC (13 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
tmp est vire

Revision 619 - Directory Listing
Modified Sat Feb 11 10:09:03 2006 UTC (13 years ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
mode debug

Revision 616 - Directory Listing
Modified Wed Feb 8 10:59:59 2006 UTC (13 years ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Optimisation des fonctions GC, GC2 et GC3

Revision 614 - Directory Listing
Modified Tue Feb 7 17:35:20 2006 UTC (13 years ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
Fonction de permutation d'une s�ence selon diff�nts mod�s

Revision 609 - Directory Listing
Modified Mon Jan 30 11:26:51 2006 UTC (13 years ago) by palmeira
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 594 - Directory Listing
Modified Thu Dec 22 19:53:36 2005 UTC (13 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 578 - Directory Listing
Modified Thu Dec 15 14:41:56 2005 UTC (13 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
latexfile

Revision 573 - Directory Listing
Modified Tue Dec 6 12:45:40 2005 UTC (13 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
reecriture complete, gain facteur 10

Revision 570 - Directory Listing
Modified Tue Dec 6 10:46:36 2005 UTC (13 years, 2 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
petites modifs du code de uco

Revision 567 - Directory Listing
Modified Mon Nov 7 14:25:02 2005 UTC (13 years, 3 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Test cvs pour leo.

Revision 566 - Directory Listing
Modified Thu Nov 3 14:02:47 2005 UTC (13 years, 3 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Suppression du bug dans gbk2g2 signale par Anouk:

je voulais juste te signaler un (tout) petit bug que je  viens de  d�uvrir dans une fonction de seqinr,  :
c'est dans  la fonction gbk2g2 :

idx5p <- grep(">", input)
   if (length(idx5p != 0))
       warning("5' partial genes encountered (no output):",
           idx5p)
   idx3p <- grep("<", input)
   if (length(idx5p != 0))
       warning("3' partial genes encountered (no output):",
           idx3p)
   idxjoin <- grep("join", input)
   if (length(idx5p != 0))
       warning("join encountered (no output):", idxjoin)

Revision 561 - Directory Listing
Modified Tue Oct 11 16:17:51 2005 UTC (13 years, 4 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Modif de R_socket.R : un nb d'annotations egale a 0 n'est plus autoris�

Revision 549 - Directory Listing
Modified Sat Jul 23 16:10:11 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
detab et polissage

Revision 546 - Directory Listing
Modified Fri Jul 22 10:14:43 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
mots clefs

Revision 545 - Directory Listing
Modified Fri Jul 22 09:52:25 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 544 - Directory Listing
Modified Fri Jul 22 09:50:50 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Resilution des bug d'affichage des annotations et de recupretation des mots-clefs

Revision 543 - Directory Listing
Modified Fri Jul 22 09:03:41 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
closebank() ferme les connections

Revision 542 - Directory Listing
Modified Thu Jul 21 23:38:03 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
backup

Revision 541 - Directory Listing
Modified Thu Jul 21 23:16:29 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
ajout de closebank()

Revision 540 - Directory Listing
Modified Thu Jul 21 21:20:20 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
choosebank(bonnebanque) retourne un resultat invisible

Revision 539 - Directory Listing
Modified Thu Jul 21 20:50:17 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
MAJEUR: changement de l'ordre des parametres de query()

Revision 538 - Directory Listing
Modified Thu Jul 21 20:35:03 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
le parametre invisible de query est maintenant TRUE par defaut

Revision 536 - Directory Listing
Modified Thu Jul 21 18:59:06 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
option tagbank dans choosebank

Revision 533 - Directory Listing
Modified Thu Jul 21 13:18:09 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
verbose de auto de query

Revision 530 - Directory Listing
Modified Thu Jul 21 13:09:56 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Modif pour recupere le socket de la banque courante qund le socket n'est pas
specifie

Revision 529 - Directory Listing
Modified Thu Jul 21 09:55:45 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Ajout de la release, du statut, et des details de la banque dans les elements
associ�a la banque

Revision 528 - Directory Listing
Modified Thu Jul 21 09:09:08 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
argument virtual

Revision 527 - Directory Listing
Modified Wed Jul 20 16:13:19 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 526 - Directory Listing
Modified Wed Jul 20 16:00:11 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 525 - Directory Listing
Modified Wed Jul 20 15:58:55 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 524 - Directory Listing
Modified Wed Jul 20 15:47:46 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
modif afficage info banque a l'ouverture

Revision 523 - Directory Listing
Modified Wed Jul 20 15:05:37 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Ajout de l'affichage du decsriptif de la banque a l'ouverture

Revision 517 - Directory Listing
Modified Tue Jul 19 17:02:12 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
un patch pas beau pour le pb du timeout dans query

Revision 516 - Directory Listing
Modified Tue Jul 19 14:16:56 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
essai

Revision 514 - Directory Listing
Modified Tue Jul 19 14:11:43 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Modif des classes SeqAcbycWeb et de query pour recupere le nom, la longueur,
 la frame et le code genetique associes a une sequence.
Modifs mineures...

Revision 512 - Directory Listing
Modified Mon Jul 18 22:24:20 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
J'ai vire la boucle de query et gagne un facteur 15 pour une requete d'une liste de 892 elements: de 60 a 4 secondes sur mon ADSL...

Revision 511 - Directory Listing
Modified Mon Jul 18 21:53:54 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Quelques commentaires sur la boucle de query

Revision 509 - Directory Listing
Modified Mon Jul 18 20:40:05 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Deplacement de prep_requete de query a choosebank

Revision 508 - Directory Listing
Modified Mon Jul 18 19:30:15 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Que du cosmetique

Revision 507 - Directory Listing
Modified Mon Jul 18 16:28:54 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
Blindage de clientID et deplacement au bon endroit

Revision 502 - Directory Listing
Modified Mon Jul 18 09:33:11 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 501 - Directory Listing
Modified Mon Jul 18 09:28:04 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 500 - Directory Listing
Modified Mon Jul 18 08:56:41 2005 UTC (13 years, 7 months ago) by penel
Original Path: branches/seqinr_cran/seqinr/R
Modifs:
	donne un identifiant (seqinr_version) au client
	plus de probleme de longueur  (formatC(length, format = "d"))
	affiche un warning alieu de s'arreter quand il ya des caracteres non iupac

Revision 499 - Directory Listing
Modified Sun Jul 17 19:57:35 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
inherits au lieu de ==

Revision 497 - Directory Listing
Modified Sat Jul 16 15:26:14 2005 UTC (13 years, 7 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
*** empty log message ***

Revision 490 - Directory Listing
Modified Wed Mar 2 09:53:49 2005 UTC (13 years, 11 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_fasta.R

Revision 489 - Directory Listing
Modified Wed Mar 2 09:41:32 2005 UTC (13 years, 11 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
	to modify the encoding in emacs: ctrl x ret f unix

Revision 487 - Directory Listing
Modified Tue Mar 1 09:26:29 2005 UTC (13 years, 11 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
	I replaced the function scan() by readLines()

Revision 485 - Directory Listing
Modified Tue Feb 8 12:47:19 2005 UTC (14 years ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
util.R

Revision 482 - Directory Listing
Modified Thu Dec 16 08:04:53 2004 UTC (14 years, 2 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R

I added some test in s2c().

Revision 481 - Directory Listing
Modified Thu Dec 16 08:02:50 2004 UTC (14 years, 2 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R

I removed the "rounds" in uco().

Revision 469 - Directory Listing
Modified Fri Oct 1 08:23:19 2004 UTC (14 years, 4 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
AAstat.R

Revision 459 - Directory Listing
Modified Tue Sep 21 09:12:18 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 451 - Directory Listing
Modified Wed Sep 15 14:11:01 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
AAstat.R

Revision 450 - Directory Listing
Modified Wed Sep 15 13:50:13 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
ClassSeq.R

Revision 449 - Directory Listing
Modified Wed Sep 15 13:39:14 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
AAstat.R

Revision 448 - Directory Listing
Modified Wed Sep 15 13:26:11 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
AAstat.R

Revision 447 - Directory Listing
Modified Wed Sep 15 13:25:45 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
PI.R

Revision 446 - Directory Listing
Modified Tue Sep 14 11:34:26 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 441 - Directory Listing
Modified Fri Sep 10 14:18:02 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 440 - Directory Listing
Modified Fri Sep 10 14:10:11 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 439 - Directory Listing
Modified Fri Sep 10 13:33:49 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 437 - Directory Listing
Modified Fri Sep 10 12:36:53 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
	kaks

Revision 429 - Directory Listing
Modified Fri Sep 3 14:21:58 2004 UTC (14 years, 5 months ago) by lobry
Original Path: branches/seqinr_cran/seqinr/R
I have added a re-try in case of failure of first estimate

Revision 421 - Directory Listing
Modified Fri Sep 3 08:54:29 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
mkbank.R

Revision 420 - Directory Listing
Modified Fri Sep 3 08:53:57 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
R_socket.R

Revision 414 - Directory Listing
Modified Fri Sep 3 08:29:38 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
ClassSeq.R

Revision 411 - Directory Listing
Modified Fri Sep 3 08:01:21 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
vesion cran

Revision 410 - Directory Listing
Modified Fri Sep 3 07:57:42 2004 UTC (14 years, 5 months ago) by charif
Original Path: branches/seqinr_cran/seqinr/R
cran version

Revision 409 - Directory Listing
Modified Wed Sep 1 12:24:48 2004 UTC (14 years, 5 months ago) by
Original Path: branches/seqinr_cran/seqinr/R
This commit was manufactured by cvs2svn to create branch 'seqinr_cran'.

Revision 407 - Directory Listing
Modified Wed Sep 1 12:24:28 2004 UTC (14 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
get.ncbi.R

Revision 406 - Directory Listing
Modified Tue Aug 31 14:50:01 2004 UTC (14 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
uco.R

Revision 403 - Directory Listing
Modified Tue Aug 31 13:48:55 2004 UTC (14 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 402 - Directory Listing
Modified Tue Aug 31 07:56:13 2004 UTC (14 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 397 - Directory Listing
Modified Fri Aug 27 08:03:46 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
uco.R

Revision 391 - Directory Listing
Modified Fri Aug 20 12:35:03 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
	I modified the function getAnnots.socket

Revision 387 - Directory Listing
Modified Thu Aug 19 09:50:08 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
	I improved the function (in particular for the calcul of the rscu)

Revision 383 - Directory Listing
Modified Thu Aug 5 13:54:29 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
kaks.R

Revision 380 - Directory Listing
Modified Thu Aug 5 13:51:27 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 379 - Directory Listing
Modified Tue Aug 3 11:25:23 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
PI.R

Revision 378 - Directory Listing
Modified Tue Aug 3 10:54:11 2004 UTC (14 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 375 - Directory Listing
Modified Fri Jul 23 12:55:18 2004 UTC (14 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
PI.R

Revision 372 - Directory Listing
Modified Tue May 18 13:29:19 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
lib.R

Revision 368 - Directory Listing
Modified Tue May 18 06:42:38 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
util.R

Revision 367 - Directory Listing
Modified Tue May 18 06:24:52 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
lib.R

Revision 366 - Directory Listing
Modified Fri May 14 13:26:00 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
uco.R

Revision 365 - Directory Listing
Modified Fri May 14 08:54:11 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
R_socket.R

Revision 362 - Directory Listing
Modified Mon May 3 08:33:50 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
R_socket.R

Revision 361 - Directory Listing
Modified Mon May 3 08:33:36 2004 UTC (14 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 360 - Directory Listing
Modified Fri Apr 2 09:16:54 2004 UTC (14 years, 10 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 355 - Directory Listing
Modified Fri Apr 2 07:10:54 2004 UTC (14 years, 10 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 354 - Directory Listing
Modified Fri Apr 2 07:09:21 2004 UTC (14 years, 10 months ago) by charif
Original Path: trunk/seqinr/R
	This function allows to read an alignment

Revision 348 - Directory Listing
Modified Tue Mar 23 15:35:39 2004 UTC (14 years, 11 months ago) by charif
Original Path: trunk/seqinr/R
	I modified the function chosebank()

Revision 347 - Directory Listing
Modified Tue Feb 24 14:56:14 2004 UTC (15 years ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 343 - Directory Listing
Modified Mon Feb 23 15:28:08 2004 UTC (15 years ago) by charif
Original Path: trunk/seqinr/R
	I modified some options

Revision 339 - Directory Listing
Modified Mon Jan 26 15:49:57 2004 UTC (15 years, 1 month ago) by charif
Original Path: trunk/seqinr/R
mase.R

Revision 336 - Directory Listing
Modified Tue Jan 20 16:23:45 2004 UTC (15 years, 1 month ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 335 - Directory Listing
Modified Tue Jan 20 16:23:24 2004 UTC (15 years, 1 month ago) by charif
Original Path: trunk/seqinr/R
	I added the following functions: getExon and getKeyword

Revision 331 - Directory Listing
Modified Sat Nov 22 11:09:02 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 329 - Directory Listing
Modified Fri Nov 21 14:53:48 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 324 - Directory Listing
Modified Fri Nov 21 09:59:37 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
lib.R

Revision 322 - Directory Listing
Modified Fri Nov 21 08:35:58 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
util.R

Revision 321 - Directory Listing
Modified Fri Nov 21 08:23:07 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	i added the RSCU

Revision 319 - Directory Listing
Modified Fri Nov 21 06:50:43 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	i changed the name of th server: pbil -> pbil.univ-lyon1.fr

Revision 314 - Directory Listing
Modified Thu Nov 20 12:44:22 2003 UTC (15 years, 3 months ago) by lobry
Original Path: trunk/seqinr/R
url changed

Revision 313 - Directory Listing
Modified Thu Nov 20 12:19:02 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
util.R

Revision 309 - Directory Listing
Modified Thu Nov 20 12:07:54 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
util.R

Revision 306 - Directory Listing
Modified Thu Nov 20 10:47:19 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 305 - Directory Listing
Modified Thu Nov 20 10:45:48 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 297 - Directory Listing
Modified Wed Nov 19 14:20:00 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 295 - Directory Listing
Modified Wed Nov 19 14:13:55 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 291 - Directory Listing
Modified Wed Nov 19 13:37:43 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 290 - Directory Listing
Modified Wed Nov 19 13:30:27 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 289 - Directory Listing
Modified Wed Nov 19 13:26:40 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 286 - Directory Listing
Modified Wed Nov 19 12:59:43 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 285 - Directory Listing
Modified Wed Nov 19 12:28:38 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
skew.R

Revision 282 - Directory Listing
Modified Wed Nov 19 12:08:30 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 280 - Directory Listing
Modified Tue Nov 18 16:01:32 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
    lalala

Revision 277 - Directory Listing
Modified Tue Nov 18 15:34:42 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
    remove .last.lib

Revision 276 - Directory Listing
Modified Mon Nov 17 16:16:43 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 275 - Directory Listing
Modified Mon Nov 17 16:07:03 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
R_fasta.R

Revision 274 - Directory Listing
Modified Mon Nov 17 15:45:52 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
R_fasta.R

Revision 266 - Directory Listing
Modified Mon Nov 17 14:36:37 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
scanAK.R

Revision 265 - Directory Listing
Modified Mon Nov 17 11:51:46 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
R_fasta.R

Revision 264 - Directory Listing
Modified Mon Nov 17 11:50:54 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
R_fasta.R

Revision 262 - Directory Listing
Modified Mon Nov 17 09:45:10 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq

Revision 260 - Directory Listing
Modified Mon Nov 17 09:18:17 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 258 - Directory Listing
Modified Mon Nov 17 09:12:06 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	j'ai rajout�es annotations comme attribut de la s�ence

Revision 257 - Directory Listing
Modified Fri Nov 14 13:04:51 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Changement du num� du port pour les sockets. Desormais le port 5557 est ouvert
�'exterieur.

Revision 254 - Directory Listing
Modified Wed Nov 12 14:40:28 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 253 - Directory Listing
Modified Mon Nov 10 15:19:43 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
R_acnuc.R

Revision 251 - Directory Listing
Modified Fri Nov 7 15:00:33 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	rajout d'un saut de ligne

Revision 249 - Directory Listing
Modified Fri Nov 7 10:05:32 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Ce fichier a � remani�n grande partie. Des classes de s�ences ont
� supprim�, d'autres ajout� et le nom des autres classes a � chang�

Revision 248 - Directory Listing
Modified Fri Nov 7 10:03:30 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Etant donn�e choix qui a � fait de repr�nter les s�uncs d'ADN
par des minuscules, les fonctions ont � corrig�. La fonction uco2 a �
rajout�

Revision 247 - Directory Listing
Modified Fri Nov 7 10:01:19 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Etant donn�e choix qui a � fait de repr�nter les s�uncs d'ADN
par des minuscules, les fonctions ont � corrig�.

Revision 246 - Directory Listing
Modified Fri Nov 7 09:59:21 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Ces fonctions sont mises entre parenth� pendant un moment

Revision 245 - Directory Listing
Modified Fri Nov 7 09:58:20 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Cette fonction se trouve d�rmais dans R_fasta.R

Revision 244 - Directory Listing
Modified Fri Nov 7 09:55:04 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	fonctions pour la  lecture de fichiers fasta.

Revision 243 - Directory Listing
Modified Fri Nov 7 09:53:20 2003 UTC (15 years, 3 months ago) by charif
Original Path: trunk/seqinr/R
	Voici les fonctions permettant d'interroger les banques ACNUC
par internet grace aux sockets.

Revision 241 - Directory Listing
Modified Fri Oct 31 16:11:31 2003 UTC (15 years, 3 months ago) by lobry
Original Path: trunk/seqinr/R
I have added a new functionality allowing to rotate the genome.

Revision 240 - Directory Listing
Modified Mon Oct 27 16:39:38 2003 UTC (15 years, 4 months ago) by charif
Original Path: trunk/seqinr/R
R_acnuc.R

Revision 239 - Directory Listing
Modified Mon Oct 27 15:57:47 2003 UTC (15 years, 4 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 238 - Directory Listing
Modified Mon Oct 27 15:40:50 2003 UTC (15 years, 4 months ago) by charif
Original Path: trunk/seqinr/R
tablecode.R

Revision 234 - Directory Listing
Modified Mon Oct 27 15:10:45 2003 UTC (15 years, 4 months ago) by charif
Original Path: trunk/seqinr/R
ClassSeq.R

Revision 232 - Directory Listing
Modified Wed Oct 22 11:51:25 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
Darwin and SunOS platforms implementation

Revision 231 - Directory Listing
Modified Wed Oct 22 11:49:02 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
Darwin and SunOS platforms implementation

Revision 229 - Directory Listing
Modified Mon Oct 20 10:53:52 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
first release

Revision 227 - Directory Listing
Modified Mon Oct 20 10:48:19 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
New functionality: works with single gbk file

Revision 226 - Directory Listing
Modified Wed Oct 15 14:11:56 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
change output separator to space

Revision 225 - Directory Listing
Modified Wed Oct 15 12:46:42 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
local use of ftp client

Revision 223 - Directory Listing
Modified Mon Oct 13 20:57:17 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
Attempt to list ftp dirs

Revision 222 - Directory Listing
Modified Mon Oct 13 12:10:04 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
adaptation to read.fasta

Revision 221 - Directory Listing
Modified Mon Oct 13 11:48:20 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 216 - Directory Listing
Modified Wed Oct 8 09:25:39 2003 UTC (15 years, 4 months ago) by lobry
Original Path: trunk/seqinr/R
bactgensize.R

Revision 215 - Directory Listing
Modified Wed Sep 24 08:24:40 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
R_acnuc.R

Revision 214 - Directory Listing
Modified Wed Sep 24 07:56:40 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
translate.R

Revision 213 - Directory Listing
Modified Mon Sep 22 12:16:39 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
R_acnuc.R

Revision 212 - Directory Listing
Modified Mon Sep 22 11:54:40 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
R_acnuc.R

Revision 211 - Directory Listing
Modified Mon Sep 22 09:48:40 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
mkbank.R

Revision 210 - Directory Listing
Modified Mon Sep 22 08:43:42 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
	I added (.

Revision 209 - Directory Listing
Modified Tue Sep 16 08:52:13 2003 UTC (15 years, 5 months ago) by lobry
Original Path: trunk/seqinr/R
Just a CVS test, ignore.

Revision 201 - Directory Listing
Modified Thu Sep 4 12:00:16 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
	Nouvelle fonction permettant de g�rer des banques structur� ACNUC

Revision 200 - Directory Listing
Modified Wed Sep 3 11:39:08 2003 UTC (15 years, 5 months ago) by charif
Original Path: trunk/seqinr/R
	I added a test to know if an ACNUC data base is already in use.

Revision 199 - Directory Listing
Modified Fri Aug 1 09:14:12 2003 UTC (15 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 196 - Directory Listing
Modified Fri Aug 1 09:08:32 2003 UTC (15 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
	I created a new function plotGC

Revision 195 - Directory Listing
Modified Wed Jul 30 12:27:04 2003 UTC (15 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 194 - Directory Listing
Modified Wed Jul 30 12:12:18 2003 UTC (15 years, 6 months ago) by charif
Original Path: trunk/seqinr/R
	I optimized the function.

Revision 193 - Directory Listing
Modified Fri Jul 25 11:36:39 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	j'ai rendu visible SEQINR.UTIL

Revision 192 - Directory Listing
Modified Thu Jul 24 12:55:38 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	J'ai modifi�es classes et rajout�a m�ode generique "summary" qui
donne le GC et la compo en base pour la classe SeqFastadna et qui donne le
pourcentage de chaque AA ainsi que le pourcentage des AA appartenant �es classes
physico-chimiques donn� pour la classe SeqFastAA.

Revision 191 - Directory Listing
Modified Thu Jul 24 12:52:47 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	J'ai ot�e . devant l'objet SEQINR.UTIL...

Revision 190 - Directory Listing
Modified Thu Jul 24 12:52:19 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	J'ai rajout�'attribut nom pour les classes de sequences SeqFastaAA et
SeqFastadna.

Revision 188 - Directory Listing
Modified Wed Jul 23 15:22:37 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	j'ai rajout�es fonctions g�riques pour les classes de s�ences

Revision 187 - Directory Listing
Modified Wed Jul 23 15:17:02 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 186 - Directory Listing
Modified Wed Jul 23 15:10:38 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	Ce fichier r�lte de la concat�tion de toutes les "petites" functions

Revision 185 - Directory Listing
Modified Wed Jul 23 15:08:44 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 166 - Directory Listing
Modified Mon Jun 30 15:18:44 2003 UTC (15 years, 7 months ago) by charif
Original Path: trunk/seqinr/R
	I corrected some errors

Revision 145 - Directory Listing
Modified Tue Jun 17 13:41:02 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
I have changed dotchart.uco() so that now an invisible list is returned
with all the infos to add extra graphics on the plot.

Revision 142 - Directory Listing
Modified Fri Jun 13 13:18:36 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
I have fixed a bug in dotchart.uco() that was linked to a non standard
use of s2c().

Revision 140 - Directory Listing
Modified Thu Jun 12 15:28:17 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
In function choosebank(), when printing ACNUC bank infos, I have changed
the print(foo) by a cat(foo,"\n") just to save space for the output (no
more line numbering and quotes).

Revision 138 - Directory Listing
Modified Thu Jun 12 12:32:30 2003 UTC (15 years, 8 months ago) by charif
Original Path: trunk/seqinr/R
	I added s2c

Revision 137 - Directory Listing
Modified Thu Jun 12 12:31:17 2003 UTC (15 years, 8 months ago) by charif
Original Path: trunk/seqinr/R
	I changed function name

Revision 136 - Directory Listing
Modified Thu Jun 12 12:11:51 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
I have added two new things within the choosebank() function:

i) Try now to detect if seqinr is running thru the RWeb interface
   at pbil.univ-lyon1.fr so as to assign correctly banks location

ii) Print the basic infos about the database

Revision 134 - Directory Listing
Modified Fri Jun 6 13:19:57 2003 UTC (15 years, 8 months ago) by charif
Original Path: trunk/seqinr/R
	I added the function s2c writing in C language. This function replace
         the old version of s2c.

Revision 133 - Directory Listing
Modified Fri Jun 6 13:17:20 2003 UTC (15 years, 8 months ago) by charif
Original Path: trunk/seqinr/R
	I removed this function in oreder to replace it by a C function
        to speed up the execution

Revision 132 - Directory Listing
Modified Fri Jun 6 13:02:36 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
I have changed the read.fasta()[[1]] to read.fasta[[1]][[1]] to get the
default genome for demo.

Revision 130 - Directory Listing
Modified Thu Jun 5 13:31:54 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
I have added a new function, dotchart.uco() to display a Cleveland dotplot
for codon usage.

Revision 129 - Directory Listing
Modified Thu Jun 5 12:02:44 2003 UTC (15 years, 8 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 126 - Directory Listing
Modified Wed May 28 16:30:08 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have shortened the title and homogenized horizontal lines length.

Revision 125 - Directory Listing
Modified Wed May 28 13:23:26 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I added two functions:
	-scanKeyword
	-scanAnnots

Revision 124 - Directory Listing
Modified Tue May 27 15:59:47 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I modified getFrag.SeqReq and getLength.SeqReq
	I added getProp.SeqReq, fto have some information about the sequence

Revision 123 - Directory Listing
Modified Tue May 27 15:58:28 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I added two functions:
		-getAnnots
		-getAttribut

Revision 122 - Directory Listing
Modified Mon May 26 13:32:59 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
new text in graph added

Revision 121 - Directory Listing
Modified Sat May 24 15:59:48 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have added a default value for the argument bankname of the function
choosebank() so that the "assign(bankname,.GlobalEnv)" statement works
even when the bankname argument is missing.

I'am not sure to understand this statment: shouldn't a value argument
be given to assign ?

Revision 119 - Directory Listing
Modified Sat May 24 15:06:33 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 118 - Directory Listing
Modified Fri May 23 22:52:53 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 115 - Directory Listing
Modified Fri May 23 16:27:30 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have just added a dot before the "SEQINR.UTIL" variable.

Revision 111 - Directory Listing
Modified Thu May 22 19:32:03 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 110 - Directory Listing
Modified Thu May 22 14:55:50 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i corrected a bug

Revision 109 - Directory Listing
Modified Thu May 22 13:34:51 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i added  assign(bankname,.GlobalEnv)

Revision 104 - Directory Listing
Modified Thu May 22 12:57:21 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I repared error I had introduiced

Revision 102 - Directory Listing
Modified Thu May 22 12:23:56 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i changed the name of the data SEQINR.UTIL : .SEQINR.UTIL

Revision 101 - Directory Listing
Modified Thu May 22 12:10:58 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i added \n

Revision 100 - Directory Listing
Modified Thu May 22 12:06:57 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i added two functions getKey and getExon

Revision 98 - Directory Listing
Modified Wed May 21 08:47:01 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I added a parenthesis

Revision 97 - Directory Listing
Modified Tue May 20 14:58:32 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
         --m

Revision 96 - Directory Listing
Modified Tue May 20 14:58:12 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i have forgotten what i changed

Revision 95 - Directory Listing
Modified Tue May 20 14:55:44 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	i initialised the class SeqReq in getreq()

Revision 94 - Directory Listing
Modified Tue May 20 14:18:16 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I removed the classes that i transfered in the file ClassSeq.R

Revision 93 - Directory Listing
Modified Tue May 20 14:15:43 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	this file contain the differents classes and methodes for the sequences

Revision 92 - Directory Listing
Modified Tue May 20 14:12:42 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I added the class of the sequences

Revision 90 - Directory Listing
Modified Tue May 20 08:29:02 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have added the require("methods") so that we can use this package

Revision 88 - Directory Listing
Modified Sun May 18 14:48:23 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 87 - Directory Listing
Modified Sun May 18 10:36:34 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
New update received from Christian Gautier by email today.

Revision 86 - Directory Listing
Modified Sat May 17 13:19:33 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
A new argument "base4 = TRUE" was added so that by default the numerical
encoding starts at 0.

Revision 84 - Directory Listing
Modified Fri May 16 14:33:14 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have added a dot-dot-dot argument to print.requete() to remove one
warning during the checking generic/method consistency.

Revision 81 - Directory Listing
Modified Fri May 16 11:27:28 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
conversion of a vector of integers into a DNA sequence

Revision 79 - Directory Listing
Modified Thu May 15 21:12:11 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
This is an alternative to seq2num.

Revision 71 - Directory Listing
Modified Thu May 15 15:20:25 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have deleted the function s2c that was already present in the package.

Revision 70 - Directory Listing
Modified Thu May 15 13:28:13 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
This file was send to me by e-mail today by Christian Gautier.

Revision 67 - Directory Listing
Modified Wed May 14 14:10:46 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have added a default behaviour to choosebank() so that it opens the
local distribution of ACNUC database if noting is available

Revision 65 - Directory Listing
Modified Tue May 13 18:54:49 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have run chmod 644 on the file to set up the mandatory permissions
for source files. These are apparently disturbed by some text editors
such as nedit on the Sun and BBEdit on the mac.

Revision 64 - Directory Listing
Modified Tue May 13 15:06:50 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I changed variable's name and i added names for the dataframe.

Revision 63 - Directory Listing
Modified Tue May 13 15:01:56 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I changed variable's name

Revision 62 - Directory Listing
Modified Tue May 13 14:34:26 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	I corrected some bugs and changed variable's name.

Revision 61 - Directory Listing
Modified Mon May 12 16:13:14 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	ajout d'un retour chariot �a fin des fonctions.

Revision 60 - Directory Listing
Modified Mon May 12 15:36:29 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	modification mineure

Revision 59 - Directory Listing
Modified Mon May 12 15:26:26 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	regroupement des trois fonctions uco.table, uco.freq, uco en une seule:
	uco(...)

Revision 58 - Directory Listing
Modified Mon May 12 14:57:26 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	fusion des fonctions codon.R et twoseq.R dans une meme fonction
splitseq.R.

Revision 57 - Directory Listing
Modified Mon May 12 14:48:06 2003 UTC (15 years, 9 months ago) by charif
Original Path: trunk/seqinr/R
	G�ralisation de la fonction count(). Desormais on peut obtenir le
        comptage des n-nucl�ides.

Revision 54 - Directory Listing
Modified Thu May 1 20:07:58 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
First preliminary release of oriloc

Revision 51 - Directory Listing
Modified Thu May 1 00:39:51 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
In getseq() I have changed class(x) <- sequence to class(x) <- c("sequence")
so that it does not complain. I have also compacted a little bit the
code thanks to the c2s() utility and by code factorization in the if/else.

Revision 50 - Directory Listing
Modified Wed Apr 30 23:52:04 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
I have moved choixbanque() to choosebank() but keep choixbanque() as
an alias so that it still runs. The function checks now that there
is an nonempty argument and that it's possible to get something from
Sys.getenv() so that it does not exit to console in these cases.

Revision 49 - Directory Listing
Modified Wed Apr 30 23:14:55 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
chmod to 644

Revision 47 - Directory Listing
Modified Wed Apr 30 23:08:42 2003 UTC (15 years, 9 months ago) by lobry
Original Path: trunk/seqinr/R
lseqinr.R

Revision 42 - Directory Listing
Modified Mon Apr 28 09:15:55 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
essai des droits du groupe seqinr

Revision 39 - Directory Listing
Modified Sun Apr 27 14:50:40 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
db.growth.R

Revision 33 - Directory Listing
Modified Sun Apr 27 08:48:37 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 31 - Directory Listing
Modified Sat Apr 26 15:27:56 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
*** empty log message ***

Revision 28 - Directory Listing
Modified Sat Apr 26 09:56:36 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
string -> chars

Revision 27 - Directory Listing
Modified Sat Apr 26 09:55:34 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
chars -> string

Revision 24 - Directory Listing
Modified Fri Apr 25 11:32:13 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
package -> seqinr

Revision 23 - Directory Listing
Modified Fri Apr 25 11:16:12 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
package -> seqinr

Revision 21 - Directory Listing
Modified Fri Apr 25 09:06:34 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
just a test of cvs

Revision 20 - Directory Listing
Modified Fri Apr 25 08:34:25 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
Ooops ! A right parenthesis was missing

Revision 18 - Directory Listing
Modified Fri Apr 25 08:20:19 2003 UTC (15 years, 10 months ago) by charif
Original Path: trunk/seqinr/R
  ajout de la fonction translateCDS

Revision 16 - Directory Listing
Modified Thu Apr 24 11:43:23 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
I have replaced "seqinr" by "package"

Revision 15 - Directory Listing
Modified Thu Apr 24 11:38:10 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
'\n' added

Revision 14 - Directory Listing
Modified Thu Apr 24 11:36:47 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
'\n' added + pretty indentation

Revision 13 - Directory Listing
Modified Thu Apr 24 11:15:21 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
I have run dos2unix

Revision 12 - Directory Listing
Modified Thu Apr 24 11:05:28 2003 UTC (15 years, 10 months ago) by lobry
Original Path: trunk/seqinr/R
I have changed the dos-like end of line into unix-like end of line
with the command: dos2unix translate.R translate.R

Revision 10 - Directory Listing
Added Wed Apr 23 08:08:21 2003 UTC (15 years, 10 months ago) by ade2001
Original Path: trunk/seqinr/R
This commit was generated by cvs2svn to compensate for changes in r3,
which included commits to RCS files with non-trunk default branches.

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