CVS log for bioperl-run/Bio/Tools/Run/EMBOSSApplication.pm

CVS log for bioperl-run/Bio/Tools/Run/EMBOSSApplication.pm
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Default branch: MAIN
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Revision 1.29 / (view) - annotate - [select for diffs] , Thu Jun 14 14:23:08 2007 UTC (12 months, 3 weeks ago) by sendu
Branch: MAIN
CVS Tags: HEAD
Changes since 1.28: +5 -5 lines
Diff to previous 1.28

removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Revision 1.28 / (view) - annotate - [select for diffs] , Sat Oct 21 19:51:59 2006 UTC (20 months, 1 week ago) by bosborne
Branch: MAIN
CVS Tags: bioperl-run-release-1-5-2
Changes since 1.27: +9 -8 lines
Diff to previous 1.27

Write executable() method, t/EMBOSS.t tests pass now

Revision 1.27 / (view) - annotate - [select for diffs] , Sat Oct 21 03:08:53 2006 UTC (20 months, 2 weeks ago) by bosborne
Branch: MAIN
Changes since 1.26: +52 -9 lines
Diff to previous 1.26

Add executable(), program_dir(), program_path()

Revision 1.26 / (view) - annotate - [select for diffs] , Sat Oct 21 02:07:46 2006 UTC (20 months, 2 weeks ago) by bosborne
Branch: MAIN
Changes since 1.25: +107 -116 lines
Diff to previous 1.25

Format code, remove old email, POD edits

Revision 1.25 / (view) - annotate - [select for diffs] , Tue Jul 4 21:23:31 2006 UTC (2 years ago) by mauricio
Branch: MAIN
Changes since 1.24: +2 -2 lines
Diff to previous 1.24

Updated bug reporting

Revision 1.24 / (view) - annotate - [select for diffs] , Sun Jul 2 05:19:42 2006 UTC (2 years ago) by mauricio
Branch: MAIN
Changes since 1.23: +3 -3 lines
Diff to previous 1.23

Fixed spaces

Revision 1.23 / (view) - annotate - [select for diffs] , Sat Jul 1 20:45:33 2006 UTC (2 years ago) by mauricio
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22

Fixed spaces and URL's

Revision 1.22 / (view) - annotate - [select for diffs] , Thu Nov 17 09:53:37 2005 UTC (2 years, 7 months ago) by heikki
Branch: MAIN
Changes since 1.21: +3 -3 lines
Diff to previous 1.21

I'll be using bioperl.org mail address from now on documens

Revision 1.21 / (view) - annotate - [select for diffs] , Sun Nov 6 21:47:45 2005 UTC (2 years, 7 months ago) by jason
Branch: MAIN
Changes since 1.20: +2 -2 lines
Diff to previous 1.20

mangle email address

Revision 1.19.2.1 / (view) - annotate - [select for diffs] , Sun Oct 9 14:19:41 2005 UTC (2 years, 8 months ago) by jason
Branch: bioperl-run-branch-1-5-1
CVS Tags: bioperl-run-release-1-5-1
Changes since 1.19: +4 -5 lines
Diff to previous 1.19 to next main 1.20

Merged from HEAD to 1.5.1 branch, changes which remove old bug email address and point to bugzilla.bioperl.org website for bug submission

Revision 1.20 / (view) - annotate - [select for diffs] , Sun Oct 9 13:49:26 2005 UTC (2 years, 8 months ago) by heikki
Branch: MAIN
Changes since 1.19: +4 -5 lines
Diff to previous 1.19

Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Revision 1.19 / (view) - annotate - [select for diffs] , Fri Oct 1 13:11:23 2004 UTC (3 years, 9 months ago) by jason
Branch: MAIN
CVS Tags: bioperl-run-release-1-5-1-rc4
Branch point for: bioperl-run-branch-1-5-1
Changes since 1.18: +3 -3 lines
Diff to previous 1.18

debugging enabled

Revision 1.18 / (view) - annotate - [select for diffs] , Fri Feb 20 20:57:47 2004 UTC (4 years, 4 months ago) by jason
Branch: MAIN
CVS Tags: bioperl-run-release-1-5-0-rc1
Changes since 1.17: +3 -3 lines
Diff to previous 1.17

allow 0 value attributes per Susan Miller's bug report

Revision 1.17 / (view) - annotate - [select for diffs] , Thu Aug 14 20:16:04 2003 UTC (4 years, 10 months ago) by jason
Branch: MAIN
CVS Tags: bioperl-run-release-1-4-0, bioperl-run-devel-1-3-01
Changes since 1.16: +4 -5 lines
Diff to previous 1.16

no need for this debugging

Revision 1.16 / (view) - annotate - [select for diffs] , Fri Mar 28 22:42:07 2003 UTC (5 years, 3 months ago) by jason
Branch: MAIN
CVS Tags: release-1-2-0, bioperl-run-release-1-2-2, bioperl-run-release-1-2-0
Changes since 1.15: +15 -11 lines
Diff to previous 1.15

rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Revision 1.15 / (view) - annotate - [select for diffs] , Mon Dec 23 19:46:32 2002 UTC (5 years, 6 months ago) by jason
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14

use debug to print out the dumper info

Revision 1.14 / (view) - annotate - [select for diffs] , Tue Dec 17 14:30:49 2002 UTC (5 years, 6 months ago) by heikki
Branch: MAIN
Changes since 1.13: +2 -2 lines
Diff to previous 1.13

added a missing semicolon to make the synopsis runnable

Revision 1.13 / (view) - annotate - [select for diffs] , Wed Oct 23 14:30:48 2002 UTC (5 years, 8 months ago) by heikki
Branch: MAIN
Changes since 1.12: +5 -42 lines
Diff to previous 1.12

no more warnings under perl 5.8.0

Revision 1.12 / (view) - annotate - [select for diffs] , Sat Jul 6 22:53:36 2002 UTC (6 years ago) by jason
Branch: MAIN
CVS Tags: bioperl-release-1-1-0
Changes since 1.11: +5 -1 lines
Diff to previous 1.11

explicitly closing some filehandles appears to do a better job freeing resources

Revision 1.11 / (view) - annotate - [select for diffs] , Sun Jun 16 16:42:18 2002 UTC (6 years ago) by heikki
Branch: MAIN
Changes since 1.10: +73 -22 lines
Diff to previous 1.10

added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Revision 1.10 / (view) - annotate - [select for diffs] , Thu May 30 02:20:32 2002 UTC (6 years, 1 month ago) by jason
Branch: MAIN
Changes since 1.9: +9 -4 lines
Diff to previous 1.9

handle some weird boundary cases

Revision 1.8.2.1 / (view) - annotate - [select for diffs] , Sun Apr 21 13:30:21 2002 UTC (6 years, 2 months ago) by jason
Branch: branch-1-0-0
CVS Tags: bioperl-release-1-0-1
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 to next main 1.9

merged changes from trunk to branch

Revision 1.9 / (view) - annotate - [select for diffs] , Tue Mar 19 19:21:00 2002 UTC (6 years, 3 months ago) by jason
Branch: MAIN
Changes since 1.8: +2 -2 lines
Diff to previous 1.8

cleanup before each run of an application

Revision 1.8 / (view) - annotate - [select for diffs] , Mon Mar 4 22:09:04 2002 UTC (6 years, 4 months ago) by jason
Branch: MAIN
CVS Tags: bioperl-release-1-0-0, bioperl-1-0-alpha2-rc, bioperl-1-0-0
Branch point for: branch-1-0-0
Changes since 1.7: +30 -17 lines
Diff to previous 1.7

added ability to dump alignments as well as sequences when running an EMBOSS application

Revision 1.7 / (view) - annotate - [select for diffs] , Mon Feb 18 22:48:40 2002 UTC (6 years, 4 months ago) by jason
Branch: MAIN
Changes since 1.6: +25 -1 lines
Diff to previous 1.6

added example documentation to the POD

Revision 1.6 / (view) - annotate - [select for diffs] , Mon Feb 18 22:34:04 2002 UTC (6 years, 4 months ago) by jason
Branch: MAIN
Changes since 1.5: +30 -2 lines
Diff to previous 1.5

handle cmd line arguments pointing to a Bio::PrimarySeqI object or array or Bio::PrimarySeqI

Revision 1.5 / (view) - annotate - [select for diffs] , Thu Feb 14 21:40:39 2002 UTC (6 years, 4 months ago) by bosborne
Branch: MAIN
CVS Tags: bioperl-1-0-alpha
Changes since 1.4: +9 -7 lines
Diff to previous 1.4

Doc clarification, fixed POD error

Revision 1.4 / (view) - annotate - [select for diffs] , Tue Nov 20 02:09:42 2001 UTC (6 years, 7 months ago) by lstein
Branch: MAIN
CVS Tags: release-0-9-3, release-0-9-2
Changes since 1.3: +3 -3 lines
Diff to previous 1.3

Sweeping change:

Bio::Root::RootI is now a pure abstract interface and cannot be
inherited from unless you implement several of its abstract methods.
Most people will want to inherit from Bio::Root::Root.

This change was necessary in order to support Bioperl objects that
were not based on hashrefs.

Revision 1.3 / (view) - annotate - [select for diffs] , Mon Nov 19 20:46:53 2001 UTC (6 years, 7 months ago) by jason
Branch: MAIN
Changes since 1.2: +5 -6 lines
Diff to previous 1.2

EMBOSS more runnable and w/ tests

Revision 1.2 / (view) - annotate - [select for diffs] , Tue Jul 24 13:43:18 2001 UTC (6 years, 11 months ago) by heikki
Branch: MAIN
CVS Tags: release-0-9-0
Changes since 1.1: +99 -46 lines
Diff to previous 1.1

claning. Needs code to compare input and ACD options

Revision 1.1 / (view) - annotate - [select for diffs] , Mon Jul 23 14:10:34 2001 UTC (6 years, 11 months ago) by heikki
Branch: MAIN

Classes for wrapping EMBOSS suite

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CVS log for bioperl-run/Bio/Tools/Run/EMBOSSApplication.pm

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