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Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 29 15:48:37 2010 UTC (9 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, myrast_33, myrast_rel40, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
fix unlink here too

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 27 16:09:28 2010 UTC (9 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.32: +22 -0 lines
Diff to previous 1.32
Clean up tmp files.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 21:55:31 2010 UTC (9 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.31: +37 -36 lines
Diff to previous 1.31
make this run with new FFs

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 23 20:24:22 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.30: +25 -5 lines
Diff to previous 1.30
use bulk lookups

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 2 09:42:27 2010 UTC (9 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.29: +11 -5 lines
Diff to previous 1.29
added support for Sapling type locations

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 16 16:01:54 2010 UTC (9 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.28: +7 -2 lines
Diff to previous 1.28
added support for locations

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 16 09:34:32 2009 UTC (10 years, 3 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_0925, rast_rel_2010_0118
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
added location for artificial features

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 2 09:38:10 2009 UTC (10 years, 3 months ago) by paczian
Branch: MAIN
Changes since 1.26: +5 -1 lines
Diff to previous 1.26
fixed size information

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 2 09:28:24 2009 UTC (10 years, 3 months ago) by paczian
Branch: MAIN
Changes since 1.25: +1 -0 lines
Diff to previous 1.25
added location to feature data

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 17 21:19:54 2009 UTC (10 years, 3 months ago) by dsouza
Branch: MAIN
Changes since 1.24: +138 -113 lines
Diff to previous 1.24
Removed code using blat.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 13 20:34:15 2009 UTC (10 years, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.23: +116 -173 lines
Diff to previous 1.23
Fixed blat code, removed fast color option.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 12 17:32:45 2009 UTC (10 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +4 -1 lines
Diff to previous 1.22
use blat

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 12 17:14:14 2009 UTC (10 years, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.21: +34 -5 lines
Diff to previous 1.21
Changed to use blat when present, otherwise use blast

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 24 19:52:31 2009 UTC (10 years, 5 months ago) by dsouza
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.20: +50 -7 lines
Diff to previous 1.20
Added sort display order of regions by similarity of pin to input peg

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 4 12:30:37 2009 UTC (10 years, 6 months ago) by paczian
Branch: MAIN
Changes since 1.19: +11 -4 lines
Diff to previous 1.19
subsystems with comments due to their variant code will now receive the correct index

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 25 18:00:13 2009 UTC (10 years, 8 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_03_26, rast_rel_2009_05_18
Changes since 1.18: +5 -1 lines
Diff to previous 1.18
fixed display of subsystems

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 17:01:25 2009 UTC (10 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.17: +1 -0 lines
Diff to previous 1.17
corrected subsystem visibility

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 12 13:50:32 2009 UTC (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.16: +5 -3 lines
Diff to previous 1.16
the extended option now causes skipping of the usable_subsystem test

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 15:43:22 2009 UTC (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.15: +66 -44 lines
Diff to previous 1.15
added optional extended information (aliases and ev codes)
optimized data retrieval

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 6 11:07:34 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05
Changes since 1.14: +3 -0 lines
Diff to previous 1.14
added functional coupling pin

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 22 18:18:31 2008 UTC (11 years, 1 month ago) by dsouza
Branch: MAIN
Changes since 1.13: +43 -20 lines
Diff to previous 1.13
Changed to handle subsystem variant codes correctly.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 18 09:56:23 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.12: +4 -3 lines
Diff to previous 1.12
Added tracing.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 16 19:26:54 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_release_2008_09_29
Changes since 1.11: +3 -2 lines
Diff to previous 1.11
Fixed a compiler warning.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 05:45:29 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.10: +452 -447 lines
Diff to previous 1.10
Added some trace messages.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 20:45:23 2008 UTC (11 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
Introduce get_figfam_data().

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 23 15:54:41 2008 UTC (11 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.8: +4 -6 lines
Diff to previous 1.8
Added tracing.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 26 17:44:16 2008 UTC (11 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.7: +58 -2 lines
Diff to previous 1.7
added add_features for features you do not get from the seed.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 20 19:23:58 2008 UTC (11 years, 9 months ago) by dsouza
Branch: MAIN
Changes since 1.6: +15 -1 lines
Diff to previous 1.6
PEG popup changed so that FigFam ID does not get repeated (was twice) for
FigFams which are not based on subsystems. This can be removed if the
FigFam function format gets changed.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 6 18:30:07 2008 UTC (11 years, 10 months ago) by dsouza
Branch: MAIN
Changes since 1.5: +19 -10 lines
Diff to previous 1.5
Bug fix for user selected genomes.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 21:04:36 2008 UTC (11 years, 10 months ago) by dsouza
Branch: MAIN
Changes since 1.4: +51 -7 lines
Diff to previous 1.4
1. Added FigFam name to feature data (for PEGs in FigFams).
2. Added support for user selection of region genomes.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 14 16:38:27 2008 UTC (11 years, 11 months ago) by dsouza
Branch: MAIN
Changes since 1.3: +7 -8 lines
Diff to previous 1.3
Comments and whitespace changes

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 21 17:22:47 2007 UTC (11 years, 11 months ago) by dsouza
Branch: MAIN
Changes since 1.2: +127 -117 lines
Diff to previous 1.2
Added protein length, subsystem information, functional coupling.
Changed behavior of 'collapse close genomes'.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 13 23:16:03 2007 UTC (12 years ago) by dsouza
Branch: MAIN
Changes since 1.1: +28 -26 lines
Diff to previous 1.1
Modified selection of PEGs for non-collapsed regions.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 17:22:16 2007 UTC (12 years ago) by dsouza
Branch: MAIN
PinnedRegions.pm creates the data structure used to create the
'compared regions' images.

It creates the list of pinned PEGs (based on similarity or PCH pins), gets
all the feature data for their contig regions required to create the image,
and packages it in a single data structure.

Mark D'Souza, 2007-11-30

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