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Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 20:47:30 2012 UTC (7 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.23: +13 -12 lines
Diff to previous 1.23
Convert image files to use new temporary file name functions.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 24 21:38:11 2012 UTC (7 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.22: +14 -47 lines
Diff to previous 1.22
Use new batch assign feature of FIG::assign_function().
Improve tracking of the reasons for assignments from similarities and trees.
Standardize the format for annotating such assignments:

Assignment projected from $id based on ...

Current reasons include identical sequence, solid rectangle, proximity
in tree, similarity and indirect similarity.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 20 05:31:04 2012 UTC (7 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.21: +30 -20 lines
Diff to previous 1.21
Changes to move multiple protein assignments to FIG.pm

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 19 17:13:48 2012 UTC (7 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.20: +29 -24 lines
Diff to previous 1.20
Minor change to all to assign_function() because this module does its own
expansion from md5 to pegs.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 18 17:21:36 2012 UTC (7 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.19: +3 -3 lines
Diff to previous 1.19
Changes to metadata access routines to be more efficient at getting just
the descired data.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 28 16:53:15 2012 UTC (7 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.18: +2 -2 lines
Diff to previous 1.18
Catch an undefined value when the reference fid is not on the local SEED.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 28 16:16:41 2012 UTC (7 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.17: +10 -4 lines
Diff to previous 1.17
Add the option 'none' to alignment coloring.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 15 04:03:27 2012 UTC (7 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.16: +44 -12 lines
Diff to previous 1.16
Add coverage information in the display of alignments that include a protein.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 3 17:18:19 2012 UTC (8 years, 1 month ago) by golsen
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
Make color by residue default for aligments.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 24 19:05:43 2012 UTC (8 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.14: +2 -1 lines
Diff to previous 1.14
Make assign_function return -1 on "successfully ignoring a reassignment to
the same role."
Make CGIAlignTreeViewer treat -1 as a failed assignment, and not write an
annotation.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 10 01:04:27 2012 UTC (8 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.13: +10 -5 lines
Diff to previous 1.13
Some speed enhancements.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 9 17:54:59 2012 UTC (8 years, 2 months ago) by fangfang
Branch: MAIN
Changes since 1.12: +2 -5 lines
Diff to previous 1.12
Improve test for valid SEED features.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 8 22:45:19 2012 UTC (8 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.11: +46 -25 lines
Diff to previous 1.11
Local dlit handling when using a SEED.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 14 21:38:16 2011 UTC (8 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.10: +122 -56 lines
Diff to previous 1.10
Update help information.
Fix Select All and Deselect All buttons to work with the Undo and Redo
functions.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 14 05:12:08 2011 UTC (8 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
Fixed a missing close quote in the JavaScipt.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 14 00:45:16 2011 UTC (8 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.8: +223 -63 lines
Diff to previous 1.8
Support for selecting subtrees (and undo and redo on selections).

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 01:18:36 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_12152011, mgrast_release_3_1_2
Changes since 1.7: +3 -1 lines
Diff to previous 1.7
Made the target of the fid links _blank.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 00:06:52 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.6: +13 -7 lines
Diff to previous 1.6
Fix issue with user name under the SEED.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 4 00:25:12 2011 UTC (8 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
Handle the case when the focus peg is not set.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 21 19:39:55 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.4: +132 -17 lines
Diff to previous 1.4
Changes in how the help information is integrated handled and linked.
Change tree links to black.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 20 06:49:22 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.3: +31 -16 lines
Diff to previous 1.3
Some more refinement of the display.
New colors for the region in alignment (more hue variation when protein
is long).
Add a help page.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 20 01:28:39 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.2: +478 -192 lines
Diff to previous 1.2
Numerous changes and improvements including collapsing identical sequences,
showing protein range covered, showing subsystems, ...

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 14 21:41:06 2011 UTC (8 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1
use batch lookup for fucntions

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 14 18:21:36 2011 UTC (8 years, 4 months ago) by olson
Branch: MAIN
Port Gary's align_tree.cgi over to a module for use in seedviewer & cgi

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