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Revision 1.63 - (view) (download) (annotate) - [select for diffs]
Thu Dec 20 20:44:52 2012 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.62: +44 -34 lines
Diff to previous 1.62
Order sequences in alignment to match the corresponding tree.

Revision 1.62 - (view) (download) (annotate) - [select for diffs]
Thu Nov 29 19:16:54 2012 UTC (6 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.61: +0 -1 lines
Diff to previous 1.61
Removed a spurious return statement that created an errror if it was hit.

Revision 1.61 - (view) (download) (annotate) - [select for diffs]
Sat Nov 24 21:38:11 2012 UTC (6 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.60: +74 -43 lines
Diff to previous 1.60
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 1.60 - (view) (download) (annotate) - [select for diffs]
Tue Aug 28 00:34:40 2012 UTC (7 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.59: +9 -2 lines
Diff to previous 1.59
Add support for an uncolored tree.

Revision 1.59 - (view) (download) (annotate) - [select for diffs]
Sat Mar 3 17:19:30 2012 UTC (7 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.58: +1 -1 lines
Diff to previous 1.58
Make color by residue default for alignments.

Revision 1.58 - (view) (download) (annotate) - [select for diffs]
Mon Nov 21 19:44:39 2011 UTC (7 years, 11 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_12152011, mgrast_release_3_1_2
Changes since 1.57: +1 -2 lines
Diff to previous 1.57
Minor changes in comments.

Revision 1.57 - (view) (download) (annotate) - [select for diffs]
Sun Oct 30 20:15:47 2011 UTC (8 years ago) by golsen
Branch: MAIN
Changes since 1.56: +11 -6 lines
Diff to previous 1.56
Log "reason" for assignments coming from similarities protein.cgi
similarities table.

Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Sat Feb 6 23:36:18 2010 UTC (9 years, 9 months ago) by golsen
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_dev_10262011, 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_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.55: +2 -1 lines
Diff to previous 1.55
Another try at getting the tree image correctly linked.

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Sat Feb 6 23:22:31 2010 UTC (9 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.54: +5 -3 lines
Diff to previous 1.54
Try to get png to display from server (chmod the image file).

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Sat Feb 6 23:01:21 2010 UTC (9 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.53: +2 -2 lines
Diff to previous 1.53
Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics

Revision 1.53 - (view) (download) (annotate) - [select for diffs]
Sat Feb 6 01:31:46 2010 UTC (9 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.52: +15 -7 lines
Diff to previous 1.52
When png tree output is requested, fall back to jpg if png is not available.

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Tue Jul 7 22:14:22 2009 UTC (10 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118
Changes since 1.51: +87 -29 lines
Diff to previous 1.51
Improved tree printer-plot graphics. Total redesign.

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Wed Jul 1 00:23:36 2009 UTC (10 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.50: +38 -10 lines
Diff to previous 1.50
Further tweeking of printerplot tree formats (particularly in fid_checked).

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Thu Jun 25 01:52:08 2009 UTC (10 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.49: +1 -1 lines
Diff to previous 1.49
Just a minor change in the PNG tree format.

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Thu Jun 25 01:19:29 2009 UTC (10 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.48: +274 -139 lines
Diff to previous 1.48
Add PNG format trees to fid_checked.cgi.  Add support elsewhere.  Some
code clean-up.  Some increases in flexibility.

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Mon Jun 22 19:18:14 2009 UTC (10 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
Do a slightly nicer midpoint rooting of the tree.

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Sat Aug 23 23:39:22 2008 UTC (11 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_release_2008_09_29
Changes since 1.46: +17 -66 lines
Diff to previous 1.46
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Thu Aug 7 16:42:13 2008 UTC (11 years, 3 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2008_08_07
Changes since 1.45: +2 -1 lines
Diff to previous 1.45
changed checkbox name for FIGfams

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Mon Jul 21 18:39:44 2008 UTC (11 years, 3 months ago) by dsouza
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806
Changes since 1.44: +30 -0 lines
Diff to previous 1.44
Handle merging FigFams

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Sat Sep 29 03:58:17 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.43: +94 -7 lines
Diff to previous 1.43
fixes to display on protein page, alternative formats for alignments and trees in fid_checked.cgi

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Thu Apr 12 00:47:54 2007 UTC (12 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.42: +20 -32 lines
Diff to previous 1.42
Change the coloring of functions in the protein page similarities table,
and the fid_checked page phylogenetic tree to match the individual roles,
rather than the function as a whole.  This will give features with multiple
roles separate colores for each role.  It will also make assignments with
different comments match, so long as the role is the same.

(Also added another pallet with more colors.)

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Mon Apr 9 22:28:35 2007 UTC (12 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.41: +8 -1 lines
Diff to previous 1.41
Add a page title.

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Mon Apr 9 21:00:24 2007 UTC (12 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.40: +328 -132 lines
Diff to previous 1.40
Major change in the alignment and tree portions of fid_checked.
Nicer alignment display.
Clean-up of tree display and underlying libraries.
Caching of the alignment and tree so that display paramters and/or
assignments can be updated without recomputing the alignment and tree.

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Thu Jan 18 03:08:57 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +1 -0 lines
Diff to previous 1.39
add comments to functions

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Mon Dec 11 19:27:49 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +18 -2 lines
Diff to previous 1.38
minor fixes to locking/unlocking PEG annotations

Revision 1.38 - (view) (download) (annotate) - [select for diffs]
Sun Dec 10 21:17:06 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +25 -12 lines
Diff to previous 1.37
annotate only successful assignments

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Fri Sep 15 18:59:30 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.36: +28 -0 lines
Diff to previous 1.36
commit code in fid_checked.cgi to lock/unlock annotations

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Sat Aug 5 03:12:15 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.35: +489 -483 lines
Diff to previous 1.35
Modified so that Sprout pages stay Sprout-like.

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Mon Mar 20 03:06:35 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +4 -2 lines
Diff to previous 1.34
RAE: Adding BUT NOT to protein.cgi

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 19:12:12 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.33: +17 -0 lines
Diff to previous 1.33
add license words

Revision 1.33 - (view) (download) (annotate) - [select for diffs]
Thu Dec 1 22:16:36 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +7 -7 lines
Diff to previous 1.32
Fix invocation of add_annotation.

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Wed Nov 30 08:44:26 2005 UTC (13 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.31: +10 -18 lines
Diff to previous 1.31
Introduce a different tree printing routine to fid_checked.  This required
a new version of align_with_clustal.pl (= align_with_clustal_2.pl) and a
new tree utilities library (gjonewicklib.pm).

The new tree printer does not require deleting the extra lines (they are
not included in the first place).  This would probably allow some other
restructuring of the code in fid_checked, but I did the minimum.

The other reason for the changes (actually the real reason) is that it is
now possible to introduce midpoint rooting to the tree, and to reorder
the taxa so that the tree is MUCH easier to read (aesthetic tree order).

Also I'm changing it to use a second-generation tree from the alignment,
not just show the guide tree.

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Thu Nov 17 07:06:25 2005 UTC (13 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.30: +90 -134 lines
Diff to previous 1.30
Loaded clean copy of version 1.29.  Put in changes to colorize the functions
on the phylogenetic tree.  Seems to work, and to restore the things that I
lost previously.

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Mon Nov 14 20:52:03 2005 UTC (14 years ago) by golsen
Branch: MAIN
Changes since 1.29: +164 -92 lines
Diff to previous 1.29
Colorize the functions in the alignment tree.

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Thu Nov 3 22:14:42 2005 UTC (14 years ago) by olson
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.28: +56 -102 lines
Diff to previous 1.28
new interface changes

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Mon Oct 3 13:13:08 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
minor fixes to align_DNA.cgi

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Sat Oct 1 20:32:19 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.26: +17 -0 lines
Diff to previous 1.26
support alignment of DNA via fid_checked.cgi

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 22:25:12 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +2 -3 lines
Diff to previous 1.25
fixing help links

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Fri Jul 22 21:50:44 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +2 -2 lines
Diff to previous 1.24
minor tweaks by Rob to make nmpdr work

Revision 1.21.2.3 - (view) (download) (annotate) - [select for diffs]
Tue Jul 12 15:39:01 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bodev_news-3
Changes since 1.21.2.2: +1 -0 lines
Diff to previous 1.21.2.2 , to branch point 1.21 , to next main 1.63
Merged changes from trunk.

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Sat Jul 9 20:22:02 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.23: +1 -0 lines
Diff to previous 1.23
adding help links

Revision 1.21.2.2 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 16:11:00 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-2
Changes since 1.21.2.1: +2 -1 lines
Diff to previous 1.21.2.1 , to branch point 1.21
Merge from trunk.

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Tue Jun 28 17:25:04 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.22: +2 -1 lines
Diff to previous 1.22
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

Revision 1.21.2.1 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 15:26:45 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-1
Changes since 1.21: +2 -1 lines
Diff to previous 1.21
Merged from trunk.

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Tue Jun 21 03:41:56 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.21: +2 -1 lines
Diff to previous 1.21
fix bug in fid_checked.cgi

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 19:44:32 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.20: +1 -71 lines
Diff to previous 1.20
interface routines hack

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Fri Jun 10 19:52:37 2005 UTC (14 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.19: +3 -3 lines
Diff to previous 1.19
Remove missign Sprout warning.

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Thu Apr 7 04:54:02 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.18: +77 -0 lines
Diff to previous 1.18
Add a "view simiarities" option to the text search report page.  Provide
the user with a form to define similarities options, and with links to
the protein similarities page for each of the selected proteins.

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Tue Feb 1 00:40:31 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
fix from restriction

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 18:04:35 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +134 -33 lines
Diff to previous 1.16
fixes to Sprout annotation

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Wed Jan 19 20:32:27 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +2 -2 lines
Diff to previous 1.15
fixes to annotation via commentary

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Wed Jan 5 20:24:14 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +18 -1 lines
Diff to previous 1.14
minor fixes to subsys.cgi and tree_utilities.pm

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Sat Jan 1 01:20:10 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +2 -2 lines
Diff to previous 1.13
fid_checked.cgi

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Wed Dec 8 23:18:01 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.12: +8 -2 lines
Diff to previous 1.12
Changes to fid_checked.cgi and check_subsys.cgi to allow you to update annotations in subsystems from the check subsystems page.

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Mon Aug 23 22:20:35 2004 UTC (15 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.11: +6 -1 lines
Diff to previous 1.11
Added javascript buttons for check all/some/none

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Mon Aug 9 21:28:45 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +5 -5 lines
Diff to previous 1.10
turn off debugging output in fid_checked.cgi

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Wed Aug 4 23:40:49 2004 UTC (15 years, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.9: +108 -9 lines
Diff to previous 1.9
Added ability to annotate entries in a CLUSTAL alignment.

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Tue Jun 8 21:33:35 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.8: +42 -1 lines
Diff to previous 1.8
added batch_assign

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Sat Mar 20 02:58:46 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.7: +3 -3 lines
Diff to previous 1.7
Convert link URL to relative; convert chop to chomp

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Fri Mar 19 22:01:26 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
fix case when function is added and an annotation is made

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Wed Mar 3 17:02:13 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fix added annotation message

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Sun Feb 15 17:12:54 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +128 -15 lines
Diff to previous 1.4
added Gary Olsen changes

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Tue Feb 3 23:08:53 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3
fix translation rules

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Fri Dec 19 19:54:48 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +49 -16 lines
Diff to previous 1.2
fixed translation rules to condense

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Tue Dec 16 16:59:42 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.1: +0 -2 lines
Diff to previous 1.1
Removed stray tool_hdr content that got copied in here

Revision 1.1.1.1 - (view) (download) (annotate) - [select for diffs] (vendor branch)
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: initial
CVS Tags: V00-00-00, V00-00-01, V00-00-02, delong-01, delong-02, init, preRossMerge-03Dec03
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 , to next main 1.63

import


Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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