jprocter [Tue, 4 Dec 2012 11:44:42 +0000 (11:44 +0000)]
JAL-1214 todo
jprocter [Tue, 4 Dec 2012 11:06:45 +0000 (11:06 +0000)]
JAL-1213 JAL-674 - import a PDB file using Jmol data api and decorate any peptide sequences with secondary structure annotation
jprocter [Tue, 4 Dec 2012 10:48:53 +0000 (10:48 +0000)]
JAL-674 commented out annotate3d calling code for Jmol external processing routine
jprocter [Tue, 4 Dec 2012 10:47:44 +0000 (10:47 +0000)]
JAL-1028 JAL-674 hooks to call external processing for peptide and nucleic acid sequences and map secondary structure annotation onto sequence imported into Jalview
jprocter [Fri, 7 Dec 2012 15:53:31 +0000 (15:53 +0000)]
revised renderer and annotation model to support different pair-patterns - needs merging and debugging
jprocter [Fri, 7 Dec 2012 15:51:52 +0000 (15:51 +0000)]
convenience function to get the RNA model for an annotation row (probably unused - need to check)
jprocter [Fri, 7 Dec 2012 15:51:28 +0000 (15:51 +0000)]
use new secstructure process algorithm
jprocter [Fri, 7 Dec 2012 15:50:23 +0000 (15:50 +0000)]
Anne's refined RNAML parser. Seems to have some bugs still (merge with jprocter's bugfixed parser)
jprocter [Fri, 7 Dec 2012 15:49:04 +0000 (15:49 +0000)]
Anne reinstated general stockholm parser code but extended to support pseudoknot annotation lines. This will need merging with Natasha's upgraded io.StockholmFile class
jprocter [Fri, 7 Dec 2012 15:11:22 +0000 (15:11 +0000)]
typing
jprocter [Fri, 7 Dec 2012 15:10:22 +0000 (15:10 +0000)]
consensus secondary structure algorithm (possibly came from VARNA)
jprocter [Fri, 7 Dec 2012 15:07:54 +0000 (15:07 +0000)]
revised RNA stem/loop processing code that copes with pseudoknots
jprocter [Fri, 7 Dec 2012 15:01:26 +0000 (15:01 +0000)]
update authors for RNA processing routines
jprocter [Fri, 7 Dec 2012 15:01:08 +0000 (15:01 +0000)]
menu for choosing between 'protein' and 'RNA' mode (unlikely to be merged into main branch)
jprocter [Fri, 7 Dec 2012 14:20:41 +0000 (14:20 +0000)]
formatting and error report cleanup
jprocter [Fri, 7 Dec 2012 14:19:57 +0000 (14:19 +0000)]
gui hooks for contrafold and RNAfold services. commented because they should be added via the web service menu framework rather than explicitly hardcoded in the popup menu
jprocter [Fri, 7 Dec 2012 14:18:55 +0000 (14:18 +0000)]
Exception signature change (will be overwritten by commit 2a7ae5)
jprocter [Fri, 7 Dec 2012 14:17:23 +0000 (14:17 +0000)]
formatting
jprocter [Fri, 7 Dec 2012 14:16:47 +0000 (14:16 +0000)]
tidy import
jprocter [Fri, 7 Dec 2012 14:15:43 +0000 (14:15 +0000)]
remove mentions of non-functional RNAInteraction colourscheme
jprocter [Fri, 7 Dec 2012 14:11:05 +0000 (14:11 +0000)]
tidy debug messages
jprocter [Fri, 7 Dec 2012 13:47:06 +0000 (13:47 +0000)]
proxy commit for Anne Menard <menard.annec@gmail.com> throw generic exceptions (just for record - finessed by
2a7ae58b8b7d619b73e8a25654fa3a12414cfd9a JAL-1140)
jprocter [Tue, 4 Dec 2012 10:17:11 +0000 (10:17 +0000)]
JAL-1028 tidy and refactor external processing and mapping to separate functions
jprocter [Mon, 19 Nov 2012 21:18:21 +0000 (21:18 +0000)]
bugfix
jprocter [Sun, 18 Nov 2012 09:04:51 +0000 (09:04 +0000)]
JAL-1205 JAL-1140 generalised exception for Anne's refactored IO
jprocter [Sat, 17 Nov 2012 21:59:42 +0000 (21:59 +0000)]
Merge branch 'develop' into menard
jprocter [Sat, 17 Nov 2012 21:59:16 +0000 (21:59 +0000)]
Merge branch 'Release_2_8_Branch' into develop
jprocter [Sat, 17 Nov 2012 21:58:30 +0000 (21:58 +0000)]
Merge branch 'master' into Release_2_8_Branch
jprocter [Sat, 17 Nov 2012 21:41:13 +0000 (21:41 +0000)]
FileParse adapter for reading directly from inputstreams
jprocter [Sat, 17 Nov 2012 21:24:42 +0000 (21:24 +0000)]
return alignmentI created from pdbfile class directly to preserve all annotation
jprocter [Sat, 17 Nov 2012 21:23:03 +0000 (21:23 +0000)]
return annotated rna sequences from rnaml returned from annotate3d
jprocter [Sat, 17 Nov 2012 21:21:49 +0000 (21:21 +0000)]
store chainid on pdbentry
jprocter [Sat, 17 Nov 2012 21:20:50 +0000 (21:20 +0000)]
format adapter should return AlignmentI
jprocter [Sat, 17 Nov 2012 21:11:12 +0000 (21:11 +0000)]
formatting
jprocter [Sat, 17 Nov 2012 21:10:59 +0000 (21:10 +0000)]
call annotate3d service and parse rnaml to alignment
jprocter [Sat, 17 Nov 2012 21:10:36 +0000 (21:10 +0000)]
formatting
jprocter [Sat, 17 Nov 2012 21:02:51 +0000 (21:02 +0000)]
sequence numbering from 1
jprocter [Sat, 17 Nov 2012 21:02:24 +0000 (21:02 +0000)]
formatting
jprocter [Sat, 17 Nov 2012 21:01:44 +0000 (21:01 +0000)]
store chaincode on pdbentry
jprocter [Sat, 17 Nov 2012 20:16:50 +0000 (20:16 +0000)]
formatting
jprocter [Sat, 17 Nov 2012 20:09:15 +0000 (20:09 +0000)]
simple HTTP multipart entity poster - may not be useful
jprocter [Sat, 17 Nov 2012 18:50:34 +0000 (18:50 +0000)]
tests for jalview.analysis.AlignSeq
jprocter [Sat, 17 Nov 2012 18:47:51 +0000 (18:47 +0000)]
openjdk7 returns null for default value selected format if it hasn't been touched
jprocter [Sat, 17 Nov 2012 18:35:43 +0000 (18:35 +0000)]
method to construct sequence mapping for matching positions in aligned sequences
jprocter [Sat, 17 Nov 2012 18:34:37 +0000 (18:34 +0000)]
convenience method for performing pairwise alignment
jprocter [Sat, 17 Nov 2012 18:33:46 +0000 (18:33 +0000)]
formatting and javadoc
Paolo Di Tommaso [Thu, 15 Nov 2012 21:43:30 +0000 (22:43 +0100)]
Fixed T-Coffee file scores parser to support extended format including residue numbers
jprocter [Thu, 15 Nov 2012 15:25:22 +0000 (15:25 +0000)]
remove java7 plugin dependency
jprocter [Thu, 15 Nov 2012 15:22:01 +0000 (15:22 +0000)]
don't set background colour for menu bar
jprocter [Thu, 15 Nov 2012 15:21:34 +0000 (15:21 +0000)]
allow .rnaml as a filename extension
jprocter [Thu, 15 Nov 2012 15:19:11 +0000 (15:19 +0000)]
comment on jalview.io.AlignFile architecture
jprocter [Thu, 15 Nov 2012 15:18:29 +0000 (15:18 +0000)]
source formatting
jprocter [Thu, 15 Nov 2012 15:15:04 +0000 (15:15 +0000)]
Merge branch 'develop' into menard
Conflicts:
src/MCview/PDBfile.java
src/jalview/analysis/Rna.java
src/jalview/analysis/StructureFrequency.java
src/jalview/appletgui/AlignFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/PopupMenu.java
src/jalview/io/FeaturesFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/workers/StrucConsensusThread.java
jprocter [Tue, 13 Nov 2012 17:49:01 +0000 (17:49 +0000)]
Merge branch 'master' into develop
jprocter [Mon, 12 Nov 2012 11:36:47 +0000 (11:36 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:36:16 +0000 (11:36 +0000)]
final tweaks to help landing page
jprocter [Mon, 12 Nov 2012 11:12:49 +0000 (11:12 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:10:12 +0000 (11:10 +0000)]
update footer for static page
jprocter [Mon, 12 Nov 2012 10:00:29 +0000 (10:00 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Sun, 11 Nov 2012 11:23:11 +0000 (11:23 +0000)]
tidy help
jprocter [Fri, 9 Nov 2012 17:00:09 +0000 (17:00 +0000)]
property to configure webstart image
jprocter [Fri, 9 Nov 2012 16:56:10 +0000 (16:56 +0000)]
tweak file association comment and make sure webstart image is published
jprocter [Fri, 9 Nov 2012 16:35:45 +0000 (16:35 +0000)]
push jalview v2.8 release date to monday 12th November
jprocter [Fri, 9 Nov 2012 16:08:50 +0000 (16:08 +0000)]
ga tracking, footers and footer link styles
jprocter [Fri, 9 Nov 2012 15:32:04 +0000 (15:32 +0000)]
more tweaking of static pages and rejigging applet parameter documentation for accessibility
jprocter [Fri, 9 Nov 2012 14:38:11 +0000 (14:38 +0000)]
tweak whats new again
jprocter [Fri, 9 Nov 2012 13:04:39 +0000 (13:04 +0000)]
tweaking welcome message and what's new
jprocter [Fri, 9 Nov 2012 08:02:00 +0000 (08:02 +0000)]
constructor takes settings from any existing feature renderer on alignment panel
jprocter [Thu, 8 Nov 2012 17:45:43 +0000 (17:45 +0000)]
JAL-1193 ensure the 'loadedComplete' method gets called for all views
after the views have been opened by using the Swing stack as a queue
cruisecontrol [Thu, 8 Nov 2012 16:49:53 +0000 (16:49 +0000)]
update installAnywhere classpath and libs for jalview 2.8
jprocter [Thu, 8 Nov 2012 16:29:30 +0000 (16:29 +0000)]
update release notes for JAL-1202
cruisecontrol [Thu, 8 Nov 2012 16:21:39 +0000 (16:21 +0000)]
JAL-1202 included examples and also added in jdas jars and the groovy library
jprocter [Thu, 8 Nov 2012 15:41:51 +0000 (15:41 +0000)]
remember to close input file!
jprocter [Thu, 8 Nov 2012 15:41:34 +0000 (15:41 +0000)]
tidy imports
jprocter [Thu, 8 Nov 2012 10:59:13 +0000 (10:59 +0000)]
embed links to major features in main page
jprocter [Thu, 8 Nov 2012 10:58:54 +0000 (10:58 +0000)]
tweak wording
jprocter [Wed, 7 Nov 2012 17:28:32 +0000 (17:28 +0000)]
patch broken link
jprocter [Wed, 7 Nov 2012 17:18:20 +0000 (17:18 +0000)]
and more tweaks.
jprocter [Wed, 7 Nov 2012 17:15:08 +0000 (17:15 +0000)]
JAL-1201 more layout tweaks
jprocter [Wed, 7 Nov 2012 17:07:05 +0000 (17:07 +0000)]
JAL-1201 tweak layout for applet page and allow monospace <pre> tags
jprocter [Wed, 7 Nov 2012 15:59:39 +0000 (15:59 +0000)]
JAL-1201 more tweaks to page layout
jprocter [Wed, 7 Nov 2012 15:42:19 +0000 (15:42 +0000)]
Jalview 2.8 release notes and whats new! text
jprocter [Wed, 7 Nov 2012 15:11:58 +0000 (15:11 +0000)]
updated release notes for Jalview Version 2.8
jprocter [Wed, 7 Nov 2012 15:11:16 +0000 (15:11 +0000)]
JAL-1201 update pages to use new website design
jprocter [Wed, 7 Nov 2012 15:04:25 +0000 (15:04 +0000)]
JAL-957 manual update to applet authorlist - need to use authorprops (JAL-1200)
jprocter [Wed, 31 Oct 2012 17:05:58 +0000 (17:05 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Wed, 31 Oct 2012 17:04:29 +0000 (17:04 +0000)]
JAL-1130 fix gif palette (arggh!)
cruisecontrol [Tue, 30 Oct 2012 18:06:48 +0000 (18:06 +0000)]
JAL-1197 tweak installer more
cruisecontrol [Tue, 30 Oct 2012 17:51:13 +0000 (17:51 +0000)]
JAL-1197 JAL-1198 migrate to IA2012 and new build VM
jprocter [Tue, 30 Oct 2012 17:22:05 +0000 (17:22 +0000)]
JAL-1130 JAL-1197 nice installer splashscreens and fireworks readable pngs for splashscreens
jprocter [Tue, 30 Oct 2012 16:59:19 +0000 (16:59 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Tue, 30 Oct 2012 16:58:32 +0000 (16:58 +0000)]
JAL-1130 fireworks editable huge jalview logo in RGB
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:17:18 +0000 (16:17 +0000)]
JAL-1130 updated installAnywhere program logos
jprocter [Tue, 30 Oct 2012 16:16:11 +0000 (16:16 +0000)]
JAL-1130 preserved old installAnywhere installer logo as logo_v2
jprocter [Mon, 29 Oct 2012 10:42:43 +0000 (10:42 +0000)]
JAL-1130 made background transparent for small logo (used for application and window icon on Windows platform)
jprocter [Wed, 24 Oct 2012 16:04:11 +0000 (17:04 +0100)]
JAL-1193 call setLoadingFromArchiveFinished(true) for any new structure views, but only after all windows have been loaded and gathered
jprocter [Wed, 24 Oct 2012 16:00:59 +0000 (17:00 +0100)]
JAL-1193 patch prevents JalviewJmolBinding from handling colourBySequence events until setLoadingFromArchiveFinished(true) called
jprocter [Thu, 4 Oct 2012 16:43:26 +0000 (17:43 +0100)]
Jalview 2.8 Source Header
git://source.jalview.org / jalview.git / log