Jim Procter [Tue, 21 Oct 2014 10:05:54 +0000 (11:05 +0100)]
JAL-1551 crlf changes
Jim Procter [Wed, 15 Oct 2014 09:16:10 +0000 (10:16 +0100)]
JAL-674 always try to extract secondary structure when importing a PDB file
Jim Procter [Wed, 15 Oct 2014 09:12:10 +0000 (10:12 +0100)]
JAL-674 support preservation of any annotation created by the MCView PDB parser by application of liftOver method
Jim Procter [Wed, 15 Oct 2014 09:09:17 +0000 (10:09 +0100)]
JAL-674 make transferAnnotation method static
Jim Procter [Wed, 15 Oct 2014 09:04:26 +0000 (10:04 +0100)]
JAL-348 JAL-674 JAL-1564 TODO and implementation error message when liftOver is attempted for a DNA/Protein mapping.
Jim Procter [Wed, 15 Oct 2014 08:56:53 +0000 (09:56 +0100)]
JAL-674 patch logic to test whether old and new sequence reference for annotation have a common dataset sequence
Jim Procter [Wed, 15 Oct 2014 08:55:13 +0000 (09:55 +0100)]
JAL-674 JAL-1305 JAL-348 new liftOver method and test to allow annotation to be propagated from one sequence to another via a sequence mapping
gmungoc [Fri, 10 Oct 2014 14:14:06 +0000 (15:14 +0100)]
JAL-1551 CRLF handling
Jim Procter [Fri, 10 Oct 2014 15:26:38 +0000 (16:26 +0100)]
JAL-674 employ new signature in Annotate3D service test
Jim Procter [Fri, 10 Oct 2014 15:25:00 +0000 (16:25 +0100)]
JAL-674 disable secondary structure annotation when data passed to MCView for display
Jim Procter [Fri, 10 Oct 2014 15:24:18 +0000 (16:24 +0100)]
JAL-674 typo
Jim Procter [Fri, 10 Oct 2014 15:23:40 +0000 (16:23 +0100)]
JAL-674 new constructors to pass flags about annotating sequence with data from PDB file
Jim Procter [Fri, 10 Oct 2014 15:22:24 +0000 (16:22 +0100)]
JAL-674 parser flag to control secondary structure processing
Jim Procter [Fri, 10 Oct 2014 15:17:01 +0000 (16:17 +0100)]
JAL-674 change jalview.io.AlignFile to allow parsing to be deferred till after the parser class has been fully initialised/configured
Jim Procter [Thu, 9 Oct 2014 15:07:15 +0000 (16:07 +0100)]
Merge branch 'bug/JAL-1558' into Release_2_8_2_Branch
Jim Procter [Thu, 9 Oct 2014 15:06:36 +0000 (16:06 +0100)]
patch fixes JAL-1558
Jim Procter [Tue, 7 Oct 2014 16:27:36 +0000 (17:27 +0100)]
Merge branch 'bugs/JAL-1151' into Release_2_8_2_Branch
Jim Procter [Tue, 7 Oct 2014 16:26:35 +0000 (17:26 +0100)]
JAL-1557 partial implementation - need to think about how to do SHIFT+double click type range selections
Jim Procter [Tue, 7 Oct 2014 16:25:37 +0000 (17:25 +0100)]
patch for JAL-1151 - select whole sequence when double clicking on associated annotation's id
Jim Procter [Tue, 7 Oct 2014 16:22:43 +0000 (17:22 +0100)]
JAL-1421 remove Vector and pass a list
Jim Procter [Tue, 7 Oct 2014 16:18:31 +0000 (17:18 +0100)]
JAL-1151 source tidy
Jim Procter [Mon, 6 Oct 2014 16:28:21 +0000 (17:28 +0100)]
Merge branch 'JAL-429_phylip-file-support' into Release_2_8_2_Branch
Jim Procter [Mon, 6 Oct 2014 16:27:56 +0000 (17:27 +0100)]
Merge branch 'patch/JAL-848' into JAL-429_phylip-file-support
Jim Procter [Mon, 6 Oct 2014 16:27:36 +0000 (17:27 +0100)]
Merge branch 'patch/JAL-848' into Release_2_8_2_Branch
Jim Procter [Mon, 6 Oct 2014 16:26:54 +0000 (17:26 +0100)]
JAL-848 reinstate netbeans files from Phylip patch branch
Jim Procter [Mon, 6 Oct 2014 16:22:12 +0000 (17:22 +0100)]
Merge branch 'JAL-429_phylip-file-support' into Release_2_8_2_Branch
Jim Procter [Mon, 6 Oct 2014 15:33:17 +0000 (16:33 +0100)]
Merge branch 'Release_2_8_2_Branch' into JAL-429_phylip-file-support
Conflicts:
src/jalview/io/AppletFormatAdapter.java
Jim Procter [Mon, 6 Oct 2014 15:18:42 +0000 (16:18 +0100)]
Merge branch 'patch/JAL-1286_JAL-1265' into Release_2_8_2_Branch
Jim Procter [Mon, 6 Oct 2014 14:49:43 +0000 (15:49 +0100)]
JAL-1286 missing file for testcase where file ends in gz but isn't a gz
file
Jim Procter [Mon, 6 Oct 2014 14:51:25 +0000 (15:51 +0100)]
JAL-1500 JAL-1265 patch to parse PDB database refs in PFAM stockholm
Jim Procter [Mon, 6 Oct 2014 11:46:56 +0000 (12:46 +0100)]
Merge branch 'feature/JAL-654_dssp' into Release_2_8_2_Branch
Jim Procter [Mon, 6 Oct 2014 11:39:13 +0000 (12:39 +0100)]
JAL-654 remove any annotation rows for chain specific query
Jim Procter [Mon, 6 Oct 2014 11:38:24 +0000 (12:38 +0100)]
JAL-654 updated pdb db fetcher test to verify the number of annotation
rows retrieved for a single chain query
Jim Procter [Mon, 6 Oct 2014 11:26:22 +0000 (12:26 +0100)]
JAL-654 JAL-1264 sequence associated annotation is duplicated before transfer to dataset sequence rather than simply relocated to preserve alignment references
Jim Procter [Mon, 6 Oct 2014 11:24:14 +0000 (12:24 +0100)]
JAL-654 format and refactor test demonstrating PDB secondary structure on alignment not properly linked to alignment sequence
Jim Procter [Mon, 6 Oct 2014 11:22:16 +0000 (12:22 +0100)]
JAL-1115 TODO remove use of java.util.Vector
Jim Procter [Mon, 6 Oct 2014 11:17:29 +0000 (12:17 +0100)]
JAL-654 javadoc createDatasetSequence and transferAnnotation
Jim Procter [Mon, 6 Oct 2014 11:11:11 +0000 (12:11 +0100)]
JAL-654_dssp formatting and javadoc
Charles Ofoegbu [Fri, 3 Oct 2014 15:33:03 +0000 (16:33 +0100)]
Integration of David Corsars Phylip File support
Jim Procter [Fri, 3 Oct 2014 13:21:34 +0000 (14:21 +0100)]
Merge branch 'Release_2_8_2_Branch_i18n' into Release_2_8_2_Branch
Jim Procter [Fri, 3 Oct 2014 13:19:04 +0000 (14:19 +0100)]
JAL-1355 removed all top level html tags from message bundles
JAL-1355 new flag to optionally add html tabs to wrapTooltip
Charles Ofoegbu [Fri, 3 Oct 2014 10:50:33 +0000 (11:50 +0100)]
removed local test data
Charles Ofoegbu [Fri, 3 Oct 2014 10:45:50 +0000 (11:45 +0100)]
Local branch test
Jim Procter [Fri, 3 Oct 2014 10:01:28 +0000 (11:01 +0100)]
Merge branch 'Release_2_8_2_Branch' into Release_2_8_2_Branch_i18n
Jim Procter [Fri, 3 Oct 2014 10:00:46 +0000 (11:00 +0100)]
Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch
Jim Procter [Fri, 3 Oct 2014 09:59:28 +0000 (10:59 +0100)]
JAL-1338 note added #fridaycommits not actually connected with JAL-1138
Jim Procter [Fri, 3 Oct 2014 09:55:18 +0000 (10:55 +0100)]
Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch
Jim Procter [Fri, 3 Oct 2014 09:54:47 +0000 (10:54 +0100)]
JAL-1499 simple test to check JABA client can
JAL-1499 send/receive data to JABA server
darolmar [Sat, 27 Sep 2014 15:35:27 +0000 (17:35 +0200)]
JAL-1355
darolmar [Fri, 26 Sep 2014 14:27:07 +0000 (16:27 +0200)]
JAL-1355
darolmar [Tue, 23 Sep 2014 14:34:33 +0000 (16:34 +0200)]
JAL-1355
darolmar [Fri, 19 Sep 2014 15:15:01 +0000 (17:15 +0200)]
JAL-1428
darolmar [Fri, 19 Sep 2014 15:12:06 +0000 (17:12 +0200)]
JAL-1355
darolmar [Fri, 19 Sep 2014 10:36:02 +0000 (12:36 +0200)]
Spanish translation
darolmar [Fri, 19 Sep 2014 06:03:57 +0000 (08:03 +0200)]
JAL-1355
gmungoc [Thu, 18 Sep 2014 13:16:21 +0000 (14:16 +0100)]
Merge branch 'JAL-1360_Branch' into Release_2_8_2_Branch
gmungoc [Thu, 18 Sep 2014 13:12:52 +0000 (14:12 +0100)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
gmungoc [Thu, 18 Sep 2014 12:59:17 +0000 (13:59 +0100)]
JAL-1360 tweaks to match help page conventions, size image properly
gmungoc [Thu, 18 Sep 2014 12:58:40 +0000 (13:58 +0100)]
JAL-1360 consistent (bold) help page headings
gmungoc [Thu, 18 Sep 2014 10:21:04 +0000 (11:21 +0100)]
JAL-1360 Javadoc, Vector replaced with ArrayList, code formatted
gmungoc [Thu, 18 Sep 2014 10:19:17 +0000 (11:19 +0100)]
JAL-1360 Javadoc/JUnit
gmungoc [Thu, 18 Sep 2014 08:31:00 +0000 (09:31 +0100)]
JAL-1360 refactored utility method to ColorUtils class
gmungoc [Thu, 18 Sep 2014 08:29:57 +0000 (09:29 +0100)]
JAL-1544 it's --> its
gmungoc [Wed, 17 Sep 2014 15:41:54 +0000 (16:41 +0100)]
JAL-1360 updates to online help for user define colour scheme
gmungoc [Wed, 17 Sep 2014 15:41:14 +0000 (16:41 +0100)]
Correct colour for text when colour set
gmungoc [Wed, 17 Sep 2014 12:42:25 +0000 (13:42 +0100)]
JAL-1360 refactored for consistent lighter/darker for
selected/unselected button foreground
gmungoc [Wed, 17 Sep 2014 09:56:45 +0000 (10:56 +0100)]
JAL-1360 workaround for user defined colours display on Java 7
gmungoc [Mon, 15 Sep 2014 14:56:27 +0000 (15:56 +0100)]
JAL-1542 script to show aligned positions of selected column(s)
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:38:46 +0000 (17:38 +0100)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:33:51 +0000 (17:33 +0100)]
Merge branch 'bug/JAL-1486_flatfile' into Release_2_8_2_Branch
patch to export of selected area so that start/end numberings are correct. main file export option still needs fixing.
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:27:47 +0000 (17:27 +0100)]
JAL-1486 JAL-1543 pushed alignment viewport->view->flat file logic into jalview.io to unify applet and application selected region export method
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:04:38 +0000 (17:04 +0100)]
formatting and organise imports
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:04:03 +0000 (17:04 +0100)]
JAL-1486 fix: pass selected region to jalview.io via alignment view and align viewport annotation methods
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:58:58 +0000 (16:58 +0100)]
JAL-1199 add stockholm output to list of AppletFormatAdapter formatters
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:56:29 +0000 (16:56 +0100)]
JAL-1486 JAL-535 refactor code for trimming alignment annotation according to selections from FormatAdapter to view model method
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:55:14 +0000 (16:55 +0100)]
JAL-535 tidy interface definition and documentation
gmungoc [Fri, 12 Sep 2014 13:59:38 +0000 (14:59 +0100)]
JAL-1516 handle null annotations
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 09:52:46 +0000 (10:52 +0100)]
JAL-1516 Annotation row score output script for jalview-discuss request from David M Garcia
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 20:09:36 +0000 (21:09 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 20:09:10 +0000 (21:09 +0100)]
JAL-1333 fix imports
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:32:45 +0000 (20:32 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:32:14 +0000 (20:32 +0100)]
JAL-1333 log4j/slf additional jars
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:25:09 +0000 (20:25 +0100)]
JAL-1333 add log4j-slf4j bridge
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:22:04 +0000 (20:22 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:21:12 +0000 (20:21 +0100)]
JAL-1333 finessing log4j and slf dependencies for strucviz and jaba-client code
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:12:48 +0000 (20:12 +0100)]
JAL-1333 JAL-1533 todo to get Chimera superposing properly we need to specify a set of atoms from each chain (or model in chimera-speak), but for chains with multiple models, each model needs to be superposed independently (potentially)
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 18:37:34 +0000 (19:37 +0100)]
JAL-1333 more superposition debugging and deadlock avoidance
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:59:26 +0000 (13:59 +0100)]
JAL-1379 Jpred JABA client test harness
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:35:32 +0000 (13:35 +0100)]
JAL-1333 allow reuse of existing chimera for new or additional structures
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:35:06 +0000 (13:35 +0100)]
JAL-1333 more refinements - deadlocks still possible with this version
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:33:42 +0000 (13:33 +0100)]
JAL-674 futzing with bugs
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:32:23 +0000 (13:32 +0100)]
JAL-795 take colour from annotation if colour is present
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:31:32 +0000 (13:31 +0100)]
ensure the dataset is instantiated before materialising alignment viewport
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:30:29 +0000 (13:30 +0100)]
JAL-1379 new look JPred results
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 11:08:09 +0000 (12:08 +0100)]
JAL-1520 switch between Protein and non-canonical RNA secondary structure rendering styles for an annotation row
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 11:00:44 +0000 (12:00 +0100)]
JAL-1028 JAL-1142 refactor test to allow reuse of secondary structure validation routine
j.procter@dundee.ac.uk [Tue, 8 Jul 2014 19:16:49 +0000 (15:16 -0400)]
JAL-1333 allow reuse of existing viewers (of a specified or currently preferred type)
j.procter@dundee.ac.uk [Tue, 8 Jul 2014 19:15:11 +0000 (15:15 -0400)]
JAL-1333 more efficient color statement
j.procter@dundee.ac.uk [Fri, 4 Jul 2014 03:09:00 +0000 (20:09 -0700)]
JAL-1333 more abstraction and refactoring and working demo of Jalview talking to Chimera
j.procter@dundee.ac.uk [Thu, 3 Jul 2014 19:53:56 +0000 (12:53 -0700)]
Merge branch 'Release_2_8_2_Branch' into features/JAL-1333
git://source.jalview.org / jalview.git / log