Jim Procter [Tue, 21 Oct 2014 10:10:52 +0000 (11:10 +0100)]
Merge branch 'features/JAL-1264_showHideAnnotations' into forpush/JAL-674_dssp
EOL changes conflict with new lines from mungo's branch
Conflicts:
resources/lang/Messages.properties
src/jalview/datamodel/SequenceI.java
Jim Procter [Tue, 21 Oct 2014 10:05:54 +0000 (11:05 +0100)]
JAL-1551 crlf changes
Jim Procter [Thu, 16 Oct 2014 12:41:05 +0000 (13:41 +0100)]
Merge branch 'feature/JAL-674_dssp' into features/JAL-1264_showHideAnnotations
Jim Procter [Wed, 15 Oct 2014 14:48:27 +0000 (15:48 +0100)]
Merge branch 'jims_crlf_hell_JAL-1551' of https://source.jalview.org/git/jalview into jims_crlf_hell_JAL-1551
Jim Procter [Wed, 15 Oct 2014 14:27:12 +0000 (15:27 +0100)]
JAL-1551 crlf changes due to checkout with text=auto
Jim Procter [Wed, 15 Oct 2014 14:27:12 +0000 (15:27 +0100)]
JAL-1551 crlf changes due to checkout with text=auto
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
gmungoc [Mon, 13 Oct 2014 13:28:13 +0000 (14:28 +0100)]
JAL-1264 unneeded setup removed
gmungoc [Mon, 13 Oct 2014 08:52:51 +0000 (09:52 +0100)]
JAL-1264 unit test corrected
gmungoc [Sun, 12 Oct 2014 17:34:23 +0000 (18:34 +0100)]
JAL-1544 SEQENCE -> SEQUENCE
gmungoc [Sun, 12 Oct 2014 17:32:48 +0000 (18:32 +0100)]
JAL-1264 help updates for show/hide annotations on
View/Annotations/Popup menus
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
gmungoc [Fri, 10 Oct 2014 14:50:00 +0000 (15:50 +0100)]
JAL-1551 project-specific settings
gmungoc [Fri, 10 Oct 2014 14:23:18 +0000 (15:23 +0100)]
JAL-1551 proposed project settings for code cleanup/Save actions
gmungoc [Fri, 10 Oct 2014 14:18:11 +0000 (15:18 +0100)]
JAL-1264 unit tests
gmungoc [Fri, 10 Oct 2014 14:17:44 +0000 (15:17 +0100)]
Suppressed test that needs user interaction to allow JUnit suite to run
gmungoc [Fri, 10 Oct 2014 14:14:06 +0000 (15:14 +0100)]
JAL-1551 CRLF handling
gmungoc [Fri, 10 Oct 2014 14:13:09 +0000 (15:13 +0100)]
JAL-1264 show/hide annotations, plus merged changes
gmungoc [Fri, 10 Oct 2014 14:05:26 +0000 (15:05 +0100)]
JAL-1481 wrap tooltip in html
gmungoc [Fri, 10 Oct 2014 14:03:58 +0000 (15:03 +0100)]
JAL-1264 added getAlignmentAnnotations(calcId, label)
gmungoc [Fri, 10 Oct 2014 13:58:37 +0000 (14:58 +0100)]
JAL-1264 reverted (removed added method)
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
gmungoc [Wed, 8 Oct 2014 11:15:45 +0000 (12:15 +0100)]
Merge branch 'Release_2_8_2_Branch' into
features/JAL-1264_showHideAnnotations
Conflicts:
resources/lang/Messages.properties
src/jalview/datamodel/Alignment.java
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
gmungoc [Tue, 7 Oct 2014 16:05:06 +0000 (17:05 +0100)]
JAL-1264 wip
gmungoc [Tue, 7 Oct 2014 14:13:53 +0000 (15:13 +0100)]
JAL-1554 handle left-then-right click on sequence id
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
gmungoc [Fri, 3 Oct 2014 11:19:59 +0000 (12:19 +0100)]
JAL-1264 javadoc update
gmungoc [Fri, 3 Oct 2014 11:08:09 +0000 (12:08 +0100)]
JAL-1264 show/hide annotations; JAL-1481 Find tooltip
gmungoc [Fri, 3 Oct 2014 11:06:23 +0000 (12:06 +0100)]
JAL-1506 delete all warning; JAL-1264 show/hide annotations
gmungoc [Fri, 3 Oct 2014 11:04:45 +0000 (12:04 +0100)]
JAL-1264 refactored show/hide annotation types including groups
gmungoc [Fri, 3 Oct 2014 11:02:09 +0000 (12:02 +0100)]
JAL-1481 search expression validation
gmungoc [Fri, 3 Oct 2014 11:01:34 +0000 (12:01 +0100)]
JAL-1506 correct exit on close align frame
gmungoc [Fri, 3 Oct 2014 11:00:10 +0000 (12:00 +0100)]
JAL-914 don't open help window twice
gmungoc [Fri, 3 Oct 2014 10:56:34 +0000 (11:56 +0100)]
JAL-1264 show/hide annotations, JAL-1481 search validation, JAL-1506
delete all warning
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
gmungoc [Thu, 25 Sep 2014 12:48:40 +0000 (13:48 +0100)]
JAL-1264 tidy up use of MouseListener for showHideAnnotations
gmungoc [Thu, 25 Sep 2014 09:26:51 +0000 (10:26 +0100)]
JAL-1264 alternative (popup menu) way to show/hide annotations by type
gmungoc [Wed, 24 Sep 2014 15:19:52 +0000 (16:19 +0100)]
JAL-1264 further refactoring of panel + unit tests
darolmar [Tue, 23 Sep 2014 14:34:33 +0000 (16:34 +0200)]
JAL-1355
gmungoc [Tue, 23 Sep 2014 13:10:45 +0000 (14:10 +0100)]
JAL-1264 first cut of panel for annotation show/hide options
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
git://source.jalview.org / jalview.git / log