Jim Procter [Fri, 21 Jun 2013 13:12:56 +0000 (14:12 +0100)]
Merge branch 'JAL-1294_iupredexportimport' into develop
Jim Procter [Fri, 21 Jun 2013 12:59:53 +0000 (13:59 +0100)]
JAL-1325 formatting
Jim Procter [Fri, 21 Jun 2013 12:59:35 +0000 (13:59 +0100)]
JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF for GRAPHLINE statements
Jim Procter [Fri, 21 Jun 2013 12:58:42 +0000 (13:58 +0100)]
JAL-1294 JAL-1325 store graphline for individual annotation rows.
Jim Procter [Fri, 21 Jun 2013 11:20:11 +0000 (12:20 +0100)]
JAL-1294 JAL-1325 bugfix equals
Jim Procter [Fri, 21 Jun 2013 10:58:47 +0000 (11:58 +0100)]
JAL-1294 JAL-1325 test annotation threshold line equivalence
Jim Procter [Fri, 21 Jun 2013 10:36:50 +0000 (11:36 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into develop
Jim Procter [Fri, 21 Jun 2013 10:36:17 +0000 (11:36 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Fri, 21 Jun 2013 10:35:07 +0000 (11:35 +0100)]
JAL-1127 set option widgets to service defaults only when showing default settings
Jim Procter [Wed, 19 Jun 2013 16:41:27 +0000 (17:41 +0100)]
JAL-1240 avoid NPE when source has no proxy available
Jim Procter [Wed, 19 Jun 2013 16:01:05 +0000 (17:01 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into develop
Jim Procter [Wed, 19 Jun 2013 16:00:37 +0000 (17:00 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Tue, 18 Jun 2013 20:57:45 +0000 (21:57 +0100)]
JAL-1320 ascending alphabetical order
Jim Procter [Tue, 18 Jun 2013 20:57:02 +0000 (21:57 +0100)]
JAL-1320 preserve option/parameter order with LinkedHashMap
Jim Procter [Tue, 18 Jun 2013 20:38:16 +0000 (21:38 +0100)]
JAL-1320 sort options and parameters according to their name
Jim Procter [Tue, 18 Jun 2013 20:29:29 +0000 (21:29 +0100)]
typo
Jim Procter [Tue, 18 Jun 2013 20:28:57 +0000 (21:28 +0100)]
JAL-1321 don't show a tooltip for empty strings
Jim Procter [Tue, 18 Jun 2013 16:06:38 +0000 (17:06 +0100)]
JAL-674 - avoid java.util.ConcurrentModificationException on the pdbfile list
Jim Procter [Tue, 18 Jun 2013 16:03:08 +0000 (17:03 +0100)]
JAL-674 tests for PDB ID retrieval and specific chain retrieval
Jim Procter [Mon, 17 Jun 2013 17:26:54 +0000 (18:26 +0100)]
Merge branch 'JAL-1319_jronn_npe' into develop
Jim Procter [Mon, 17 Jun 2013 17:26:47 +0000 (18:26 +0100)]
Merge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 17:25:54 +0000 (18:25 +0100)]
JAL-1319 (blacklist fix) check for presence of a score object before we start making annotation
Jim Procter [Mon, 17 Jun 2013 16:52:15 +0000 (17:52 +0100)]
Merge branch 'JAL-1312_ambiguity_na' into develop
Jim Procter [Mon, 17 Jun 2013 16:51:33 +0000 (17:51 +0100)]
Merge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 16:45:23 +0000 (17:45 +0100)]
JAL-1027 fix errors in alternative codon table
Jim Procter [Mon, 17 Jun 2013 16:45:03 +0000 (17:45 +0100)]
JAL-1027 check that ResidueProperties.codonHash2 is actually identical to the codon table used in previous versions
Jim Procter [Mon, 17 Jun 2013 16:41:40 +0000 (17:41 +0100)]
JAL-1027 use alternative codon table in ResidueProperties.codonHash2 for translation
Jim Procter [Mon, 17 Jun 2013 14:23:00 +0000 (15:23 +0100)]
JAL-1035 option to allow 'STOP' codon to translate as '*'
Jim Procter [Mon, 17 Jun 2013 14:14:40 +0000 (15:14 +0100)]
JAL-1312 patch for regression noticed after patch to jalview.analysis.Dna cdna translation
Jim Procter [Mon, 17 Jun 2013 14:13:13 +0000 (15:13 +0100)]
JAL-1312 rewrite of code for first reported exception - note - maintaining scontigs may not even be necessary !
Jim Procter [Mon, 17 Jun 2013 14:10:22 +0000 (15:10 +0100)]
JAL-1312 formatting and more comprehensive test
Jim Procter [Mon, 17 Jun 2013 14:09:04 +0000 (15:09 +0100)]
JAL-1312 remove unnecessary methods
Jim Procter [Mon, 17 Jun 2013 12:52:21 +0000 (13:52 +0100)]
JAL-1312 more helpful error message when translation breaks
Jim Procter [Mon, 17 Jun 2013 09:40:26 +0000 (10:40 +0100)]
JAL-529 - IUBMB nucleotide ambiguity codes and programmatic generation of codons and inverse tables
Jim Procter [Mon, 17 Jun 2013 09:35:28 +0000 (10:35 +0100)]
JAL-1318 - route warnings to stderr (need to find a better solution for JAL-1069)
Jim Procter [Mon, 17 Jun 2013 09:33:11 +0000 (10:33 +0100)]
JAL-1318 avoid failure if SequenceI objects don't have valid dataset references
Jim Procter [Mon, 17 Jun 2013 09:31:58 +0000 (10:31 +0100)]
JAL-966 avoid using java.util.Vector
Jim Procter [Mon, 17 Jun 2013 09:21:32 +0000 (10:21 +0100)]
test for JAL-1312
Jim Procter [Fri, 14 Jun 2013 15:23:31 +0000 (16:23 +0100)]
Merge branch 'JAL-1316' into develop
Jim Procter [Fri, 14 Jun 2013 15:23:22 +0000 (16:23 +0100)]
Merge branch 'JAL-1316' into Release_2_8_Branch
Jim Procter [Fri, 14 Jun 2013 15:18:23 +0000 (16:18 +0100)]
JAL-1316 compact '' to '
Jim Procter [Fri, 14 Jun 2013 15:17:58 +0000 (16:17 +0100)]
JAL-1316 recognise and extract quoted region as nodename
Jim Procter [Fri, 14 Jun 2013 14:06:42 +0000 (15:06 +0100)]
JAL-1316 JAL-1313 newick IO test harness
Jim Procter [Thu, 13 Jun 2013 16:38:24 +0000 (17:38 +0100)]
Merge branch 'JAL-1314_headlessFlag' into develop
Jim Procter [Thu, 13 Jun 2013 16:38:08 +0000 (17:38 +0100)]
Merge branch 'JAL-1314_headlessFlag' into Release_2_8_Branch
Jim Procter [Thu, 13 Jun 2013 16:37:43 +0000 (17:37 +0100)]
JAL-1314 allow 'nogui' and 'headless' as synonyms for 'nodisplay' argument and ensure awt.gui.headless=true is set as early as possible.
Jim Procter [Thu, 13 Jun 2013 16:36:46 +0000 (17:36 +0100)]
JAL-1314 test for common variants of -nodisplay performing the same for EPS generation
JAL-1314 test for identical termination behaviour with/without java.awt.headless=true
Jim Procter [Thu, 13 Jun 2013 15:55:18 +0000 (16:55 +0100)]
Merge branch 'JAL-1315_headlessEPS' into develop
Jim Procter [Thu, 13 Jun 2013 15:55:11 +0000 (16:55 +0100)]
Merge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch
Jim Procter [Thu, 13 Jun 2013 15:53:33 +0000 (16:53 +0100)]
fix for JAL-1315
Jim Procter [Thu, 13 Jun 2013 15:53:10 +0000 (16:53 +0100)]
JAL-1315 test for exit and successful generation of EPS using commandline
Jim Procter [Tue, 11 Jun 2013 10:50:27 +0000 (11:50 +0100)]
change to release version of VARNA-3-9
Jim Procter [Sun, 9 Jun 2013 18:34:47 +0000 (19:34 +0100)]
JAL-674 avoid runtime dependency on annotate3d webservice in applet
Jim Procter [Sun, 9 Jun 2013 18:33:54 +0000 (19:33 +0100)]
JAL-674 - update applet build dependency on VARNA
Jim Procter [Sun, 9 Jun 2013 14:30:55 +0000 (15:30 +0100)]
Merge branch '2_8_1_patch_multiharmony' into develop
Jim Procter [Sun, 9 Jun 2013 14:30:33 +0000 (15:30 +0100)]
Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
Jim Procter [Sun, 9 Jun 2013 14:29:43 +0000 (15:29 +0100)]
fix for JAL-1298
Jim Procter [Sun, 9 Jun 2013 14:29:14 +0000 (15:29 +0100)]
JAL-715 - TODO
Jim Procter [Fri, 7 Jun 2013 15:33:07 +0000 (16:33 +0100)]
Merge branch '2_8_1_patch_multiharmony' into develop
Jim Procter [Fri, 7 Jun 2013 15:32:54 +0000 (16:32 +0100)]
Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
Jim Procter [Fri, 7 Jun 2013 12:31:37 +0000 (13:31 +0100)]
JAL-1309 fix broken partition computation for adding in ungrouped sequences as final group
Jim Procter [Fri, 7 Jun 2013 12:24:47 +0000 (13:24 +0100)]
JAL-945 uniquify prior to submission
Jim Procter [Fri, 7 Jun 2013 12:24:16 +0000 (13:24 +0100)]
formatting
Jim Procter [Fri, 7 Jun 2013 12:24:08 +0000 (13:24 +0100)]
JAL-715 allow headless construction for testing
Jim Procter [Fri, 7 Jun 2013 12:23:28 +0000 (13:23 +0100)]
JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony service
Jim Procter [Tue, 4 Jun 2013 13:23:08 +0000 (14:23 +0100)]
fix for JAL-1246
Jim Procter [Tue, 4 Jun 2013 10:50:19 +0000 (11:50 +0100)]
JAL-1307 patch to squash number format exceptions when pressing return
Jim Procter [Tue, 4 Jun 2013 09:45:19 +0000 (10:45 +0100)]
JAL-1300 documentation
Jim Procter [Fri, 7 Jun 2013 13:55:23 +0000 (14:55 +0100)]
Merge branch 'JAL-1161_optimisingAnnotationPanel' into develop
Conflicts:
src/jalview/datamodel/Annotation.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/StockholmFile.java
src/jalview/renderer/AnnotationRenderer.java
Feature conflict left unresolved - JAL-1081 (Pseuodknots) which utilises VARNA to process stockholm annotation data
Jim Procter [Fri, 31 May 2013 16:09:33 +0000 (17:09 +0100)]
JAL-1259 patch to avoid NPE
Jim Procter [Fri, 31 May 2013 16:10:11 +0000 (17:10 +0100)]
Merge branch 'JAL-1259_hotfix' into Release_2_8_Branch
Jim Procter [Fri, 31 May 2013 16:09:33 +0000 (17:09 +0100)]
JAL-1259 patch to avoid NPE
Jim Procter [Fri, 24 May 2013 14:14:01 +0000 (15:14 +0100)]
Merge branch 'JAL-1161_optimisingAnnotationPanel' (early part) into Release_2_8_Branch
Jim Procter [Sun, 19 May 2013 18:25:49 +0000 (19:25 +0100)]
JAL-???? notes on summarisation and analysis of annotation tracks
Jim Procter [Fri, 24 May 2013 13:14:45 +0000 (14:14 +0100)]
JAL-1291 reinstate fastPaint flag manipulation to make trackPad scrolling smooth
Jim Procter [Fri, 24 May 2013 12:34:55 +0000 (13:34 +0100)]
JAL-1291 TODO: revised graphGroup model so grouped graphs are more efficiently rendered
Jim Procter [Fri, 24 May 2013 12:27:49 +0000 (13:27 +0100)]
JAL-1291 - don't touch the graphics object until after deciding to skip annotation row
Jim Procter [Fri, 24 May 2013 12:27:06 +0000 (13:27 +0100)]
JAL-1291 conditional output of rendering debugging info
Jim Procter [Thu, 23 May 2013 14:48:31 +0000 (15:48 +0100)]
patch for JAL-1300 fixes JAL-1294: read and write COMBINE statements that use SEQUENCE_REF and GROUP_REF scope to conserve annotation rows with seqeunce and group references
Jim Procter [Thu, 23 May 2013 14:47:16 +0000 (15:47 +0100)]
JAL-1300 test and example data for parsing annotation files with COMBINE statements to group sequence associated annotation
Jim Procter [Thu, 23 May 2013 11:04:24 +0000 (12:04 +0100)]
JAL-1295 test to demonstrate JAL-1294 (caused by JAL-1297)
Jim Procter [Thu, 23 May 2013 11:03:09 +0000 (12:03 +0100)]
JAL-1295 refactored Jws2 discovery bootstrap code to test utility class
Jim Procter [Thu, 23 May 2013 10:58:20 +0000 (11:58 +0100)]
JAL-1295 relaxed test for Annotation element equivalence and javadoc to clarify format for Annotation.toString
Jim Procter [Thu, 23 May 2013 10:57:02 +0000 (11:57 +0100)]
JAL-381 Desktop.addInternalFrame cannot be called in headless mode
Jim Procter [Thu, 23 May 2013 09:15:59 +0000 (10:15 +0100)]
JAL-1299 fix: ensure a new graphGroup is created if first row identified in COMBINE statement doesn't have existing graphGroup assignment
Jim Procter [Thu, 23 May 2013 09:12:17 +0000 (10:12 +0100)]
JAL-1295 JAL-1296 clearer assertion failed message
Jim Procter [Wed, 22 May 2013 17:06:21 +0000 (18:06 +0100)]
JAL-1295 JAL-1297 enhance test to check graph visiblity and graphGroup set equivalence
Jim Procter [Wed, 22 May 2013 16:53:03 +0000 (17:53 +0100)]
fix for JAL-1297: COMBINE output now follows specification and all additional annotation rows included in output (not just the first one which wasn't hidden)
Jim Procter [Wed, 22 May 2013 16:49:09 +0000 (17:49 +0100)]
JAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294
test alignment annotation file IO for example given in documentation and for multiple combine statement
Jim Procter [Wed, 22 May 2013 16:46:25 +0000 (17:46 +0100)]
JAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment+annotation equivalence test to be used in other tests
Jim Procter [Wed, 22 May 2013 16:45:42 +0000 (17:45 +0100)]
javadoc and formatting
Jim Procter [Wed, 22 May 2013 16:45:29 +0000 (17:45 +0100)]
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefit of annotation IO test
Jim Procter [Wed, 22 May 2013 16:43:40 +0000 (17:43 +0100)]
JAL-1297 JAL-1295 JAL-1294 improve test logic for comparing annotation elements
Jim Procter [Tue, 21 May 2013 14:05:47 +0000 (15:05 +0100)]
JAL-1296 reinstated tab characters so example annotation file can be copied and pasted to a file and imported
Jim Procter [Tue, 21 May 2013 13:12:15 +0000 (14:12 +0100)]
JAL-1070 - [ not a real patch ] - include offending line number and content in output when an Alignment annotation file parsing exception stacktraces to stderr
Jim Procter [Tue, 21 May 2013 09:53:37 +0000 (10:53 +0100)]
JAL-966 paintrefresher should be abstract [ Merge branch 'jv3_notes' into JAL-1161_optAnnotPanelRendering ]
Jim Procter [Tue, 21 May 2013 09:52:14 +0000 (10:52 +0100)]
JAL-1161 conditional parameters for controlling clipping
Jim Procter [Tue, 21 May 2013 08:33:56 +0000 (09:33 +0100)]
JAL-1292 avoid exception by using bitset of arbitrary width for remembering which graphgroups have been drawn
Jim Procter [Mon, 20 May 2013 14:35:04 +0000 (15:35 +0100)]
JAL-1161 changed signature to allow clipping bounds for panel to be obtained
Jim Procter [Mon, 20 May 2013 14:33:46 +0000 (15:33 +0100)]
formatting
git://source.jalview.org / jalview.git / log