tcofoegbu [Mon, 27 Apr 2015 14:39:32 +0000 (15:39 +0100)]
JAL-1714 improved the new PDB Sequence fetcher by enabling it query multiple PDB entries in one operation
tcofoegbu [Tue, 21 Apr 2015 16:26:17 +0000 (17:26 +0100)]
Resolved diffs from 2.8.3
gmungoc [Tue, 31 Mar 2015 15:12:49 +0000 (16:12 +0100)]
JAL-1681 ensure cDNA consensus computed on startup (project/applet)
gmungoc [Tue, 31 Mar 2015 15:07:48 +0000 (16:07 +0100)]
JAL-1544 "true of false" -> "true or false"
gmungoc [Tue, 31 Mar 2015 15:06:20 +0000 (16:06 +0100)]
JAL-1264 reinstated 'show annotations' menu item (and set from params)
gmungoc [Mon, 30 Mar 2015 15:31:14 +0000 (16:31 +0100)]
JAL-1264 fix broken applet build dependencies
gmungoc [Wed, 25 Mar 2015 13:46:16 +0000 (13:46 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 25 Mar 2015 13:43:13 +0000 (13:43 +0000)]
JAL-1264 adding show/hide annotation options to applet
tcofoegbu [Wed, 25 Mar 2015 10:28:46 +0000 (10:28 +0000)]
Merge branch 'features/JAL-1667_PDBe_Search_API' into develop
tcofoegbu [Wed, 25 Mar 2015 10:27:43 +0000 (10:27 +0000)]
JAL-1667 clean up commented codes in PopupMenu.java and StructureChooser.java
tcofoegbu [Wed, 25 Mar 2015 10:15:02 +0000 (10:15 +0000)]
Merge commit
tcofoegbu [Wed, 25 Mar 2015 09:39:53 +0000 (09:39 +0000)]
JAL-1668 Tab for summary config, auto refresh after config and table column sorting
gmungoc [Mon, 23 Mar 2015 14:41:57 +0000 (14:41 +0000)]
JAL-1681 (import reorder only)
gmungoc [Mon, 23 Mar 2015 14:39:24 +0000 (14:39 +0000)]
JAL-845 restore SplitFrame size from project; enable Find in SplitFrame
gmungoc [Mon, 23 Mar 2015 14:37:29 +0000 (14:37 +0000)]
StringBuffer --> StringBuilder
gmungoc [Mon, 23 Mar 2015 10:00:41 +0000 (10:00 +0000)]
Merge branch 'features/sequenceFeatureRefactor' into develop
Conflicts:
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Dna.java
src/jalview/bin/JalviewLite.java
src/jalview/gui/PopupMenu.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
test/jalview/datamodel/SequenceTest.java
and minor unit test refactoring
tcofoegbu [Thu, 19 Mar 2015 14:50:29 +0000 (14:50 +0000)]
JAL-1668 finally clean up
gmungoc [Thu, 19 Mar 2015 12:59:07 +0000 (12:59 +0000)]
JAL-845 fix bug in 3-to-1 scaling of protein from cDNA
gmungoc [Wed, 18 Mar 2015 20:32:18 +0000 (20:32 +0000)]
JAL-1680 small tidy
gmungoc [Wed, 18 Mar 2015 20:31:15 +0000 (20:31 +0000)]
JAL-845 adjust both sides of split frame when changing fonts etc
gmungoc [Wed, 18 Mar 2015 20:29:08 +0000 (20:29 +0000)]
JAL-1675 Chimera highlight side-chain; timeout added to REST calls
gmungoc [Wed, 18 Mar 2015 20:27:08 +0000 (20:27 +0000)]
Merge hack/JAL-1617 fake DBRef to develop
gmungoc [Wed, 18 Mar 2015 20:24:48 +0000 (20:24 +0000)]
JAL-845 map 'STOP' codons correctly
Charles Ofoegbu [Wed, 18 Mar 2015 17:05:03 +0000 (17:05 +0000)]
JAL-1668 house keeping
Charles Ofoegbu [Wed, 18 Mar 2015 10:58:26 +0000 (10:58 +0000)]
JAL-1668 added PDBDocFieldPreference for configuring rest response summary fields
gmungoc [Tue, 17 Mar 2015 16:18:22 +0000 (16:18 +0000)]
JAL-1687 ignore case when determining if sequence matches consensus
gmungoc [Tue, 17 Mar 2015 14:01:06 +0000 (14:01 +0000)]
JAL-845 ensure cDNA consensus scales with font size
gmungoc [Tue, 17 Mar 2015 14:00:12 +0000 (14:00 +0000)]
JAL-845 provide a moveable divider for SplitFrame (Desktop)
gmungoc [Mon, 16 Mar 2015 17:34:58 +0000 (17:34 +0000)]
JAL-845 tweaks and bug fixes for split frame view
Charles Ofoegbu [Mon, 16 Mar 2015 17:31:16 +0000 (17:31 +0000)]
JAL-1668 added validation for manual entry of pdb structures
Charles Ofoegbu [Sun, 15 Mar 2015 15:10:40 +0000 (15:10 +0000)]
JAL-1667 updated test and internationalization messages
gmungoc [Fri, 13 Mar 2015 17:03:39 +0000 (17:03 +0000)]
JAL-845 refinements + tests for making mappings between alignments
gmungoc [Fri, 13 Mar 2015 17:02:56 +0000 (17:02 +0000)]
JAL-1686 @Override and/or TODO added to equals(Object) methods
gmungoc [Fri, 13 Mar 2015 09:04:01 +0000 (09:04 +0000)]
JAL-1684 allow X in protein to map to untranslatable in DNA (grc in
EMBLCDS AAK20930)
gmungoc [Fri, 13 Mar 2015 08:53:01 +0000 (08:53 +0000)]
JAL-1685 fixed
gmungoc [Thu, 12 Mar 2015 15:18:31 +0000 (15:18 +0000)]
JAL-1544 sequece now sequence
gmungoc [Wed, 11 Mar 2015 15:53:47 +0000 (15:53 +0000)]
JAL-1684 better window size parameters; match up sequence id lengths
gmungoc [Wed, 11 Mar 2015 14:18:32 +0000 (14:18 +0000)]
JAL-1684 fix bug in AlignmentView constructor
gmungoc [Wed, 11 Mar 2015 12:02:19 +0000 (12:02 +0000)]
JAL-1684 include JMOL jar for applet
gmungoc [Wed, 11 Mar 2015 12:00:44 +0000 (12:00 +0000)]
JAL-1684 fix jars list, parameters for new example
gmungoc [Wed, 11 Mar 2015 11:45:56 +0000 (11:45 +0000)]
JAL-845 start cDNA consensus on 'add alignment' (as well as translate or
show cross-ref)
gmungoc [Wed, 11 Mar 2015 11:27:44 +0000 (11:27 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 11 Mar 2015 11:20:57 +0000 (11:20 +0000)]
JAL-1685 further tests
gmungoc [Wed, 11 Mar 2015 10:55:08 +0000 (10:55 +0000)]
JAL-845 smarter test for 'mappability' when adding sequences to an
alignment
gmungoc [Wed, 11 Mar 2015 10:54:30 +0000 (10:54 +0000)]
JAL-1421 changed Vector to List<String> for protein-to-codon mappings
gmungoc [Wed, 11 Mar 2015 10:52:50 +0000 (10:52 +0000)]
JAL-1685 tests added for ambiguity codes (including failing test for R)
gmungoc [Wed, 11 Mar 2015 08:47:00 +0000 (08:47 +0000)]
JAL-845 cDNA mapping: select on sequence translation instead of name
gmungoc [Wed, 11 Mar 2015 08:45:01 +0000 (08:45 +0000)]
JAL-845 handle no profile without NPE!
gmungoc [Wed, 11 Mar 2015 08:44:08 +0000 (08:44 +0000)]
JAL-1684 applet example for SplitFrame view of cDNA/Protein
gmungoc [Tue, 10 Mar 2015 11:45:26 +0000 (11:45 +0000)]
JAL-1680 group consensus speeded up with a different QuickSort algorithm
gmungoc [Tue, 10 Mar 2015 11:44:42 +0000 (11:44 +0000)]
JAL-1681 show cDNA consensus on protein alignment - first version
Jim Procter [Mon, 9 Mar 2015 12:54:38 +0000 (12:54 +0000)]
Merge branch 'features/JAL-1565_jpred4' into develop
Jim Procter [Mon, 9 Mar 2015 12:51:46 +0000 (12:51 +0000)]
JAL-1565 loading a concise file causes insertions to be automatically hidden in desktop
Charles Ofoegbu [Fri, 6 Mar 2015 19:17:14 +0000 (19:17 +0000)]
JAL-1668 added filtering and sorting capabilites
Jim Procter [Fri, 6 Mar 2015 15:43:05 +0000 (15:43 +0000)]
Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop
Jim Procter [Fri, 6 Mar 2015 15:40:33 +0000 (15:40 +0000)]
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
JAL-1645 bring JAL-845 feature branch up to date ready for develop merge
Conflicts:
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
test/jalview/analysis/DnaTranslation.java
Jim Procter [Fri, 6 Mar 2015 15:29:03 +0000 (15:29 +0000)]
JAL-1683 bump version for r2.8.3 branch
Jim Procter [Fri, 6 Mar 2015 15:26:45 +0000 (15:26 +0000)]
JAL-1683 replace year/version strings with tokens in source
Jim Procter [Fri, 6 Mar 2015 15:13:51 +0000 (15:13 +0000)]
reassign features already created/documented for 2.9 to 2.8.3 JAL-1682
Jim Procter [Fri, 6 Mar 2015 14:44:39 +0000 (14:44 +0000)]
Jim Procter [Fri, 6 Mar 2015 14:42:01 +0000 (14:42 +0000)]
Charles Ofoegbu [Fri, 6 Mar 2015 08:59:38 +0000 (08:59 +0000)]
JAL-1667 refactoring to support JAL-1668
Jim Procter [Thu, 5 Mar 2015 15:48:04 +0000 (15:48 +0000)]
JAL-1678 fix replace token for launchApp in a buildwq
Jim Procter [Thu, 5 Mar 2015 15:05:31 +0000 (15:05 +0000)]
JAL-1678 fix replace token for launchApp in a buildwq
Jim Procter [Thu, 5 Mar 2015 14:36:18 +0000 (14:36 +0000)]
JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this in the future
Jim Procter [Thu, 5 Mar 2015 14:26:38 +0000 (14:26 +0000)]
JAL-1678 add version parameter to example files in publish phase
Jim Procter [Thu, 5 Mar 2015 14:22:21 +0000 (14:22 +0000)]
JAL-1678 add version parameter to example files in publish phase
gmungoc [Thu, 5 Mar 2015 13:50:58 +0000 (13:50 +0000)]
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
Conflicts:
src/jalview/datamodel/SequenceGroup.java
Jim Procter [Thu, 5 Mar 2015 13:28:35 +0000 (13:28 +0000)]
Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop
Jim Procter [Thu, 5 Mar 2015 13:28:00 +0000 (13:28 +0000)]
JAL-1643 add quaqua libs as OSX specific resources
gmungoc [Thu, 5 Mar 2015 12:47:39 +0000 (12:47 +0000)]
JAL-845 minor tidy / tests / javadoc tweaks
gmungoc [Thu, 5 Mar 2015 10:38:43 +0000 (10:38 +0000)]
JAL-1270 tests added
Charles Ofoegbu [Wed, 4 Mar 2015 20:49:30 +0000 (20:49 +0000)]
JAL-1668 First version JAL-1668
gmungoc [Wed, 4 Mar 2015 13:37:13 +0000 (13:37 +0000)]
JAL-845 bug fixes correcting linked editing
gmungoc [Tue, 3 Mar 2015 15:55:46 +0000 (15:55 +0000)]
JAL-845 refactor / typo fix
gmungoc [Tue, 3 Mar 2015 10:35:19 +0000 (10:35 +0000)]
JAL-845 implement alignment of protein to match cDNA alignment
gmungoc [Tue, 3 Mar 2015 10:34:01 +0000 (10:34 +0000)]
JAL-1452 nucleotide/protein default colour; JAL-845 SplitFrame refactor
Charles Ofoegbu [Mon, 2 Mar 2015 17:33:27 +0000 (17:33 +0000)]
house keeping
Jim Procter [Fri, 27 Feb 2015 17:01:25 +0000 (17:01 +0000)]
Merge branch 'bug/addcustomlaunchdesktopparams' into develop
Jim Procter [Fri, 27 Feb 2015 17:01:08 +0000 (17:01 +0000)]
JAL-1678 - patch to make sure we only compare positions of the last / or ?
Jim Procter [Fri, 27 Feb 2015 16:58:45 +0000 (16:58 +0000)]
fix for JAL-1678
gmungoc [Fri, 27 Feb 2015 14:45:09 +0000 (14:45 +0000)]
JAL-1452 distinct colour preferences for nucleotide and protein
gmungoc [Fri, 27 Feb 2015 14:43:36 +0000 (14:43 +0000)]
JAL-845 SplitFrame for "show product" and after aligning from SplitFrame
Charles Ofoegbu [Thu, 26 Feb 2015 18:20:38 +0000 (18:20 +0000)]
JAL-1667 PDBe Search Interface implementation
gmungoc [Wed, 25 Feb 2015 10:42:13 +0000 (10:42 +0000)]
JAL-1677 commenting use of AlignViewport.gatherViewsHere
gmungoc [Tue, 24 Feb 2015 16:37:55 +0000 (16:37 +0000)]
JAL-1677 Castor source changes
gmungoc [Tue, 24 Feb 2015 16:29:21 +0000 (16:29 +0000)]
JAL-845 set top and bottom seq id widths the same
gmungoc [Tue, 24 Feb 2015 16:10:16 +0000 (16:10 +0000)]
JAL-1677 save/restore SplitFrame to Jalview project
gmungoc [Mon, 23 Feb 2015 15:48:13 +0000 (15:48 +0000)]
JAL-845 repaint of complementary selection (applet)
gmungoc [Mon, 23 Feb 2015 12:15:30 +0000 (12:15 +0000)]
JAL-1619 split frame now offered in applet 'input from textbox'
gmungoc [Fri, 20 Feb 2015 17:22:19 +0000 (17:22 +0000)]
JAL-1673 additional test (and trim of PDB resnum value)
gmungoc [Fri, 20 Feb 2015 17:19:21 +0000 (17:19 +0000)]
JAL-1675 correct highlighting in Chimera for mouseover of sequence
gmungoc [Fri, 20 Feb 2015 11:53:18 +0000 (11:53 +0000)]
JAL-1665 create dataset sequences in applet
gmungoc [Fri, 20 Feb 2015 11:51:56 +0000 (11:51 +0000)]
JAL-1674 update both status bars when mousing over linked sequences
gmungoc [Thu, 19 Feb 2015 13:14:06 +0000 (13:14 +0000)]
JAL-1665 refactored Sequence.getSequenceFeatures
gmungoc [Thu, 19 Feb 2015 10:31:38 +0000 (10:31 +0000)]
JAL-845 applet colour by tree; translate as cDNA; pull up history list
gmungoc [Fri, 13 Feb 2015 17:10:22 +0000 (17:10 +0000)]
JAL-845 first rough applet SplitFrame (add parameter file2)
Jim Procter [Thu, 12 Feb 2015 17:20:51 +0000 (17:20 +0000)]
JAL-1350 added to 2.9 release notes
Jim Procter [Thu, 12 Feb 2015 17:16:04 +0000 (17:16 +0000)]
JAL-1350 document changed behaviour
Jim Procter [Thu, 12 Feb 2015 17:10:45 +0000 (17:10 +0000)]
JAL-1350 forgot to remove empty test
git://source.jalview.org / jalview.git / log