gmungoc [Wed, 25 Mar 2015 13:43:13 +0000 (13:43 +0000)]
JAL-1264 adding show/hide annotation options to applet
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
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
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
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
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)]
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
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
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
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
Jim Procter [Thu, 12 Feb 2015 16:50:31 +0000 (16:50 +0000)]
JAL-1350 pass the columnselection rather then selected sequence strings if column-selection exists.
Jim Procter [Thu, 12 Feb 2015 16:49:32 +0000 (16:49 +0000)]
JAL-1350 cloned method and tested equivalence for using column selection to subdivide groups
Jim Procter [Thu, 12 Feb 2015 16:47:49 +0000 (16:47 +0000)]
JAL-1115 switch to lists in SequenceGroup
Jim Procter [Thu, 12 Feb 2015 16:47:18 +0000 (16:47 +0000)]
JAL-1115 typecast
Jim Procter [Thu, 12 Feb 2015 16:46:57 +0000 (16:46 +0000)]
javadoc
Jim Procter [Thu, 12 Feb 2015 16:46:44 +0000 (16:46 +0000)]
JAL-1115 List rather than vector for sequence groups (minimal additional synchronized clauses added)
gmungoc [Thu, 12 Feb 2015 11:04:45 +0000 (11:04 +0000)]
JAL-1633 set file format on 'translate cDNA'
gmungoc [Thu, 12 Feb 2015 09:33:05 +0000 (09:33 +0000)]
Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into
features/JAL-845splitPaneMergeDevelop
Conflicts:
src/jalview/gui/Desktop.java
gmungoc [Wed, 11 Feb 2015 12:26:31 +0000 (12:26 +0000)]
JAL-845 handling eXpand/Gather split frame views
gmungoc [Wed, 11 Feb 2015 12:24:51 +0000 (12:24 +0000)]
JAL-1264 button labels (for panel currently not linked in menu)
Jim Procter [Wed, 11 Feb 2015 09:23:42 +0000 (09:23 +0000)]
JAL-1655 JAL-845 special support to set column width of protein panel 3*width of dna panel - probably should refactor logic to a SplitFrame.setStyle method call..
Jim Procter [Wed, 11 Feb 2015 09:19:55 +0000 (09:19 +0000)]
JAL-845 avoid OOBException when method is called with only one view
Jim Procter [Wed, 11 Feb 2015 09:16:45 +0000 (09:16 +0000)]
JAL-969 use AlignViewportI interface instance where ever possible in method signatures
Jim Procter [Wed, 11 Feb 2015 09:06:22 +0000 (09:06 +0000)]
JAL-1654 allow font to be specified without modifying column width
Jim Procter [Tue, 10 Feb 2015 17:11:11 +0000 (17:11 +0000)]
note about preserving/reinstating custom grid geometry for alignment (JAL-470) and for cDNA/protein JAL-845
Jim Procter [Tue, 10 Feb 2015 17:08:51 +0000 (17:08 +0000)]
JAL-1640 make font-size changes modify grid size again
Jim Procter [Tue, 10 Feb 2015 16:21:54 +0000 (16:21 +0000)]
JAL-845 - portability patch - workaround for lastToken failing for '\'
Jim Procter [Tue, 10 Feb 2015 15:57:41 +0000 (15:57 +0000)]
added comment to @gmungoc todo about referencing PDB entities in Javascript - also verified JAL-592 is now a bug again and can be reproduced :(
Jim Procter [Tue, 10 Feb 2015 15:35:48 +0000 (15:35 +0000)]
JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought
Jim Procter [Tue, 10 Feb 2015 14:57:50 +0000 (14:57 +0000)]
JAL-1382 slightly more efficient detection of non-gap entry in deleted region of sequence
Jim Procter [Tue, 10 Feb 2015 14:56:36 +0000 (14:56 +0000)]
JAL-1382 @mungo TODO done: use StringUtils for delete chars
git://source.jalview.org / jalview.git / log