Jim Procter [Thu, 30 Oct 2014 17:05:36 +0000 (17:05 +0000)]
Merge branch 'develop' into features/ssFromPDBEntry
Jim Procter [Thu, 30 Oct 2014 16:53:20 +0000 (16:53 +0000)]
JAL-674 hang on to sequences created by secondary parsiing process to manage transfer of annotation
Jim Procter [Thu, 30 Oct 2014 16:51:10 +0000 (16:51 +0000)]
JAL-674 count number of annotation transferred in test
Jim Procter [Thu, 30 Oct 2014 15:51:54 +0000 (15:51 +0000)]
JAL-674 propagate annotation onto mapped sequence and its dataset sequence
Jim Procter [Thu, 30 Oct 2014 15:50:30 +0000 (15:50 +0000)]
JAL-674 register PDB IDs when ever they are resolved on file IO
Jim Procter [Thu, 30 Oct 2014 15:47:07 +0000 (15:47 +0000)]
JAL-674 use PDB ID<>File registry to look up correct ID for PDB file derived annotation on a mapped sequence
Jim Procter [Thu, 30 Oct 2014 15:44:50 +0000 (15:44 +0000)]
JAL-674 return original and replacement sequences and the alignment to allow more processing if needed
Jim Procter [Thu, 30 Oct 2014 15:40:31 +0000 (15:40 +0000)]
JAL-674 helpful javadoc for remap method
Jim Procter [Thu, 30 Oct 2014 15:39:53 +0000 (15:39 +0000)]
JAL-674 flag and proxy method to distinguish setMapping calls which create a mapping for a displayed structure and those which transfer annotation
Jim Procter [Thu, 30 Oct 2014 15:30:50 +0000 (15:30 +0000)]
JAL-674 map on StructureSelectionManager to record PDB IDs extracted/assigned to PDB files
Jim Procter [Thu, 30 Oct 2014 15:26:11 +0000 (15:26 +0000)]
patch for JAL-795 - use base secondary structure colour if no colour defined on annotation row element
Jim Procter [Thu, 30 Oct 2014 15:24:00 +0000 (15:24 +0000)]
JAL-674 patch test to verify presence of annotation on the sequence associated with the PDB file
Jim Procter [Thu, 30 Oct 2014 15:21:31 +0000 (15:21 +0000)]
JAL-1551 format and tidy
Jim Procter [Wed, 29 Oct 2014 10:47:13 +0000 (10:47 +0000)]
JAL-1264 JAL-674 test to exercise the AlignmentAnnotation.remap method via
the jalview.structure.StructureMapping.transfer method
Jim Procter [Wed, 29 Oct 2014 10:44:33 +0000 (10:44 +0000)]
JAL-1264 JAL-674 method to copy annotation on structure positions to associated sequence positions
Jim Procter [Wed, 29 Oct 2014 10:41:32 +0000 (10:41 +0000)]
JAL-674 JAL-1264 remap method to allow annotation positions to be updated from simple int-pair arrays (like those used in the StructureManager mappings)
gmungoc [Tue, 28 Oct 2014 15:52:53 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 28 Oct 2014 15:51:46 +0000 (15:51 +0000)]
JAL-1264 refactor to add menu options to _both_ sequence and selection
pop-ups, plus unit tests.
Jim Procter [Mon, 27 Oct 2014 13:39:38 +0000 (13:39 +0000)]
Merge branch 'Release_2_8_2_Branch' into merge_r282_dev
normalised HTML messages and line endings for JAL-1420 JAL-1428 JAL-1355
(darolmar commits)
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Jim Procter [Thu, 23 Oct 2014 22:08:56 +0000 (23:08 +0100)]
Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
Conflicts:
.classpath
RELEASE
src/castor.properties
Jim Procter [Thu, 23 Oct 2014 22:02:54 +0000 (23:02 +0100)]
Merge branch 'hotfix/JAL-1521' into develop
Conflicts:
.classpath
RELEASE
unknown [Thu, 23 Oct 2014 21:28:31 +0000 (22:28 +0100)]
JAL-1521 updated xerces to 2.11 along with xml-apis
Jim Procter [Thu, 23 Oct 2014 16:24:12 +0000 (17:24 +0100)]
JAL-1521 patch is to remove xerces from classpath. This may cause problems for java 1.6 builds
Jim Procter [Thu, 23 Oct 2014 16:23:16 +0000 (17:23 +0100)]
JAL-1521 test to check registry is returning sources
Jim Procter [Thu, 9 Oct 2014 15:06:36 +0000 (16:06 +0100)]
patch fixes JAL-1558
Jim Procter [Thu, 23 Oct 2014 15:18:59 +0000 (16:18 +0100)]
JAL-1503 tag 2.8.1b1 hotfix - last in 2.8.1 line
gmungoc [Thu, 23 Oct 2014 14:39:44 +0000 (15:39 +0100)]
JAL-1264 new unit tests
gmungoc [Thu, 23 Oct 2014 14:37:42 +0000 (15:37 +0100)]
JAL-1264 further refactoring and tests
gmungoc [Wed, 22 Oct 2014 08:20:50 +0000 (09:20 +0100)]
JAL-1304 repositioned tab to correct example
Jim Procter [Tue, 21 Oct 2014 16:36:34 +0000 (17:36 +0100)]
Merge branch 'forpush/JAL-674_dssp' into develop
Jim Procter [Tue, 21 Oct 2014 16:36:13 +0000 (17:36 +0100)]
JAL-674 check for null vector before ...
Jim Procter [Tue, 21 Oct 2014 15:54:58 +0000 (16:54 +0100)]
Merge branch 'patch_sjf4j_typo' into develop
Jim Procter [Tue, 21 Oct 2014 15:54:46 +0000 (16:54 +0100)]
JAL-1216 update varna dependency string in jalviewLite build
Jim Procter [Tue, 21 Oct 2014 14:25:15 +0000 (15:25 +0100)]
Merge branch 'patch_sjf4j_typo' into develop
Jim Procter [Tue, 21 Oct 2014 14:24:59 +0000 (15:24 +0100)]
JWS-59 JAL-1216 patch broken InstallAnywhere build
Jim Procter [Tue, 21 Oct 2014 11:06:49 +0000 (12:06 +0100)]
Merge branch 'forpush/JAL-674_dssp' into develop
Jim Procter [Tue, 21 Oct 2014 11:06:08 +0000 (12:06 +0100)]
JAL-1551 reinstate missing import
Jim Procter [Tue, 21 Oct 2014 11:03:02 +0000 (12:03 +0100)]
JAL-674 initial implementation - only need to extract PDB id from file, no SS transfer at this stage
Jim Procter [Tue, 21 Oct 2014 10:49:31 +0000 (11:49 +0100)]
JAL-1551 crlf
Jim Procter [Tue, 21 Oct 2014 10:48:45 +0000 (11:48 +0100)]
JAL-674 JAL-1551 imports dropped during merge
Jim Procter [Fri, 17 Oct 2014 14:20:50 +0000 (15:20 +0100)]
JAL-1216 update to VARNA 3.91
Jim Procter [Tue, 21 Oct 2014 08:37:24 +0000 (09:37 +0100)]
JAL-674 remove any spurious PDBEntrys generated by Jmol/RNAView parsing processes
Jim Procter [Mon, 20 Oct 2014 17:24:41 +0000 (18:24 +0100)]
JAL-674 methods and test for PDB derived annotation stored and recovered in project
Jim Procter [Mon, 20 Oct 2014 17:23:28 +0000 (18:23 +0100)]
JAL-674 store ID in MCview.PDBfile calcId string, not PDB filename
Jim Procter [Mon, 20 Oct 2014 12:48:40 +0000 (13:48 +0100)]
JAL-674 don't create multiple secondary structure lines for a particular sequence/PDB mapping
Jim Procter [Mon, 20 Oct 2014 12:46:36 +0000 (13:46 +0100)]
JAL-674 test for the test for presence of annotation derived from particular PDB file
Jim Procter [Mon, 20 Oct 2014 12:46:05 +0000 (13:46 +0100)]
JAL-674 test for presence of annotation derived from particular PDB file
Jim Procter [Mon, 20 Oct 2014 12:35:59 +0000 (13:35 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 20 Oct 2014 12:34:04 +0000 (13:34 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 20 Oct 2014 10:21:05 +0000 (11:21 +0100)]
JAL-674 patch for duplicate row bug
Jim Procter [Mon, 20 Oct 2014 10:20:27 +0000 (11:20 +0100)]
JAL-674 test for duplicate alignment annotation rows on aligment
Jim Procter [Mon, 20 Oct 2014 10:19:55 +0000 (11:19 +0100)]
JAL-1551 formatting
Conflicts:
src/MCview/PDBfile.java
Jim Procter [Mon, 20 Oct 2014 09:58:54 +0000 (10:58 +0100)]
JAL-674 patch to ensure existing annotation is properly wired up when
transferred to newly annotated version
Jim Procter [Mon, 20 Oct 2014 09:57:59 +0000 (10:57 +0100)]
JAL-674 test to ensure sequence and annotation on sequence reference
eachother (consider refactoring to a general alignment annotation
validation suite)
Jim Procter [Mon, 20 Oct 2014 08:34:15 +0000 (09:34 +0100)]
JAL-1551 source formatting
Jim Procter [Mon, 20 Oct 2014 08:29:55 +0000 (09:29 +0100)]
JAL-674 JAL-207 getTers for aligned sequences in dataset context
Jim Procter [Mon, 20 Oct 2014 08:27:57 +0000 (09:27 +0100)]
JAL-674 refactor method to match and transfer annotation between aligned
sequences
Jim Procter [Mon, 20 Oct 2014 08:25:08 +0000 (09:25 +0100)]
JAL-1551 formatting
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)
darolmar [Fri, 10 Oct 2014 06:36:17 +0000 (08:36 +0200)]
JAL-1428 (related with JAL-1420)
darolmar [Fri, 10 Oct 2014 06:35:44 +0000 (08:35 +0200)]
JAL-1420
darolmar [Fri, 10 Oct 2014 06:26:46 +0000 (08:26 +0200)]
JAL-1428
darolmar [Fri, 10 Oct 2014 06:20:53 +0000 (08:20 +0200)]
JAL-1355
darolmar [Fri, 10 Oct 2014 06:10:47 +0000 (08:10 +0200)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview into Release_2_8_2_Branch
darolmar [Fri, 10 Oct 2014 06:09:40 +0000 (08:09 +0200)]
JAL-1428
Jim Procter [Thu, 9 Oct 2014 15:07:35 +0000 (16:07 +0100)]
Merge branch 'bug/JAL-1558' into develop
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
git://source.jalview.org / jalview.git / log