gmungoc [Tue, 24 Oct 2017 12:45:15 +0000 (13:45 +0100)]
Merge branch 'develop' into features/JAL-1793VCF; lambda Function for
EnsemblLookup parsing
Conflicts:
src/jalview/ext/ensembl/EnsemblInfo.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblRestClient.java
gmungoc [Tue, 24 Oct 2017 10:28:56 +0000 (11:28 +0100)]
JAL-2788 corrected merge error in propertyChange
gmungoc [Tue, 24 Oct 2017 08:31:38 +0000 (09:31 +0100)]
JAL-2787 set start/end seq explicitly for test
Jim Procter [Mon, 23 Oct 2017 16:17:09 +0000 (17:17 +0100)]
Merge branch 'bug/JAL-2609attemptedmerge' into develop
Jim Procter [Mon, 23 Oct 2017 16:15:51 +0000 (17:15 +0100)]
JAL-2609 remove unused AlignPanel.fastPaint flag and broken conditional preventing repaints on vertical scroll
Jim Procter [Mon, 23 Oct 2017 15:37:29 +0000 (16:37 +0100)]
Merge branch 'bug/JAL-2609attemptedmerge' into develop
Jim Procter [Mon, 23 Oct 2017 15:36:14 +0000 (16:36 +0100)]
JAL-2768 release notes
Jim Procter [Mon, 23 Oct 2017 15:27:46 +0000 (16:27 +0100)]
JAL-2739 release notes
Jim Procter [Mon, 23 Oct 2017 15:20:54 +0000 (16:20 +0100)]
Merge branch 'bug/JAL-2739' into develop
Jim Procter [Mon, 23 Oct 2017 15:09:23 +0000 (16:09 +0100)]
JAL-2682 release notes
Jim Procter [Mon, 23 Oct 2017 14:59:30 +0000 (15:59 +0100)]
Merge branch 'bug/JAL-2682parseId' into develop
Jim Procter [Mon, 23 Oct 2017 14:33:12 +0000 (15:33 +0100)]
JAL-2253 release notes
Jim Procter [Mon, 23 Oct 2017 14:00:38 +0000 (15:00 +0100)]
Merge branch 'bug/JAL-2253' into develop
JAL-2253 resolve diffrences between patches post-code review and diverging develop
gmungoc [Mon, 23 Oct 2017 10:25:42 +0000 (11:25 +0100)]
JAL-1854 keep fallthrough but with comment to suppress error
gmungoc [Mon, 23 Oct 2017 09:58:44 +0000 (10:58 +0100)]
JAL-1854 remove fallthrough of switch case (Checkstyle error)
gmungoc [Mon, 23 Oct 2017 09:57:54 +0000 (10:57 +0100)]
JAL-2737 JAL-1854 corrected package suppressions, updated import
controls
Jim Procter [Fri, 20 Oct 2017 14:28:47 +0000 (15:28 +0100)]
Merge branch 'patch/JAL-547_pid_groovyscript' into develop
Jim Procter [Fri, 20 Oct 2017 14:28:08 +0000 (15:28 +0100)]
JAL-547 fix NPE when no selection available
Jim Procter [Fri, 20 Oct 2017 14:25:49 +0000 (15:25 +0100)]
JAL-547 only generate matrix for current selection if available. better comments.
Jim Procter [Fri, 20 Oct 2017 14:12:49 +0000 (15:12 +0100)]
JAL-547 PID script in release notes
Jim Procter [Fri, 20 Oct 2017 14:10:56 +0000 (15:10 +0100)]
Merge branch 'patch/JAL-547_pid_groovyscript' into develop
Jim Procter [Fri, 20 Oct 2017 14:09:29 +0000 (15:09 +0100)]
JAL-547 updated the PID script for 2.10.x series score model architecture
gmungoc [Fri, 20 Oct 2017 13:05:40 +0000 (14:05 +0100)]
JAL-2253 pull up constant, additional unit test
gmungoc [Fri, 20 Oct 2017 09:22:26 +0000 (10:22 +0100)]
JAL-2755 update caller for method rename!
gmungoc [Fri, 20 Oct 2017 07:44:17 +0000 (08:44 +0100)]
JAL-2609 fully erase scale above, tidy code change
gmungoc [Thu, 19 Oct 2017 15:45:56 +0000 (16:45 +0100)]
JAL-2609 adjustments for test findings
gmungoc [Thu, 19 Oct 2017 14:02:45 +0000 (15:02 +0100)]
JAL-2755 find gene loci for fetched xrefs where possible
gmungoc [Thu, 19 Oct 2017 14:01:56 +0000 (15:01 +0100)]
JAL-2755 put chromosomal dbref first in report
gmungoc [Thu, 19 Oct 2017 14:01:16 +0000 (15:01 +0100)]
JAL-2755 add lookup of cds/cdna gene loci
gmungoc [Thu, 19 Oct 2017 14:00:34 +0000 (15:00 +0100)]
JAL-2755 add species lookup
gmungoc [Thu, 19 Oct 2017 13:57:12 +0000 (14:57 +0100)]
JAL-2755 add missing Javadoc
gmungoc [Thu, 19 Oct 2017 13:56:13 +0000 (14:56 +0100)]
JAL-2755 rename EnsemblInfo as EnsemblData, add 'true' EnsemblInfo
kiramt [Thu, 19 Oct 2017 13:14:59 +0000 (14:14 +0100)]
Merge branch 'develop' into bug/JAL-2609attemptedmerge
Jim Procter [Wed, 18 Oct 2017 14:28:30 +0000 (15:28 +0100)]
JAL-2782 remark about possible exception due to unsafe regex
Jim Procter [Wed, 18 Oct 2017 13:25:37 +0000 (14:25 +0100)]
JAL-2777 JAL-2773 release notes
Jim Procter [Wed, 18 Oct 2017 13:22:57 +0000 (14:22 +0100)]
Merge branch 'bugs/JAL-2777_whitespaceChain' into develop
Jim Procter [Wed, 18 Oct 2017 13:20:00 +0000 (14:20 +0100)]
JAL-2777 remove duplicate code outside conditional from rebase artefact
Jim Procter [Tue, 17 Oct 2017 13:46:09 +0000 (14:46 +0100)]
JAL-2777 release notes
Jim Procter [Tue, 17 Oct 2017 13:43:20 +0000 (14:43 +0100)]
Merge branch 'features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview' into develop
Jim Procter [Tue, 17 Oct 2017 13:42:56 +0000 (14:42 +0100)]
JAL-2773 renamed flags for clarity
Jim Procter [Mon, 16 Oct 2017 14:04:57 +0000 (15:04 +0100)]
JAL-2777 patch for whitespace chain
Jim Procter [Mon, 16 Oct 2017 14:03:40 +0000 (15:03 +0100)]
JAL-2777 test for the whitespace chain
Jim Procter [Mon, 16 Oct 2017 13:35:17 +0000 (14:35 +0100)]
JAL-2481 patch to fix findFeatureColour for end-of-sequence test
Jim Procter [Mon, 16 Oct 2017 13:34:20 +0000 (14:34 +0100)]
JAL-2481 test correct behaviour of findFeatureColour for final residue in sequence
Jim Procter [Fri, 13 Oct 2017 16:27:57 +0000 (17:27 +0100)]
JAL-2777 noticed exception raised on construction of feature settings because transparency slider 'setMax' triggers a repaint
Jim Procter [Thu, 12 Oct 2017 16:40:50 +0000 (17:40 +0100)]
JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first pass at limiting updates of structure to just those that are necessary.
gmungoc [Wed, 11 Oct 2017 17:46:16 +0000 (18:46 +0100)]
JAL-2609 tests updated for revised label width
gmungoc [Wed, 11 Oct 2017 15:17:13 +0000 (16:17 +0100)]
JAL-2772 check array bounds for sequence access
gmungoc [Wed, 11 Oct 2017 14:01:16 +0000 (15:01 +0100)]
JAL-2609 tidy label width code, some checkstyle warnings
gmungoc [Wed, 11 Oct 2017 12:41:13 +0000 (13:41 +0100)]
Merge branch 'bug/JAL-2742' into develop
gmungoc [Wed, 11 Oct 2017 12:39:34 +0000 (13:39 +0100)]
JAL-2742 set HiddenColumns null for no hidden coluns test to match
Jalview usage
Jim Procter [Wed, 11 Oct 2017 11:46:33 +0000 (12:46 +0100)]
JAL-2757 release notes
gmungoc [Wed, 11 Oct 2017 11:12:54 +0000 (12:12 +0100)]
Merge branch 'bug/JAL-2757_uniprotftsbadquery' into develop
gmungoc [Wed, 11 Oct 2017 11:12:11 +0000 (12:12 +0100)]
JAL-2757 fix PDB also; suppress stack trace and compiler warnings
kiramt [Wed, 11 Oct 2017 11:11:03 +0000 (12:11 +0100)]
JAL-2742 test updates following review
kiramt [Wed, 11 Oct 2017 11:08:25 +0000 (12:08 +0100)]
JAL-2742 minor test updates following review
gmungoc [Wed, 11 Oct 2017 07:59:54 +0000 (08:59 +0100)]
JAL-2738 javadoc correction
kiramt [Wed, 11 Oct 2017 07:20:21 +0000 (08:20 +0100)]
JAL-2742 removed unused getViewAsCigars
kiramt [Tue, 10 Oct 2017 13:38:30 +0000 (14:38 +0100)]
JAL-2609attemptedmerge tidy
kiramt [Tue, 10 Oct 2017 13:34:50 +0000 (14:34 +0100)]
Merge remote-tracking branch 'origin/features/JAL-2609fastPaintWrapped'
into bug/JAL-2690attemptedmerge
Conflicts:
src/jalview/gui/SeqCanvas.java
kiramt [Tue, 10 Oct 2017 13:30:43 +0000 (14:30 +0100)]
JAL-2690attemptedmerge seems to work
Jim Procter [Tue, 10 Oct 2017 11:11:02 +0000 (12:11 +0100)]
JAL-2523 release notes
Jim Procter [Tue, 10 Oct 2017 11:08:51 +0000 (12:08 +0100)]
Merge branch 'features/JAL-2523httpRetries' into develop
kiramt [Tue, 10 Oct 2017 10:59:51 +0000 (11:59 +0100)]
JAL-2690attemptedmerge partial merge
gmungoc [Tue, 10 Oct 2017 07:35:30 +0000 (08:35 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 9 Oct 2017 15:03:22 +0000 (16:03 +0100)]
JAL-2480 use interface type for sequenceFeatureStore
gmungoc [Mon, 9 Oct 2017 14:31:13 +0000 (15:31 +0100)]
JAL-2523 basic sleep and retry (3 times) on 429 response code with
Retry-After
gmungoc [Mon, 9 Oct 2017 14:24:10 +0000 (15:24 +0100)]
JAL-2523 convenience method to get model organisms
Jim Procter [Mon, 9 Oct 2017 13:47:00 +0000 (14:47 +0100)]
Merge branch 'patch/JAL-2446_mergeconflictmissed' into develop
Jim Procter [Mon, 9 Oct 2017 13:46:24 +0000 (14:46 +0100)]
JAL-2446 remove duplicate code from pulled up method.
gmungoc [Mon, 9 Oct 2017 10:55:55 +0000 (11:55 +0100)]
JAL-2738 ensure variant feature is in forward sense
gmungoc [Mon, 9 Oct 2017 09:27:06 +0000 (10:27 +0100)]
JAL-2738 assertion for derived protein variant added
gmungoc [Mon, 9 Oct 2017 08:47:42 +0000 (09:47 +0100)]
JAL-2738 remove commented code, unit test coverage
Jim Procter [Fri, 6 Oct 2017 16:02:42 +0000 (17:02 +0100)]
Merge branch 'patch/JAL-2116_java9_antjnlpfix' into develop
Jim Procter [Fri, 6 Oct 2017 16:01:38 +0000 (17:01 +0100)]
JAL-2116 fix jnlp file post-processing so java 9 module path and java version added correctly
gmungoc [Fri, 6 Oct 2017 08:44:35 +0000 (09:44 +0100)]
JAL-2753 add new jar to lib folder!
gmungoc [Fri, 6 Oct 2017 08:40:05 +0000 (09:40 +0100)]
JAL-2753 update to htsjdk 2.12.0 (requires Java 8)
gmungoc [Fri, 6 Oct 2017 08:39:02 +0000 (09:39 +0100)]
JAL-2754 update to Java 1.8
gmungoc [Fri, 6 Oct 2017 08:16:13 +0000 (09:16 +0100)]
JAL-2738 unit test for mapping failure case
Jim Procter [Thu, 5 Oct 2017 17:59:09 +0000 (18:59 +0100)]
JAL-2757 reset textbox after a non HTTP 200 response
gmungoc [Thu, 5 Oct 2017 14:18:01 +0000 (15:18 +0100)]
JAL-2738 warn (in console) when non chromosomal coordinates on sequence
gmungoc [Thu, 5 Oct 2017 14:17:19 +0000 (15:17 +0100)]
JAL-2738 helper method for convolving mappings
gmungoc [Thu, 5 Oct 2017 14:16:49 +0000 (15:16 +0100)]
JAL-2755 transfer chromosomal reference from transcript to CDS
gmungoc [Thu, 5 Oct 2017 14:15:41 +0000 (15:15 +0100)]
JAL-2738 method to compound / traverse / convolve two mappings
gmungoc [Thu, 5 Oct 2017 09:41:46 +0000 (10:41 +0100)]
JAL-2744 add score to feature details report, description to menu item
gmungoc [Wed, 4 Oct 2017 14:19:02 +0000 (15:19 +0100)]
JAL-2738 fix bug of premature exit from adding attributes
gmungoc [Wed, 4 Oct 2017 12:55:17 +0000 (13:55 +0100)]
JAL-2523 start of refactoring...
gmungoc [Wed, 4 Oct 2017 10:31:12 +0000 (11:31 +0100)]
JAL-2738 match consequence "Allele" to VCF allele; add non-SNP variants
on nucleotide
gmungoc [Wed, 4 Oct 2017 10:29:03 +0000 (11:29 +0100)]
JAL-2744 handle null features list
Jim Procter [Tue, 3 Oct 2017 14:25:34 +0000 (15:25 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' into develop
Conflicts:
help/html/releases.html
help/html/whatsNew.html
src/jalview/ws/dbsources/Uniprot.java
gmungoc [Tue, 3 Oct 2017 10:21:52 +0000 (11:21 +0100)]
JAL-2738 update test for threaded VCFLoader
gmungoc [Tue, 3 Oct 2017 10:21:11 +0000 (11:21 +0100)]
JAL-2738 code formatting
gmungoc [Mon, 2 Oct 2017 17:52:23 +0000 (18:52 +0100)]
JAL-2738 code tidy up, null checks &c
gmungoc [Mon, 2 Oct 2017 14:45:33 +0000 (15:45 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 2 Oct 2017 14:41:02 +0000 (15:41 +0100)]
JAL-2525 lookup transcript features by Ontology
gmungoc [Mon, 2 Oct 2017 14:37:01 +0000 (15:37 +0100)]
JAL-2738 filter VEP consequence data to that for current transcript
Jim Procter [Sun, 1 Oct 2017 11:43:41 +0000 (12:43 +0100)]
Merge branch 'documentation/JAL-2751patch2102b2' into releases/Release_2_10_2b1_Branch
Jim Procter [Sun, 1 Oct 2017 11:42:32 +0000 (12:42 +0100)]
JAL-2751 what's new for 2.10.2b2 patch
Jim Procter [Sun, 1 Oct 2017 11:40:53 +0000 (12:40 +0100)]
JAL-2751 patch release notes
Jim Procter [Sat, 30 Sep 2017 10:26:15 +0000 (11:26 +0100)]
JAL-2751 bump version and new releases entry
git://source.jalview.org / jalview.git / log