jalview.git
8 years agoJAL-2164 clear the desktop before testStoreAndRecoverExpandedViews
Jim Procter [Mon, 1 Aug 2016 12:45:05 +0000 (13:45 +0100)]
JAL-2164 clear the desktop before testStoreAndRecoverExpandedViews

8 years agoJAL-1772 make sure we actually return reference to AlignFrame that is visible after...
Jim Procter [Mon, 1 Aug 2016 07:49:54 +0000 (08:49 +0100)]
JAL-1772 make sure we actually return reference to AlignFrame that is visible after views are gathered

8 years agoJAL-1772 JAL-2164 make expanded view save/restore test pass when run in isolation...
Jim Procter [Fri, 29 Jul 2016 16:37:32 +0000 (17:37 +0100)]
JAL-1772 JAL-2164 make expanded view save/restore test pass when run in isolation (problem may be that load returns an alignFrame that isn’t actually the one shown in the desktop…)

8 years agoJAL-2164 JAL-1772 explodeViews can be static, so make it so
Jim Procter [Fri, 29 Jul 2016 16:36:51 +0000 (17:36 +0100)]
JAL-2164 JAL-1772 explodeViews can be static, so make it so

8 years agoJAL-2164 revert tests depending on import of legacy jalview projects
Jim Procter [Fri, 29 Jul 2016 15:07:38 +0000 (16:07 +0100)]
JAL-2164 revert tests depending on import of legacy jalview projects

8 years agoJAL-2157 fixed Jalview2xmlTest
tcofoegbu [Fri, 29 Jul 2016 09:38:38 +0000 (10:38 +0100)]
JAL-2157 fixed Jalview2xmlTest

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 27 Jul 2016 12:02:46 +0000 (13:02 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

8 years agoJAL-1919 added codes for End-2-End scan for sequence consistency for PDB files parse...
tcofoegbu [Wed, 27 Jul 2016 12:02:07 +0000 (13:02 +0100)]
JAL-1919 added codes for End-2-End scan for sequence consistency for PDB files parse with JmolParser vs. Jalview's PDBfile parser

8 years agoJAL-2157 todo: verify parser/file format enums and static/dynamic status these fields
Jim Procter [Tue, 26 Jul 2016 11:59:31 +0000 (12:59 +0100)]
JAL-2157 todo: verify parser/file format enums and static/dynamic status these fields

8 years agoJAL-2157 bugfix for issues from enum refactoring
tcofoegbu [Tue, 26 Jul 2016 10:57:46 +0000 (11:57 +0100)]
JAL-2157 bugfix for issues from enum refactoring

8 years agoJAL-2157 bugfix for regression from commit 82a6c8e2e25b7534168b68b2c89b9cf195f815a5
tcofoegbu [Mon, 25 Jul 2016 14:05:01 +0000 (15:05 +0100)]
JAL-2157 bugfix for regression from commit 82a6c8e2e25b7534168b68b2c89b9cf195f815a5

8 years agoJAL-2148 Bugfix in structureImportSettings string-to-enum conversion and further...
tcofoegbu [Fri, 22 Jul 2016 16:13:53 +0000 (17:13 +0100)]
JAL-2148 Bugfix in structureImportSettings string-to-enum conversion and further enhancement to deal with Atoms from multi-model entries

8 years agoResolve merge conflict for StructureImportSettings
tcofoegbu [Thu, 21 Jul 2016 16:20:56 +0000 (17:20 +0100)]
Resolve merge conflict for StructureImportSettings

8 years agoJAL-2148 fix to heuristically determine chain termination positions. This aids in...
tcofoegbu [Thu, 21 Jul 2016 16:12:10 +0000 (17:12 +0100)]
JAL-2148 fix to heuristically determine chain termination positions. This aids in decision making w.r.t CA HETATMs inclusion

8 years agoMerge branch 'apifix/JAL-1926_JAL-2106' into develop
Jim Procter [Thu, 21 Jul 2016 12:03:21 +0000 (13:03 +0100)]
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
JAL-1919 JAL-2148 regularise use of jalview.datamodel.PDBEntry.Type for PDB/mmCIF file type
JAL-1919 JAL-2148 use new enum jalview.structure.StructureImportSettings.StructureParser

8 years agoJAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annot...
Jim Procter [Wed, 20 Jul 2016 15:25:25 +0000 (16:25 +0100)]
JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annotation from 3D data

8 years agoJAL-1926 JAL-2106 don’t use PDB database constant as a file format string
Jim Procter [Wed, 20 Jul 2016 15:19:08 +0000 (16:19 +0100)]
JAL-1926 JAL-2106 don’t use PDB database constant as a file format string

8 years agoJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMAT’ property values
Jim Procter [Wed, 20 Jul 2016 15:18:01 +0000 (16:18 +0100)]
JAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMAT’ property values

8 years agoJAL-1926 JAL-2106 remove startRes/endRes fields - not used
Jim Procter [Wed, 20 Jul 2016 13:30:29 +0000 (14:30 +0100)]
JAL-1926 JAL-2106 remove startRes/endRes fields - not used

8 years agoJAL-2023 stronger check for whether to start cdna consensus
gmungoc [Wed, 20 Jul 2016 09:00:57 +0000 (10:00 +0100)]
JAL-2023 stronger check for whether to start cdna consensus

8 years agoJAL-2023 avoid writing / loading empty mappings
gmungoc [Wed, 20 Jul 2016 09:00:24 +0000 (10:00 +0100)]
JAL-2023 avoid writing / loading empty mappings

8 years agoJAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons
gmungoc [Wed, 20 Jul 2016 08:05:29 +0000 (09:05 +0100)]
JAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons

8 years agoJAL-2068 AnnotationWorker create/update annotation, not delete / re-add
gmungoc [Wed, 20 Jul 2016 05:09:01 +0000 (06:09 +0100)]
JAL-2068 AnnotationWorker create/update annotation, not delete / re-add

8 years agoJAL-2068 small refactor to reuse shared method
gmungoc [Tue, 19 Jul 2016 17:31:02 +0000 (18:31 +0100)]
JAL-2068 small refactor to reuse shared method

8 years agoJAL-2068 update rather than recreate AlignmentAnnotation on run()
gmungoc [Tue, 19 Jul 2016 17:30:24 +0000 (18:30 +0100)]
JAL-2068 update rather than recreate AlignmentAnnotation on run()

8 years agoJAL-391 corrected handling of gapped sequences
gmungoc [Tue, 19 Jul 2016 15:21:18 +0000 (16:21 +0100)]
JAL-391 corrected handling of gapped sequences

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 19 Jul 2016 11:49:48 +0000 (12:49 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

8 years agoJAL-1919 set default structure file format to mmCIF, refactored some StructureImportS...
tcofoegbu [Tue, 19 Jul 2016 11:49:35 +0000 (12:49 +0100)]
JAL-1919 set default structure file format to mmCIF, refactored some StructureImportSetting variables, removed mmCIF from DBRefSource, updated tests

8 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Mon, 18 Jul 2016 16:03:04 +0000 (17:03 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

8 years agoJAL-666 patch JAL-1947 in applet where overview is under sampled when lost of sequenc...
Jim Procter [Tue, 27 Oct 2015 12:17:25 +0000 (12:17 +0000)]
JAL-666 patch JAL-1947 in applet where overview is under sampled when lost of sequences are hidden in the viewport (hangover from applet not supporting hidden rows)

8 years agoJAL-2105 check content of Ensembl REST ping response
gmungoc [Mon, 18 Jul 2016 15:39:34 +0000 (16:39 +0100)]
JAL-2105 check content of Ensembl REST ping response

8 years agoJAL-2099 ensure initial setting of scaleAbove reaches viewport
gmungoc [Mon, 18 Jul 2016 15:38:53 +0000 (16:38 +0100)]
JAL-2099 ensure initial setting of scaleAbove reaches viewport

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 18 Jul 2016 15:36:58 +0000 (16:36 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-2099 JAL-2100 port scale number / hidden column mark changes to
gmungoc [Mon, 18 Jul 2016 15:36:44 +0000 (16:36 +0100)]
JAL-2099 JAL-2100 port scale number / hidden column mark changes to
applet

8 years agoJAL-2068 clearer instructions on how to use script (and modify it!)
Jim Procter [Mon, 18 Jul 2016 15:29:34 +0000 (16:29 +0100)]
JAL-2068 clearer instructions on how to use script (and modify it!)

8 years agoJAL-2068 clarify comments
Jim Procter [Mon, 18 Jul 2016 15:29:15 +0000 (16:29 +0100)]
JAL-2068 clarify comments

8 years agoJAL-2068 scale annotation display character to width for feature count annotation
Jim Procter [Mon, 18 Jul 2016 15:28:31 +0000 (16:28 +0100)]
JAL-2068 scale annotation display character to width for feature count annotation

8 years agoJAL-2121 cleanup TODO
Jim Procter [Mon, 18 Jul 2016 13:20:07 +0000 (14:20 +0100)]
JAL-2121 cleanup TODO

8 years agoJAL-2110 JAL-2145 fix out of date test for 2baee069f9edaef280f0115bae42d4ac7b77bb9b
Jim Procter [Mon, 18 Jul 2016 13:17:42 +0000 (14:17 +0100)]
JAL-2110 JAL-2145 fix out of date test for 2baee069f9edaef280f0115bae42d4ac7b77bb9b

8 years agoJAL-1976 Spanish version of new message
gmungoc [Mon, 18 Jul 2016 13:15:31 +0000 (14:15 +0100)]
JAL-1976 Spanish version of new message

8 years agoJAL-2015 restore check for null colour in paint()
gmungoc [Mon, 18 Jul 2016 13:10:40 +0000 (14:10 +0100)]
JAL-2015 restore check for null colour in paint()

8 years agoMerge branch 'features/JAL-2068groovyAnnotationWorker' into develop
Jim Procter [Mon, 18 Jul 2016 13:01:49 +0000 (14:01 +0100)]
Merge branch 'features/JAL-2068groovyAnnotationWorker' into develop
minor conflicts in constructor/imports for unification of Graduated/FeatureColour

8 years agoJAL-2145 improvement: ensure conservation calculation performed between istart &...
Jim Procter [Mon, 18 Jul 2016 08:31:06 +0000 (09:31 +0100)]
JAL-2145 improvement: ensure conservation calculation performed between istart & alwidth only!

8 years agoJAL-2145 documentation of getWidth()
Jim Procter [Mon, 18 Jul 2016 08:24:39 +0000 (09:24 +0100)]
JAL-2145 documentation of getWidth()

8 years agoJAL-2145 JAL-1551 formatting
Jim Procter [Mon, 18 Jul 2016 08:22:18 +0000 (09:22 +0100)]
JAL-2145 JAL-1551 formatting

8 years agoJAL-2145 fix: build alignments before building AlignFrame/SplitFrame pair
Jim Procter [Mon, 18 Jul 2016 08:21:56 +0000 (09:21 +0100)]
JAL-2145 fix: build alignments before building AlignFrame/SplitFrame pair

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 14 Jul 2016 14:07:22 +0000 (15:07 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

8 years agoJAL-1919 house-keeping
tcofoegbu [Thu, 14 Jul 2016 14:07:11 +0000 (15:07 +0100)]
JAL-1919 house-keeping

8 years agofix for JAL-2147
Jim Procter [Thu, 14 Jul 2016 13:53:33 +0000 (14:53 +0100)]
fix for JAL-2147
- scope search for codonmappings to local alignment
- efficiency - use discovered mappings directly rather than letting highlight search results do the work again

8 years agoJAL-2147 findMappingsBetweenSequenceAndOthers for scoping search to sequences in...
Jim Procter [Thu, 14 Jul 2016 13:49:35 +0000 (14:49 +0100)]
JAL-2147 findMappingsBetweenSequenceAndOthers for scoping search to sequences in an alignment

8 years agoJAL-1115 change implementation to avoid possibility of deadlock
Jim Procter [Thu, 14 Jul 2016 10:43:53 +0000 (11:43 +0100)]
JAL-1115 change implementation to avoid possibility of deadlock

8 years agoJAL-1270 test coverage TODO Alignment.append(AlignmentI)
Jim Procter [Thu, 14 Jul 2016 10:42:51 +0000 (11:42 +0100)]
JAL-1270 test coverage TODO Alignment.append(AlignmentI)

8 years agoJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstructed from aligned proteins
Jim Procter [Thu, 14 Jul 2016 10:28:14 +0000 (11:28 +0100)]
JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstructed from aligned proteins

8 years agoMerge branch 'features/JAL-2110_crossRefDuplications' into develop
Jim Procter [Wed, 13 Jul 2016 15:52:20 +0000 (16:52 +0100)]
Merge branch 'features/JAL-2110_crossRefDuplications' into develop

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications
Jim Procter [Wed, 13 Jul 2016 15:51:30 +0000 (16:51 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 13 Jul 2016 10:28:11 +0000 (11:28 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

8 years agoJAL-2135 minor house-keeping
tcofoegbu [Wed, 13 Jul 2016 10:28:06 +0000 (11:28 +0100)]
JAL-2135 minor house-keeping

8 years agoJAL-2144 TODO - new methods for canonicalisation and comparison of source strings...
Jim Procter [Tue, 12 Jul 2016 16:41:50 +0000 (17:41 +0100)]
JAL-2144 TODO - new methods for canonicalisation and comparison of source strings, regularisation of properties from SequenceDbSource implementations, recognition of coding databases in a more generic way.

8 years agoJAL-2110 avoid potential race condition where user changes selection after ‘show...
Jim Procter [Tue, 12 Jul 2016 16:28:55 +0000 (17:28 +0100)]
JAL-2110 avoid potential race condition where user changes selection after ‘show cross refs’ option has been selected

8 years agoJAL-2110 TODO for JAL-2131
Jim Procter [Tue, 12 Jul 2016 16:19:43 +0000 (17:19 +0100)]
JAL-2110 TODO for JAL-2131

8 years agoJAL-2110 note about use case for when alignAsSameSequences fails due to missing share...
Jim Procter [Tue, 12 Jul 2016 16:18:06 +0000 (17:18 +0100)]
JAL-2110 note about use case for when alignAsSameSequences fails due to missing shared dataset refs

8 years agoJAL-2110 test demonstrating limitation of current implementation of alignAs (simple...
Jim Procter [Tue, 12 Jul 2016 16:15:23 +0000 (17:15 +0100)]
JAL-2110 test demonstrating limitation of current implementation of alignAs (simple case)

8 years agoJAL-2110 javadoc and TODO re shortcomings of implementation
Jim Procter [Tue, 12 Jul 2016 16:14:28 +0000 (17:14 +0100)]
JAL-2110 javadoc and TODO re shortcomings of implementation

8 years agoJAL-2110 javadoc
Jim Procter [Tue, 12 Jul 2016 16:12:10 +0000 (17:12 +0100)]
JAL-2110 javadoc

8 years agoJAL-2110 scalability todo
Jim Procter [Tue, 12 Jul 2016 15:37:19 +0000 (16:37 +0100)]
JAL-2110 scalability todo

8 years agoJAL-1381 JAL-2110 efficiency TODO
Jim Procter [Tue, 12 Jul 2016 15:36:31 +0000 (16:36 +0100)]
JAL-1381 JAL-2110 efficiency TODO

8 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 12 Jul 2016 10:35:18 +0000 (11:35 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

8 years agoJAL-1369 release notes for patch of save/restore representative group when only one...
Jim Procter [Tue, 12 Jul 2016 10:31:52 +0000 (11:31 +0100)]
JAL-1369 release notes for patch of save/restore representative group when only one sequence represented

8 years agoJAL-2135 NPE bugfix when parsing a structure file with Jmol and id & inFile is null
tcofoegbu [Tue, 12 Jul 2016 10:03:50 +0000 (11:03 +0100)]
JAL-2135 NPE bugfix when parsing a structure file with Jmol and id & inFile is null

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications features/JAL-2110_crossRefDuplications
gmungoc [Sat, 9 Jul 2016 06:12:09 +0000 (07:12 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications

8 years agoJAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be...
tcofoegbu [Fri, 8 Jul 2016 16:16:54 +0000 (17:16 +0100)]
JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be configurable. Minor refactorings (StructureViewSettings class renamed to StructureImportSettings, fileName variables of AlignFile class renamed to dataObject since in realty it could be a file, url or pasted string)

8 years agoJAL-2110 added alignAsSameSequences to handle 'direct' (copy) case
gmungoc [Thu, 7 Jul 2016 15:51:51 +0000 (16:51 +0100)]
JAL-2110 added alignAsSameSequences to handle 'direct' (copy) case

8 years agoJAL-2110 field 'cf' moved to stack
gmungoc [Thu, 7 Jul 2016 15:51:21 +0000 (16:51 +0100)]
JAL-2110 field 'cf' moved to stack

8 years agoJAL-2110 generic rather than specific check for gap character
gmungoc [Wed, 6 Jul 2016 15:34:32 +0000 (16:34 +0100)]
JAL-2110 generic rather than specific check for gap character

8 years agoJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
gmungoc [Wed, 6 Jul 2016 15:34:01 +0000 (16:34 +0100)]
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented

8 years agoJAL-2110 ensuring mapped dbrefs between protein and cds
gmungoc [Wed, 6 Jul 2016 12:08:28 +0000 (13:08 +0100)]
JAL-2110 ensuring mapped dbrefs between protein and cds

8 years agoJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL CDS protein_id)
gmungoc [Wed, 6 Jul 2016 11:47:04 +0000 (12:47 +0100)]
JAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL CDS protein_id)

8 years agoJAL-2110 cross-refs from protein to show cds not non-coding sequences
gmungoc [Wed, 6 Jul 2016 11:42:11 +0000 (12:42 +0100)]
JAL-2110 cross-refs from protein to show cds not non-coding sequences

8 years agoJAL-2110 fixes and tests for adding dbrefs to EMBL sequence and products
gmungoc [Wed, 6 Jul 2016 09:10:53 +0000 (10:10 +0100)]
JAL-2110 fixes and tests for adding dbrefs to EMBL sequence and products

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Mon, 4 Jul 2016 14:57:01 +0000 (15:57 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications

8 years agoJAL-2110 use shared dataset when copying alignment for split frame
gmungoc [Mon, 4 Jul 2016 14:35:13 +0000 (15:35 +0100)]
JAL-2110 use shared dataset when copying alignment for split frame

8 years agoJAL-2110 added another test case (should fail but doesn't)
gmungoc [Mon, 4 Jul 2016 14:34:51 +0000 (15:34 +0100)]
JAL-2110 added another test case (should fail but doesn't)

8 years agoRevert "JAL-2110 use shared alignment dataset when copying alignment for split frame"
gmungoc [Mon, 4 Jul 2016 14:27:21 +0000 (15:27 +0100)]
Revert "JAL-2110 use shared alignment dataset when copying alignment for split frame"

This reverts commit f931c557266d95b3f4ab5b64bd108123c90e85ab.

8 years agoJAL-2110 use shared alignment dataset when copying alignment for split
gmungoc [Mon, 4 Jul 2016 14:21:49 +0000 (15:21 +0100)]
JAL-2110 use shared alignment dataset when copying alignment for split
frame

8 years agoJAL-2110 bug fix / test for searchDataset mappings created
gmungoc [Mon, 4 Jul 2016 14:21:17 +0000 (15:21 +0100)]
JAL-2110 bug fix / test for searchDataset mappings created

8 years agoJAL-2110 unused method removed
gmungoc [Mon, 4 Jul 2016 14:20:27 +0000 (15:20 +0100)]
JAL-2110 unused method removed

8 years agoJAL-2110 defensive check in code
gmungoc [Mon, 4 Jul 2016 14:19:43 +0000 (15:19 +0100)]
JAL-2110 defensive check in code

8 years agoJAL-2110 bug fixing and tidying for get cross-refs
gmungoc [Fri, 1 Jul 2016 15:54:01 +0000 (16:54 +0100)]
JAL-2110 bug fixing and tidying for get cross-refs

8 years agoJAL-2110 set reasonable bounds to initial split of SplitFrame divider
gmungoc [Fri, 1 Jul 2016 14:01:00 +0000 (15:01 +0100)]
JAL-2110 set reasonable bounds to initial split of SplitFrame divider

8 years agoJAL-2135 bugfix for error preventing processing of secondary structure annotation...
tcofoegbu [Fri, 1 Jul 2016 10:08:43 +0000 (11:08 +0100)]
JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2

8 years agoJAL-2110 add 'products' parameter to filter results in madeCdsAlignment
gmungoc [Fri, 1 Jul 2016 09:19:20 +0000 (10:19 +0100)]
JAL-2110 add 'products' parameter to filter results in madeCdsAlignment

8 years agoJAL-2110 code/comment tidy
gmungoc [Fri, 1 Jul 2016 09:07:31 +0000 (10:07 +0100)]
JAL-2110 code/comment tidy

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Thu, 30 Jun 2016 15:24:19 +0000 (16:24 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications

8 years agoJAL-2074 Improvement to StructureChooser and FTS interfaces to remember the user...
tcofoegbu [Thu, 30 Jun 2016 14:59:00 +0000 (15:59 +0100)]
JAL-2074 Improvement to StructureChooser and FTS interfaces to remember the user preferences for summary table columns, window size & positions

8 years agoJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN dbrefs
gmungoc [Thu, 30 Jun 2016 14:49:51 +0000 (15:49 +0100)]
JAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN dbrefs

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Thu, 30 Jun 2016 13:01:23 +0000 (14:01 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications

8 years agoJAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable...
tcofoegbu [Thu, 30 Jun 2016 09:46:51 +0000 (10:46 +0100)]
JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable proper processing of mmCIF files

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 29 Jun 2016 13:58:41 +0000 (14:58 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

8 years agoJAL-1479 added test case to elaborate getEntityByMostOptimalMatchedId method
tcofoegbu [Wed, 29 Jun 2016 13:58:34 +0000 (14:58 +0100)]
JAL-1479 added test case to elaborate getEntityByMostOptimalMatchedId method

8 years agoMerge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Wed, 29 Jun 2016 13:21:32 +0000 (14:21 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications