jalview.git
8 years agoJAL-2089 JAL-2119 help link fixups
Jim Procter [Thu, 8 Sep 2016 13:35:58 +0000 (14:35 +0100)]
JAL-2089 JAL-2119 help link fixups

8 years agoJAL-2119 linkcheck target. runs before build indices
Jim Procter [Thu, 8 Sep 2016 13:30:06 +0000 (14:30 +0100)]
JAL-2119 linkcheck target. runs before build indices

8 years agoMerge branch 'bug/JAL-1803_JAL-2157' into develop
Jim Procter [Wed, 7 Sep 2016 14:38:59 +0000 (15:38 +0100)]
Merge branch 'bug/JAL-1803_JAL-2157' into develop

8 years agoJAL-1670 groundhog day: fix FeaturesFileTest by redacting last commit:53dd28432308dda... bug/JAL-1803_JAL-2157
Jim Procter [Wed, 7 Sep 2016 14:38:36 +0000 (15:38 +0100)]
JAL-1670 groundhog day: fix FeaturesFileTest by redacting last commit:53dd28432308dda9cc73d6887bcd43fcfe17907d

8 years agoMerge branch 'bug/JAL-1803_JAL-2157' into develop
Jim Procter [Wed, 7 Sep 2016 11:47:30 +0000 (12:47 +0100)]
Merge branch 'bug/JAL-1803_JAL-2157' into develop

8 years agoMerge branch 'develop' into bug/JAL-1803_JAL-2157
Jim Procter [Wed, 7 Sep 2016 11:46:28 +0000 (12:46 +0100)]
Merge branch 'develop' into bug/JAL-1803_JAL-2157

8 years agoJAL-2192 TODO
Jim Procter [Wed, 7 Sep 2016 11:43:37 +0000 (12:43 +0100)]
JAL-2192 TODO

8 years agoJAL-2191 comments re chimera view code redundancy and JAL-1803
Jim Procter [Wed, 7 Sep 2016 11:32:04 +0000 (12:32 +0100)]
JAL-2191 comments re chimera view code redundancy and JAL-1803

8 years agoJAL-282 TODO - Sequence name from PDB had redundant info
Jim Procter [Wed, 7 Sep 2016 11:26:32 +0000 (12:26 +0100)]
JAL-282 TODO - Sequence name from PDB had redundant info

8 years agoJAL-1803 transfer mapped chain’s PDBEntry to the *dataset* SequenceI it was mapped to
Jim Procter [Wed, 7 Sep 2016 10:57:09 +0000 (11:57 +0100)]
JAL-1803 transfer mapped chain’s PDBEntry to the *dataset* SequenceI it was mapped to

8 years agoJAL-1803 JAL-1919 set type when structure file is parsed
Jim Procter [Wed, 7 Sep 2016 10:55:51 +0000 (11:55 +0100)]
JAL-1803 JAL-1919 set type when structure file is parsed

8 years agoJAL-1803 first pass at updatePDBEntry
Jim Procter [Wed, 7 Sep 2016 10:54:14 +0000 (11:54 +0100)]
JAL-1803 first pass at updatePDBEntry
* merge PDBEntry if same ID, existing is null or identical filename, and chaincode is unspecified or identical to new one.
* merge propagates type, chainCode, filename, and all properties to parent.

Note TODOs: we don’t recognise and merge 1QIPA onto 1QIP (yet)

8 years agoJAL-1803 switched so ‘expected’ is constant in assert
Jim Procter [Wed, 7 Sep 2016 10:50:41 +0000 (11:50 +0100)]
JAL-1803 switched so ‘expected’ is constant in assert

8 years agoJAL-2164 fix failing test
gmungoc [Wed, 7 Sep 2016 09:26:25 +0000 (10:26 +0100)]
JAL-2164 fix failing test

8 years agoJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandidate()
gmungoc [Tue, 6 Sep 2016 14:31:42 +0000 (15:31 +0100)]
JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandidate()

8 years agoJAL-2147 additional test coverage for findMappingsForSequenceAndOthers
gmungoc [Tue, 6 Sep 2016 13:46:45 +0000 (14:46 +0100)]
JAL-2147 additional test coverage for findMappingsForSequenceAndOthers

8 years agoMerge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Tue, 6 Sep 2016 07:00:08 +0000 (08:00 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop

8 years agoJAL-1563 UniProt FTS doc revisions
Jim Procter [Mon, 5 Sep 2016 16:20:10 +0000 (17:20 +0100)]
JAL-1563 UniProt FTS doc revisions

8 years agoJAL-2089 reworked and formatted doc for
Jim Procter [Mon, 5 Sep 2016 16:17:37 +0000 (17:17 +0100)]
JAL-2089 reworked and formatted doc for
JAL-1479 - SIFTS

8 years agoJAL-2089 reworked and formatted doc for
Jim Procter [Mon, 5 Sep 2016 16:16:43 +0000 (17:16 +0100)]
JAL-2089 reworked and formatted doc for
JAL-1666 PDB search interface and ‘3D structure…’ viewing option
JAL-1919 mmcif

8 years agoJAL-2089 update Uniprot to UniProt in help docs.
Jim Procter [Mon, 5 Sep 2016 16:12:50 +0000 (17:12 +0100)]
JAL-2089 update Uniprot to UniProt in help docs.

8 years agoJAL-2089 drop MCView documentation from contents.
Jim Procter [Mon, 5 Sep 2016 16:11:09 +0000 (17:11 +0100)]
JAL-2089 drop MCView documentation from contents.

8 years agoJAL-2154 made Java 7 compatible
gmungoc [Mon, 5 Sep 2016 15:30:03 +0000 (16:30 +0100)]
JAL-2154 made Java 7 compatible

8 years agoJAL-2106 increased coverage for testGetPrimaryDbRefs
gmungoc [Mon, 5 Sep 2016 15:13:31 +0000 (16:13 +0100)]
JAL-2106 increased coverage for testGetPrimaryDbRefs

8 years agoJAL-1919 revised mmCIF documentation
Jim Procter [Mon, 5 Sep 2016 14:31:02 +0000 (15:31 +0100)]
JAL-1919 revised mmCIF documentation

8 years agoJAL-2089 bump release date for 2.10
Jim Procter [Mon, 5 Sep 2016 14:18:25 +0000 (15:18 +0100)]
JAL-2089 bump release date for 2.10

8 years agoJAL-2106 corrections to DBRefEntry.isPrimary code and tests
gmungoc [Mon, 5 Sep 2016 14:07:52 +0000 (15:07 +0100)]
JAL-2106 corrections to DBRefEntry.isPrimary code and tests

8 years agoJAL-1919 preserve filename on restore of project so Chimera recognises mmCIF files...
Jim Procter [Sun, 4 Sep 2016 16:42:28 +0000 (17:42 +0100)]
JAL-1919 preserve filename on restore of project so Chimera recognises mmCIF files from .cif suffix

8 years agoJAL-1803 JAL-2106 patch tests for tighter PDB Primary DBRef definition
Jim Procter [Sun, 4 Sep 2016 14:15:03 +0000 (15:15 +0100)]
JAL-1803 JAL-2106 patch tests for tighter PDB Primary DBRef definition

8 years agoJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loaded from local file system
Jim Procter [Sun, 4 Sep 2016 13:40:19 +0000 (14:40 +0100)]
JAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loaded from local file system

8 years agoJAL-1803 recover type field faithfully for mmCIF/PDB file type info
Jim Procter [Sun, 4 Sep 2016 12:20:40 +0000 (13:20 +0100)]
JAL-1803 recover type field faithfully for mmCIF/PDB file type info

8 years agoJAL-1803 restore property array for a sequence’s associated PDBEntry from project.
Jim Procter [Sun, 4 Sep 2016 12:20:01 +0000 (13:20 +0100)]
JAL-1803 restore property array for a sequence’s associated PDBEntry from project.

8 years agoJAL-1803 chainCode moved onto property hashtable as chain_code
Jim Procter [Sun, 4 Sep 2016 12:13:46 +0000 (13:13 +0100)]
JAL-1803 chainCode moved onto property hashtable as chain_code

8 years agoJAL-1803 patch test: PDBEntry.getFile() will always be different, but never null
Jim Procter [Sun, 4 Sep 2016 12:11:44 +0000 (13:11 +0100)]
JAL-1803 patch test: PDBEntry.getFile() will always be different, but never null

8 years agoMerge branch 'bug/JAL-2034_fix' into develop
Jim Procter [Thu, 1 Sep 2016 17:44:26 +0000 (18:44 +0100)]
Merge branch 'bug/JAL-2034_fix' into develop

8 years agoJAL-2077 don't mess with the look and feel
gmungoc [Thu, 1 Sep 2016 15:41:49 +0000 (16:41 +0100)]
JAL-2077 don't mess with the look and feel

8 years agoJAL-2077 less drastic exit on close
gmungoc [Thu, 1 Sep 2016 15:37:10 +0000 (16:37 +0100)]
JAL-2077 less drastic exit on close

8 years agoJAL-2034 - remember to reset needsOverviewUpdate at beginning of new select/drag...
Jim Procter [Thu, 1 Sep 2016 15:11:15 +0000 (16:11 +0100)]
JAL-2034 - remember to reset needsOverviewUpdate at beginning of new select/drag event

8 years agoJAL-2077 test harness for inspecting mouse events
gmungoc [Thu, 1 Sep 2016 15:09:00 +0000 (16:09 +0100)]
JAL-2077 test harness for inspecting mouse events

8 years agoJAL-2077 check isPopupTrigger in mouseReleased not mouseClicked
gmungoc [Thu, 1 Sep 2016 13:46:53 +0000 (14:46 +0100)]
JAL-2077 check isPopupTrigger in mouseReleased not mouseClicked
(Windows)

8 years agoJAL-1421 add generics to NJTree, refactor recursive search
gmungoc [Thu, 1 Sep 2016 12:47:02 +0000 (13:47 +0100)]
JAL-1421 add generics to NJTree, refactor recursive search

8 years agoJAL-2034 check context of selection group to catch case when selection was added...
Jim Procter [Thu, 1 Sep 2016 12:27:42 +0000 (13:27 +0100)]
JAL-2034 check context of selection group to catch case when selection was added/removed from alignment without deselection/reselection

8 years agoJAL-1854 rule to disallow import of swing in appletgui
gmungoc [Thu, 1 Sep 2016 11:08:25 +0000 (12:08 +0100)]
JAL-1854 rule to disallow import of swing in appletgui

8 years agoJAL-2077 do nothing in mousePressed if right button down (on Windows)
gmungoc [Thu, 1 Sep 2016 11:07:44 +0000 (12:07 +0100)]
JAL-2077 do nothing in mousePressed if right button down (on Windows)

8 years agoJAL-2077 force defer right-click handling to mouseReleased on Windows
gmungoc [Thu, 1 Sep 2016 09:53:37 +0000 (10:53 +0100)]
JAL-2077 force defer right-click handling to mouseReleased on Windows

8 years agoJAL-1803 JAL-2188 experimental:
Jim Procter [Thu, 1 Sep 2016 09:16:48 +0000 (10:16 +0100)]
JAL-1803 JAL-2188 experimental:
Don’t go looking for new cross-references if we already have a mapping between a PDBEntry and a sequence - speeds up viewing already downloaded structure data.

8 years agoJAL-1926 JAL-2106 source DB refs come from SequenceI.getPrimaryDBRefs()
Jim Procter [Wed, 31 Aug 2016 16:22:32 +0000 (17:22 +0100)]
JAL-1926 JAL-2106 source DB refs come from SequenceI.getPrimaryDBRefs()

8 years agoJAL-1926 JAL-2106 resolve source DB refs using canonical dbsource match
Jim Procter [Wed, 31 Aug 2016 16:21:58 +0000 (17:21 +0100)]
JAL-1926 JAL-2106 resolve source DB refs using canonical dbsource match

8 years agoJAL-1926 JAL-2106 fix PDB primary DBRef semantics: must have a matching PDBEntry...
Jim Procter [Wed, 31 Aug 2016 16:13:22 +0000 (17:13 +0100)]
JAL-1926 JAL-2106 fix PDB primary DBRef semantics: must have a matching PDBEntry with non-null File. type field doesn’t matter

8 years agoJAL-2077 test isPopupTrigger in mouseReleased or mouseClicked (for
gmungoc [Wed, 31 Aug 2016 15:37:49 +0000 (16:37 +0100)]
JAL-2077 test isPopupTrigger in mouseReleased or mouseClicked (for
Windows) as well as mousePressed (Mac)

8 years agoJAL-2077 more javadoc
gmungoc [Wed, 31 Aug 2016 15:37:14 +0000 (16:37 +0100)]
JAL-2077 more javadoc

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 31 Aug 2016 15:35:42 +0000 (16:35 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-2157 JAL-2154 simplify CanshowProducts code to avoid one source of NPE
Jim Procter [Wed, 31 Aug 2016 15:16:06 +0000 (16:16 +0100)]
JAL-2157 JAL-2154 simplify CanshowProducts code to avoid one source of NPE

8 years agoJAL-2034 fix logic so recalcConservation(true) returns true if conservation updates...
Jim Procter [Wed, 31 Aug 2016 14:38:21 +0000 (15:38 +0100)]
JAL-2034 fix logic so recalcConservation(true) returns true if conservation updates were performed on group

8 years agoJAL-2034 moved ‘isDefinedGroup’ flag to a test method on AlignViewportI so controller...
Jim Procter [Wed, 31 Aug 2016 14:36:33 +0000 (15:36 +0100)]
JAL-2034 moved ‘isDefinedGroup’ flag to a test method on AlignViewportI so controller doesn’t have to track datamodel state.

8 years agoJAL-2034 remove todo - answer is yes!
Jim Procter [Wed, 31 Aug 2016 14:34:19 +0000 (15:34 +0100)]
JAL-2034 remove todo - answer is yes!

8 years agoJAL-2077 check for isPopupTrigger() in mousePressed as well as
gmungoc [Wed, 31 Aug 2016 13:59:42 +0000 (14:59 +0100)]
JAL-2077 check for isPopupTrigger() in mousePressed as well as
mouseClicked.

8 years agoJAL-2148 further enhancment to CA HETATM processing
tcofoegbu [Wed, 31 Aug 2016 13:18:53 +0000 (14:18 +0100)]
JAL-2148 further enhancment to CA HETATM processing

8 years agoJAL-1670 repositioned feature for backwards compatibility of feature
gmungoc [Wed, 31 Aug 2016 10:00:23 +0000 (11:00 +0100)]
JAL-1670 repositioned feature for backwards compatibility of feature
order

8 years agoMerge branch 'develop' into merge/develop_bug/JAL-2154projectMappings merge/develop_bug/JAL-2154projectMappings
Jim Procter [Tue, 30 Aug 2016 17:06:00 +0000 (18:06 +0100)]
Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings

8 years agoJAL-2154 doc & AssertError trap for known failure case due to JAL-2179
Jim Procter [Tue, 30 Aug 2016 15:18:38 +0000 (16:18 +0100)]
JAL-2154 doc & AssertError trap for known failure case due to JAL-2179

8 years agoJAL-2154 always compare canonicalised DBRefEntry source strings!
Jim Procter [Tue, 30 Aug 2016 15:17:12 +0000 (16:17 +0100)]
JAL-2154 always compare canonicalised DBRefEntry source strings!

8 years agoJAL-2154 simplify expression
Jim Procter [Tue, 30 Aug 2016 15:16:35 +0000 (16:16 +0100)]
JAL-2154 simplify expression

8 years agoJAL-2183 defensive check for openFrameCount < 0 (shouldn't happen but
gmungoc [Tue, 30 Aug 2016 14:58:47 +0000 (15:58 +0100)]
JAL-2183 defensive check for openFrameCount < 0 (shouldn't happen but
did)

8 years agoJAL-2183 simplified database tree actionPerformed, accept dbl-click
gmungoc [Tue, 30 Aug 2016 14:49:34 +0000 (15:49 +0100)]
JAL-2183 simplified database tree actionPerformed, accept dbl-click

8 years agoJAL-2183 revised change (= no change)
gmungoc [Tue, 30 Aug 2016 14:45:45 +0000 (15:45 +0100)]
JAL-2183 revised change (= no change)

8 years agoJAL-2183 formatter added @Override (only)
gmungoc [Tue, 30 Aug 2016 14:27:14 +0000 (15:27 +0100)]
JAL-2183 formatter added @Override (only)

8 years agoJAL-2183 removed redundant (overriden) add panel to container
gmungoc [Tue, 30 Aug 2016 14:26:31 +0000 (15:26 +0100)]
JAL-2183 removed redundant (overriden) add panel to container

8 years agoJAL-2154 javadoc, fix underloaded version of assertDatasetIsNormalised
Jim Procter [Tue, 30 Aug 2016 13:44:49 +0000 (14:44 +0100)]
JAL-2154 javadoc, fix underloaded version of assertDatasetIsNormalised

8 years agoMerge branch 'develop' into merge/develop_bug/JAL-2154projectMappings
Jim Procter [Tue, 30 Aug 2016 13:30:34 +0000 (14:30 +0100)]
Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings

8 years agoJAL-2154 don’t synthesise multiple CDS|<Acc> sequences when one is already available...
Jim Procter [Mon, 29 Aug 2016 21:20:23 +0000 (22:20 +0100)]
JAL-2154 don’t synthesise multiple CDS|<Acc> sequences when one is already available on dataset (fixes crossRefs2XML failure - CDS|ENST00000288602 found duplicated
"Pass (0,0,0): before start of pass3: ENSEMBL ENSG00000157764 -> UNIPROT{0}:”)

8 years agoJAL-2154 filter out dbrefs that already match primary refs for sequences already...
Jim Procter [Mon, 29 Aug 2016 21:15:58 +0000 (22:15 +0100)]
JAL-2154 filter out dbrefs that already match primary refs for sequences already retrieved. This is a patch for ENA records where protein products were not reconstructed (AC006347) resulting in duplicate sequence fetches

8 years agoJAL-2154 refactor if (for easier breakpoint) and formatting
Jim Procter [Mon, 29 Aug 2016 21:13:13 +0000 (22:13 +0100)]
JAL-2154 refactor if (for easier breakpoint) and formatting

8 years agoJAL-2154 canonical dbsources are lowercased before matching
Jim Procter [Mon, 29 Aug 2016 21:10:27 +0000 (22:10 +0100)]
JAL-2154 canonical dbsources are lowercased before matching

8 years agoJAL-2154 ENA specific Ensembl canonical db prefixes
Jim Procter [Mon, 29 Aug 2016 21:09:50 +0000 (22:09 +0100)]
JAL-2154 ENA specific Ensembl canonical db prefixes

8 years agoJAL-2154 endless loop fixed (hopefully :) )
Jim Procter [Mon, 29 Aug 2016 21:09:02 +0000 (22:09 +0100)]
JAL-2154 endless loop fixed (hopefully :) )

8 years agoJAL-1854 tweaks to rules and README
gmungoc [Mon, 29 Aug 2016 11:31:34 +0000 (12:31 +0100)]
JAL-1854 tweaks to rules and README

8 years agoJAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignm...
Jim Procter [Mon, 29 Aug 2016 11:10:10 +0000 (12:10 +0100)]
JAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignment.assertDatasetIsNormaised

8 years agoJAL-2154 Optional message parameter for assertDatasetNormalised
Jim Procter [Mon, 29 Aug 2016 11:07:13 +0000 (12:07 +0100)]
JAL-2154 Optional message parameter for assertDatasetNormalised

8 years agoJAL-2154 new assertDatasetIsNormalised to trivially test for the addition of identica...
Jim Procter [Mon, 29 Aug 2016 11:02:03 +0000 (12:02 +0100)]
JAL-2154 new assertDatasetIsNormalised to trivially test for the addition of identical sequence data in the dataset (e.g. due to faulty create CDS sequence processes)

8 years agoJAL-2154 additional test that removing a duplicate sequence reinstates dataset refere...
Jim Procter [Mon, 29 Aug 2016 10:59:47 +0000 (11:59 +0100)]
JAL-2154 additional test that removing a duplicate sequence reinstates dataset reference validity

8 years agoJAL-1854 checkstyle relocated to /utils, newlines to Unix (?)
gmungoc [Mon, 29 Aug 2016 10:23:58 +0000 (11:23 +0100)]
JAL-1854 checkstyle relocated to /utils, newlines to Unix (?)

8 years agoMerge branch 'bug/JAL-1841rnaSecStr' into develop
gmungoc [Mon, 29 Aug 2016 09:24:23 +0000 (10:24 +0100)]
Merge branch 'bug/JAL-1841rnaSecStr' into develop

8 years agoJAL-1448 updated unit test for last change
gmungoc [Mon, 29 Aug 2016 09:23:59 +0000 (10:23 +0100)]
JAL-1448 updated unit test for last change

8 years agoJAL-1841 robustness fix bug/JAL-1841rnaSecStr
gmungoc [Mon, 29 Aug 2016 09:10:20 +0000 (10:10 +0100)]
JAL-1841 robustness fix

8 years agoMerge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Mon, 29 Aug 2016 08:01:06 +0000 (09:01 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr

8 years agoJAL-1854 two more rules, readme notes
gmungoc [Fri, 26 Aug 2016 15:28:53 +0000 (16:28 +0100)]
JAL-1854 two more rules, readme notes

8 years agoJAL-2154 patch regression on DbRefFetcher due to PDB being dropped from NUCLEOTIDEDBS...
Jim Procter [Fri, 26 Aug 2016 15:09:16 +0000 (16:09 +0100)]
JAL-2154 patch regression on DbRefFetcher due to PDB being dropped from NUCLEOTIDEDBS and PROTEINDBS lists

8 years agoMerge branch 'bug/JAL-2154projectMappings' into merge/develop_bug/JAL-2154projectMappings
Jim Procter [Fri, 26 Aug 2016 14:37:36 +0000 (15:37 +0100)]
Merge branch 'bug/JAL-2154projectMappings' into merge/develop_bug/JAL-2154projectMappings

8 years agoJAL-2106 fix (last one!) remove the Sequence.sourceDBRef field! bug/JAL-2154projectMappings
Jim Procter [Fri, 26 Aug 2016 13:53:31 +0000 (14:53 +0100)]
JAL-2106 fix (last one!) remove the Sequence.sourceDBRef field!

8 years agoJAL-2154 ENSEMBL and Uniprot tests
Jim Procter [Fri, 26 Aug 2016 12:43:22 +0000 (13:43 +0100)]
JAL-2154 ENSEMBL and Uniprot tests

8 years agoJAL-2154 report any db fetch failures as a fail at end
Jim Procter [Fri, 26 Aug 2016 12:43:06 +0000 (13:43 +0100)]
JAL-2154 report any db fetch failures as a fail at end

8 years agoJAL-2154 ensure pass increments actually result in a termination
Jim Procter [Fri, 26 Aug 2016 12:24:05 +0000 (13:24 +0100)]
JAL-2154 ensure pass increments actually result in a termination

8 years agoJAL-2154 catch and report a failures when xrefed project didn’t seem to have associat...
Jim Procter [Fri, 26 Aug 2016 12:22:56 +0000 (13:22 +0100)]
JAL-2154 catch and report a failures when xrefed project didn’t seem to have associated file (possibly due to failed ref retrieval)

8 years agoJAL-2154 check that xref is a coding xref before adding sequence to retrieved xrefs
Jim Procter [Fri, 26 Aug 2016 12:21:33 +0000 (13:21 +0100)]
JAL-2154 check that xref is a coding xref before adding sequence to retrieved xrefs

8 years agoJAL-2154 don’t add any remaining xrefed sequences of the wrong molecule type to the...
Jim Procter [Fri, 26 Aug 2016 12:20:51 +0000 (13:20 +0100)]
JAL-2154 don’t add any remaining xrefed sequences of the wrong molecule type to the alignment

8 years agoMerge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Fri, 26 Aug 2016 11:15:06 +0000 (12:15 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr

8 years agoJAL-1854 commented FallThrough rule
gmungoc [Fri, 26 Aug 2016 11:11:57 +0000 (12:11 +0100)]
JAL-1854 commented FallThrough rule

8 years agoJAL-1854 corrected nested package rule
gmungoc [Fri, 26 Aug 2016 11:11:22 +0000 (12:11 +0100)]
JAL-1854 corrected nested package rule

8 years agoJAL-2049 set Ensembl variant source to ENSEMBL if '.' (not provided) and
gmungoc [Fri, 26 Aug 2016 11:09:27 +0000 (12:09 +0100)]
JAL-2049 set Ensembl variant source to ENSEMBL if '.' (not provided) and
in computed peptide variants