jalview.git
7 years agoJAL-2694 StructureSelectionManager.getMapping takes a list of Chain IDs per sequence... patch/JAL-2694_maptoallchainsworkaround
Jim Procter [Fri, 1 Sep 2017 16:22:42 +0000 (17:22 +0100)]
JAL-2694 StructureSelectionManager.getMapping takes a list of Chain IDs per sequence to be bound to structure, and resolveChains adjusted accordingly. targetChains also dropped in StructureViewer constructor since resolveChains discovers extant chain mappings, and StructureSelectionManager infers any sequence/chain mappings that remain.

one failing test in this commit

7 years agoJAL-2694 utility to transform single String to List<String>[1]
Jim Procter [Thu, 31 Aug 2017 06:04:43 +0000 (07:04 +0100)]
JAL-2694 utility to transform single String to List<String>[1]

7 years agoJAL-2694 formatting
Jim Procter [Wed, 30 Aug 2017 16:48:55 +0000 (17:48 +0100)]
JAL-2694 formatting

7 years agoJAL-2694 add maximal set of chain mappings between a PDBEntry and a sequence
Jim Procter [Wed, 30 Aug 2017 16:48:35 +0000 (17:48 +0100)]
JAL-2694 add maximal set of chain mappings between a PDBEntry and a sequence

7 years agoJAL-2698 spawn a thread to test for and raise auto associate dialogs for PDB file...
Jim Procter [Tue, 29 Aug 2017 13:35:37 +0000 (14:35 +0100)]
JAL-2698 spawn a thread to test for and raise auto associate dialogs for PDB file drops on the alignment view

7 years agoJAL-2691 assert chains are recovered by AAStructureBindingModel bug/JAL-2691_nomultimermapping
Jim Procter [Sun, 27 Aug 2017 14:50:03 +0000 (15:50 +0100)]
JAL-2691 assert chains are recovered by AAStructureBindingModel

7 years agoJAL-2691 catchall if passed dataset sequences (tests only)
Jim Procter [Sun, 27 Aug 2017 14:49:02 +0000 (15:49 +0100)]
JAL-2691 catchall if passed dataset sequences (tests only)

7 years agoJAL-2693 TODO comments
Jim Procter [Sun, 27 Aug 2017 13:25:01 +0000 (14:25 +0100)]
JAL-2693 TODO comments

7 years agoJAL-2691 discover any existing chain mappings for a structure view
Jim Procter [Sun, 27 Aug 2017 13:23:06 +0000 (14:23 +0100)]
JAL-2691 discover any existing chain mappings for a structure view

7 years agoJAL-2691 cached view combo box value javadoc
Jim Procter [Sun, 27 Aug 2017 13:17:30 +0000 (14:17 +0100)]
JAL-2691 cached view combo box value javadoc

7 years agoJAL-2435 last lost commit e926a5d redone
gmungoc [Wed, 23 Aug 2017 13:42:32 +0000 (14:42 +0100)]
JAL-2435 last lost commit e926a5d redone

7 years agoMerge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 21 Aug 2017 13:47:22 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch

7 years agoJAL-2675 typo in what's new href
Jim Procter [Mon, 21 Aug 2017 13:46:45 +0000 (14:46 +0100)]
JAL-2675 typo in what's new href

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:17:50 +0000 (14:17 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2675 bump version for branch to 2.10.2b1
Jim Procter [Fri, 18 Aug 2017 13:15:40 +0000 (14:15 +0100)]
JAL-2675 bump version for branch to 2.10.2b1

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:14:17 +0000 (14:14 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-1551 formatting
Jim Procter [Fri, 18 Aug 2017 13:13:28 +0000 (14:13 +0100)]
JAL-1551 formatting

7 years agoJAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest...
Jim Procter [Fri, 18 Aug 2017 13:08:03 +0000 (14:08 +0100)]
JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.

7 years agoJAL-2418 ahem - correct year for what's new releases/Release_2_10_2_Branch
Jim Procter [Thu, 17 Aug 2017 12:07:53 +0000 (13:07 +0100)]
JAL-2418 ahem - correct year for what's new

7 years agoJAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to...
Jim Procter [Thu, 17 Aug 2017 11:37:50 +0000 (12:37 +0100)]
JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9

7 years agoJAL-2418 JAL-2116 make sure java 8,7 vm args are also listed
Jim Procter [Thu, 17 Aug 2017 10:41:33 +0000 (11:41 +0100)]
JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 22:24:25 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 22:24:13 +0000 (23:24 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 formatting
Jim Procter [Wed, 16 Aug 2017 22:23:59 +0000 (23:23 +0100)]
JAL-2418 formatting

7 years agoJAL-2418 occupancy row in What’s New
Jim Procter [Wed, 16 Aug 2017 22:23:53 +0000 (23:23 +0100)]
JAL-2418 occupancy row in What’s New

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 21:37:37 +0000 (22:37 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2418 add GPL to main sources
Jim Procter [Wed, 16 Aug 2017 21:30:21 +0000 (22:30 +0100)]
JAL-2418 add GPL to main sources

7 years agoJAL-2418 source formatting
Jim Procter [Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)]
JAL-2418 source formatting

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 20:52:55 +0000 (21:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 20:52:36 +0000 (21:52 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 mirror fonts option doc tweak
Jim Procter [Wed, 16 Aug 2017 20:52:07 +0000 (21:52 +0100)]
JAL-2418 mirror fonts option doc tweak

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 19:17:43 +0000 (20:17 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 whats new for 2.10.2
Jim Procter [Wed, 16 Aug 2017 19:17:03 +0000 (20:17 +0100)]
JAL-2418 whats new for 2.10.2

7 years agoJAL-2418 reclassify some issues to features/bugs resolved
Jim Procter [Wed, 16 Aug 2017 19:16:52 +0000 (20:16 +0100)]
JAL-2418 reclassify some issues to features/bugs resolved

7 years agoJAL-2418 typos in release notes
Jim Procter [Wed, 16 Aug 2017 18:23:33 +0000 (19:23 +0100)]
JAL-2418 typos in release notes

7 years agoJAL-2418 check groovy script one-liners for restoring legacy score model behaviour
Jim Procter [Wed, 16 Aug 2017 18:16:08 +0000 (19:16 +0100)]
JAL-2418 check groovy script one-liners for restoring legacy score model behaviour

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 16:15:25 +0000 (17:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 fix typo in build.xml for j2se element
Jim Procter [Tue, 15 Aug 2017 16:14:32 +0000 (17:14 +0100)]
JAL-2116 fix typo in build.xml for j2se element

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 15:55:22 +0000 (16:55 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 15 Aug 2017 15:55:06 +0000 (16:55 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 bump release to Thursday
Jim Procter [Tue, 15 Aug 2017 14:02:19 +0000 (15:02 +0100)]
JAL-2418 bump release to Thursday

7 years agoMerge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Tue, 15 Aug 2017 13:54:20 +0000 (14:54 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 16:25:16 +0000 (17:25 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2418 release notes for JAL-2663
Jim Procter [Mon, 14 Aug 2017 16:23:46 +0000 (17:23 +0100)]
JAL-2418 release notes for JAL-2663

7 years agoMerge branch 'patch/JAL-2335_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 16:21:45 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2335_filterAACons' into develop

7 years agoMerge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 16:21:16 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop

7 years agoJAL-2116 add 1.8 1.7 compatible launch string
Jim Procter [Mon, 14 Aug 2017 16:20:28 +0000 (17:20 +0100)]
JAL-2116 add 1.8 1.7 compatible launch string

7 years agoJAL-2335 choose appropriate alphabet for filtering nonstandard symbols
Jim Procter [Mon, 14 Aug 2017 13:17:35 +0000 (14:17 +0100)]
JAL-2335 choose appropriate alphabet for filtering nonstandard symbols

7 years agoJAL-2335 source formatting
Jim Procter [Mon, 14 Aug 2017 13:16:27 +0000 (14:16 +0100)]
JAL-2335 source formatting

7 years agoJAL-2335 filterNonStandardResidues configurable for jabaws clients
Jim Procter [Mon, 14 Aug 2017 13:16:17 +0000 (14:16 +0100)]
JAL-2335 filterNonStandardResidues configurable for jabaws clients

7 years agoMerge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 09:45:14 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop

7 years agoMerge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:45:05 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 switch to java.se.ee https://bugs.openjdk.java.net/browse/JDK-8166438
Jim Procter [Mon, 14 Aug 2017 09:44:25 +0000 (10:44 +0100)]
JAL-2116 switch to java.se.ee https://bugs.openjdk.java.net/browse/JDK-8166438

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:35:00 +0000 (10:35 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'patch/JAL-2663_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 09:34:44 +0000 (10:34 +0100)]
Merge branch 'patch/JAL-2663_filterAACons' into develop

7 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Mon, 14 Aug 2017 09:33:33 +0000 (10:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

7 years agoJAL-2663 flag and filter to exclude non-standard amino acids from submission
Jim Procter [Sun, 13 Aug 2017 14:34:58 +0000 (15:34 +0100)]
JAL-2663 flag and filter to exclude non-standard amino acids from submission

7 years agoJAL-2663 source formatting
Jim Procter [Sun, 13 Aug 2017 14:34:20 +0000 (15:34 +0100)]
JAL-2663 source formatting

7 years agoMerge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 20:11:21 +0000 (21:11 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 try '=' syntax http://jigsaw-dev.1059479.n5.nabble.com/Java-9-EA-169-Webstar...
Jim Procter [Thu, 10 Aug 2017 20:10:23 +0000 (21:10 +0100)]
JAL-2116 try '=' syntax jigsaw-dev.1059479.n5.nabble.com/Java-9-EA-169-Webstart-NoClassDefFoundError-javax-xml-ws-Service-td5716769.html

7 years agoMerge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 19:42:30 +0000 (20:42 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 test java 9 only JNLP launch
Jim Procter [Thu, 10 Aug 2017 19:38:36 +0000 (20:38 +0100)]
JAL-2116 test java 9 only JNLP launch

7 years agoMerge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 15:38:21 +0000 (16:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 explicit replace j2se element with a java9 specific one since orangevolt...
Jim Procter [Thu, 10 Aug 2017 15:37:30 +0000 (16:37 +0100)]
JAL-2116 explicit replace j2se element with a java9 specific one since orangevolt-tasks don't support the java-vm-args attribute

7 years agoMerge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 14:38:30 +0000 (15:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch

7 years agoJAL-2116 java9 modules dependency for JNLP file
Jim Procter [Thu, 10 Aug 2017 14:37:16 +0000 (15:37 +0100)]
JAL-2116 java9 modules dependency for JNLP file

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 10 Aug 2017 11:56:12 +0000 (12:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

7 years agoJAL-2660 used saved value of ignoreGapsInConsensus when loading
gmungoc [Thu, 10 Aug 2017 11:29:52 +0000 (12:29 +0100)]
JAL-2660 used saved value of ignoreGapsInConsensus when loading
(/copying) viewport

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 09:31:54 +0000 (10:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Thu, 10 Aug 2017 09:31:39 +0000 (10:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 set final release date to 15th August 2017 for 2.10.2

Jim Procter [Thu, 10 Aug 2017 09:31:23 +0000 (10:31 +0100)]
JAL-2418 set final release date to 15th August 2017 for 2.10.2


Signed-off-by: Jim Procter <jprocter@issues.jalview.org>

7 years agoJAL-2418 typo in release notes
Jim Procter [Thu, 10 Aug 2017 09:30:00 +0000 (10:30 +0100)]
JAL-2418 typo in release notes

7 years agoJAL-2418 known defect for JAL-2321 in release notes
Jim Procter [Thu, 10 Aug 2017 09:29:53 +0000 (10:29 +0100)]
JAL-2418 known defect for JAL-2321 in release notes

7 years agoJAL-2418 reorganised release notes to topic sections rather than General/Application...
Jim Procter [Thu, 10 Aug 2017 09:19:29 +0000 (10:19 +0100)]
JAL-2418 reorganised release notes to topic sections rather than General/Application/Applet

7 years agoMerge branch 'documentation/JAL-2418_release2102' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 9 Aug 2017 20:40:35 +0000 (21:40 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 9 Aug 2017 20:40:25 +0000 (21:40 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 JAL-2398 JAL-2397 simpler documentation for reinstating legacy behaviour
Jim Procter [Wed, 9 Aug 2017 20:40:05 +0000 (21:40 +0100)]
JAL-2418 JAL-2398 JAL-2397 simpler documentation for reinstating legacy behaviour

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 9 Aug 2017 20:15:55 +0000 (21:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 9 Aug 2017 20:15:27 +0000 (21:15 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2397 JAL-2398 documentation for reinstating legacy PCA calculation with asymmetri...
Jim Procter [Wed, 9 Aug 2017 20:14:58 +0000 (21:14 +0100)]
JAL-2397 JAL-2398 documentation for reinstating legacy PCA calculation with asymmetric Blosum62 matrix.

7 years agoJAL-2426 Rfam download suffix
Jim Procter [Wed, 9 Aug 2017 19:24:00 +0000 (20:24 +0100)]
JAL-2426 Rfam download suffix

7 years agoJAL-2426 JAL-1270 report Xfam download URL used if debug enabled
Jim Procter [Wed, 9 Aug 2017 18:32:05 +0000 (19:32 +0100)]
JAL-2426 JAL-1270 report Xfam download URL used if debug enabled

7 years agoJAL-2425 raw stockholm download URLs
Jim Procter [Wed, 9 Aug 2017 18:31:29 +0000 (19:31 +0100)]
JAL-2425 raw stockholm download URLs

7 years agoJAL-1270 testProps should also enable debug logging
Jim Procter [Wed, 9 Aug 2017 18:29:54 +0000 (19:29 +0100)]
JAL-1270 testProps should also enable debug logging

7 years agoJAL-2425 test for alignment metadata retrieved from Pfam and Rfam
Jim Procter [Wed, 9 Aug 2017 18:29:05 +0000 (19:29 +0100)]
JAL-2425 test for alignment metadata retrieved from Pfam and Rfam

7 years agoJAL-2425 remove overloaded getSequenceRecords method (don’t need it ?)
Jim Procter [Wed, 9 Aug 2017 18:27:53 +0000 (19:27 +0100)]
JAL-2425 remove overloaded getSequenceRecords method (don’t need it ?)

7 years agoJAL-2418 release notes
Jim Procter [Wed, 9 Aug 2017 15:44:02 +0000 (16:44 +0100)]
JAL-2418 release notes

7 years agoJAL-2418 more release notes
Jim Procter [Wed, 9 Aug 2017 08:46:08 +0000 (09:46 +0100)]
JAL-2418 more release notes

7 years agoJAL-2418 JAL-2611 and rejigged overview documentation
Jim Procter [Wed, 9 Aug 2017 08:45:50 +0000 (09:45 +0100)]
JAL-2418 JAL-2611 and rejigged overview documentation

7 years agoMerge branch 'bug/JAL-2634' into develop
Jim Procter [Wed, 9 Aug 2017 08:09:56 +0000 (09:09 +0100)]
Merge branch 'bug/JAL-2634' into develop

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 9 Aug 2017 07:56:01 +0000 (08:56 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2560 alternative fix (reinstate lost line of code)
gmungoc [Tue, 8 Aug 2017 15:44:45 +0000 (16:44 +0100)]
JAL-2560 alternative fix (reinstate lost line of code)

7 years agoJAL-2649 JAL-2650 wait for Conservation calc to complete before setting
gmungoc [Tue, 8 Aug 2017 10:18:12 +0000 (11:18 +0100)]
JAL-2649 JAL-2650 wait for Conservation calc to complete before setting
on new View coloured by Conservation

7 years agoJAL-2650 configure new viewport settings before selecting view tab
gmungoc [Tue, 8 Aug 2017 09:08:46 +0000 (11:08 +0200)]
JAL-2650 configure new viewport settings before selecting view tab

7 years agoMerge branch 'bug/JAL-2592userDefinedScheme' into develop
Jim Procter [Mon, 7 Aug 2017 14:33:47 +0000 (15:33 +0100)]
Merge branch 'bug/JAL-2592userDefinedScheme' into develop

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 7 Aug 2017 13:31:35 +0000 (14:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 7 Aug 2017 13:31:13 +0000 (14:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 JAL-2468 known issue
Jim Procter [Mon, 7 Aug 2017 11:24:05 +0000 (12:24 +0100)]
JAL-2418 JAL-2468 known issue

7 years agoJAL-2482 JAL-2487 documented in release notes
Jim Procter [Mon, 7 Aug 2017 11:07:45 +0000 (12:07 +0100)]
JAL-2482 JAL-2487 documented in release notes

7 years agoJAL-2482 release notes
Jim Procter [Mon, 7 Aug 2017 11:04:48 +0000 (12:04 +0100)]
JAL-2482 release notes