Jim Procter [Mon, 14 Aug 2017 13:17:35 +0000 (14:17 +0100)]
JAL-2335 choose appropriate alphabet for filtering nonstandard symbols
Jim Procter [Mon, 14 Aug 2017 13:16:27 +0000 (14:16 +0100)]
JAL-2335 source formatting
Jim Procter [Mon, 14 Aug 2017 13:16:17 +0000 (14:16 +0100)]
JAL-2335 filterNonStandardResidues configurable for jabaws clients
TZVanaalten [Mon, 14 Aug 2017 10:43:46 +0000 (11:43 +0100)]
JAL-2629 remove redundant options from HMMER menu
TZVanaalten [Mon, 14 Aug 2017 10:43:21 +0000 (11:43 +0100)]
JAL-2629 add validation for HMMER path
TZVanaalten [Mon, 14 Aug 2017 10:41:04 +0000 (11:41 +0100)]
JAL-2629 fix incorrect gap insertions on HMM sequence
Jim Procter [Mon, 14 Aug 2017 09:45:14 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
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
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
Jim Procter [Mon, 14 Aug 2017 09:35:00 +0000 (10:35 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:34:44 +0000 (10:34 +0100)]
Merge branch 'patch/JAL-2663_filterAACons' 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
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
Jim Procter [Sun, 13 Aug 2017 14:34:20 +0000 (15:34 +0100)]
JAL-2663 source formatting
TZVanaalten [Sun, 13 Aug 2017 11:38:13 +0000 (12:38 +0100)]
JAL-2629 fix issue where trim termini setting would not update
TZVanaalten [Sun, 13 Aug 2017 11:00:40 +0000 (12:00 +0100)]
JAL-2629 hmmalign can now be run from the sequence pop-up menu
TZVanaalten [Sun, 13 Aug 2017 11:00:13 +0000 (12:00 +0100)]
JAL-2629 add force alphabet type for HMMER commands
TZVanaalten [Sun, 13 Aug 2017 10:58:35 +0000 (11:58 +0100)]
JAL-2629 fix issue where HMM sequences would be too long
TZVanaalten [Sun, 13 Aug 2017 10:55:28 +0000 (11:55 +0100)]
JAL-2629 add HMMER tab in preferences menu
TZVanaalten [Fri, 11 Aug 2017 15:11:41 +0000 (16:11 +0100)]
JAL-2629 delete unnecessary buffer files for hmmer commands
TZVanaalten [Fri, 11 Aug 2017 15:09:39 +0000 (16:09 +0100)]
JAL-2629 add ability to build a HMM from a group
TZVanaalten [Fri, 11 Aug 2017 15:09:01 +0000 (16:09 +0100)]
JAL-2629 add ability to select HMMs
TZVanaalten [Fri, 11 Aug 2017 15:05:18 +0000 (16:05 +0100)]
JAL-2599 HMMs can now be dropped onto the desktop
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
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
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
Jim Procter [Thu, 10 Aug 2017 19:38:36 +0000 (20:38 +0100)]
JAL-2116 test java 9 only JNLP launch
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
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
TZVanaalten [Thu, 10 Aug 2017 15:24:22 +0000 (16:24 +0100)]
JAL-2629 hmmalign now correctly creates a new frame
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
Jim Procter [Thu, 10 Aug 2017 14:37:16 +0000 (15:37 +0100)]
JAL-2116 java9 modules dependency for JNLP file
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
gmungoc [Thu, 10 Aug 2017 11:29:52 +0000 (12:29 +0100)]
JAL-2660 used saved value of ignoreGapsInConsensus when loading
(/copying) viewport
tzvanaalten [Thu, 10 Aug 2017 10:15:57 +0000 (11:15 +0100)]
Merge branch 'features/hmmer' of https://source.jalview.org/git/jalview.git into features/hmmer
tzvanaalten [Thu, 10 Aug 2017 10:01:22 +0000 (11:01 +0100)]
JAL-2629 fix files permission issue on Mac
Jim Procter [Thu, 10 Aug 2017 09:31:54 +0000 (10:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 09:31:39 +0000 (10:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
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>
Jim Procter [Thu, 10 Aug 2017 09:30:00 +0000 (10:30 +0100)]
JAL-2418 typo 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
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
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
Jim Procter [Wed, 9 Aug 2017 20:40:25 +0000 (21:40 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
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
Jim Procter [Wed, 9 Aug 2017 20:15:55 +0000 (21:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 9 Aug 2017 20:15:27 +0000 (21:15 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
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.
Jim Procter [Wed, 9 Aug 2017 19:24:00 +0000 (20:24 +0100)]
JAL-2426 Rfam download suffix
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
Jim Procter [Wed, 9 Aug 2017 18:31:29 +0000 (19:31 +0100)]
JAL-2425 raw stockholm download URLs
Jim Procter [Wed, 9 Aug 2017 18:29:54 +0000 (19:29 +0100)]
JAL-1270 testProps should also enable debug logging
Jim Procter [Wed, 9 Aug 2017 18:29:05 +0000 (19:29 +0100)]
JAL-2425 test for alignment metadata retrieved from Pfam and Rfam
Jim Procter [Wed, 9 Aug 2017 18:27:53 +0000 (19:27 +0100)]
JAL-2425 remove overloaded getSequenceRecords method (don’t need it ?)
TZVanaalten [Wed, 9 Aug 2017 15:52:32 +0000 (16:52 +0100)]
JAL-2599 fix for issue where info annot would not display
tzvanaalten [Wed, 9 Aug 2017 15:51:10 +0000 (16:51 +0100)]
JAL-2599 fix for issue where info annot would not display
Jim Procter [Wed, 9 Aug 2017 15:44:02 +0000 (16:44 +0100)]
JAL-2418 release notes
TZVanaalten [Wed, 9 Aug 2017 15:42:50 +0000 (16:42 +0100)]
JAL-2599 add uniref 50 hmm example
TZVanaalten [Wed, 9 Aug 2017 15:19:45 +0000 (16:19 +0100)]
JAL-2629 buffers are now temporary files
TZVanaalten [Wed, 9 Aug 2017 11:01:05 +0000 (12:01 +0100)]
JAL-2629 removed unnecessary exception throws from Jalview main method
TZVanaalten [Wed, 9 Aug 2017 09:06:06 +0000 (10:06 +0100)]
JAL-2629 disable AAFrequencyTest compilation error
Jim Procter [Wed, 9 Aug 2017 08:46:08 +0000 (09:46 +0100)]
JAL-2418 more release notes
Jim Procter [Wed, 9 Aug 2017 08:45:50 +0000 (09:45 +0100)]
JAL-2418 JAL-2611 and rejigged overview documentation
Jim Procter [Wed, 9 Aug 2017 08:09:56 +0000 (09:09 +0100)]
Merge branch 'bug/JAL-2634' into develop
Jim Procter [Wed, 9 Aug 2017 07:56:01 +0000 (08:56 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
TZVanaalten [Tue, 8 Aug 2017 16:56:35 +0000 (17:56 +0100)]
JAL-2616 fix allowing clan sorting to work
TZVanaalten [Tue, 8 Aug 2017 16:55:56 +0000 (17:55 +0100)]
JAL-2599 fix for index issue on node lookup
TZVanaalten [Tue, 8 Aug 2017 16:55:12 +0000 (17:55 +0100)]
JAL-2629 add ability to select hmmer binaries folder
gmungoc [Tue, 8 Aug 2017 15:44:45 +0000 (16:44 +0100)]
JAL-2560 alternative fix (reinstate lost line of code)
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
gmungoc [Tue, 8 Aug 2017 09:08:46 +0000 (11:08 +0200)]
JAL-2650 configure new viewport settings before selecting view tab
TZVanaalten [Mon, 7 Aug 2017 15:33:39 +0000 (16:33 +0100)]
JAL-2629 fixed hmmalign failing due to differing sequence lengths
TZVanaalten [Mon, 7 Aug 2017 15:22:23 +0000 (16:22 +0100)]
JAL-2629 current hmmer commands are now executed in threads
Jim Procter [Mon, 7 Aug 2017 14:33:47 +0000 (15:33 +0100)]
Merge branch 'bug/JAL-2592userDefinedScheme' into develop
Jim Procter [Mon, 7 Aug 2017 13:31:35 +0000 (14:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 7 Aug 2017 13:31:13 +0000 (14:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 7 Aug 2017 11:24:05 +0000 (12:24 +0100)]
JAL-2418 JAL-2468 known issue
Jim Procter [Mon, 7 Aug 2017 11:07:45 +0000 (12:07 +0100)]
JAL-2482 JAL-2487 documented in release notes
Jim Procter [Mon, 7 Aug 2017 11:04:48 +0000 (12:04 +0100)]
JAL-2482 release notes
Jim Procter [Mon, 7 Aug 2017 10:56:46 +0000 (11:56 +0100)]
JAL-2418 release notes formatting
Jim Procter [Mon, 7 Aug 2017 10:56:01 +0000 (11:56 +0100)]
JAL-2418 release notes
Jim Procter [Mon, 7 Aug 2017 10:55:46 +0000 (11:55 +0100)]
JAL-2418 typo and formatting of search.html
Jim Procter [Mon, 7 Aug 2017 10:54:25 +0000 (11:54 +0100)]
JAL-1648 documentation of search history for Find command
Jim Procter [Mon, 7 Aug 2017 08:50:33 +0000 (09:50 +0100)]
JAL-2418 reformatting and scripting section in what’s new
Jim Procter [Mon, 7 Aug 2017 08:49:38 +0000 (09:49 +0100)]
JAL-2418 release notes
Jim Procter [Mon, 7 Aug 2017 08:49:10 +0000 (09:49 +0100)]
JAL-2418 formatting
Jim Procter [Mon, 7 Aug 2017 08:48:58 +0000 (09:48 +0100)]
JAL-1476 JAL-2418 insufficient columns for superposition docs/release notes
TZVanaalten [Fri, 4 Aug 2017 11:29:11 +0000 (12:29 +0100)]
JAL-2599 fixed information annotation buttons not working
TZVanaalten [Fri, 4 Aug 2017 11:19:51 +0000 (12:19 +0100)]
JAL-2629 hmmbuild now runs on alignments of different lengths
TZVanaalten [Fri, 4 Aug 2017 10:13:17 +0000 (11:13 +0100)]
JAL-2629 multiple HMMs can now be dropped onto an alignment
Jim Procter [Fri, 4 Aug 2017 12:40:20 +0000 (13:40 +0100)]
JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes
Jim Procter [Fri, 4 Aug 2017 10:28:36 +0000 (11:28 +0100)]
JAL-2418 new features in release notes JAL-1933 JAL-2375
Jim Procter [Fri, 4 Aug 2017 10:10:43 +0000 (11:10 +0100)]
JAL-2418 release notes
Jim Procter [Fri, 4 Aug 2017 10:10:09 +0000 (11:10 +0100)]
JAL-1551 JAL-2418 reformat releases.html to remove tabs
Jim Procter [Fri, 4 Aug 2017 08:13:06 +0000 (09:13 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 4 Aug 2017 08:12:44 +0000 (09:12 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Fri, 4 Aug 2017 08:12:35 +0000 (09:12 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
gmungoc [Thu, 3 Aug 2017 11:47:18 +0000 (13:47 +0200)]
JAL-2500 JAL-2365 lightGray changed to lightgray for backwards
compatibility!
JAL-1551 source formatting definition for eclipse
gmungoc [Thu, 3 Aug 2017 11:45:25 +0000 (13:45 +0200)]
JAL-2500 JAL-2365 lightGray changed to gray in example file for
backwards compatibility
Jim Procter [Thu, 3 Aug 2017 13:09:25 +0000 (14:09 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
git://source.jalview.org / jalview.git / log