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
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 09:44:25 +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 09:34:44 +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
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 19:38:36 +0000 (20:38 +0100)]
JAL-2116 test java 9 only JNLP launch
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
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
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 20:40:25 +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 20:15:27 +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 ?)
Jim Procter [Wed, 9 Aug 2017 15:44:02 +0000 (16:44 +0100)]
JAL-2418 release notes
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
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
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 13:31:13 +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
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 08:12:44 +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 13:09:10 +0000 (14:09 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Thu, 3 Aug 2017 13:07:51 +0000 (14:07 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Thu, 3 Aug 2017 13:05:30 +0000 (14:05 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 3 Aug 2017 13:05:14 +0000 (14:05 +0100)]
JAL-2418 what’s new - faster PCA, calculations UI and score model framework
Jim Procter [Thu, 3 Aug 2017 13:04:43 +0000 (14:04 +0100)]
JAL-2418 release notes
Jim Procter [Thu, 3 Aug 2017 12:59:31 +0000 (13:59 +0100)]
JAL-1551 updated source code formatting settings from gmungoc and README on how to compare between versions
gmungoc [Thu, 3 Aug 2017 12:13:00 +0000 (14:13 +0200)]
JAL-2500 JAL-2365 feature colour "gray" _not_ "lightgray" for backwards
compatibility!!
gmungoc [Thu, 3 Aug 2017 11:47:18 +0000 (13:47 +0200)]
JAL-2500 JAL-2365 lightGray changed to lightgray for backwards
compatibility!
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
gmungoc [Thu, 3 Aug 2017 11:18:03 +0000 (13:18 +0200)]
JAL-2435 test for 'mirror font' option visible (not enabled) (safer)
Jim Procter [Thu, 3 Aug 2017 10:33:46 +0000 (11:33 +0100)]
Merge branch 'bug/JAL-2591overviewupdate' into develop
Jim Procter [Wed, 2 Aug 2017 16:02:06 +0000 (17:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 2 Aug 2017 16:01:50 +0000 (17:01 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 2 Aug 2017 16:01:02 +0000 (17:01 +0100)]
Merge branch 'bug/JAL-2321_merged' into develop
Jim Procter [Wed, 2 Aug 2017 14:31:01 +0000 (15:31 +0100)]
Merge branch 'bug/JAL-2321' into bug/JAL-2321_merged
Jim Procter [Wed, 2 Aug 2017 14:28:12 +0000 (15:28 +0100)]
JAL-2418 release notes for JAL-2582
gmungoc [Wed, 2 Aug 2017 14:02:14 +0000 (16:02 +0200)]
JAL-2418 corrected link url for "overview" target
Jim Procter [Tue, 1 Aug 2017 16:12:05 +0000 (17:12 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 16:11:32 +0000 (17:11 +0100)]
JAL-2418 known defect for eggnog tree import (JAL-2590)
Jim Procter [Tue, 1 Aug 2017 15:42:52 +0000 (16:42 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 15:42:43 +0000 (16:42 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Tue, 1 Aug 2017 15:42:28 +0000 (16:42 +0100)]
Merge branch 'bug/JAL-2632' into develop
Jim Procter [Tue, 1 Aug 2017 15:39:23 +0000 (16:39 +0100)]
JAL-2418 documentation
Jim Procter [Tue, 1 Aug 2017 15:16:05 +0000 (16:16 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 15:15:46 +0000 (16:15 +0100)]
JAL-2631 JAL-2623 JAL-2624 JAL-2630 JAL-147 JAL-2034 release notes and signoff
Jim Procter [Tue, 1 Aug 2017 15:14:53 +0000 (16:14 +0100)]
JAL-2418 update 2.10.2 release date
gmungoc [Tue, 1 Aug 2017 10:08:34 +0000 (12:08 +0200)]
JAL-2611 reinstate missed merge - again!
gmungoc [Tue, 1 Aug 2017 09:55:35 +0000 (11:55 +0200)]
Merge branch 'feature/JAL-2611' into develop
gmungoc [Tue, 1 Aug 2017 09:39:24 +0000 (11:39 +0200)]
Merge branch 'bug/JAL-2630gradColourUpdateOverview' into develop
kiramt [Mon, 31 Jul 2017 10:01:55 +0000 (12:01 +0200)]
JAL-2634 Make overview box full height when alignment is wrapped
gmungoc [Mon, 31 Jul 2017 09:28:09 +0000 (11:28 +0200)]
JAL-2623 updated Overview/structure on input of threshold value
kiramt [Mon, 31 Jul 2017 09:23:04 +0000 (11:23 +0200)]
JAL-2634 Added null test for graphics in AnnotationPanel::fastPaint
gmungoc [Mon, 31 Jul 2017 09:20:15 +0000 (11:20 +0200)]
JAL-2622 don't vertical scroll wrapped alignment id panel from trackpad
gmungoc [Mon, 31 Jul 2017 08:36:34 +0000 (10:36 +0200)]
JAL-2631 test updated for added kd graduated feature colour
gmungoc [Mon, 31 Jul 2017 08:32:11 +0000 (10:32 +0200)]
JAL-2623 JAL-2015 set Below Threshold on FeatureColour when selected!
gmungoc [Mon, 31 Jul 2017 08:10:24 +0000 (10:10 +0200)]
JAL-2630 applet update overview on release of threshold slider
kiramt [Fri, 28 Jul 2017 15:35:32 +0000 (17:35 +0200)]
JAL-2632 Added paintAlignment(true) to show cols code
gmungoc [Fri, 28 Jul 2017 13:17:08 +0000 (15:17 +0200)]
JAL-147 corrected status bar message for wrapped scrolled right view
gmungoc [Fri, 28 Jul 2017 11:12:50 +0000 (13:12 +0200)]
JAL-2622 no vertical scroll of wrapped alignment from trackpad / mouse
button
gmungoc [Fri, 28 Jul 2017 10:06:39 +0000 (12:06 +0200)]
JAL-147 unit test for no vertical move of Overview box in wrapped mode
gmungoc [Fri, 28 Jul 2017 08:45:57 +0000 (10:45 +0200)]
JAL-2006 squash rounding errors at min/max threshold slider positions
git://source.jalview.org / jalview.git / log