Jim Procter [Tue, 11 Sep 2018 15:06:03 +0000 (16:06 +0100)]
JAL-3112 increased TEST_TIMEOUT to 9000ms - needed after inclusion discovered class path entries
Jim Procter [Tue, 11 Sep 2018 15:05:02 +0000 (16:05 +0100)]
JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview
gmungoc [Tue, 11 Sep 2018 14:04:29 +0000 (15:04 +0100)]
JAL-3048 recoded edit View Name dialog for JalviewJS
Jim Procter [Tue, 11 Sep 2018 13:05:00 +0000 (14:05 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
Jim Procter [Tue, 11 Sep 2018 13:03:50 +0000 (14:03 +0100)]
JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)
Jim Procter [Tue, 11 Sep 2018 12:56:41 +0000 (13:56 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
gmungoc [Tue, 11 Sep 2018 12:41:43 +0000 (13:41 +0100)]
JAL-3056 offer New / Expand / Gather View in JalviewJS
Jim Procter [Tue, 11 Sep 2018 12:31:09 +0000 (13:31 +0100)]
Merge branch 'releases/Release_2_11_Branch' into merge/JAL-3091_develop_211
Jim Procter [Tue, 11 Sep 2018 12:29:37 +0000 (13:29 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch
JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge
Jim Procter [Sun, 9 Sep 2018 13:14:52 +0000 (14:14 +0100)]
JAL-3091 changed release date to 10th September - tweaked release notes.
Jim Procter [Sun, 9 Sep 2018 13:04:28 +0000 (14:04 +0100)]
JAL-3106 normalise extension before checking if it is '.jar' when constructing fileformat/extension name index
Jim Procter [Fri, 7 Sep 2018 14:05:27 +0000 (15:05 +0100)]
JAL-3107 update any group associated annotation rows when a new group is created
Jim Procter [Fri, 7 Sep 2018 13:51:13 +0000 (14:51 +0100)]
JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar
Jim Procter [Fri, 7 Sep 2018 13:24:20 +0000 (14:24 +0100)]
JAL-2988 if selected file is null (On Java 10/OSX - happens if user has entered text after selecting a file), try and get the filename from the UI. If no file can be gotten, cancel the save operation
Jim Procter [Fri, 7 Sep 2018 13:23:16 +0000 (14:23 +0100)]
JAL-2988 workaround: overload getSelectedFile() because calling setSelectedFile(..) results in getSelectedFile()==null on OSX/Java 10/VAqua4/5.
Jim Procter [Fri, 7 Sep 2018 13:19:28 +0000 (14:19 +0100)]
JAL-3106 use .jvp as default
Jim Procter [Fri, 7 Sep 2018 11:24:10 +0000 (12:24 +0100)]
JAL-3105 fix for focus transfer after window closed on OSX
Jim Procter [Thu, 6 Sep 2018 19:51:47 +0000 (20:51 +0100)]
JAL-3091 code committed in error (failed patch for JAL-2854)
Jim Procter [Thu, 6 Sep 2018 19:41:29 +0000 (20:41 +0100)]
JAL-3091 release notes for JAL-3104
Jim Procter [Thu, 6 Sep 2018 19:37:06 +0000 (20:37 +0100)]
JAL-3105 reallocate quality and consensus annotation rows so old values aren’t rendered when alignments become shorter
Jim Procter [Thu, 6 Sep 2018 19:33:43 +0000 (20:33 +0100)]
JAL-2854 compute visible annotation panel height and provide it directly to via Scrollable interface
Jim Procter [Wed, 5 Sep 2018 17:12:14 +0000 (18:12 +0100)]
JAL-3065 don’t quote class path args for Runtime.exec java launch command (needs to be ported to 2.11)
Jim Procter [Wed, 5 Sep 2018 16:58:24 +0000 (17:58 +0100)]
JAL-3091 update whats new!
Jim Procter [Wed, 5 Sep 2018 14:14:08 +0000 (15:14 +0100)]
JAL-3091 update Java 10 known issues/workarounds in whats new
Jim Procter [Wed, 5 Sep 2018 13:59:24 +0000 (14:59 +0100)]
JAL-3091 known defect in whats new for Java 10 issues: JAL-3103 JAL-3102
Jim Procter [Wed, 5 Sep 2018 13:34:25 +0000 (14:34 +0100)]
JAL-3091 add Ben Soares to authors list and switch ordering of Toch and Kira (since Kira left after Toch).
Jim Procter [Wed, 5 Sep 2018 13:28:50 +0000 (14:28 +0100)]
JAL-3091 release notes for updated memory settings
Jim Procter [Wed, 5 Sep 2018 12:59:51 +0000 (13:59 +0100)]
JAL-3091 release notes
Jim Procter [Wed, 5 Sep 2018 12:57:15 +0000 (13:57 +0100)]
JAL-3101 increase default heap size in IA and JNLP generation, and generate a jalview_256MB.jnlp file for backwards compatibility
Jim Procter [Wed, 5 Sep 2018 10:06:54 +0000 (11:06 +0100)]
Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
Jim Procter [Wed, 5 Sep 2018 10:06:00 +0000 (11:06 +0100)]
JAL-2988 update InstallAnywhere install dependencies for VAqua5
Jim Procter [Wed, 5 Sep 2018 09:42:11 +0000 (10:42 +0100)]
Merge branch 'bug/JAL-3076ensemblGeneId' into develop
Jim Procter [Wed, 5 Sep 2018 08:04:19 +0000 (09:04 +0100)]
JAL-3091 release date set for Thursday 6th September
Jim Procter [Wed, 5 Sep 2018 08:03:37 +0000 (09:03 +0100)]
Merge branch 'bug/JAL-3065_DH_keyPair_Exception_nogroovysettings' into releases/Release_2_10_5_Branch
Jim Procter [Wed, 5 Sep 2018 08:01:50 +0000 (09:01 +0100)]
JAL-3065 - amended commit
4906697ab6e5a79fbce3baae89f7f64178c9a739 to exclude .settings/..groovy
Added notes to the instructions, also adjusted the jalviewDesktopRunner
test to lookup OS and use ';' or ':' accordingly.
All the CommandLineOperations tests failed on my (hastily set up) linux
box, so I'm committing and will test on MacOS too.
Jim Procter [Tue, 4 Sep 2018 12:02:44 +0000 (13:02 +0100)]
JAL-3091 JAL-2988 release notes re Java 10 and OSX
Jim Procter [Mon, 3 Sep 2018 18:58:18 +0000 (19:58 +0100)]
Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 18:48:42 +0000 (19:48 +0100)]
Merge branch 'releases/Release_2_10_5_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 15:45:51 +0000 (16:45 +0100)]
JAL-3091 -Dnosign to disable jar signing phase of build
Jim Procter [Mon, 3 Sep 2018 15:45:51 +0000 (16:45 +0100)]
JAL-3091 -Dnosign to disable jar signing phase of build
Jim Procter [Mon, 3 Sep 2018 15:45:23 +0000 (16:45 +0100)]
JAL-3091 release notes and whats new !
gmungoc [Mon, 3 Sep 2018 14:04:14 +0000 (15:04 +0100)]
Merge branch 'trialMerge' into releases/Release_2_10_5_Branch
gmungoc [Fri, 10 Aug 2018 09:59:42 +0000 (10:59 +0100)]
JAL-3076 fetch Ensembl sequence as JSON instead of Fasta
Conflicts:
src/jalview/ext/ensembl/EnsemblInfo.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
gmungoc [Mon, 3 Sep 2018 13:42:17 +0000 (14:42 +0100)]
JAL-3079 drop use of clip region while drawing wrapped alignment
Jim Procter [Mon, 3 Sep 2018 13:26:54 +0000 (14:26 +0100)]
JAL-3065 release notes
Jim Procter [Mon, 3 Sep 2018 13:22:58 +0000 (14:22 +0100)]
Merge branch 'bug/JAL-3065_DH_keyPair_Exception' into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 13:03:54 +0000 (14:03 +0100)]
JAL-3076 clarify javadoc handling single sequence response for Ensembl REST sequence_id endpoint
Jim Procter [Mon, 3 Sep 2018 12:33:35 +0000 (13:33 +0100)]
JAL-3087 release notes
Jim Procter [Fri, 31 Aug 2018 15:08:32 +0000 (16:08 +0100)]
JAL-3095 account for sequence start when highlighting selections in trimmed VARNA model
Jim Procter [Fri, 31 Aug 2018 15:03:42 +0000 (16:03 +0100)]
JAL-3053 JAL-3061 JAL-3095 release notes
Jim Procter [Fri, 31 Aug 2018 14:04:32 +0000 (15:04 +0100)]
Merge branch 'bug/JAL-3061_RNA_secondary_structure_annotation_gap_character' into releases/Release_2_10_5_Branch
Jim Procter [Fri, 31 Aug 2018 11:12:46 +0000 (12:12 +0100)]
Merge branch 'releases/Release_2_10_5_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_5_Branch
Jim Procter [Fri, 31 Aug 2018 11:12:20 +0000 (12:12 +0100)]
JAL-3095 release notes
Jim Procter [Fri, 31 Aug 2018 11:10:26 +0000 (12:10 +0100)]
java doc and fix for JAL-3095 - region of trimmed RNA model to highlight is indexed relative to SeuqenceI.getStart()
gmungoc [Fri, 31 Aug 2018 10:49:00 +0000 (11:49 +0100)]
JAL-3003 remove redundant call to drawSelectionGroup
gmungoc [Fri, 31 Aug 2018 08:49:55 +0000 (09:49 +0100)]
Merge branch 'bug/JAL-3003epsWithSelection' into trialMerge
Conflicts:
src/jalview/gui/SeqCanvas.java
Jim Procter [Thu, 30 Aug 2018 15:34:58 +0000 (16:34 +0100)]
JAL-3092 release notes
Jim Procter [Thu, 30 Aug 2018 15:31:37 +0000 (16:31 +0100)]
JAL-3092 make sure base pair counter is always moved in loop that computes the helix count for a strand of RNA secondary structure
gmungoc [Thu, 30 Aug 2018 15:30:32 +0000 (16:30 +0100)]
Merge branch 'bug/JAL-247pngShowHiddenSeqMarks' into trialMerge
gmungoc [Thu, 30 Aug 2018 15:28:01 +0000 (16:28 +0100)]
JAL-3055 refinements to alternatives to deriveFont
gmungoc [Thu, 30 Aug 2018 15:27:33 +0000 (16:27 +0100)]
JAL-3079 don't create new Graphics to draw as it confuses PDFGraphics
Jim Procter [Wed, 29 Aug 2018 09:17:25 +0000 (10:17 +0100)]
JAL-3091 release notes for JAL-3003 JAL-3059
Jim Procter [Tue, 28 Aug 2018 16:11:48 +0000 (17:11 +0100)]
JAL-3003 different coloured borders in demo annotation file
gmungoc [Thu, 23 Aug 2018 12:28:52 +0000 (13:28 +0100)]
JAL-3059 use correct border colour for groups
gmungoc [Thu, 23 Aug 2018 12:27:10 +0000 (13:27 +0100)]
JAL-3003 draw selection group outline on main graphics context
gmungoc [Tue, 28 Aug 2018 15:55:58 +0000 (16:55 +0100)]
JAL-3055 corrected logo drawing in JS
Jim Procter [Tue, 28 Aug 2018 15:28:38 +0000 (16:28 +0100)]
JAL-247 release notes
gmungoc [Mon, 27 Aug 2018 09:19:28 +0000 (10:19 +0100)]
JAL-247 comment to clarify wrapped print algorithm
gmungoc [Fri, 24 Aug 2018 15:16:08 +0000 (16:16 +0100)]
JAL-247 print/export wrapped uses common code to draw seq ids and
annotation labels
gmungoc [Fri, 24 Aug 2018 14:32:44 +0000 (15:32 +0100)]
JAL-3087 include full alignment height in repeating wrapped height
gmungoc [Fri, 24 Aug 2018 09:06:41 +0000 (10:06 +0100)]
JAL-247 draw/print sequence ids now uses common code (unwrapped case)
Jim Procter [Tue, 28 Aug 2018 15:16:56 +0000 (16:16 +0100)]
JAL-3091 release 2.10.5 added to release notes
gmungoc [Tue, 28 Aug 2018 11:32:01 +0000 (12:32 +0100)]
JAL-3055 corrections to use of AffineTransform to scale characters
hansonr [Tue, 28 Aug 2018 03:43:18 +0000 (22:43 -0500)]
Button/mouse tests
hansonr [Tue, 28 Aug 2018 03:35:35 +0000 (22:35 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 28 Aug 2018 03:34:40 +0000 (22:34 -0500)]
JAL-3026 mouse event overhaul; Jmol working (some "black label" issue?
pull, build-site
hansonr [Mon, 27 Aug 2018 16:09:53 +0000 (11:09 -0500)]
JAL-3026 alignmentFrame.statusBar.setText -> .setStatus
Ben Soares [Mon, 27 Aug 2018 15:50:20 +0000 (16:50 +0100)]
JAL-3061 / JAL-3053
Fixed broken StockholmFileTest tests
curlyWUSSsecondaryStructureForRNASequence
fullWUSSsecondaryStructureForRNASequence
by adding " ." as a recognised Annotation.isWhiteSpace displayCharacter
(which happens for StockholmFile '.' RNA SS annotations)
gmungoc [Mon, 27 Aug 2018 14:30:25 +0000 (15:30 +0100)]
JAL-3055 restore original deriveFont code for Java runtime
hansonr [Mon, 27 Aug 2018 13:39:36 +0000 (08:39 -0500)]
Bob's site directory JAL-3026
gmungoc [Mon, 27 Aug 2018 09:19:28 +0000 (10:19 +0100)]
JAL-247 comment to clarify wrapped print algorithm
hansonr [Mon, 27 Aug 2018 08:36:29 +0000 (03:36 -0500)]
JAL-3026 Jmol functioning; some issues
Reworked mouse event handling. Temporarily lost out-of-frame business.
Or, more specifically, hovering over the scroll bar to auto-scroll.
gmungoc [Fri, 24 Aug 2018 15:16:08 +0000 (16:16 +0100)]
JAL-247 print/export wrapped uses common code to draw seq ids and
annotation labels
gmungoc [Fri, 24 Aug 2018 14:32:44 +0000 (15:32 +0100)]
JAL-3087 include full alignment height in repeating wrapped height
gmungoc [Fri, 24 Aug 2018 09:06:41 +0000 (10:06 +0100)]
JAL-247 draw/print sequence ids now uses common code (unwrapped case)
hansonr [Fri, 24 Aug 2018 07:35:44 +0000 (02:35 -0500)]
JAL-3026 Java bug associated with File/String mods
in AlignFrame lines 4586,4592
hansonr [Fri, 24 Aug 2018 07:26:06 +0000 (02:26 -0500)]
JAL-3026 GD#107,128,130,139 build-site.xml
JInternalFrame z-order issues resolved
EBIFeching via server proxy as no access-control-origin:*
Temp file creation by File.createTempFile
Jmol app fixes for virtual key issues and starting to display now. Still
not dynamic, though. (No mouse action)
URL downloads now allow checking of status code (actually a hack, just
200 or 404, but we can get access to the real code.
gmungoc [Thu, 23 Aug 2018 12:28:52 +0000 (13:28 +0100)]
JAL-3059 use correct border colour for groups
gmungoc [Thu, 23 Aug 2018 12:27:10 +0000 (13:27 +0100)]
JAL-3003 draw selection group outline on main graphics context
hansonr [Wed, 22 Aug 2018 16:32:03 +0000 (11:32 -0500)]
JAL-3026 GD#127 frame selection/toFront
Jim Procter [Wed, 22 Aug 2018 13:54:29 +0000 (14:54 +0100)]
JAL-2988 workaround for jalview save as dialogs - clear filename before displaying
Jim Procter [Wed, 22 Aug 2018 13:53:11 +0000 (14:53 +0100)]
JAL-2988 JAL-2976 update to latest VAqua release: VAqua5
hansonr [Wed, 22 Aug 2018 10:49:20 +0000 (05:49 -0500)]
JAL-3026 JavaScript tests moved to utils/test
gmungoc [Wed, 22 Aug 2018 10:31:04 +0000 (11:31 +0100)]
JAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration
hansonr [Tue, 21 Aug 2018 19:30:23 +0000 (14:30 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 21 Aug 2018 18:36:43 +0000 (13:36 -0500)]
JAL-3026 GD #118 tooltip not showing for components.
hansonr [Tue, 21 Aug 2018 18:36:43 +0000 (13:36 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 21 Aug 2018 18:30:37 +0000 (13:30 -0500)]
JAL-3026 Boolean upgrade to Java 8
hansonr [Tue, 21 Aug 2018 18:30:37 +0000 (13:30 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of
https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
Conflicts:
swingjs/SwingJS-site.zip
swingjs/timestamp
swingjs/ver/3.2.2/SwingJS-site.zip
swingjs/ver/3.2.2/timestamp
hansonr [Tue, 21 Aug 2018 18:21:16 +0000 (13:21 -0500)]
JAL-3026 GD#137 Boolean upgrade requires build-site.xml only
git://source.jalview.org / jalview.git / log