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
hansonr [Tue, 21 Aug 2018 18:21:16 +0000 (13:21 -0500)]
JAL-3026 GD#137 Boolean upgrade requires build-site.xml only
hansonr [Tue, 21 Aug 2018 17:15:55 +0000 (12:15 -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 17:15:08 +0000 (12:15 -0500)]
JAL-3027 GD#140 checkbox/radio text alignment not coded in
JSRadioButtonUI - requires build-site.xml
gmungoc [Tue, 21 Aug 2018 13:59:50 +0000 (14:59 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Tue, 21 Aug 2018 13:59:38 +0000 (14:59 +0100)]
JAL-3032 MCview package renamed mc_view in test classes
hansonr [Tue, 21 Aug 2018 13:00:09 +0000 (08:00 -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 12:59:38 +0000 (07:59 -0500)]
JAL-3026 fixes Jmol going into debug mode
much faster PDB file processing if it doesn't print every line as it
goes!
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names
hansonr [Tue, 21 Aug 2018 12:14:33 +0000 (07:14 -0500)]
JAL-3026 fixes ?j2strace=xxx message, user.home, error msg in
ItentifiersUrlProvider
gmungoc [Tue, 21 Aug 2018 11:16:50 +0000 (12:16 +0100)]
JAL-3032 JAL-3084 test class for JS layout bug(s)
hansonr [Tue, 21 Aug 2018 05:00:16 +0000 (00:00 -0500)]
JAL-3026 JSONObject: removing annotation sensing
hansonr [Tue, 21 Aug 2018 04:33:09 +0000 (23:33 -0500)]
swingjs.JSSAXParser working for Jalview
hansonr [Tue, 21 Aug 2018 02:12:36 +0000 (21:12 -0500)]
JAL-3026 JmolData running; new run time and transpiler.
Run build-site.xml and possibly do a clean build.
hansonr [Tue, 21 Aug 2018 02:10:41 +0000 (21:10 -0500)]
mc_view references were MCview
hansonr [Tue, 21 Aug 2018 02:09:25 +0000 (21:09 -0500)]
JAL-3026 MCview -> mc_view
SwingJS requires standard package and class capitalization;
_ added to avoid PC capitalization issue
hansonr [Mon, 20 Aug 2018 15:24:19 +0000 (10:24 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 20 Aug 2018 15:23:49 +0000 (10:23 -0500)]
JAL-3026 j2sClazz.js fixes
// BH 8/20/2018 3.2.2.04 adds character.isJavaIdentifierPart$C and
several Character...$I equivalents
// BH 8/19/2018 3.2.2.04 fixes Enum .name being .$name
// BH 8/16/2018 3.2.2.04 fixes Character.toTitleCase$C,
[Integer,Long,Short,Byte].toString(i,radix)
gmungoc [Mon, 20 Aug 2018 12:52:46 +0000 (13:52 +0100)]
JAL-3032 Feature Settings menu item always enabled (restored)
gmungoc [Mon, 20 Aug 2018 10:52:01 +0000 (11:52 +0100)]
JAL-3032 variant of Sequence Details panel for JalviewJS
gmungoc [Mon, 20 Aug 2018 09:57:09 +0000 (10:57 +0100)]
JAL-3084 force EPS output to "Text" for JalviewJS
gmungoc [Mon, 20 Aug 2018 09:32:14 +0000 (10:32 +0100)]
JAL-3084 hide startup file, Chimera, HTML/SVG, Web Services options/tab
in JalviewJS
hansonr [Mon, 20 Aug 2018 05:39:18 +0000 (00:39 -0500)]
Adds org.json (along with "org.json.simple") for
jalview.io.JSONFile.java
hansonr [Mon, 20 Aug 2018 04:23:06 +0000 (23:23 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 20 Aug 2018 04:22:24 +0000 (23:22 -0500)]
fixes for anonymous classes; preliminary Jmol classes
Problem: anonymous classes that reference superclass finals may not
escape them properly with $. (drag-drop of PDB file)
Jmol classes into libjs, but not working yet, since we need to now
distinguish between JavaScript/AWT for application and JavaScript/noAWT
for standard JSmol applet
gmungoc [Fri, 17 Aug 2018 13:57:49 +0000 (14:57 +0100)]
JAL-3048 remove obsolete way of handling dialogs in JalviewJS
gmungoc [Fri, 17 Aug 2018 13:57:12 +0000 (14:57 +0100)]
JAL-3048 adapt 'input from URL' dialog for JalviewJS
gmungoc [Fri, 17 Aug 2018 10:38:33 +0000 (11:38 +0100)]
JAL-3038 unit test updates for JalviewJS workaround hack
gmungoc [Thu, 16 Aug 2018 14:07:35 +0000 (15:07 +0100)]
JAL-3038 workaround to replace editable combobox with text field in JS
hansonr [Thu, 16 Aug 2018 13:13:45 +0000 (08:13 -0500)]
JAL-3026 Character.toUpperCase
hansonr [Thu, 16 Aug 2018 12:55:30 +0000 (07:55 -0500)]
JAL-3026 SwingJS-site.zip fix
gmungoc [Thu, 16 Aug 2018 09:08:49 +0000 (10:08 +0100)]
Merge branch 'bug/JAL-3082selectRegex' into Jalview-BH/JAL-3026
git://source.jalview.org / jalview.git / log