hansonr [Mon, 1 Apr 2019 02:50:20 +0000 (21:50 -0500)]
embedded core-file demo for faster loading
hansonr [Mon, 1 Apr 2019 02:42:17 +0000 (21:42 -0500)]
Ajax enhancements
hansonr [Mon, 1 Apr 2019 02:41:49 +0000 (21:41 -0500)]
first demo of embedding components as simple divs with known ids
hansonr [Mon, 1 Apr 2019 02:41:20 +0000 (21:41 -0500)]
jsmol2.php?? must have been just for testing
hansonr [Mon, 1 Apr 2019 02:40:37 +0000 (21:40 -0500)]
JSON refactoring of a few methods; fixing JavaScript issues
hansonr [Mon, 1 Apr 2019 02:39:35 +0000 (21:39 -0500)]
jalview-pca-div added
hansonr [Mon, 1 Apr 2019 02:38:34 +0000 (21:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
Jim Procter [Sun, 31 Mar 2019 17:57:06 +0000 (18:57 +0100)]
JAL-3033 build.xml:build-site runs build-site.xml to populate site/ with prebuilt/deps
hansonr [Sun, 31 Mar 2019 17:21:52 +0000 (12:21 -0500)]
adds TreePanel name jalview-tree
hansonr [Sun, 31 Mar 2019 17:21:30 +0000 (12:21 -0500)]
adds StructureViewer name jalview-structureviewer
hansonr [Sun, 31 Mar 2019 17:20:31 +0000 (12:20 -0500)]
adds SplitFrame name jalview-splitframe;
hansonr [Sun, 31 Mar 2019 17:20:07 +0000 (12:20 -0500)]
adds RnaStructureViewer name jalview-rnastructureviewer;
hansonr [Sun, 31 Mar 2019 17:19:30 +0000 (12:19 -0500)]
adds Desktop name jalview-desktop;
hansonr [Sun, 31 Mar 2019 17:19:07 +0000 (12:19 -0500)]
adds AlignFrame name jalview-alignment;
hansonr [Sun, 31 Mar 2019 17:18:36 +0000 (12:18 -0500)]
clean up implicit object refs
hansonr [Sun, 31 Mar 2019 17:17:15 +0000 (12:17 -0500)]
Cache JS adds search of Info for jalview_xxx properties
hansonr [Sun, 31 Mar 2019 12:18:31 +0000 (07:18 -0500)]
#210 Ensembl fix; adds embedding test
was incorrect catch parameter in close() of swingjs/json/JSON.js
gmungoc [Fri, 29 Mar 2019 11:15:46 +0000 (11:15 +0000)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
gmungoc [Fri, 29 Mar 2019 11:15:31 +0000 (11:15 +0000)]
Merge branch 'develop' into Jalview-JS/develop
Conflicts:
.classpath
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
gmungoc [Fri, 29 Mar 2019 10:31:02 +0000 (10:31 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)
Jim Procter [Fri, 29 Mar 2019 09:54:49 +0000 (09:54 +0000)]
JAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete
hansonr [Thu, 28 Mar 2019 18:55:39 +0000 (14:55 -0400)]
#211 corrects swingjs.JSUtil.parseJSONRaw$S call
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:11 +0000 (17:34 +0000)]
JAL-3111 biojava dependencies
Jim Procter [Thu, 28 Mar 2019 17:20:31 +0000 (17:20 +0000)]
JAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere
Jim Procter [Thu, 28 Mar 2019 17:20:04 +0000 (17:20 +0000)]
JAL-3111 fix jabaws dependency name in IA config
Jim Procter [Thu, 28 Mar 2019 16:59:51 +0000 (16:59 +0000)]
JAL-3111 intervalstore library on IA classpath
gmungoc [Thu, 28 Mar 2019 16:13:39 +0000 (16:13 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Thu, 28 Mar 2019 15:55:08 +0000 (15:55 +0000)]
JAL-3111 typo in IA config
gmungoc [Thu, 28 Mar 2019 15:52:34 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 28 Mar 2019 15:52:23 +0000 (15:52 +0000)]
JAL-1889 patch for failing isControDown test on build server
Jim Procter [Thu, 28 Mar 2019 15:40:20 +0000 (15:40 +0000)]
JAL-3111 update InstallAnywhere dependencies for changed libraries
gmungoc [Thu, 28 Mar 2019 08:07:01 +0000 (08:07 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 28 Mar 2019 07:56:40 +0000 (07:56 +0000)]
Merge branch 'feature/JAL-3181linkOrdering' into develop
gmungoc [Wed, 27 Mar 2019 17:07:24 +0000 (17:07 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Wed, 27 Mar 2019 17:06:12 +0000 (17:06 +0000)]
JAL-2620 improved error reporting on failure to load resource files
gmungoc [Wed, 27 Mar 2019 16:29:29 +0000 (16:29 +0000)]
JAL-3032 small formatting and isJS() tidy
hansonr [Wed, 27 Mar 2019 12:30:50 +0000 (08:30 -0400)]
reinstating test data for JalviewJS
hansonr [Wed, 27 Mar 2019 11:33:59 +0000 (07:33 -0400)]
comment out of @j2sNative block
hansonr [Wed, 27 Mar 2019 11:00:52 +0000 (07:00 -0400)]
allows web-page embedding
hansonr [Wed, 27 Mar 2019 10:06:38 +0000 (06:06 -0400)]
consolidation of Platform isJS calls
hansonr [Wed, 27 Mar 2019 09:40:22 +0000 (05:40 -0400)]
isJS cleanup
hansonr [Wed, 27 Mar 2019 09:39:05 +0000 (05:39 -0400)]
clean-up of isJS business for (temporarily) noneditable JS JComboBox
hansonr [Wed, 27 Mar 2019 00:33:12 +0000 (20:33 -0400)]
Platform comment about isPopupTrigger
hansonr [Tue, 26 Mar 2019 11:18:14 +0000 (07:18 -0400)]
upgraded Platform.java
gmungoc [Mon, 25 Mar 2019 16:37:39 +0000 (16:37 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change
gmungoc [Sat, 23 Mar 2019 08:57:59 +0000 (08:57 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Sat, 23 Mar 2019 08:49:52 +0000 (08:49 +0000)]
JAL-1889 explicit recalc of geometry for scale left/right/above on/off
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server
gmungoc [Wed, 20 Mar 2019 15:19:48 +0000 (15:19 +0000)]
Merge branch 'develop' into Jalview-JS/develop
Conflicts:
src/jalview/gui/AlignFrame.java
src/jalview/gui/ScalePanel.java
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug
gmungoc [Wed, 20 Mar 2019 09:19:38 +0000 (09:19 +0000)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
gmungoc [Tue, 19 Mar 2019 15:40:21 +0000 (15:40 +0000)]
JAL-3210 code formatting only
Jim Procter [Tue, 19 Mar 2019 15:37:04 +0000 (15:37 +0000)]
JAL-3192 corefile after loading in exampleFile_2_7.jvp
gmungoc [Mon, 18 Mar 2019 15:11:33 +0000 (15:11 +0000)]
JAL-1551 reinstate formatting and save actions (with Java 1.8 additions)
gmungoc [Mon, 18 Mar 2019 14:31:11 +0000 (14:31 +0000)]
JAL-3141 JAL-3056 backups regime option suppressed in JalviewJS
gmungoc [Mon, 18 Mar 2019 10:39:10 +0000 (10:39 +0000)]
JAL-3210 JAL-3063 JAL-3035 remove Castor and Spring libraries
gmungoc [Mon, 18 Mar 2019 10:26:58 +0000 (10:26 +0000)]
JAL-3210 JAL-3140 intervalstore.jar in .classpath.js also
gmungoc [Sun, 17 Mar 2019 11:00:44 +0000 (11:00 +0000)]
JAL-3210 remove unnecessary (and malformed?) .classpath from .gitignore
gmungoc [Fri, 15 Mar 2019 15:55:31 +0000 (15:55 +0000)]
JAL-3210 ensure tooltips on FeatureSettings in JS
gmungoc [Fri, 15 Mar 2019 14:58:30 +0000 (14:58 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:18:19 +0000 (14:18 +0000)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences
gmungoc [Fri, 15 Mar 2019 09:08:01 +0000 (09:08 +0000)]
JAL-3071 corrections to IdPanel$ScrollThread
gmungoc [Fri, 15 Mar 2019 08:04:46 +0000 (08:04 +0000)]
JAL-2814 updated unit test for code change
gmungoc [Thu, 14 Mar 2019 13:05:33 +0000 (13:05 +0000)]
JAL-2814 JAL-3032 targeted help URL links for JalviewJS
gmungoc [Thu, 14 Mar 2019 12:40:43 +0000 (12:40 +0000)]
JAL-3056 open Help web page instead of internal (targeted) help link
gmungoc [Thu, 14 Mar 2019 10:51:01 +0000 (10:51 +0000)]
JAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS
gmungoc [Thu, 14 Mar 2019 10:05:07 +0000 (10:05 +0000)]
JAL-3210 relocate setMinimumSize so it works in JS
gmungoc [Thu, 14 Mar 2019 08:39:15 +0000 (08:39 +0000)]
JAL-3210 JAL-3140 intervalstore library added to JS as zip
gmungoc [Wed, 13 Mar 2019 15:54:42 +0000 (15:54 +0000)]
JAL-3210 merge conflict tidying
gmungoc [Wed, 13 Mar 2019 11:57:54 +0000 (11:57 +0000)]
JAL-1889 hack to ensure endRes is computed in setUp
gmungoc [Wed, 13 Mar 2019 10:50:39 +0000 (10:50 +0000)]
JAL-3141 fix up merge artefact so BackupFilesTest passes
gmungoc [Wed, 13 Mar 2019 09:26:03 +0000 (09:26 +0000)]
Merge branch 'develop' into trialMerge
Conflicts:
.classpath
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/api/AlignViewportI.java
src/jalview/fts/core/GFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqPanel.java
src/jalview/io/JalviewFileChooser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/io/CrossRef2xmlTests.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/ws/dbsources/UniprotTest.java
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport
gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge
gmungoc [Mon, 11 Mar 2019 15:07:39 +0000 (15:07 +0000)]
Merge branch 'develop' into merge/JAL-3127
Conflicts:
src/jalview/viewmodel/AlignmentViewport.java
gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project
gmungoc [Mon, 11 Mar 2019 11:37:58 +0000 (11:37 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
Conflicts:
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
test/jalview/io/Jalview2xmlTests.java
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file
git://source.jalview.org / jalview.git / log