hansonr [Tue, 20 Nov 2018 12:50:14 +0000 (06:50 -0600)]
untested new SwingJS-site.zip so that at least we all have the same one.
hansonr [Tue, 20 Nov 2018 05:00:58 +0000 (23:00 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Tue, 20 Nov 2018 05:00:12 +0000 (23:00 -0600)]
should fix issue with hover-activated scrollbar
gmungoc [Mon, 19 Nov 2018 15:14:34 +0000 (15:14 +0000)]
JAL-3032 J2S variant for painting JTable
gmungoc [Mon, 19 Nov 2018 15:13:19 +0000 (15:13 +0000)]
JAL-3032 reinstate methods now available in SwingJS
hansonr [Sun, 18 Nov 2018 06:57:30 +0000 (00:57 -0600)]
JAL-3026-JAL-3063 fix for JTable row/col dragging
hansonr [Sun, 18 Nov 2018 06:56:58 +0000 (00:56 -0600)]
adds JS hook for JTable repaint
hansonr [Sun, 18 Nov 2018 06:02:15 +0000 (00:02 -0600)]
BH - suggestion to turn off column dragging in Java (and JavaScript)
hansonr [Sun, 18 Nov 2018 05:21:31 +0000 (23:21 -0600)]
misc fixes
adds move cursor for JSplitPane
corrects EventDispatchThread miscoding
adds dummy frame consideration for SwingUtilities.SharedOwnerFrame
sets mouse click for multiple click from jqevent.originalEvent
adds JSplitPane drag cursor on mouse move
fixes JComboBox not being disabled
fixes early setCursor before peer is created
hansonr [Sun, 18 Nov 2018 00:37:39 +0000 (18:37 -0600)]
JAL-3026-JAL-3063 #98, #141
hansonr [Sat, 17 Nov 2018 21:00:38 +0000 (15:00 -0600)]
JAL-3026-JAL-3063 Menu font line spacing fix
hansonr [Sat, 17 Nov 2018 20:37:50 +0000 (14:37 -0600)]
JAL-3026-JAL-3063 menu fonts
hansonr [Sat, 17 Nov 2018 19:37:54 +0000 (13:37 -0600)]
SwingJS-site.zip for menus JAL-3026
hansonr [Sat, 17 Nov 2018 19:24:07 +0000 (13:24 -0600)]
JAL-3026-JAL-3063 menus dyanamic; better alignment
hansonr [Fri, 16 Nov 2018 09:16:37 +0000 (03:16 -0600)]
JAL-3026-JAL-3063 fix for panel layout failure
SwingJS-site.zip
gmungoc [Fri, 16 Nov 2018 08:04:54 +0000 (08:04 +0000)]
JAL-2069 wider dialog so all fields show!
hansonr [Fri, 16 Nov 2018 00:19:07 +0000 (18:19 -0600)]
fixing several GD# -- see green colors
hansonr [Thu, 15 Nov 2018 18:54:02 +0000 (12:54 -0600)]
Jmol/SwingJS-site update for handling communally cached files
gmungoc [Thu, 15 Nov 2018 14:04:08 +0000 (14:04 +0000)]
JAL-3063 remove commented code, suppress debug output
gmungoc [Thu, 15 Nov 2018 14:02:52 +0000 (14:02 +0000)]
JAL-2344 unit test updated for code change
gmungoc [Thu, 15 Nov 2018 13:59:34 +0000 (13:59 +0000)]
JAL-3032 JAL-2344 project files are 'identifiable'
hansonr [Thu, 15 Nov 2018 12:57:13 +0000 (06:57 -0600)]
JAL-3026-JAL-3063 aliases JSFrame/JSDialog as Frame/Dialog
hansonr [Thu, 15 Nov 2018 04:38:08 +0000 (22:38 -0600)]
JMenu selected/deselected events implemented
gmungoc [Wed, 14 Nov 2018 16:34:09 +0000 (16:34 +0000)]
JAL-3032 don't throw Exception to signal chain not found, return null
gmungoc [Wed, 14 Nov 2018 15:18:23 +0000 (15:18 +0000)]
JAL-3152 holding patch for colour Jmol by sequence
hansonr [Wed, 14 Nov 2018 13:50:08 +0000 (07:50 -0600)]
JAL-3026-JAL-3063 fixes title-bar overflow
hansonr [Tue, 13 Nov 2018 22:57:02 +0000 (16:57 -0600)]
new jmol-app.zip fixes unnecessary Exception calling in COLOR cmd
hansonr [Tue, 13 Nov 2018 20:32:41 +0000 (14:32 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Tue, 13 Nov 2018 20:32:21 +0000 (14:32 -0600)]
JAL-3026-JAL-3063 fixes tooltip persistence problem GD#148
gmungoc [Tue, 13 Nov 2018 19:08:32 +0000 (19:08 +0000)]
JAL-3026 add equals() to test
gmungoc [Tue, 13 Nov 2018 18:49:17 +0000 (18:49 +0000)]
JAL-3026 tweak to test class
gmungoc [Tue, 13 Nov 2018 17:52:42 +0000 (17:52 +0000)]
JAL-3026 test for File.hashCode problem
gmungoc [Tue, 13 Nov 2018 08:19:37 +0000 (08:19 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Mon, 12 Nov 2018 17:43:59 +0000 (17:43 +0000)]
JAL-3076 JalviewJS requires lower case content-type parameter in URL
hansonr [Mon, 12 Nov 2018 10:44:03 +0000 (04:44 -0600)]
0-length SwingJS-site
hansonr [Mon, 12 Nov 2018 00:54:43 +0000 (18:54 -0600)]
JAL-3026-JAL-3063 removes antialiasing
trying to make lines thinner, but this is not the way, apparently.
hansonr [Sun, 11 Nov 2018 23:42:21 +0000 (17:42 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Sun, 11 Nov 2018 20:36:41 +0000 (14:36 -0600)]
Fixes for JInternalFrame, JAXB, String
hansonr [Sun, 11 Nov 2018 20:36:41 +0000 (14:36 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Sun, 11 Nov 2018 20:35:27 +0000 (14:35 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
swingjs/SwingJS-site.zip
swingjs/timestamp
swingjs/ver/3.2.4/SwingJS-site.zip
swingjs/ver/3.2.4/timestamp
hansonr [Sun, 11 Nov 2018 20:35:27 +0000 (14:35 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
swingjs/SwingJS-site.zip
swingjs/timestamp
swingjs/ver/3.2.4/SwingJS-site.zip
swingjs/ver/3.2.4/timestamp
hansonr [Sun, 11 Nov 2018 20:13:15 +0000 (14:13 -0600)]
JAL-3026-JAL-3063 JTable and JSplitPane
JTable performance improved; still rendering twice?
JSplitPane implemented.
JFrame and JInternalFrame jumping fixed.
hansonr [Sun, 11 Nov 2018 20:13:15 +0000 (14:13 -0600)]
JAL-3026-JAL-3063 JTable and JSplitPane
JTable performance improved; still rendering twice?
JSplitPane implmented.
hansonr [Sun, 11 Nov 2018 15:47:17 +0000 (09:47 -0600)]
better JTable performance, 1/2
hansonr [Sun, 11 Nov 2018 10:26:45 +0000 (04:26 -0600)]
pivot table summary of @Xml*
hansonr [Sun, 11 Nov 2018 10:26:10 +0000 (04:26 -0600)]
adds explicit AJAX-allowed
hansonr [Sun, 11 Nov 2018 00:41:44 +0000 (18:41 -0600)]
JAL-3026-JAL-3063 transpiler and runtime update
Adds @XmlElements for UniProt and EMBL
Fixes missing border UIResource
Removes debugging messages in JTable and JAXB*
hansonr [Sun, 11 Nov 2018 00:37:07 +0000 (18:37 -0600)]
minor org.json JavaScript version update
hansonr [Sun, 11 Nov 2018 00:35:59 +0000 (18:35 -0600)]
adds static declaration of AJAX-readable domains
hansonr [Fri, 9 Nov 2018 02:52:37 +0000 (20:52 -0600)]
JAL-3026-JAL-3063 SwingJS-site.zip fix
- JTable null cell value,
- JAXB fix for xmlns in uniprot
hansonr [Thu, 8 Nov 2018 13:28:13 +0000 (07:28 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Thu, 8 Nov 2018 13:27:49 +0000 (13:27 +0000)]
JAL-3116 better unmarshalling of EMBL/Uniprot XML
hansonr [Thu, 8 Nov 2018 13:27:18 +0000 (07:27 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Thu, 8 Nov 2018 13:26:20 +0000 (07:26 -0600)]
removed jalview test code truncated ObjectFactory
gmungoc [Thu, 8 Nov 2018 11:04:20 +0000 (11:04 +0000)]
JAL-3048 use JalviewJS compatible JalviewFileChooser.showOpenDialog
gmungoc [Thu, 8 Nov 2018 11:00:00 +0000 (11:00 +0000)]
JAL-3048 override showOpenDialog with JalviewJS compatible code
hansonr [Wed, 7 Nov 2018 18:03:26 +0000 (12:03 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Wed, 7 Nov 2018 13:40:57 +0000 (07:40 -0600)]
JAL-3026-JAL-3063 JAXB unmarshaller fix
hansonr [Wed, 7 Nov 2018 13:40:57 +0000 (07:40 -0600)]
JAL-3026-JAL-3063 session test files
JS loads java50.jvx, but not java50b.jvx.
hansonr [Wed, 7 Nov 2018 04:23:56 +0000 (22:23 -0600)]
JAL-3026-JAL-3063-JAXB marshalling
JAXB marshalling/unmarshalling successful
JavaScript marshal -> Java unmarshal
JavaScript marshal -> JavaScript unmarshal
Java marshal -> JavaScript unmarshal
hansonr [Tue, 6 Nov 2018 01:38:12 +0000 (19:38 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
swingjs/SwingJS-site.zip
swingjs/timestamp
swingjs/ver/3.2.4/SwingJS-site.zip
swingjs/ver/3.2.4/timestamp
hansonr [Fri, 2 Nov 2018 06:50:46 +0000 (01:50 -0500)]
JAXB marshalling by JavaScript successfully unmarshalled in Java
JalviewJS session save JAXB; Jalview (Java app) drag drop.
hansonr [Fri, 2 Nov 2018 06:50:46 +0000 (01:50 -0500)]
Marshalling produces valid ZIP file. Unmarshalling hanging on getting a
system JAXBContextFactory -- simple enough to do, just haven't done it.
hansonr [Fri, 2 Nov 2018 01:39:39 +0000 (20:39 -0500)]
JAXB update site + transpiler
- ObjectFactory hack (does not actually use the methods)
- removal of jalviewBH
- new SwingJS-site and transpiler
hansonr [Thu, 1 Nov 2018 17:06:13 +0000 (12:06 -0500)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Thu, 1 Nov 2018 17:05:41 +0000 (12:05 -0500)]
SwingJS-site and net.sf.j2s.core.jar
Note that this does include a new transpiler.
gmungoc [Thu, 1 Nov 2018 14:31:16 +0000 (14:31 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
src/jalview/gui/FeatureTypeSettings.java
gmungoc [Thu, 1 Nov 2018 11:33:44 +0000 (11:33 +0000)]
JAXB default namespace from ObjectFactory
gmungoc [Thu, 1 Nov 2018 11:33:44 +0000 (11:33 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
swingjs/timestamp
gmungoc [Thu, 1 Nov 2018 11:32:20 +0000 (11:32 +0000)]
Merge branch 'feature/JAL-3144noJTree' into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
src/jalview/ext/ensembl/EnsemblRestClient.java
hansonr [Thu, 1 Nov 2018 11:21:32 +0000 (06:21 -0500)]
JAXB upgrade for package-info.java namespace
gmungoc [Thu, 1 Nov 2018 10:33:35 +0000 (10:33 +0000)]
Merge branch 'Jalview-BH/JAL-3026' into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/gui/Desktop.java
src/jalview/gui/UserDefinedColours.java
src/jalview/jbgui/GDesktop.java
gmungoc [Thu, 1 Nov 2018 10:01:53 +0000 (10:01 +0000)]
JAL-3048 JAL-3056 reinstate save/load project, colour scheme dialogs in
JS
gmungoc [Wed, 31 Oct 2018 16:30:24 +0000 (16:30 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into trialMerge
Conflicts:
src/jalview/ext/ensembl/EnsemblRestClient.java
swingjs/timestamp
gmungoc [Wed, 31 Oct 2018 15:12:58 +0000 (15:12 +0000)]
Merge branch 'Jalview-BH/JAL-3026' into feature/JAL-3144noJTree
gmungoc [Wed, 31 Oct 2018 15:10:22 +0000 (15:10 +0000)]
JAL-3026 skip unsupported HttpURLConnection methods in JS
Jim Procter [Wed, 31 Oct 2018 12:27:58 +0000 (12:27 +0000)]
JAL-3063-JAL-3026 propagate classpath changes to classpath.js
hansonr [Wed, 31 Oct 2018 06:04:36 +0000 (01:04 -0500)]
JAXB upgrade; URLConnection.getResourceCode()
Conflicts:
swingjs/SwingJS-site.zip
swingjs/net.sf.j2s.core.jar
swingjs/timestamp
swingjs/ver/3.2.4/SwingJS-site.zip
swingjs/ver/3.2.4/net.sf.j2s.core.jar
swingjs/ver/3.2.4/timestamp
hansonr [Wed, 31 Oct 2018 06:04:36 +0000 (01:04 -0500)]
JAXB upgrade; URLConnection.getResourceCode()
gmungoc [Tue, 30 Oct 2018 15:48:42 +0000 (15:48 +0000)]
JAL-3144 left aligned looks better (and works in JalviewJS!)
gmungoc [Tue, 30 Oct 2018 14:08:21 +0000 (14:08 +0000)]
JAL-3144 query URL corrected
gmungoc [Tue, 30 Oct 2018 12:43:26 +0000 (12:43 +0000)]
JAL-3144 close SequenceFetcher before opening PDB/Uniprot panel
hansonr [Tue, 30 Oct 2018 12:18:38 +0000 (07:18 -0500)]
JAL-3026-JAL-3063 adds binary ext to J2S
J2S needs to know any binary extensions for its file saving mechanism.
gmungoc [Tue, 30 Oct 2018 10:32:27 +0000 (10:32 +0000)]
JAL-3144 spelling, Javadoc, abstract method for JalviewJS
hansonr [Tue, 30 Oct 2018 08:40:13 +0000 (03:40 -0500)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Tue, 30 Oct 2018 08:39:05 +0000 (03:39 -0500)]
JAL-3026-JAL-3063-JAXB swingjs/ upgrade
gmungoc [Tue, 30 Oct 2018 08:05:43 +0000 (08:05 +0000)]
Merge branch 'Jalview-BH/JAL-3026' into feature/JAL-3144noJTree
gmungoc [Mon, 29 Oct 2018 16:13:23 +0000 (16:13 +0000)]
JAL-3144 SequenceFetcher without JDatabaseTree
gmungoc [Mon, 29 Oct 2018 15:02:39 +0000 (15:02 +0000)]
JAL-3038 add ActionListener and FocusListener to SwingJS mode
gmungoc [Thu, 25 Oct 2018 19:27:16 +0000 (20:27 +0100)]
JAL-3143 unit tests updated for code changes!
gmungoc [Thu, 25 Oct 2018 14:41:21 +0000 (15:41 +0100)]
JAL-3143 comma-delimited feature attributes for alleles,
clinical_significance
gmungoc [Thu, 25 Oct 2018 13:56:01 +0000 (14:56 +0100)]
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
Jim Procter [Tue, 23 Oct 2018 10:06:47 +0000 (11:06 +0100)]
JAL-3026 JAL-3063 patch jalview.project.Jalview2XmlTests with updates in jalview.io.Jalview2XmlTests due to changed way of accessing result of call to result of AlignFrame.saveAlignment
hansonr [Wed, 17 Oct 2018 17:17:05 +0000 (12:17 -0500)]
nonfunctional testing directory - just so I can see how it compiles.
Jim Procter [Wed, 17 Oct 2018 16:21:11 +0000 (17:21 +0100)]
JAL-3047 - create the clover output dir in the working directory before going any further !
Jim Procter [Wed, 17 Oct 2018 15:52:01 +0000 (16:52 +0100)]
Merge branch 'feature/JAL-3063JAXB' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Fri, 28 Sep 2018 11:29:55 +0000 (12:29 +0100)]
JAL-3063 service param files read/saved using JAXB not Castor binding
gmungoc [Fri, 28 Sep 2018 11:29:28 +0000 (12:29 +0100)]
JAL-3063 top level element added to JalviewWsParamSet.xsd
gmungoc [Fri, 28 Sep 2018 11:28:54 +0000 (12:28 +0100)]
JAL-3063 comments re use of xjc to generate Java binding classes
gmungoc [Mon, 24 Sep 2018 07:53:16 +0000 (08:53 +0100)]
JAL-3063 tidy commented out code
git://source.jalview.org / jalview.git / log