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
gmungoc [Fri, 21 Sep 2018 13:52:20 +0000 (14:52 +0100)]
JAL-3063 wrappers with check for null getting optional Integer, Float,
Boolean XML attributes
gmungoc [Thu, 20 Sep 2018 11:23:14 +0000 (12:23 +0100)]
JAL-2843 tweaks to help text for filters
gmungoc [Thu, 20 Sep 2018 10:54:31 +0000 (11:54 +0100)]
JAL-2843 help text for colour by attribute, feature filters
Jim Procter [Wed, 19 Sep 2018 14:45:29 +0000 (15:45 +0100)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into develop
gmungoc [Wed, 19 Sep 2018 13:59:44 +0000 (14:59 +0100)]
JAL-3120 preserve plain colour value when changing to Colour by Label
gmungoc [Wed, 19 Sep 2018 12:44:58 +0000 (13:44 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 19 Sep 2018 11:39:17 +0000 (12:39 +0100)]
Merge branch 'cherrypick/JAL-2808_notabs' into develop
Jim Procter [Thu, 5 Jul 2018 13:38:42 +0000 (14:38 +0100)]
JAL-2808 JAL-3026 deleted all commented out tab code from the dialog
Omitted dialog refactoring from JAL-3058
gmungoc [Thu, 5 Jul 2018 13:27:44 +0000 (14:27 +0100)]
JAL-2808 JAL-3032 drop tabbed layout for Colours and Filters
gmungoc [Wed, 19 Sep 2018 08:07:49 +0000 (09:07 +0100)]
JAL-3063 use JAXB for 'Save as Project' and load project from parameter
gmungoc [Wed, 19 Sep 2018 07:03:38 +0000 (08:03 +0100)]
JAL-3063 unit test for save/load project switched to JAXB
gmungoc [Tue, 18 Sep 2018 16:43:03 +0000 (17:43 +0100)]
JAL-3063 Save/Load user defined colours using JAXB
gmungoc [Tue, 18 Sep 2018 15:58:25 +0000 (16:58 +0100)]
JAL-3063 Save/Load user colour scheme using JAXB
gmungoc [Tue, 18 Sep 2018 15:57:42 +0000 (16:57 +0100)]
JAL-3063 top level element added to colours schema, JAXB classes regen'd
gmungoc [Tue, 18 Sep 2018 15:18:13 +0000 (16:18 +0100)]
JAL-3063 New View via JAXB
gmungoc [Tue, 18 Sep 2018 15:03:09 +0000 (16:03 +0100)]
JAL-3063 temporary extra menu option to save/load project as JAXB
gmungoc [Tue, 18 Sep 2018 15:02:34 +0000 (16:02 +0100)]
JAL-3063 first version of Jalview2XML using JAXB to (un)marshal
gmungoc [Tue, 18 Sep 2018 15:01:52 +0000 (16:01 +0100)]
JAL-3063 JAXB binding classes generated by xjc from jalview.xsd
git://source.jalview.org / jalview.git / log