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 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()
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.
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 [Mon, 29 Oct 2018 15:02:39 +0000 (15:02 +0000)]
JAL-3038 add ActionListener and FocusListener to SwingJS mode
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 [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
gmungoc [Tue, 18 Sep 2018 15:01:07 +0000 (16:01 +0100)]
JAL-3063 tweak schema so JAXB tool xjc recognises XML root element
gmungoc [Tue, 18 Sep 2018 15:00:20 +0000 (16:00 +0100)]
JAL-3063 tweak schema so JAXB generates enums for enumerated values
hansonr [Tue, 18 Sep 2018 05:05:30 +0000 (00:05 -0500)]
Jmol/SwingJS update. Includes new transpiler and runtime
install transpiler
run build-site.xml
gmungoc [Mon, 17 Sep 2018 10:51:43 +0000 (11:51 +0100)]
JAL-3116 test method renamed to match code
gmungoc [Mon, 17 Sep 2018 10:47:51 +0000 (11:47 +0100)]
JAL-3116 unit tests adapted to EMBL over JAXB
gmungoc [Fri, 14 Sep 2018 16:11:40 +0000 (17:11 +0100)]
JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)
gmungoc [Thu, 13 Sep 2018 15:28:27 +0000 (16:28 +0100)]
JAL-3116 Uniprot XML unmarshalled using JAXB not Castor
gmungoc [Wed, 12 Sep 2018 15:30:52 +0000 (16:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 12 Sep 2018 15:20:51 +0000 (16:20 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
gmungoc [Wed, 12 Sep 2018 11:27:21 +0000 (12:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 12 Sep 2018 10:59:39 +0000 (11:59 +0100)]
JAL-1551 reinstated Save actions
gmungoc [Tue, 11 Sep 2018 16:37:30 +0000 (17:37 +0100)]
JAL-3113 override minimum frame size in a way that works in JalviewJS
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
git://source.jalview.org / jalview.git / log