Jim Procter [Mon, 25 Nov 2013 16:18:56 +0000 (16:18 +0000)]
Merge branch 'JAL-1139_proguard' into develop
Jim Procter [Mon, 25 Nov 2013 16:17:39 +0000 (16:17 +0000)]
JAL-1139 latest version of proguard needed for Java 1.7 builds
Jim Procter [Thu, 7 Nov 2013 13:56:07 +0000 (13:56 +0000)]
Merge branch 'JAL-1286' into develop
slightly dirty merge - JAL-1400 patches brought in too
Conflicts:
build.xml
Jim Procter [Thu, 7 Nov 2013 13:49:15 +0000 (13:49 +0000)]
JAL-1286 additional tests to ensure that non-GZ files with a .gz at end
are read in correctly
Jim Procter [Thu, 7 Nov 2013 13:43:30 +0000 (13:43 +0000)]
JAL-1286 check if local file ends with .gz and opens as a gzip stream
Jim Procter [Thu, 7 Nov 2013 13:42:35 +0000 (13:42 +0000)]
JAL-1286 test input of gzip stream from local file
Jim Procter [Tue, 5 Nov 2013 17:33:29 +0000 (17:33 +0000)]
JAL-1400 found a fix for the sandbox exception - need a 'permissions' parameter
http://stackoverflow.com/questions/
18914650/can-you-sign-a-java-applet-but-keep-it-in-the-sandbox-not-give-it-full-access-t
http://docs.oracle.com/javase/tutorial/deployment/applet/html.html
Jim Procter [Tue, 5 Nov 2013 17:26:55 +0000 (17:26 +0000)]
experiment with reinstating the sandbox permissions
Jim Procter [Tue, 5 Nov 2013 17:07:20 +0000 (17:07 +0000)]
JAL-1400 try putting explicit domain for jalviewLite applet
Jim Procter [Mon, 21 Oct 2013 16:52:51 +0000 (17:52 +0100)]
JAL-1400 Always create indices for jar before signing
Jim Procter [Mon, 21 Oct 2013 16:54:12 +0000 (17:54 +0100)]
JAL-1400 sign everything !
Jim Procter [Mon, 21 Oct 2013 16:53:45 +0000 (17:53 +0100)]
JAL-1400 explicit security settings for applet
Jim Procter [Mon, 21 Oct 2013 16:53:25 +0000 (17:53 +0100)]
JAL-1400 explicit security permissions for Desktop
Jalview build Manager [Fri, 1 Nov 2013 17:04:18 +0000 (17:04 +0000)]
JAL-1403 make sure MacOS installer searchers for the Apple Java install, otherwise it silently fails due to a JVM not being found.
Jalview build Manager [Fri, 1 Nov 2013 17:02:37 +0000 (17:02 +0000)]
JAL-1403 make sure MacOS installer searchers for the Apple Java install, otherwise it silently fails due to a JVM not being found.
Jalview build Manager [Wed, 23 Oct 2013 10:52:42 +0000 (11:52 +0100)]
Merge branch 'JAL-1403' into develop
Jalview build Manager [Wed, 23 Oct 2013 10:37:12 +0000 (11:37 +0100)]
JAL-1403 updated paths to IA 2013 and additional build parameter to disable the update thread so builds happen quicker
Jalview build Manager [Wed, 23 Oct 2013 10:36:24 +0000 (11:36 +0100)]
JAL-1403 upgraded the InstallAnywhere build file to IA Professional 2013
Jim Procter [Thu, 17 Oct 2013 11:42:35 +0000 (12:42 +0100)]
Merge branch 'JAL-1397' into develop
Jim Procter [Thu, 17 Oct 2013 11:33:32 +0000 (12:33 +0100)]
fix for JAL-1398 - original colourscheme is enabled if colourscheme has a BaseColour setting.
See JAL-1399 for future improvements.
Jim Procter [Thu, 17 Oct 2013 10:25:11 +0000 (11:25 +0100)]
JAL-1233 TODO concerning the way we propagate annotation colourschemes to new groups.
Jim Procter [Thu, 17 Oct 2013 10:14:46 +0000 (11:14 +0100)]
JAL-1397 make sure annotation colourscheme is up to date after loading the project
Jim Procter [Thu, 17 Oct 2013 10:13:02 +0000 (11:13 +0100)]
JAL-1397 store colour by sequence and originalColour flags for AnnotationColourScheme
Jim Procter [Thu, 17 Oct 2013 10:10:44 +0000 (11:10 +0100)]
JAL-1397 make sure ColourschemeI instances are up to date after a new view is created
Jim Procter [Thu, 17 Oct 2013 10:09:24 +0000 (11:09 +0100)]
JAL-1397 propagate any consensus/conservation colourscheme state changes to the background colourscheme being thresholded by annotation colourscheme
Jim Procter [Thu, 17 Oct 2013 10:06:50 +0000 (11:06 +0100)]
JAL-1397 getters for originalColours flag
Jim Procter [Wed, 16 Oct 2013 16:41:54 +0000 (17:41 +0100)]
Merge branch 'JAL-1395' into Release_2_8_1_Branch
Jim Procter [Wed, 16 Oct 2013 16:41:46 +0000 (17:41 +0100)]
Merge branch 'JAL-1395' into develop
Jim Procter [Wed, 16 Oct 2013 16:40:16 +0000 (17:40 +0100)]
JAL-1395 do not calculate non-gap consensus when no symbols present in column (regression on JAL-1373
Jim Procter [Tue, 15 Oct 2013 11:33:27 +0000 (12:33 +0100)]
workaround for JAL-1395
Jim Procter [Tue, 15 Oct 2013 10:23:44 +0000 (11:23 +0100)]
Merge branch 'dev_from_2_8_1' into develop
Jim Procter [Tue, 15 Oct 2013 10:21:04 +0000 (11:21 +0100)]
JAL-1159 Merging 2.8.1 patches and Anne Menards work from 2012 into development branch
Merge branch 'develop_m2_8_1_2' into dev_from_2_8_1
Conflicts:
src/jalview/appletgui/AlignFrame.java
src/jalview/renderer/AnnotationRenderer.java
Jim Procter [Mon, 14 Oct 2013 16:26:20 +0000 (17:26 +0100)]
Merge branch 'develop' into dev_from_2_8_1
Conflicts:
.classpath
.project
src/jalview/appletgui/AlignFrame.java
src/jalview/io/FileLoader.java
Jim Procter [Fri, 11 Oct 2013 16:51:52 +0000 (17:51 +0100)]
Merge branch 'JAL-1292_regression' into Release_2_8_1_Branch
Jim Procter [Fri, 11 Oct 2013 16:20:08 +0000 (17:20 +0100)]
JAL-1164 regression on JAL-1292 use bitset to mark graphGroup as rendered
Jim Procter [Fri, 11 Oct 2013 16:22:59 +0000 (17:22 +0100)]
Merge branch 'JAL-1164_disorderforselection' into Release_2_8_Branch
Jim Procter [Fri, 11 Oct 2013 16:20:08 +0000 (17:20 +0100)]
JAL-1164 regression on JAL-1292 use bitset to mark graphGroup as rendered
Jim Procter [Fri, 11 Oct 2013 11:24:08 +0000 (12:24 +0100)]
Merge branch 'JAL-1164_disorderforselection' into Release_2_8_1_Branch
Conflicts:
src/jalview/api/AlignViewportI.java
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
Jim Procter [Fri, 11 Oct 2013 10:45:26 +0000 (11:45 +0100)]
JAL-1164 scope bySequence analysis methods to start/end of selected region or alignment region.
Jim Procter [Fri, 11 Oct 2013 10:44:19 +0000 (11:44 +0100)]
JAL-1114 javadoc
Jim Procter [Fri, 11 Oct 2013 10:44:03 +0000 (11:44 +0100)]
JAL-1114 promote start/end attributes to gettable fields of annotatable collections
Jim Procter [Fri, 11 Oct 2013 10:40:23 +0000 (11:40 +0100)]
JAL-1114 API javadoc
Jim Procter [Fri, 11 Oct 2013 09:58:00 +0000 (10:58 +0100)]
JAL-1164 only predict on currently selected sequences for perSequence
Jim Procter [Mon, 7 Oct 2013 16:02:45 +0000 (17:02 +0100)]
JAL-1385 expose core view model methods in interface
Jim Procter [Fri, 11 Oct 2013 09:37:48 +0000 (10:37 +0100)]
Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_Branch
Jim Procter [Fri, 11 Oct 2013 09:37:21 +0000 (10:37 +0100)]
JAL-1354 watch for exceptions when initialising (Security exceptions can occur in the JalviewLite applet when running in default sandbox)
Jim Procter [Fri, 11 Oct 2013 09:34:28 +0000 (10:34 +0100)]
JAL-1354 ensure resource bundles are copied into JalviewApplet jar.
JAL-1390 consider splitting language resources from main Jars
Jim Procter [Tue, 8 Oct 2013 15:08:30 +0000 (16:08 +0100)]
reindexed Jmol jar with 'jar -i' to fix JAL-1389
Jim Procter [Tue, 8 Oct 2013 14:28:34 +0000 (15:28 +0100)]
Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_Branch
Jim Procter [Tue, 8 Oct 2013 14:26:39 +0000 (15:26 +0100)]
localisation for JAL-1384 and JAL-1388
Jim Procter [Tue, 8 Oct 2013 14:23:40 +0000 (15:23 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
Jim Procter [Tue, 8 Oct 2013 14:05:11 +0000 (15:05 +0100)]
Merge branch 'JAL-643_JAL-1384' into Release_2_8_1_Branch
Jim Procter [Tue, 8 Oct 2013 14:02:42 +0000 (15:02 +0100)]
JAL-1384 JAL-1388 revised popup menu documentation for group create/edit/remove
Jim Procter [Tue, 8 Oct 2013 13:51:01 +0000 (14:51 +0100)]
JAL-1384 Create Group in selection popup menu
JAL-1388 move Remove Group option to selection menu
JAL-1388 Group editing menu is now context dependent (either 'Edit Group' or 'Edit New Group')
Jim Procter [Tue, 8 Oct 2013 13:33:53 +0000 (14:33 +0100)]
fix for JAL-1387
Jim Procter [Tue, 8 Oct 2013 10:53:33 +0000 (11:53 +0100)]
JAL-1384 documentation and consistent ordering for new items in select menu
Jim Procter [Mon, 7 Oct 2013 16:44:11 +0000 (17:44 +0100)]
JAL-1384 group/ungroup sequences with command/ctrl+G and shift+command/ctrl+G
Jim Procter [Mon, 7 Oct 2013 16:39:06 +0000 (17:39 +0100)]
JAL-1385 refactor logic to AlignmentViewController
Jim Procter [Mon, 7 Oct 2013 16:33:16 +0000 (17:33 +0100)]
JAL-1385 JAL-535 refactor sequence colour settings to abstract alignment view model
Jim Procter [Mon, 7 Oct 2013 16:02:45 +0000 (17:02 +0100)]
JAL-1385 expose core view model methods in interface
Jim Procter [Mon, 7 Oct 2013 15:59:52 +0000 (16:59 +0100)]
JAL-1385 Alignment view controller logic implementation and API
Jim Procter [Sat, 5 Oct 2013 14:02:04 +0000 (15:02 +0100)]
Merge branch 'JAL-1378_jb2.1cli' into Release_2_8_1_Branch
Jim Procter [Sat, 5 Oct 2013 13:01:00 +0000 (14:01 +0100)]
JAL-1379 graceful degradation to legacy service when JABAWS Jpred service not available
Jim Procter [Sat, 5 Oct 2013 12:59:40 +0000 (13:59 +0100)]
JAL-1379 JAL-1378 exclusion list property to ignore services not fully integrated with Jalview
Jim Procter [Sat, 5 Oct 2013 11:20:52 +0000 (12:20 +0100)]
JAL-1378 hack to place 'Predictors' into Secondary struture predictors (may be redacted later)
Jim Procter [Sat, 5 Oct 2013 11:20:15 +0000 (12:20 +0100)]
JAL-1364 use gapMap to map RNAalifold annotation onto correct columns
Jim Procter [Sat, 5 Oct 2013 11:13:12 +0000 (12:13 +0100)]
JAL-1379 JAL-1358 only enable/disable menu entries associated with services not applicable for the current sequence type
Jim Procter [Fri, 4 Oct 2013 15:27:01 +0000 (16:27 +0100)]
JAL-1383 - disable startup of the Envision2 workflow discovery thread
Jim Procter [Fri, 4 Oct 2013 15:22:16 +0000 (16:22 +0100)]
JAL-940 JAL-1378 EOL comment on JWS v1 services
Jim Procter [Fri, 4 Oct 2013 14:08:38 +0000 (15:08 +0100)]
update JABA client dependency in InstallAnywhere build
Jim Procter [Fri, 4 Oct 2013 14:07:00 +0000 (15:07 +0100)]
Merge branch 'RNAalifold' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Oct 2013 14:03:52 +0000 (15:03 +0100)]
fix for JAL-1380 and efficiency todo for JAL-1381
Jim Procter [Fri, 4 Oct 2013 12:48:34 +0000 (13:48 +0100)]
JAL-1378 JWS-71 update to from-source build of JABA v2.1 client for use with JABA test server
Jim Procter [Wed, 25 Sep 2013 15:36:24 +0000 (16:36 +0100)]
JAL-1365 test that RNAAliFold service settings are stored and recovered from Jalview projects
Jim Procter [Wed, 25 Sep 2013 15:34:55 +0000 (16:34 +0100)]
formatting
Jim Procter [Wed, 25 Sep 2013 15:33:41 +0000 (16:33 +0100)]
JAL-1365 unified GUI building for AACon and RNAAliFold service clients
Jim Procter [Wed, 25 Sep 2013 15:30:37 +0000 (16:30 +0100)]
JAL-1365 use AlignAnalysisUIText class to provide metadata for a service's UI elements
Jim Procter [Wed, 25 Sep 2013 15:28:31 +0000 (16:28 +0100)]
JAL-1365 refactored core methods from RNAAliFold and AACon service clients to a common Alignment Analysis client class
Jim Procter [Wed, 25 Sep 2013 15:17:07 +0000 (16:17 +0100)]
JAL-1365 new metadata class to describe instantaneous calculation services like AACon and RNAAliFold
Jim Procter [Wed, 25 Sep 2013 15:13:56 +0000 (16:13 +0100)]
JAL-1270 nominal jalview version string for projects written during development tests
Jim Procter [Wed, 25 Sep 2013 15:10:43 +0000 (16:10 +0100)]
JAL-1270 Desktop.instance is null during headless jalview tests
Jim Procter [Fri, 20 Sep 2013 17:33:14 +0000 (18:33 +0100)]
formatting
Jim Procter [Wed, 18 Sep 2013 09:09:57 +0000 (10:09 +0100)]
JAL-1355 - fix compilation errors: typos and missing imports
Jim Procter [Fri, 13 Sep 2013 16:51:48 +0000 (17:51 +0100)]
tweak - v is lowercase in Jalview
darolmar [Fri, 13 Sep 2013 11:44:01 +0000 (13:44 +0200)]
i18n how to
Jim Procter [Tue, 3 Sep 2013 13:27:54 +0000 (14:27 +0100)]
Merge branch 'JAL-1373_precision' into RNAalifold
Jim Procter [Tue, 3 Sep 2013 13:27:29 +0000 (14:27 +0100)]
Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch
Jim Procter [Tue, 3 Sep 2013 13:26:47 +0000 (14:26 +0100)]
JAL-1373 tweak precision calculation so alignments of less than 100 sequences don't include any decimal points.
Jim Procter [Tue, 3 Sep 2013 13:25:28 +0000 (14:25 +0100)]
JAL-920 compute a consensus for single sequence
Jim Procter [Mon, 2 Sep 2013 17:14:45 +0000 (18:14 +0100)]
Merge branch 'JAL-1373_precision' into develop
Jim Procter [Mon, 2 Sep 2013 17:14:07 +0000 (18:14 +0100)]
Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch
Jim Procter [Mon, 2 Sep 2013 17:11:29 +0000 (18:11 +0100)]
JAL-1373 JAL-520 wrap tooltips for columns in annotation rows
Jim Procter [Mon, 2 Sep 2013 17:09:08 +0000 (18:09 +0100)]
JAL-1373 generate percentages with appropriate precision
Jim Procter [Mon, 2 Sep 2013 17:07:42 +0000 (18:07 +0100)]
JAL-1373 pass size of sequence set to consensus rendering routines so appropriate precision can be chosen
Jim Procter [Mon, 2 Sep 2013 09:42:43 +0000 (10:42 +0100)]
JAL-1358 monday morning commits :(
Jim Procter [Mon, 2 Sep 2013 09:37:45 +0000 (10:37 +0100)]
JAL-1358 jabaws not jaba
Jim Procter [Mon, 2 Sep 2013 09:27:46 +0000 (10:27 +0100)]
JAL-1358 update jabaws client for installanywhere
Jim Procter [Mon, 2 Sep 2013 09:20:21 +0000 (10:20 +0100)]
JAL-1358 remove old v2 jaba min-client
Daniel Barton [Sat, 31 Aug 2013 16:42:19 +0000 (17:42 +0100)]
Brief html documentation entry for RNAalifold under webServices
Daniel Barton [Fri, 30 Aug 2013 16:11:12 +0000 (17:11 +0100)]
Colour be RNA helices bug fixed
git://source.jalview.org / jalview.git / log