jalview.git
14 years ago2.6 release date change
jprocter [Sun, 26 Sep 2010 08:28:04 +0000 (08:28 +0000)]
2.6 release date change

14 years agoremove overrides
jprocter [Thu, 23 Sep 2010 16:27:29 +0000 (16:27 +0000)]
remove overrides

14 years agoupdate release branch to 2.6
jprocter [Thu, 23 Sep 2010 08:53:11 +0000 (08:53 +0000)]
update release branch to 2.6

14 years agotypos and indicate 'legacy' service documentation
jprocter [Thu, 23 Sep 2010 08:31:44 +0000 (08:31 +0000)]
typos and indicate 'legacy' service documentation

14 years agoNPE race condition alert - see JAL-661
jprocter [Thu, 23 Sep 2010 08:31:10 +0000 (08:31 +0000)]
NPE race condition alert - see JAL-661

14 years agorevised author list
jprocter [Thu, 23 Sep 2010 07:15:17 +0000 (07:15 +0000)]
revised author list

14 years agoJalview 2.6 source licence
jprocter [Thu, 23 Sep 2010 07:11:07 +0000 (07:11 +0000)]
Jalview 2.6 source licence

14 years agoapply jalview code style
jprocter [Thu, 23 Sep 2010 07:06:55 +0000 (07:06 +0000)]
apply jalview code style

14 years agoJalview 2.6 source licence
jprocter [Thu, 23 Sep 2010 07:01:18 +0000 (07:01 +0000)]
Jalview 2.6 source licence

14 years ago2.6 highlights
jprocter [Wed, 22 Sep 2010 21:48:14 +0000 (21:48 +0000)]
2.6 highlights

14 years agoupdate 2.6 history
jprocter [Wed, 22 Sep 2010 11:39:22 +0000 (11:39 +0000)]
update 2.6 history

14 years agoJmol 12 update
jprocter [Wed, 22 Sep 2010 10:43:01 +0000 (10:43 +0000)]
Jmol 12 update

14 years agoFix and documentation for JAL-657
jprocter [Wed, 22 Sep 2010 10:08:28 +0000 (10:08 +0000)]
Fix and documentation for JAL-657

14 years agoFix and documentation for JAL-657
jprocter [Wed, 22 Sep 2010 09:59:51 +0000 (09:59 +0000)]
Fix and documentation for JAL-657

14 years agonew web service dialogs and JABA
jprocter [Wed, 22 Sep 2010 01:04:24 +0000 (01:04 +0000)]
new web service dialogs and JABA

14 years agonew export options
jprocter [Wed, 22 Sep 2010 01:03:48 +0000 (01:03 +0000)]
new export options

14 years agojmol update
jprocter [Wed, 22 Sep 2010 01:03:16 +0000 (01:03 +0000)]
jmol update

14 years agojabaws, not jws2
jprocter [Wed, 22 Sep 2010 00:58:45 +0000 (00:58 +0000)]
jabaws, not jws2

14 years agotrap out of memory errors specifically associated with Jmol view creation (needs...
jprocter [Wed, 22 Sep 2010 00:58:32 +0000 (00:58 +0000)]
trap out of memory errors specifically associated with Jmol view creation (needs refinement)

14 years agoensure presets and parameters are discovered when service is discovered
jprocter [Wed, 22 Sep 2010 00:57:59 +0000 (00:57 +0000)]
ensure presets and parameters are discovered when service is discovered

14 years agolayout the menu with a minimum number of host labels
jprocter [Mon, 20 Sep 2010 08:57:28 +0000 (08:57 +0000)]
layout the menu with a minimum number of host labels

14 years agomore attempts to fix NPE from race condition
jprocter [Mon, 20 Sep 2010 08:57:02 +0000 (08:57 +0000)]
more attempts to fix NPE from race condition

14 years agoonly indicate that job is broken if it wasn't submitted correctly
jprocter [Mon, 20 Sep 2010 07:22:00 +0000 (07:22 +0000)]
only indicate that job is broken if it wasn't submitted correctly

14 years agostop race condition when submenu being populated before workflows are discovered
jprocter [Mon, 20 Sep 2010 06:43:46 +0000 (06:43 +0000)]
stop race condition when submenu being populated before workflows are discovered

14 years agoensure host is shown for all non-host indexed submenus
jprocter [Mon, 20 Sep 2010 06:43:12 +0000 (06:43 +0000)]
ensure host is shown for all non-host indexed submenus

14 years agoresolve pdb id/chain to pdb file/model number and chain
jprocter [Sun, 19 Sep 2010 22:37:25 +0000 (22:37 +0000)]
resolve pdb id/chain to pdb file/model number and chain

14 years agoname change for jaba
jprocter [Sun, 19 Sep 2010 22:36:55 +0000 (22:36 +0000)]
name change for jaba

14 years agocache the runner config so the preset list can be retrieved quickly
jprocter [Sun, 19 Sep 2010 22:36:33 +0000 (22:36 +0000)]
cache the runner config so the preset list can be retrieved quickly

14 years agoprogress bar and OOM/Exception traps for project marshalling
jprocter [Sun, 19 Sep 2010 22:35:29 +0000 (22:35 +0000)]
progress bar and OOM/Exception traps for project marshalling

14 years agocatch case when a service has no parameters (or the service's servicerunner does...
jprocter [Sun, 19 Sep 2010 16:36:25 +0000 (16:36 +0000)]
catch case when a service has no parameters (or the service's servicerunner does not init correctly) and only display a 'default' submission entry for it.

14 years agomake sure only one sequence datasource initialization thread runs at any one time
jprocter [Sun, 19 Sep 2010 16:35:34 +0000 (16:35 +0000)]
make sure only one sequence datasource initialization thread runs at any one time

14 years agohack to ensure that if window geometry was not stored correctly, windows are not...
jprocter [Sun, 19 Sep 2010 16:34:58 +0000 (16:34 +0000)]
hack to ensure that if window geometry was not stored correctly, windows are not placed outside the current screen dimensions (occurs with console occasionally in 2.5.x)

14 years agothread off sequence fetcher initialisation to make initial alignment window display...
jprocter [Sun, 19 Sep 2010 16:34:07 +0000 (16:34 +0000)]
thread off sequence fetcher initialisation to make initial alignment window display smoother

14 years agoshow a save dialog box!
jprocter [Fri, 17 Sep 2010 17:14:38 +0000 (17:14 +0000)]
show a save dialog box!

14 years agoposs fix for JAL-656
jprocter [Fri, 17 Sep 2010 17:14:16 +0000 (17:14 +0000)]
poss fix for JAL-656

14 years agomake sure web service menu is always refreshed on 'OK'
jprocter [Fri, 17 Sep 2010 17:13:30 +0000 (17:13 +0000)]
make sure web service menu is always refreshed on 'OK'

14 years agoreflect the state of a failed Job in the GUI (e.g. trying to align protein seqs with...
jprocter [Thu, 16 Sep 2010 11:54:27 +0000 (11:54 +0000)]
reflect the state of a failed Job in the GUI (e.g. trying to align protein seqs with a nucleotide parameter set)

14 years agopatch to prevent NPE - which occurs if no features are available (see JAL-650)
jprocter [Thu, 16 Sep 2010 11:53:45 +0000 (11:53 +0000)]
patch to prevent NPE - which occurs if no features are available (see JAL-650)

14 years agoclean the dist directory before copying Jars
jprocter [Wed, 15 Sep 2010 20:31:14 +0000 (20:31 +0000)]
clean the dist directory before copying Jars

14 years agoupdate jmol
jprocter [Wed, 15 Sep 2010 20:12:06 +0000 (20:12 +0000)]
update jmol

14 years agoadded colour by label to feature type colourspec and gff statement to allow mixed...
jprocter [Wed, 15 Sep 2010 14:03:03 +0000 (14:03 +0000)]
added colour by label to feature type colourspec and gff statement to allow mixed jalview colour specs and gff feature specs

14 years agoreinstated the splitpanes with better size placement, and made tooltips button labels...
jprocter [Wed, 15 Sep 2010 11:12:06 +0000 (11:12 +0000)]
reinstated the splitpanes with better size placement, and made tooltips button labels more helpful

14 years agofix the javac issue for JmolApplet references in application build
jprocter [Tue, 14 Sep 2010 16:24:48 +0000 (16:24 +0000)]
fix the javac issue for JmolApplet references in application build

14 years agoupdate Jmol jar ref
jprocter [Tue, 14 Sep 2010 16:15:59 +0000 (16:15 +0000)]
update Jmol jar ref

14 years agoappletgui should ve excluded from normal application build
jprocter [Tue, 14 Sep 2010 15:59:06 +0000 (15:59 +0000)]
appletgui should ve excluded from normal application build

14 years agostreamlined app and applet jmol console + event handling via component listener
jprocter [Tue, 14 Sep 2010 15:49:31 +0000 (15:49 +0000)]
streamlined app and applet jmol console + event handling via component listener

14 years agorefactored to remove App reference in Applet (JAL-638)
jprocter [Mon, 13 Sep 2010 21:03:05 +0000 (21:03 +0000)]
refactored to remove App reference in Applet (JAL-638)

14 years agorefactored to remove App reference in Applet (JAL-638)
jprocter [Mon, 13 Sep 2010 19:55:05 +0000 (19:55 +0000)]
refactored to remove App reference in Applet (JAL-638)

14 years agopatched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)
jprocter [Mon, 13 Sep 2010 19:03:37 +0000 (19:03 +0000)]
patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

14 years agopatched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)
jprocter [Mon, 13 Sep 2010 18:24:06 +0000 (18:24 +0000)]
patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

14 years agojabaws, not jaba
jprocter [Fri, 10 Sep 2010 16:23:12 +0000 (16:23 +0000)]
jabaws, not jaba

14 years agothreaded off ws menu building to avoid initial pause when services are discovered
jprocter [Fri, 10 Sep 2010 16:22:52 +0000 (16:22 +0000)]
threaded off ws menu building to avoid initial pause when services are discovered

14 years agoproperly report invalid jobs (server doesn't support service, seuqence set too big...
jprocter [Fri, 10 Sep 2010 15:22:11 +0000 (15:22 +0000)]
properly report invalid jobs (server doesn't support service, seuqence set too big/wide, invalid input parameters) in a pop up dialog

14 years agoearly bail out for long urls, and threaded off group url construction: JAL-402
jprocter [Fri, 10 Sep 2010 15:21:04 +0000 (15:21 +0000)]
early bail out for long urls, and threaded off group url construction: JAL-402

14 years agowrap preset description tooltips
jprocter [Thu, 9 Sep 2010 15:48:56 +0000 (15:48 +0000)]
wrap preset description tooltips

14 years agoremove duplicate host URLs in service list when not indexing services by host
jprocter [Thu, 9 Sep 2010 15:48:36 +0000 (15:48 +0000)]
remove duplicate host URLs in service list when not indexing services by host

14 years agowrap tooltips and revise layout (JAL-644)
jprocter [Thu, 9 Sep 2010 15:33:03 +0000 (15:33 +0000)]
wrap tooltips and revise layout (JAL-644)

14 years agowrap tooltips
jprocter [Thu, 9 Sep 2010 15:32:45 +0000 (15:32 +0000)]
wrap tooltips

14 years agotabbed panes for parameters and options.
jprocter [Thu, 9 Sep 2010 08:56:46 +0000 (08:56 +0000)]
tabbed panes for parameters and options.

14 years agoJAL-634 and JAL-635
jprocter [Wed, 8 Sep 2010 14:15:02 +0000 (14:15 +0000)]
JAL-634 and JAL-635

14 years agoJAL-634
jprocter [Wed, 8 Sep 2010 14:14:39 +0000 (14:14 +0000)]
JAL-634

14 years agotodos & added simple method for other classes to monitor when fileUpdate events have...
jprocter [Wed, 8 Sep 2010 14:12:51 +0000 (14:12 +0000)]
todos & added simple method for other classes to monitor when fileUpdate events have occured

14 years agotrap NPE possiblity for trees that have no associated alignment panels (usually becau...
jprocter [Wed, 8 Sep 2010 14:10:29 +0000 (14:10 +0000)]
trap NPE possiblity for trees that have no associated alignment panels (usually because they've been closed)

14 years agoright click opens view URL popup for both parameters and option boxes JAL-601
jprocter [Tue, 7 Sep 2010 15:14:28 +0000 (15:14 +0000)]
right click opens view URL popup for both parameters and option boxes JAL-601

14 years agofix for JAL-631
jprocter [Tue, 7 Sep 2010 13:24:45 +0000 (13:24 +0000)]
fix for JAL-631

14 years agodebug warning / option dialog box display
jprocter [Tue, 7 Sep 2010 12:09:49 +0000 (12:09 +0000)]
debug warning / option dialog box display

14 years agokick off the first time service parameter set discovery thread when service is discovered
jprocter [Tue, 7 Sep 2010 12:09:17 +0000 (12:09 +0000)]
kick off the first time service parameter set discovery thread when service is discovered

14 years agoJAL-591
jprocter [Mon, 6 Sep 2010 16:39:44 +0000 (16:39 +0000)]
JAL-591

14 years agonew XML representation for web services parameters
jprocter [Mon, 6 Sep 2010 16:37:44 +0000 (16:37 +0000)]
new XML representation for web services parameters

14 years agopass user preset arguments to job
jprocter [Mon, 6 Sep 2010 11:08:50 +0000 (11:08 +0000)]
pass user preset arguments to job

14 years agoabstracted GUI to use jalview.ws.params objects (JAL-591, JAL-633). User defined...
jprocter [Mon, 6 Sep 2010 10:53:27 +0000 (10:53 +0000)]
abstracted GUI to use jalview.ws.params objects (JAL-591, JAL-633). User defined presets shown in menu - which is dynamically populated

14 years agoabstracted GUI to use jalview.ws.params objects (JAL-591, JAL-633)
jprocter [Mon, 6 Sep 2010 10:53:04 +0000 (10:53 +0000)]
abstracted GUI to use jalview.ws.params objects (JAL-591, JAL-633)

14 years agodistinguish between userdefined parameter set job and preset job
jprocter [Fri, 3 Sep 2010 08:19:39 +0000 (08:19 +0000)]
distinguish between userdefined parameter set job and preset job

14 years agoparameter set serialization/deserialization and preset/userdefined parameter set...
jprocter [Fri, 3 Sep 2010 08:19:23 +0000 (08:19 +0000)]
parameter set serialization/deserialization and preset/userdefined parameter set recall

14 years agofix occasional arrayIndexOutOfBounds when sequences in subgroup are shorter than...
jprocter [Thu, 2 Sep 2010 15:59:26 +0000 (15:59 +0000)]
fix occasional arrayIndexOutOfBounds when sequences in subgroup are shorter than alignment width

14 years agodebugged option changed logic and layout
jprocter [Thu, 2 Sep 2010 15:18:01 +0000 (15:18 +0000)]
debugged option changed logic and layout

14 years agoupdate gui in gui thread - not structure loading thread
jprocter [Thu, 2 Sep 2010 12:31:51 +0000 (12:31 +0000)]
update gui in gui thread - not structure loading thread

14 years agoincrement if strings *dont* match
jprocter [Thu, 2 Sep 2010 12:31:38 +0000 (12:31 +0000)]
increment if strings *dont* match

14 years ago1.1 compatibility
jprocter [Thu, 2 Sep 2010 10:06:59 +0000 (10:06 +0000)]
1.1 compatibility

14 years agore-implemented user prefs logic - still need to debug option change detection.
jprocter [Thu, 2 Sep 2010 10:03:24 +0000 (10:03 +0000)]
re-implemented user prefs logic - still need to debug option change detection.

14 years agonotes re JAL-623 and JAL-583, new api methods for adding several structure/seq mappin...
jprocter [Tue, 31 Aug 2010 16:18:55 +0000 (16:18 +0000)]
notes re JAL-623 and JAL-583, new api methods for adding several structure/seq mappings at once

14 years agonotes re JAL-629
jprocter [Tue, 31 Aug 2010 16:16:51 +0000 (16:16 +0000)]
notes re JAL-629

14 years agofixed various null pointer exceptions that occur when PDB files imported into Jmol...
jprocter [Tue, 31 Aug 2010 16:16:31 +0000 (16:16 +0000)]
fixed various null pointer exceptions that occur when PDB files imported into Jmol which do not map to a sequence. Notes re JAL-623

14 years agofixed various null pointer exceptions that occur when PDB files imported into Jmol...
jprocter [Tue, 31 Aug 2010 16:16:06 +0000 (16:16 +0000)]
fixed various null pointer exceptions that occur when PDB files imported into Jmol which do not map to a sequence

14 years agoadded URL display for parameters/options and debugged parameter set switching
jprocter [Tue, 31 Aug 2010 16:15:31 +0000 (16:15 +0000)]
added URL display for parameters/options and debugged parameter set switching

14 years agoutilities for cloning and manipulating JabaWS parameter objects.
jprocter [Tue, 31 Aug 2010 16:14:38 +0000 (16:14 +0000)]
utilities for cloning and manipulating JabaWS parameter objects.

14 years agorefactored seq/str binding methods and ensured that structures added to existing...
jprocter [Fri, 27 Aug 2010 15:44:06 +0000 (15:44 +0000)]
refactored seq/str binding methods and ensured that structures added to existing view get loaded first

14 years agopatch for structures with multiple models, and refactored seq/str binding methods
jprocter [Fri, 27 Aug 2010 15:43:15 +0000 (15:43 +0000)]
patch for structures with multiple models, and refactored seq/str binding methods

14 years ago1.2 compatibility
jprocter [Fri, 27 Aug 2010 13:02:02 +0000 (13:02 +0000)]
1.2 compatibility

14 years agorevised sequence/structure binding so one structure associated with x-seuqenceI's...
jprocter [Fri, 27 Aug 2010 11:35:14 +0000 (11:35 +0000)]
revised sequence/structure binding so one structure associated with x-seuqenceI's, and bugfixed superposition code(See JAL-583)

14 years agorevised sequence/structure binding so one structure associated with x-seuqenceI's
jprocter [Fri, 27 Aug 2010 11:34:50 +0000 (11:34 +0000)]
revised sequence/structure binding so one structure associated with x-seuqenceI's

14 years agopatch re http://issues.jalview.org/browse/JAL-583 : hack to prevent chains being...
jprocter [Fri, 27 Aug 2010 11:32:40 +0000 (11:32 +0000)]
patch re issues.jalview.org/browse/JAL-583 : hack to prevent chains being mapped to sequences with different chainspecs

14 years agoupdate to Jmol 12.1.5 (will become 12.2.X when released)
jprocter [Wed, 25 Aug 2010 14:52:14 +0000 (14:52 +0000)]
update to Jmol 12.1.5 (will become 12.2.X when released)

14 years agoapplet now requires java 1.5 minimum (jmol 12.1.xx series is 1.5 only).
jprocter [Wed, 25 Aug 2010 14:17:55 +0000 (14:17 +0000)]
applet now requires java 1.5 minimum (jmol 12.1.xx series is 1.5 only).

14 years agoupdate to Jmol 12.1.5 (will become 12.2.X when released)
jprocter [Wed, 25 Aug 2010 14:16:31 +0000 (14:16 +0000)]
update to Jmol 12.1.5 (will become 12.2.X when released)

14 years agoinit Jmol with 'SmarterJmolAdapter'
jprocter [Wed, 25 Aug 2010 14:14:31 +0000 (14:14 +0000)]
init Jmol with 'SmarterJmolAdapter'

14 years agocorrect initing of JmolViewer to avoid security exception in unsigned applet moed
jprocter [Wed, 25 Aug 2010 14:13:52 +0000 (14:13 +0000)]
correct initing of JmolViewer to avoid security exception in unsigned applet moed

14 years agoexcluded methods related to broken Jmol applet binding mechanism (JAL-621)
jprocter [Wed, 25 Aug 2010 14:13:22 +0000 (14:13 +0000)]
excluded methods related to broken Jmol applet binding mechanism (JAL-621)

14 years agoexcluded methods related to broken Jmol applet binding mechanism (JAL-621) and implem...
jprocter [Wed, 25 Aug 2010 14:12:10 +0000 (14:12 +0000)]
excluded methods related to broken Jmol applet binding mechanism (JAL-621) and implemented default 'search all alignment' mode when opening a new PDB structure view

14 years agoensure template InstallAnywhere build file is always copied before file locations...
jprocter [Mon, 23 Aug 2010 15:08:48 +0000 (15:08 +0000)]
ensure template InstallAnywhere build file is always copied before file locations are updated