jalview.git
14 years agoextend jmol binding handles selection events and add in a 'refreshPdbEntries' step...
jprocter [Fri, 20 Aug 2010 11:54:04 +0000 (11:54 +0000)]
extend jmol binding handles selection events and add in a 'refreshPdbEntries' step so the list of PDB entries jalview knows about can be updated before a Jmol notifyUpdate event is handled

14 years agobinding between JalviewLite alignment windows and some external Jmol viewer
jprocter [Fri, 20 Aug 2010 11:52:40 +0000 (11:52 +0000)]
binding between JalviewLite alignment windows and some external Jmol viewer

14 years agoJAL-617 - new menu items for exporting current view or complete PCA pointset
jprocter [Wed, 18 Aug 2010 16:52:54 +0000 (16:52 +0000)]
JAL-617 - new menu items for exporting current view or complete PCA pointset

14 years agooutput the eigenvector matrix in full: JAL-616
jprocter [Wed, 18 Aug 2010 16:51:35 +0000 (16:51 +0000)]
output the eigenvector matrix in full: JAL-616

14 years agoJAL-612 - catch hidden OOM related to filling in cut and paste text boxes
jprocter [Wed, 18 Aug 2010 16:50:34 +0000 (16:50 +0000)]
JAL-612 - catch hidden OOM related to filling in cut and paste text boxes

14 years agonew appletlib path for jars specific to the applet
jprocter [Wed, 18 Aug 2010 12:57:39 +0000 (12:57 +0000)]
new appletlib path for jars specific to the applet

14 years agonew appletlib path for jars specific to the applet
jprocter [Wed, 18 Aug 2010 12:51:31 +0000 (12:51 +0000)]
new appletlib path for jars specific to the applet

14 years agosource level now 1.5
jprocter [Wed, 18 Aug 2010 12:50:30 +0000 (12:50 +0000)]
source level now 1.5

14 years agosource level now 1.5
jprocter [Wed, 18 Aug 2010 12:49:57 +0000 (12:49 +0000)]
source level now 1.5

14 years agosource level now 1.5
jprocter [Wed, 18 Aug 2010 12:49:30 +0000 (12:49 +0000)]
source level now 1.5

14 years agonew appletlib path for jars specific to the applet
jprocter [Wed, 18 Aug 2010 12:48:55 +0000 (12:48 +0000)]
new appletlib path for jars specific to the applet

14 years agoupdate Jmol to 12.0.6
jprocter [Wed, 18 Aug 2010 11:16:54 +0000 (11:16 +0000)]
update Jmol to 12.0.6

14 years ago1.5 annotation removal
jprocter [Wed, 18 Aug 2010 11:04:14 +0000 (11:04 +0000)]
1.5 annotation removal

14 years agoupdate jmol instance
jprocter [Wed, 18 Aug 2010 10:18:25 +0000 (10:18 +0000)]
update jmol instance

14 years agothread safe construction of Jmol instance and hack to translate invalid jmol state...
jprocter [Wed, 18 Aug 2010 10:16:36 +0000 (10:16 +0000)]
thread safe construction of Jmol instance and hack to translate invalid jmol state statements.

14 years agorefactor to abstract jmol/jalview binding and applet and application specific sequenc...
jprocter [Wed, 18 Aug 2010 10:15:01 +0000 (10:15 +0000)]
refactor to abstract jmol/jalview binding and applet and application specific sequence structure binding.

14 years agocode design comment
jprocter [Wed, 18 Aug 2010 10:13:30 +0000 (10:13 +0000)]
code design comment

14 years ago1.5 annotation fix and thread safe menu update
jprocter [Wed, 18 Aug 2010 10:12:47 +0000 (10:12 +0000)]
1.5 annotation fix and thread safe menu update

14 years agorefactor to jalview.api methods
jprocter [Wed, 18 Aug 2010 10:11:41 +0000 (10:11 +0000)]
refactor to jalview.api methods

14 years ago1.5 annotation fix
jprocter [Wed, 18 Aug 2010 10:10:02 +0000 (10:10 +0000)]
1.5 annotation fix

14 years agocolour menu items are in same radiobutton group
jprocter [Wed, 18 Aug 2010 10:09:04 +0000 (10:09 +0000)]
colour menu items are in same radiobutton group

14 years agocutn'paste fix so rna residue chains are assembled correctly
jprocter [Wed, 18 Aug 2010 10:08:10 +0000 (10:08 +0000)]
cutn'paste fix so rna residue chains are assembled correctly

14 years agoimproved parameter set store/save/rename logic and debugged parameter/option display
jprocter [Fri, 13 Aug 2010 13:07:53 +0000 (13:07 +0000)]
improved parameter set store/save/rename logic and debugged parameter/option display

14 years agojaba ws client revision 2680
jprocter [Wed, 11 Aug 2010 15:30:38 +0000 (15:30 +0000)]
jaba ws client revision 2680

14 years agoreverted dodgy test code
jprocter [Wed, 11 Aug 2010 15:29:22 +0000 (15:29 +0000)]
reverted dodgy test code

14 years agoimproved dialog layout and flow and fixed switching between presets. No preset save...
jprocter [Wed, 11 Aug 2010 14:15:45 +0000 (14:15 +0000)]
improved dialog layout and flow and fixed switching between presets. No preset save/load support yet.

14 years agoask user if they want to run the JabaWS tester on new URLs
jprocter [Wed, 11 Aug 2010 14:14:34 +0000 (14:14 +0000)]
ask user if they want to run the JabaWS tester on new URLs

14 years agorender jnlp artefacts for 1G and 2G machines (jalview_1G and jalview_2G.jnlp)
jprocter [Fri, 6 Aug 2010 14:30:16 +0000 (14:30 +0000)]
render jnlp artefacts for 1G and 2G machines (jalview_1G and jalview_2G.jnlp)

14 years agointeractive/batch mode test for groovy scripting (See JAL-611)
jprocter [Fri, 6 Aug 2010 11:04:56 +0000 (11:04 +0000)]
interactive/batch mode test for groovy scripting (See JAL-611)

14 years agoensure that both null and undefined colourscheme names resolve to 'None' when the...
jprocter [Wed, 4 Aug 2010 12:09:56 +0000 (12:09 +0000)]
ensure that both null and undefined colourscheme names resolve to 'None' when the applied colour scheme is reflected in the gui

14 years agoreorganised colourscheme enumeration to make it easier to add hardwired schemes.
jprocter [Wed, 4 Aug 2010 12:08:48 +0000 (12:08 +0000)]
reorganised colourscheme enumeration to make it easier to add hardwired schemes.

14 years agojabaws is the new jaba!
jprocter [Mon, 2 Aug 2010 16:05:35 +0000 (16:05 +0000)]
jabaws is the new jaba!

14 years agojaba!=jws2
jprocter [Wed, 21 Jul 2010 15:10:16 +0000 (15:10 +0000)]
jaba!=jws2

14 years agoURLs that begin with javascript: are opened in the same window. See
jprocter [Wed, 21 Jul 2010 15:06:07 +0000 (15:06 +0000)]
URLs that begin with javascript: are opened in the same window. See
http://issues.jalview.org/browse/JAL-604

14 years agoless ambiguous feature style description
jprocter [Tue, 20 Jul 2010 09:07:22 +0000 (09:07 +0000)]
less ambiguous feature style description

14 years agoremoved 'method notes' comment in job output.
jprocter [Tue, 20 Jul 2010 09:06:19 +0000 (09:06 +0000)]
removed 'method notes' comment in job output.

14 years agoupdate to Jaba_r1 minimal client distribution, and resolve issues JAL-602
jprocter [Tue, 20 Jul 2010 09:05:46 +0000 (09:05 +0000)]
update to Jaba_r1 minimal client distribution, and resolve issues JAL-602

14 years agowrong config string
jprocter [Sun, 11 Jul 2010 18:24:34 +0000 (18:24 +0000)]
wrong config string

14 years agojaba on classpath
jprocter [Sun, 11 Jul 2010 17:18:18 +0000 (17:18 +0000)]
jaba on classpath

14 years agono tooltip and cleaner parameter layout
jprocter [Sun, 11 Jul 2010 13:48:48 +0000 (13:48 +0000)]
no tooltip and cleaner parameter layout

14 years agodivide services by host within the menu
jprocter [Sun, 11 Jul 2010 13:48:25 +0000 (13:48 +0000)]
divide services by host within the menu

14 years agojaba is the new name.
jprocter [Sun, 11 Jul 2010 13:47:43 +0000 (13:47 +0000)]
jaba is the new name.

14 years agodefault public service URL
jprocter [Thu, 1 Jul 2010 15:48:56 +0000 (15:48 +0000)]
default public service URL

14 years agojmol 12 patch - ensure we replace the correct filename in the jmol script before...
jprocter [Tue, 29 Jun 2010 16:24:11 +0000 (16:24 +0000)]
jmol 12 patch - ensure we replace the correct filename in the jmol script before it gets executed

14 years agoupgrading structure/sequence binding so that a structure view can contain many pdb...
jprocter [Tue, 29 Jun 2010 16:23:00 +0000 (16:23 +0000)]
upgrading structure/sequence binding so that a structure view can contain many pdb files

14 years agonew ajax api methods for linking existing jmol viewers with sequences in an alignframe
jprocter [Tue, 29 Jun 2010 16:22:02 +0000 (16:22 +0000)]
new ajax api methods for linking existing jmol viewers with sequences in an alignframe

14 years agointerfaces implemented by jalview renderers
jprocter [Tue, 29 Jun 2010 16:20:37 +0000 (16:20 +0000)]
interfaces implemented by jalview renderers

14 years agoproxy interface for structure viewers that jalview works with
jprocter [Tue, 29 Jun 2010 16:20:11 +0000 (16:20 +0000)]
proxy interface for structure viewers that jalview works with

14 years agonew abstract proxy for use by applet and application
jprocter [Tue, 29 Jun 2010 16:19:32 +0000 (16:19 +0000)]
new abstract proxy for use by applet and application

14 years agoupgrade to InstallAnywhere 2010 and ensure minimum vm size is 32M, and max is 256M
jprocter [Tue, 29 Jun 2010 16:14:40 +0000 (16:14 +0000)]
upgrade to InstallAnywhere 2010 and ensure minimum vm size is 32M, and max is 256M

14 years agopatch for npe that occurs for importing Jalview projects where group conservation...
jprocter [Tue, 29 Jun 2010 15:21:16 +0000 (15:21 +0000)]
patch for npe that occurs for importing Jalview projects where group conservation is displayed but no conservation for alignment is displayed - (observed during Jmol patching)

14 years agotypo bugfix
jprocter [Tue, 29 Jun 2010 09:43:53 +0000 (09:43 +0000)]
typo bugfix

14 years agocatch OOM earlier * JAL-595
jprocter [Tue, 29 Jun 2010 09:42:46 +0000 (09:42 +0000)]
catch OOM earlier * JAL-595

14 years agodrop down selection of different parameter sets
jprocter [Mon, 28 Jun 2010 13:56:13 +0000 (13:56 +0000)]
drop down selection of different parameter sets

14 years agoedit jws2 job parameters before running job
jprocter [Sun, 27 Jun 2010 17:17:17 +0000 (17:17 +0000)]
edit jws2 job parameters before running job

14 years agoprototype - implementation in progress JAL-591
jprocter [Tue, 22 Jun 2010 12:37:22 +0000 (12:37 +0000)]
prototype - implementation in progress JAL-591

14 years agoset program name to service type (see related issues to JAL-493 re setting provenance...
jprocter [Mon, 21 Jun 2010 10:16:50 +0000 (10:16 +0000)]
set program name to service type (see related issues to JAL-493 re setting provenance correctly)

14 years agoorganisation by host and service type
jprocter [Mon, 21 Jun 2010 10:16:14 +0000 (10:16 +0000)]
organisation by host and service type

14 years agogeneric action text method
jprocter [Mon, 21 Jun 2010 10:15:46 +0000 (10:15 +0000)]
generic action text method

14 years agoensure service menu is rebuilt after update listeners registered, and flatten JWS2...
jprocter [Mon, 21 Jun 2010 10:15:25 +0000 (10:15 +0000)]
ensure service menu is rebuilt after update listeners registered, and flatten JWS2 service tree.

14 years ago2.6 docs
jprocter [Sat, 19 Jun 2010 17:03:52 +0000 (17:03 +0000)]
2.6 docs

14 years agonew web services preference tab (JAL-589)
jprocter [Sat, 19 Jun 2010 16:44:37 +0000 (16:44 +0000)]
new web services preference tab (JAL-589)

14 years agorejigged change support to make it (more) reliable
jprocter [Sat, 19 Jun 2010 16:43:39 +0000 (16:43 +0000)]
rejigged change support to make it (more) reliable

14 years agonew jmol/pdb relates api calls
jprocter [Fri, 18 Jun 2010 08:15:04 +0000 (08:15 +0000)]
new jmol/pdb relates api calls

14 years agoadded new jmol to install manifest
jprocter [Thu, 17 Jun 2010 16:31:34 +0000 (16:31 +0000)]
added new jmol to install manifest

14 years agoupdate jmol jar version for applet
jprocter [Thu, 17 Jun 2010 16:21:51 +0000 (16:21 +0000)]
update jmol jar version for applet

14 years agoremove source annotations
jprocter [Thu, 17 Jun 2010 16:07:49 +0000 (16:07 +0000)]
remove source annotations

14 years agoupdate to Jmol series 12 (JAL-582)
jprocter [Thu, 17 Jun 2010 15:53:13 +0000 (15:53 +0000)]
update to Jmol series 12 (JAL-582)

14 years agoNPE in hashtable constructor
jprocter [Tue, 15 Jun 2010 10:16:55 +0000 (10:16 +0000)]
NPE in hashtable constructor

14 years agoupdate latest version
jprocter [Tue, 15 Jun 2010 07:11:20 +0000 (07:11 +0000)]
update latest version

14 years agostop multiple dialogs appearing one after another (in progress for JAL-414)
jprocter [Mon, 14 Jun 2010 12:47:21 +0000 (12:47 +0000)]
stop multiple dialogs appearing one after another (in progress for JAL-414)

14 years agoadd patch for JAL-572 to release history
jprocter [Mon, 14 Jun 2010 11:43:47 +0000 (11:43 +0000)]
add patch for JAL-572 to release history

14 years agopatch for JAL-572
jprocter [Mon, 14 Jun 2010 11:21:34 +0000 (11:21 +0000)]
patch for JAL-572

14 years agoadded min-jws2 jar to classpath
jprocter [Mon, 14 Jun 2010 10:51:48 +0000 (10:51 +0000)]
added min-jws2 jar to classpath

14 years agoJGoogleAnalytics on classpath.
jprocter [Mon, 14 Jun 2010 10:18:04 +0000 (10:18 +0000)]
JGoogleAnalytics on classpath.

14 years agodocumented the -colour command line argument.
jprocter [Sat, 12 Jun 2010 12:45:52 +0000 (12:45 +0000)]
documented the -colour command line argument.

14 years agostockholm added as readable format (Lauren Lui commit)
jprocter [Fri, 11 Jun 2010 15:06:12 +0000 (15:06 +0000)]
stockholm added as readable format (Lauren Lui commit)

14 years agoensure enfin service is started in background when desktop is displayed
jprocter [Fri, 11 Jun 2010 14:57:02 +0000 (14:57 +0000)]
ensure enfin service is started in background when desktop is displayed

14 years agojalview 2.5.1 release notes
jprocter [Fri, 11 Jun 2010 14:39:04 +0000 (14:39 +0000)]
jalview 2.5.1 release notes

14 years agopatch for JAL-556 - more robust mapping of sequence to structure sequence with correc...
jprocter [Fri, 11 Jun 2010 09:54:26 +0000 (09:54 +0000)]
patch for JAL-556 - more robust mapping of sequence to structure sequence with correct substitution matrix

14 years agopatch for JAL-556
jprocter [Fri, 11 Jun 2010 09:54:14 +0000 (09:54 +0000)]
patch for JAL-556

14 years agopatched for JAL-531 - only display full symbol distribution stats on tooltip/annotati...
jprocter [Fri, 11 Jun 2010 07:59:54 +0000 (07:59 +0000)]
patched for JAL-531 - only display full symbol distribution stats on tooltip/annotation label when the sequenceLogo is displayed.

14 years agopatch for JAL-545 - make deep copy of feature settings
jprocter [Wed, 9 Jun 2010 14:06:02 +0000 (14:06 +0000)]
patch for JAL-545 - make deep copy of feature settings

14 years agopatch for JAL-555
jprocter [Wed, 9 Jun 2010 12:09:58 +0000 (12:09 +0000)]
patch for JAL-555

14 years agopaste menu display on OSX Leopard * JAL-557
jprocter [Wed, 9 Jun 2010 12:09:07 +0000 (12:09 +0000)]
paste menu display on OSX Leopard * JAL-557

14 years agoOSX look and feel JAL-577
jprocter [Wed, 9 Jun 2010 12:07:57 +0000 (12:07 +0000)]
OSX look and feel JAL-577

14 years agofollowSelections flag now set via user preferences, and disabled for 2.5.1 * JAL...
jprocter [Tue, 8 Jun 2010 14:48:29 +0000 (14:48 +0000)]
followSelections flag now set via user preferences, and disabled for 2.5.1 * JAL-574 and * JAL-576

14 years agobetter test for when to update column selection when receiving a selection message...
jprocter [Tue, 8 Jun 2010 14:30:34 +0000 (14:30 +0000)]
better test for when to update column selection when receiving a selection message * JAL-574

14 years agotrim hidden regions outside selection when copying selected region to clipboard ...
jprocter [Tue, 8 Jun 2010 14:27:20 +0000 (14:27 +0000)]
trim hidden regions outside selection when copying selected region to clipboard * JAL-573

14 years agoPatch for incorrect column selection when hidden regions are present * JAL-558
jprocter [Tue, 8 Jun 2010 14:25:35 +0000 (14:25 +0000)]
Patch for incorrect column selection when hidden regions are present * JAL-558

14 years agopatch for JAL-542
jprocter [Sun, 6 Jun 2010 14:57:15 +0000 (14:57 +0000)]
patch for JAL-542

14 years agoFix for * JAL-541
jprocter [Sun, 6 Jun 2010 14:27:48 +0000 (14:27 +0000)]
Fix for * JAL-541

14 years agoresolution for * JAL-553
jprocter [Fri, 4 Jun 2010 16:18:54 +0000 (16:18 +0000)]
resolution for * JAL-553

14 years agoupdate group annotation for new treegroups (JAL-552)
jprocter [Fri, 4 Jun 2010 16:09:49 +0000 (16:09 +0000)]
update group annotation for new treegroups (JAL-552)

14 years agocorrect popup menu, ensure panel doesn't disappear when empty (patches for JAL-554...
jprocter [Fri, 4 Jun 2010 15:45:44 +0000 (15:45 +0000)]
correct popup menu, ensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL-562) and first patch for annotation label redraw (JAL-563)

14 years agofirst patch for JAL-563 - attempt to relayout annotation panel after adjusting heights
jprocter [Fri, 4 Jun 2010 15:44:14 +0000 (15:44 +0000)]
first patch for JAL-563 - attempt to relayout annotation panel after adjusting heights

14 years agoensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL...
jprocter [Fri, 4 Jun 2010 15:39:01 +0000 (15:39 +0000)]
ensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL-562)

14 years agopatches for JAL-554 and JAL-570
jprocter [Fri, 4 Jun 2010 15:32:37 +0000 (15:32 +0000)]
patches for JAL-554 and JAL-570
focus is explicitly handed back to caller (JAL-566)

14 years agofocus is explicitly handed back to caller (JAL-566)
jprocter [Fri, 4 Jun 2010 15:26:44 +0000 (15:26 +0000)]
focus is explicitly handed back to caller (JAL-566)

14 years agofocus is explicitly handed back to caller (JAL-566)
jprocter [Fri, 4 Jun 2010 15:20:46 +0000 (15:20 +0000)]
focus is explicitly handed back to caller (JAL-566)