jalview.git
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

14 years agoavoid race condition by setting sequence logo flag directly rather than via accessor...
jprocter [Fri, 20 Aug 2010 14:56:26 +0000 (14:56 +0000)]
avoid race condition by setting sequence logo flag directly rather than via accessor. See todo for further threadsafety

14 years agorollback to 1.58 - since excludes are unnecessary
jprocter [Fri, 20 Aug 2010 13:14:28 +0000 (13:14 +0000)]
rollback to 1.58 - since excludes are unnecessary

14 years agobroken xml ? (could be old ant issue)
jprocter [Fri, 20 Aug 2010 13:00:28 +0000 (13:00 +0000)]
broken xml ? (could be old ant issue)

14 years agocomplete the sequence-structure mapping details. * JAL-582
jprocter [Fri, 20 Aug 2010 12:32:51 +0000 (12:32 +0000)]
complete the sequence-structure mapping details. * JAL-582

14 years agorefactor jmol api so it doesn't clash with Swing component method. * JAL-582
jprocter [Fri, 20 Aug 2010 12:32:13 +0000 (12:32 +0000)]
refactor jmol api so it doesn't clash with Swing component method. * JAL-582

14 years agocheck that we have mappings before trying to broadcast mouseovers involving them
jprocter [Fri, 20 Aug 2010 12:31:33 +0000 (12:31 +0000)]
check that we have mappings before trying to broadcast mouseovers involving them

14 years ago(probably unnecessary) explicit inclusion of jalview/ext package
jprocter [Fri, 20 Aug 2010 11:59:09 +0000 (11:59 +0000)]
(probably unnecessary) explicit inclusion of jalview/ext package

14 years agorefactored external structure viewer binding API calls so they do not reference Jmol...
jprocter [Fri, 20 Aug 2010 11:58:12 +0000 (11:58 +0000)]
refactored external structure viewer binding API calls so they do not reference Jmol classes (re-instate's Jmol free launch of JalviewLite).

14 years agowrapped code from URL retrieval tester as a function to determine correct protocol...
jprocter [Fri, 20 Aug 2010 11:56:45 +0000 (11:56 +0000)]
wrapped code from URL retrieval tester as a function to determine correct protocol to retrieve data of a certain type from a datasource string. note - not rigourously tested

14 years agoimproved debug output when Jmol viewer creation fails
jprocter [Fri, 20 Aug 2010 11:55:01 +0000 (11:55 +0000)]
improved debug output when Jmol viewer creation fails

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)