jalview.git
13 years agopatched XML parser to ensure it properly escapes non-html friendly characters prior...
jprocter [Tue, 19 Apr 2011 13:55:01 +0000 (13:55 +0000)]
patched XML parser to ensure it properly escapes non-html friendly characters prior to tooltip generation (resolves JAL-808)

13 years agotodo
jprocter [Fri, 8 Apr 2011 17:22:04 +0000 (17:22 +0000)]
todo

13 years agoimported properties via -props should never be overwritten
jprocter [Fri, 8 Apr 2011 16:10:21 +0000 (16:10 +0000)]
imported properties via -props should never be overwritten

13 years agoallow groovy scripts to be run when in headless mode - pass startupAlFrame as context
jprocter [Fri, 8 Apr 2011 10:57:44 +0000 (10:57 +0000)]
allow groovy scripts to be run when in headless mode - pass startupAlFrame as context

13 years agoallow groovy scripts to be run when in headless mode - pass startupAlFrame as context
jprocter [Thu, 7 Apr 2011 22:18:22 +0000 (22:18 +0000)]
allow groovy scripts to be run when in headless mode - pass startupAlFrame as context

13 years agoallow groovy scripts to be run when in headless mode - pass startupAlFrame as context
jprocter [Thu, 7 Apr 2011 22:08:42 +0000 (22:08 +0000)]
allow groovy scripts to be run when in headless mode - pass startupAlFrame as context

13 years agoresolves JAL-805
jprocter [Thu, 7 Apr 2011 13:05:39 +0000 (13:05 +0000)]
resolves JAL-805

13 years agoresolves JAL-804
jprocter [Thu, 7 Apr 2011 11:04:46 +0000 (11:04 +0000)]
resolves JAL-804

13 years agoexcess imports
jprocter [Mon, 28 Feb 2011 10:48:21 +0000 (10:48 +0000)]
excess imports

13 years agopatch for JAL-780
jprocter [Sun, 27 Feb 2011 18:37:45 +0000 (18:37 +0000)]
patch for JAL-780

13 years agopatch for occasional ArrayIndexOutOfBounds
jprocter [Sun, 27 Feb 2011 18:35:54 +0000 (18:35 +0000)]
patch for occasional ArrayIndexOutOfBounds

13 years agopatch for JAL-792
jprocter [Sun, 27 Feb 2011 18:35:28 +0000 (18:35 +0000)]
patch for JAL-792

13 years agofirst patch for JAL-774 - ensure end is a valid bound to limit search for last sequen...
jprocter [Sun, 27 Feb 2011 17:13:47 +0000 (17:13 +0000)]
first patch for JAL-774 - ensure end is a valid bound to limit search for last sequence position (at least as long as sequence)

13 years agofirst approximation for JAL-782 - hint that opaque groupName is actually the name
jprocter [Fri, 25 Feb 2011 17:10:24 +0000 (17:10 +0000)]
first approximation for JAL-782 - hint that opaque groupName is actually the name

13 years agoJAL-777/JAL-641 debugging
jprocter [Fri, 18 Feb 2011 17:33:41 +0000 (17:33 +0000)]
JAL-777/JAL-641 debugging

13 years agonew alignmentPanel api + JAL-777/JAL-641 debugging
jprocter [Fri, 18 Feb 2011 17:33:30 +0000 (17:33 +0000)]
new alignmentPanel api  + JAL-777/JAL-641 debugging

13 years agofix scrolltoposition behaviour and new alignmentPanel api
jprocter [Fri, 18 Feb 2011 17:31:29 +0000 (17:31 +0000)]
fix scrolltoposition behaviour and new alignmentPanel api

13 years agofix scrolltoposition behaviour
jprocter [Fri, 18 Feb 2011 17:30:49 +0000 (17:30 +0000)]
fix scrolltoposition behaviour

13 years agoJAL-574
jprocter [Fri, 18 Feb 2011 17:30:18 +0000 (17:30 +0000)]
JAL-574

13 years agoconvenience method to discover all Jmols
jprocter [Fri, 18 Feb 2011 17:29:50 +0000 (17:29 +0000)]
convenience method to discover all Jmols

13 years agoJAL-779 and some redraw refinements
jprocter [Fri, 18 Feb 2011 17:24:29 +0000 (17:24 +0000)]
JAL-779 and some redraw refinements

13 years agoJAl-574
jprocter [Fri, 18 Feb 2011 17:19:53 +0000 (17:19 +0000)]
JAl-574

13 years agoavoid exceptions for orphaned windows
jprocter [Fri, 18 Feb 2011 17:18:57 +0000 (17:18 +0000)]
avoid exceptions for orphaned windows

13 years agobugfixing for JAL-778
jprocter [Fri, 18 Feb 2011 17:18:25 +0000 (17:18 +0000)]
bugfixing for JAL-778

13 years agonew multiple multiple view associations JAL-777
jprocter [Fri, 18 Feb 2011 17:18:12 +0000 (17:18 +0000)]
new multiple multiple view associations JAL-777

13 years agocall to release any explicit event handler references and fix for occasional arrayInd...
jprocter [Fri, 18 Feb 2011 17:16:39 +0000 (17:16 +0000)]
call to release any explicit event handler references and fix for occasional arrayIndexOutOfboundsErrors

13 years agodynamic alignmentPanel menu class
jprocter [Fri, 18 Feb 2011 17:16:00 +0000 (17:16 +0000)]
dynamic alignmentPanel menu class

13 years agocall to release any explicit event handler references
jprocter [Fri, 18 Feb 2011 17:15:36 +0000 (17:15 +0000)]
call to release any explicit event handler references

13 years agoremoved explicit 'linkedAlignmentPanel' flag
jprocter [Fri, 18 Feb 2011 17:12:41 +0000 (17:12 +0000)]
removed explicit 'linkedAlignmentPanel' flag

13 years agofix for occasional race conditions
jprocter [Fri, 18 Feb 2011 17:12:22 +0000 (17:12 +0000)]
fix for occasional race conditions

13 years agofixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view...
jprocter [Thu, 17 Feb 2011 11:29:57 +0000 (11:29 +0000)]
fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view for colouring and optionally for superposition as well.

13 years agoprotype api
jprocter [Thu, 17 Feb 2011 11:26:05 +0000 (11:26 +0000)]
protype api

13 years agoclassCast exception - attempting to update registry to bind jalview object to the...
jprocter [Thu, 17 Feb 2011 11:25:42 +0000 (11:25 +0000)]
classCast exception - attempting to update registry to bind jalview object to the VorbaId rather than the actual Vamsas data object the VorbaId refers to.

13 years agofix for JAL-776
jprocter [Tue, 15 Feb 2011 16:30:33 +0000 (16:30 +0000)]
fix for JAL-776

13 years agofixes JAL-775
jprocter [Tue, 15 Feb 2011 14:43:07 +0000 (14:43 +0000)]
fixes JAL-775

13 years agoJAL-769
jprocter [Mon, 14 Feb 2011 12:58:37 +0000 (12:58 +0000)]
JAL-769

13 years agoJAL-564 (annotation panel height adjustment) and alignment annotation popup menu...
jprocter [Mon, 14 Feb 2011 10:56:51 +0000 (10:56 +0000)]
JAL-564 (annotation panel height adjustment) and alignment annotation popup menu items for JAL-759

13 years agoJAL-621 (mouseover debugging) and JAL-564 (annotation panel height adjustment)
jprocter [Mon, 14 Feb 2011 10:55:13 +0000 (10:55 +0000)]
JAL-621 (mouseover debugging) and JAL-564 (annotation panel height adjustment)

13 years agoJAL-621 and JAL-564
jprocter [Mon, 14 Feb 2011 10:53:59 +0000 (10:53 +0000)]
JAL-621 and JAL-564

13 years agoJAL-621 - also renamed list of javascript handlers
jprocter [Mon, 14 Feb 2011 10:52:32 +0000 (10:52 +0000)]
JAL-621 - also renamed list of javascript handlers

13 years agorefactored annotation panel height calculation
jprocter [Mon, 14 Feb 2011 10:51:25 +0000 (10:51 +0000)]
refactored annotation panel height calculation

13 years agoJAL-621 - also renamed list of javascript handlers
jprocter [Mon, 14 Feb 2011 10:46:29 +0000 (10:46 +0000)]
JAL-621 - also renamed list of javascript handlers

13 years agojavadoc
jprocter [Mon, 14 Feb 2011 10:40:53 +0000 (10:40 +0000)]
javadoc

13 years agoBalascz reported problems - jalview tries to write back to the URL. Fixed this so...
jprocter [Fri, 4 Feb 2011 16:10:54 +0000 (16:10 +0000)]
Balascz reported problems - jalview tries to write back to the URL. Fixed this so that Jalview will only write back to properties files, and also ensured properties are modified before potentially failing writes occur.

13 years agoJAL-761
jprocter [Fri, 4 Feb 2011 15:30:50 +0000 (15:30 +0000)]
JAL-761

13 years ago1.2ish awt methods
jprocter [Fri, 4 Feb 2011 12:04:46 +0000 (12:04 +0000)]
1.2ish awt methods

13 years agojava 1.4.2 applet build
jprocter [Fri, 4 Feb 2011 12:00:28 +0000 (12:00 +0000)]
java 1.4.2 applet build

13 years ago1.2ish awt methods and excluding unused code
jprocter [Fri, 4 Feb 2011 11:34:20 +0000 (11:34 +0000)]
1.2ish awt methods and excluding unused code

13 years agodon't need to retrieve idwidthadjuster
jprocter [Fri, 4 Feb 2011 11:26:34 +0000 (11:26 +0000)]
don't need to retrieve idwidthadjuster

13 years agojavadoc
jprocter [Fri, 4 Feb 2011 11:16:03 +0000 (11:16 +0000)]
javadoc

13 years agopatch for JAL-760
jprocter [Fri, 4 Feb 2011 11:11:26 +0000 (11:11 +0000)]
patch for JAL-760

13 years agogroup associated annotation and logos JAL-516 JAL-759
jprocter [Fri, 4 Feb 2011 11:07:42 +0000 (11:07 +0000)]
group associated annotation and logos JAL-516 JAL-759

13 years agoadjustable annotation panel height and vertical scrollbar JAL-516,JAL-338,JAL-306
jprocter [Fri, 4 Feb 2011 10:44:26 +0000 (10:44 +0000)]
adjustable annotation panel height and vertical scrollbar JAL-516,JAL-338,JAL-306

13 years agofixes JAL-757
jprocter [Tue, 1 Feb 2011 14:17:11 +0000 (14:17 +0000)]
fixes JAL-757

13 years agoextended mouseover message with absolute sequence position info JAL-433, relaxed...
jprocter [Fri, 21 Jan 2011 17:15:21 +0000 (17:15 +0000)]
extended mouseover message with absolute sequence position info JAL-433, relaxed id matching for order/selection/highlighting JAL-753 and order/getOrder methods JAL-754

13 years agosearch result highlighting and scrolling and some patches for JAL-695
jprocter [Fri, 21 Jan 2011 17:12:03 +0000 (17:12 +0000)]
search result highlighting and scrolling and some patches for JAL-695

13 years agomore efficient highlighting and selection display JAL-469
jprocter [Fri, 21 Jan 2011 17:10:23 +0000 (17:10 +0000)]
more efficient highlighting and selection display JAL-469

13 years agomore efficient highlighting and selection display
jprocter [Fri, 21 Jan 2011 17:09:43 +0000 (17:09 +0000)]
more efficient highlighting and selection display

13 years agologic bug for auto scrolling
jprocter [Fri, 21 Jan 2011 17:08:29 +0000 (17:08 +0000)]
logic bug for auto scrolling

13 years agorelaxed ID matching parameter JAL-753 and sortBy JAL-754
jprocter [Fri, 21 Jan 2011 17:07:31 +0000 (17:07 +0000)]
relaxed ID matching parameter JAL-753 and sortBy JAL-754

13 years agorelaxed ID matching parameter JAL-753
jprocter [Fri, 21 Jan 2011 17:05:43 +0000 (17:05 +0000)]
relaxed ID matching parameter JAL-753

13 years agoensure source is rarely null
jprocter [Fri, 21 Jan 2011 17:03:40 +0000 (17:03 +0000)]
ensure source is rarely null

13 years agoextended mouseover message with absolute sequence position info JAL-433
jprocter [Fri, 21 Jan 2011 17:03:10 +0000 (17:03 +0000)]
extended mouseover message with absolute sequence position info JAL-433

13 years agopatch for JAL-695 - need to test if this is observed in applet
jprocter [Tue, 18 Jan 2011 17:46:08 +0000 (17:46 +0000)]
patch for JAL-695 - need to test if this is observed in applet

13 years agopatch for JAL-695
jprocter [Tue, 18 Jan 2011 17:43:16 +0000 (17:43 +0000)]
patch for JAL-695

13 years agojavadoc
jprocter [Tue, 18 Jan 2011 17:41:48 +0000 (17:41 +0000)]
javadoc

13 years agojavadoc
jprocter [Tue, 18 Jan 2011 17:40:53 +0000 (17:40 +0000)]
javadoc

13 years agoavoid creating lots of identical search results. patch for JAL-751
jprocter [Tue, 18 Jan 2011 17:40:16 +0000 (17:40 +0000)]
avoid creating lots of identical search results. patch for JAL-751

13 years agoremoved securityException caused by accessing class directly from sun. package
jprocter [Tue, 18 Jan 2011 10:42:20 +0000 (10:42 +0000)]
removed securityException caused by accessing class directly from sun. package

13 years agorefactored VamsasListener to allow the source of the event to be passed to handlers
jprocter [Tue, 18 Jan 2011 10:33:11 +0000 (10:33 +0000)]
refactored VamsasListener to allow the source of the event to be passed to handlers

13 years agoadditional test - http://www.koders.com/java/fid4C9593FE80CE8AA81158AF712B50C7A689488...
jprocter [Mon, 17 Jan 2011 15:54:27 +0000 (15:54 +0000)]
additional test - koders.com/java/fid4C9593FE80CE8AA81158AF712B50C7A689488FD8.aspx c.f. JAL-749

13 years agowarn user that no JS callbacks will work by default, and show stacktrace if debug...
jprocter [Mon, 17 Jan 2011 15:36:06 +0000 (15:36 +0000)]
warn user that no JS callbacks will work by default, and show stacktrace if debug is enabled JAL-749

13 years agoneed to own lock to notify
jprocter [Mon, 17 Jan 2011 15:11:46 +0000 (15:11 +0000)]
need to own lock to notify

13 years agoneed to own lock to notify
jprocter [Mon, 17 Jan 2011 14:48:52 +0000 (14:48 +0000)]
need to own lock to notify

13 years agoavoid 1.5 specific methods
jprocter [Mon, 17 Jan 2011 14:32:45 +0000 (14:32 +0000)]
avoid 1.5 specific methods

13 years agorevised default separator string expression to avoid utf8 warnings. Regularised new...
jprocter [Mon, 17 Jan 2011 14:28:35 +0000 (14:28 +0000)]
revised default separator string expression to avoid utf8 warnings. Regularised new api methods (select, selectIn(alignFrame..), ). improved separatorList routines and added onInit javascript callback.

13 years agoallow debug messages to be output before jscallback execution
jprocter [Mon, 17 Jan 2011 14:27:06 +0000 (14:27 +0000)]
allow debug messages to be output before jscallback execution

13 years agorefactored javascript callback to parent class.
jprocter [Mon, 17 Jan 2011 13:59:00 +0000 (13:59 +0000)]
refactored javascript callback to parent class.

13 years agoeliminate utf8 compilation errors
jprocter [Mon, 17 Jan 2011 13:57:51 +0000 (13:57 +0000)]
eliminate utf8 compilation errors

13 years agouse local reference for current target frame as set by JAL-451
jprocter [Mon, 17 Jan 2011 13:56:09 +0000 (13:56 +0000)]
use local reference for current target frame as set by JAL-451

13 years agoJAL-750 and JAL-451
jprocter [Mon, 17 Jan 2011 13:51:25 +0000 (13:51 +0000)]
JAL-750 and JAL-451

13 years agooutput jsexception message
jprocter [Thu, 13 Jan 2011 11:03:47 +0000 (11:03 +0000)]
output jsexception message

13 years agohandlers with no specified alignframe broadcast events from all applet's alignFrames
jprocter [Wed, 12 Jan 2011 23:01:10 +0000 (23:01 +0000)]
handlers with no specified alignframe broadcast events from all applet's alignFrames

13 years agoapplication compilation time dependency plugin.jar needed for jalview.javascript...
jprocter [Wed, 12 Jan 2011 22:14:57 +0000 (22:14 +0000)]
application compilation time dependency plugin.jar needed for jalview.javascript interfaces

13 years agoupdated jar dependencies
jprocter [Wed, 12 Jan 2011 22:01:29 +0000 (22:01 +0000)]
updated jar dependencies

13 years ago1.1 compat
jprocter [Wed, 12 Jan 2011 18:41:02 +0000 (18:41 +0000)]
1.1 compat

13 years agojavascript callback for selection, mousover, and functions for selection and highligh...
jprocter [Wed, 12 Jan 2011 17:05:05 +0000 (17:05 +0000)]
javascript callback for selection, mousover, and functions for selection and highlighting JAL-469 JAL-433 JAL-744

13 years agoselection should be sent after refresh happens
jprocter [Wed, 12 Jan 2011 17:02:47 +0000 (17:02 +0000)]
selection should be sent after refresh happens

13 years agojavadoc
jprocter [Wed, 12 Jan 2011 16:59:19 +0000 (16:59 +0000)]
javadoc

13 years agojava side javascript callback enactors JAL-469
jprocter [Wed, 12 Jan 2011 16:59:00 +0000 (16:59 +0000)]
java side javascript callback enactors JAL-469

13 years agoupdated dependencies for project
jprocter [Wed, 12 Jan 2011 16:57:50 +0000 (16:57 +0000)]
updated dependencies for project

13 years agojalviewLite now needs plugin.jar from jre so it can access JSObject class for javascr...
jprocter [Wed, 12 Jan 2011 16:57:24 +0000 (16:57 +0000)]
jalviewLite now needs plugin.jar from jre so it can access JSObject class for javascript/java callbacks JAL-469

13 years agopatch for JAL-740
jprocter [Mon, 10 Jan 2011 17:00:30 +0000 (17:00 +0000)]
patch for JAL-740

13 years agorefactored dropFile allowing known information to be passed in if available
jprocter [Fri, 7 Jan 2011 13:17:22 +0000 (13:17 +0000)]
refactored dropFile allowing known information to be passed in if available

13 years agobulk associate pdb files dropped on to alignment : JAL-732
jprocter [Fri, 7 Jan 2011 13:16:49 +0000 (13:16 +0000)]
bulk associate pdb files dropped on to alignment : JAL-732

13 years agorefactored guts of pdb file association code
jprocter [Fri, 7 Jan 2011 13:16:24 +0000 (13:16 +0000)]
refactored guts of pdb file association code

13 years agocheck for all http protocols
jprocter [Fri, 7 Jan 2011 13:11:36 +0000 (13:11 +0000)]
check for all http protocols

13 years agorefactored to use SequenceI
jprocter [Fri, 7 Jan 2011 13:10:41 +0000 (13:10 +0000)]
refactored to use SequenceI

13 years agoJAL-730
jprocter [Thu, 6 Jan 2011 15:53:25 +0000 (15:53 +0000)]
JAL-730

13 years agomore robust calculation of partition from possibly overlapping groups, and check...
jprocter [Wed, 5 Jan 2011 16:06:36 +0000 (16:06 +0000)]
more robust calculation of partition from possibly overlapping groups, and check to ensure minimum group size is honoured