jalview.git
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

13 years agoinline submission of alignment with correct crlf
jprocter [Wed, 5 Jan 2011 16:06:03 +0000 (16:06 +0000)]
inline submission of alignment with correct crlf

13 years agoensure group props are recalculated before alignment displayed
jprocter [Wed, 5 Jan 2011 16:05:47 +0000 (16:05 +0000)]
ensure group props are recalculated before alignment displayed

13 years agorevised shmr service
jprocter [Wed, 5 Jan 2011 16:05:15 +0000 (16:05 +0000)]
revised shmr service

13 years agotodo and ensure old annotation/groups are removed before new ones loaded back
jprocter [Wed, 5 Jan 2011 16:04:56 +0000 (16:04 +0000)]
todo and ensure old annotation/groups are removed before new ones loaded back

13 years agotodo
jprocter [Wed, 5 Jan 2011 16:04:17 +0000 (16:04 +0000)]
todo

13 years agoexception reporting for bad URLs
jprocter [Wed, 5 Jan 2011 16:03:33 +0000 (16:03 +0000)]
exception reporting for bad URLs

13 years agoJAL-727
jprocter [Wed, 5 Jan 2011 15:52:16 +0000 (15:52 +0000)]
JAL-727

13 years agoJAL-727
jprocter [Wed, 5 Jan 2011 15:37:11 +0000 (15:37 +0000)]
JAL-727

13 years agopropagated groups trimmed to correct region on viscontig
jprocter [Wed, 5 Jan 2011 15:36:30 +0000 (15:36 +0000)]
propagated groups trimmed to correct region on viscontig

13 years agographThreshold not being copied by constructor
jprocter [Wed, 5 Jan 2011 15:36:05 +0000 (15:36 +0000)]
graphThreshold not being copied by constructor

13 years agofirst publicly accessible test of JAL-724
jprocter [Fri, 17 Dec 2010 16:54:42 +0000 (16:54 +0000)]
first publicly accessible test of JAL-724

13 years agoJAL-715 and JAL-724
jprocter [Fri, 17 Dec 2010 16:53:32 +0000 (16:53 +0000)]
JAL-715 and JAL-724

13 years agoJAL-715
jprocter [Fri, 17 Dec 2010 16:53:13 +0000 (16:53 +0000)]
JAL-715

13 years agorefined modification test
jprocter [Fri, 17 Dec 2010 16:48:26 +0000 (16:48 +0000)]
refined modification test

13 years agorefactored gap insert/visible view modification code from JPredThread
jprocter [Fri, 17 Dec 2010 16:47:51 +0000 (16:47 +0000)]
refactored gap insert/visible view modification code from JPredThread

13 years agoadjust start and end of intersecting group relative to selected region
jprocter [Fri, 17 Dec 2010 16:47:26 +0000 (16:47 +0000)]
adjust start and end of intersecting group relative to selected region

13 years ago1.1 compat
jprocter [Fri, 17 Dec 2010 14:24:26 +0000 (14:24 +0000)]
1.1 compat

13 years ago1.1 compat
jprocter [Fri, 17 Dec 2010 13:56:04 +0000 (13:56 +0000)]
1.1 compat

13 years agorefactored gap insert/visible view modification code from JPredThread
jprocter [Fri, 17 Dec 2010 13:17:29 +0000 (13:17 +0000)]
refactored gap insert/visible view modification code from JPredThread

13 years agojavadoc
jprocter [Fri, 17 Dec 2010 13:17:03 +0000 (13:17 +0000)]
javadoc

13 years agoincremental refinement of results parsing
jprocter [Wed, 15 Dec 2010 14:54:18 +0000 (14:54 +0000)]
incremental refinement of results parsing

13 years agoallow client to check if the original alignment data was annotated by results from...
jprocter [Wed, 15 Dec 2010 14:53:25 +0000 (14:53 +0000)]
allow client to check if the original alignment data was annotated by results from service

13 years agojavadoc
jprocter [Wed, 15 Dec 2010 14:51:23 +0000 (14:51 +0000)]
javadoc