jalview.git
13 years agoexample applet and desktop application files that should be published
jprocter [Thu, 19 May 2011 14:24:03 +0000 (15:24 +0100)]
example applet and desktop application files that should be published
to website at www.jalview.org/examples (JAL-815)
base version is 2.6.1 release of Jalview

13 years agoRevert "just a test"
jprocter [Thu, 19 May 2011 13:29:57 +0000 (14:29 +0100)]
Revert "just a test"

This reverts commit 0f56a75191c95a02b5f5ee90d9a6a57f72b0433b.

13 years agojust a test
jprocter [Wed, 18 May 2011 14:28:38 +0000 (15:28 +0100)]
just a test

13 years agorefactor to allow distinct StructureSelectionManager instances for
jprocter [Tue, 17 May 2011 12:49:57 +0000 (13:49 +0100)]
refactor to allow distinct StructureSelectionManager instances for
each jalview context in a JVM (JAL-621, JAL-569, JAL-731, JAL-735,
JAL-832)

13 years agointerface for objects at root of a jalview session's
jprocter [Tue, 17 May 2011 12:39:14 +0000 (13:39 +0100)]
interface for objects at root of a jalview session's
selection/highlighting/colouring message context

13 years agointerface for handlers of alignmentViewPanel events
jprocter [Tue, 17 May 2011 12:37:05 +0000 (13:37 +0100)]
interface for handlers of alignmentViewPanel events

13 years agocruisecontrol again
jprocter [Tue, 17 May 2011 09:25:23 +0000 (10:25 +0100)]
cruisecontrol again

13 years agoanother cc test
jprocter [Tue, 17 May 2011 09:13:08 +0000 (10:13 +0100)]
another cc test

13 years agoMerge branch 'master' of https://source.jalview.org/git/jalview
jprocter [Tue, 17 May 2011 09:07:32 +0000 (10:07 +0100)]
Merge branch 'master' of https://source.jalview.org/git/jalview

13 years agotest cruisecontrol
jprocter [Tue, 17 May 2011 09:04:19 +0000 (10:04 +0100)]
test cruisecontrol

13 years agotest cruisecontrol
jprocter [Tue, 17 May 2011 08:52:46 +0000 (09:52 +0100)]
test cruisecontrol

13 years agoensure all colour statements added to string set
jprocter [Tue, 17 May 2011 08:25:44 +0000 (09:25 +0100)]
ensure all colour statements added to string set

13 years agouncommentable debug message for JAL-771
jprocter [Thu, 5 May 2011 14:07:48 +0000 (14:07 +0000)]
uncommentable debug message for JAL-771

13 years agohtml tags
jprocter [Thu, 5 May 2011 14:02:13 +0000 (14:02 +0000)]
html tags

13 years agoimproved javascript callback execution thread and provided 'large string' asynchronou...
jprocter [Thu, 5 May 2011 14:01:26 +0000 (14:01 +0000)]
improved javascript callback execution thread and provided 'large string' asynchronous retrieval interface (JAL-735)

13 years agoseparation of jmol script command generation from jmol binding
jprocter [Thu, 5 May 2011 13:56:53 +0000 (13:56 +0000)]
separation of jmol script command generation from jmol binding

13 years agojavadoc and informative error message when external binding to PDB fails
jprocter [Thu, 5 May 2011 13:55:16 +0000 (13:55 +0000)]
javadoc and informative error message when external binding to PDB fails

13 years agoensure feature renderer settings come from the given view
jprocter [Thu, 5 May 2011 13:53:46 +0000 (13:53 +0000)]
ensure feature renderer settings come from the given view

13 years agoadded simple stdout debug function
jprocter [Thu, 5 May 2011 13:40:20 +0000 (13:40 +0000)]
added simple stdout debug function

13 years agoJAL-824 - additional methods to allow jmol colouring state indicator to be passed...
jprocter [Mon, 25 Apr 2011 16:22:19 +0000 (16:22 +0000)]
JAL-824 - additional methods to allow jmol colouring state indicator to be passed in and modified on an instantiated view

13 years agoJAL-824 - patch to schema to allow jmol colouring state to be stored
jprocter [Mon, 25 Apr 2011 16:21:40 +0000 (16:21 +0000)]
JAL-824 - patch to schema to allow jmol colouring state to be stored

13 years agotoggle of inclusion/exclusion of views for colouring was't working
jprocter [Mon, 25 Apr 2011 13:55:48 +0000 (13:55 +0000)]
toggle of inclusion/exclusion of views for colouring was't working

13 years agoJAL-824 - ensure Jmol colouring is a radio button
jprocter [Mon, 25 Apr 2011 13:08:11 +0000 (13:08 +0000)]
JAL-824 - ensure Jmol colouring is a radio button

13 years agodocumentation for JAL-824 and JAL-621
jprocter [Mon, 25 Apr 2011 12:57:43 +0000 (12:57 +0000)]
documentation for JAL-824 and JAL-621

13 years agodocumentation for JAL-732
jprocter [Mon, 25 Apr 2011 12:56:13 +0000 (12:56 +0000)]
documentation for JAL-732

13 years agohtmlfix
jprocter [Mon, 25 Apr 2011 12:54:49 +0000 (12:54 +0000)]
htmlfix

13 years agoformatting
jprocter [Fri, 22 Apr 2011 14:26:04 +0000 (14:26 +0000)]
formatting

13 years agoremoved useless flag (was always null for button press) to ensure default view colour...
jprocter [Fri, 22 Apr 2011 14:24:52 +0000 (14:24 +0000)]
removed useless flag (was always null for button press) to ensure default view colouring behaviour for JAL-824 when sequence colouring is chosen

13 years agoJAL-823 and JAL-824 - seqColour no longer the default colouring state unless PDB...
jprocter [Fri, 22 Apr 2011 11:41:41 +0000 (11:41 +0000)]
JAL-823 and JAL-824 - seqColour no longer the default colouring state unless PDB file opened from alignment window

13 years agocomments re JAL-823 legacy issue
jprocter [Fri, 22 Apr 2011 11:40:53 +0000 (11:40 +0000)]
comments re JAL-823 legacy issue

13 years agoclarify tooltip
jprocter [Fri, 22 Apr 2011 11:39:54 +0000 (11:39 +0000)]
clarify tooltip

13 years agomoved loadingFromArchive flag modification to after GUI refreshes are completed and...
jprocter [Fri, 22 Apr 2011 11:39:27 +0000 (11:39 +0000)]
moved loadingFromArchive flag modification to after GUI refreshes are completed and javadoc.

13 years agooption for enabling Jmol colouring mode JAL-824
jprocter [Fri, 22 Apr 2011 11:37:55 +0000 (11:37 +0000)]
option for enabling Jmol colouring mode JAL-824

13 years agoJAL-641 patch
jprocter [Thu, 21 Apr 2011 16:55:54 +0000 (16:55 +0000)]
JAL-641 patch

13 years agopatch for JAL-733
jprocter [Thu, 21 Apr 2011 16:54:09 +0000 (16:54 +0000)]
patch for JAL-733

13 years agopatch for JAL-820 and JAL-821
jprocter [Thu, 21 Apr 2011 14:51:08 +0000 (14:51 +0000)]
patch for JAL-820 and JAL-821

13 years agoseparated alignment annotation height calculation from panel height adjustment
jprocter [Thu, 21 Apr 2011 14:49:48 +0000 (14:49 +0000)]
separated alignment annotation height calculation from panel height adjustment

13 years agomoved to same place as in jalview.gui
jprocter [Thu, 21 Apr 2011 14:48:21 +0000 (14:48 +0000)]
moved to same place as in jalview.gui

13 years agosave and recover graph height, visibility and row position for autocalculated annotat...
jprocter [Thu, 21 Apr 2011 13:19:38 +0000 (13:19 +0000)]
save and recover graph height, visibility and row position for autocalculated annotation rows (JAL-785) and column label formatting attributes (JAL-817 and JAL-818).

13 years agoallow an alignment annotation row to be removed and re-inserted without losing any...
jprocter [Thu, 21 Apr 2011 13:17:07 +0000 (13:17 +0000)]
allow an alignment annotation row to be removed and re-inserted without losing any of its sequence or group associations (JAL-784)

13 years agoallow an existing alignment annotation row to be bound to a sequenceGroup as its...
jprocter [Thu, 21 Apr 2011 13:16:27 +0000 (13:16 +0000)]
allow an existing alignment annotation row to be bound to a sequenceGroup as its consensus or conservation row (JAL-784)

13 years agoadded graphHeight attribute to schema (JAL-784)
jprocter [Thu, 21 Apr 2011 13:14:43 +0000 (13:14 +0000)]
added graphHeight attribute to schema (JAL-784)

13 years agoavoid race condition when featureRenderer for structure is updated by its associated...
jprocter [Tue, 19 Apr 2011 13:56:07 +0000 (13:56 +0000)]
avoid race condition when featureRenderer for structure is updated by its associated view.

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