jalview.git
13 years agodocumentation (JAL-859, JAL-816, JAL-621)
jprocter [Sun, 3 Jul 2011 12:42:29 +0000 (13:42 +0100)]
documentation (JAL-859, JAL-816, JAL-621)

13 years agoextracted jalviewlite API calls as separate interface (JAL-859)
jprocter [Sun, 3 Jul 2011 12:39:54 +0000 (13:39 +0100)]
extracted jalviewlite API calls as separate interface (JAL-859)

13 years agogroovy scripting examples (JAL-???)
jprocter [Sun, 3 Jul 2011 12:05:24 +0000 (13:05 +0100)]
groovy scripting examples (JAL-???)

13 years agojavadoc built under dist directory for all Jalview source (JAL-858)
jprocter [Sun, 3 Jul 2011 11:56:11 +0000 (12:56 +0100)]
javadoc built under dist directory for all Jalview source (JAL-858)

13 years agoset initial annotation panel height appropriately (JAL-564, JAL-306)
jprocter [Thu, 30 Jun 2011 11:50:45 +0000 (12:50 +0100)]
set initial annotation panel height appropriately (JAL-564, JAL-306)

13 years agostandard embedded jalviewLite example (JAL-815)
jprocter [Wed, 29 Jun 2011 17:34:20 +0000 (18:34 +0100)]
standard embedded jalviewLite example (JAL-815)

13 years agodocumentation and targets for building a working applet examples
jprocter [Wed, 29 Jun 2011 17:33:37 +0000 (18:33 +0100)]
documentation and targets for building a working applet examples
directory (JAL-834)

13 years agorepaint image buffer height change (JAL-564) and ensure annotation panel
jprocter [Wed, 29 Jun 2011 16:56:57 +0000 (17:56 +0100)]
repaint image buffer height change (JAL-564) and ensure annotation panel
height drag events do not result in annotation row reordering (JAL-769)

13 years agorepaint image buffer resize when panel height changes (JAL-564)
jprocter [Wed, 29 Jun 2011 16:54:37 +0000 (17:54 +0100)]
repaint image buffer resize when panel height changes (JAL-564)

13 years agopreliminary patch to reduce problem observed in JAL-546
jprocter [Wed, 29 Jun 2011 16:52:22 +0000 (17:52 +0100)]
preliminary patch to reduce problem observed in JAL-546

13 years agoensure annotation height adjuster doesn't disappear off top of screen on
jprocter [Wed, 29 Jun 2011 16:51:15 +0000 (17:51 +0100)]
ensure annotation height adjuster doesn't disappear off top of screen on
resize, and fixed some bugs with height calculation for annotation panel
JAL-564

13 years agofixes JAL-849 - double check after waiting a bit that there is no more
jprocter [Tue, 28 Jun 2011 16:40:45 +0000 (17:40 +0100)]
fixes JAL-849 - double check after waiting a bit that there is no more
job output to retrieve from server.

13 years agoreinstated valid XML content : additional for JAL-775
jprocter [Sun, 26 Jun 2011 15:50:22 +0000 (16:50 +0100)]
reinstated valid XML content : additional for JAL-775

13 years agobasic Netbeans project files and enriched build documentation: fixes JAL-848
jprocter [Sun, 26 Jun 2011 15:44:51 +0000 (16:44 +0100)]
basic Netbeans project files and enriched build documentation: fixes JAL-848

13 years agofix to preserve sequence numbering in MSF (JAL-847)
jprocter [Fri, 24 Jun 2011 15:55:15 +0000 (16:55 +0100)]
fix to preserve sequence numbering in MSF (JAL-847)

13 years agojmb isn't created yet, so use another SSM provider
jprocter [Thu, 23 Jun 2011 14:48:07 +0000 (15:48 +0100)]
jmb isn't created yet, so use another SSM provider

13 years agopatch for JAL-846 made targetChain mapping constraint selective so
jprocter [Thu, 23 Jun 2011 14:45:07 +0000 (15:45 +0100)]
patch for JAL-846 made targetChain mapping constraint selective so
computed mappings are limited to cases where chain codes were explicitly
supplied

13 years agobug for clients using NJTree directly - pwtype should be valid score
jprocter [Mon, 30 May 2011 06:35:37 +0000 (07:35 +0100)]
bug for clients using NJTree directly - pwtype should be valid score
matrix or PID, otherwise it is set by default to BLOSUM62

13 years agofirst patch for JAL-838 - allow new typed of PID calcs
jprocter [Mon, 30 May 2011 06:34:28 +0000 (07:34 +0100)]
first patch for JAL-838 - allow new typed of PID calcs

13 years agoexample applet and desktop application files that should be published
jprocter [Thu, 19 May 2011 14:24:22 +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 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