jalview.git
12 years agojavatidy
jprocter [Wed, 13 Jun 2012 08:09:08 +0000 (09:09 +0100)]
javatidy

12 years agoJAL-1115 refactor reordering code operating directly on Sequence collection as Alignm...
jprocter [Tue, 12 Jun 2012 11:48:03 +0000 (12:48 +0100)]
JAL-1115 refactor reordering code operating directly on Sequence collection as AlignmentI method

12 years agoJAL-1115 refactor base collection for Alignment from Vector to locally synchronized...
jprocter [Tue, 12 Jun 2012 11:35:56 +0000 (12:35 +0100)]
JAL-1115 refactor base collection for Alignment from Vector to locally synchronized List<SequenceI>

12 years agoJAL-1115 - use local reference for annotation row
jprocter [Tue, 12 Jun 2012 10:58:18 +0000 (11:58 +0100)]
JAL-1115 - use local reference for annotation row

12 years agoJAL-961, JAL-1115 - pending test to ensure only one worker waits around for another...
jprocter [Tue, 12 Jun 2012 10:57:52 +0000 (11:57 +0100)]
JAL-961, JAL-1115 - pending test to ensure only one worker waits around for another one for the same type to complete.

12 years agojavatidy
jprocter [Thu, 7 Jun 2012 17:10:32 +0000 (18:10 +0100)]
javatidy

12 years agoJAL-967, JAL-1114, JAL-1115 more concurrent access hacks
jprocter [Thu, 7 Jun 2012 17:07:46 +0000 (18:07 +0100)]
JAL-967, JAL-1114, JAL-1115 more concurrent access hacks

12 years agojavatidy
jprocter [Thu, 7 Jun 2012 17:06:49 +0000 (18:06 +0100)]
javatidy

12 years agofix for bug introduced with commit:b81d4d7d46ea8b1c89df086fb847baab6b69d427
jprocter [Thu, 7 Jun 2012 14:25:20 +0000 (15:25 +0100)]
fix for bug introduced with commit:b81d4d7d46ea8b1c89df086fb847baab6b69d427

12 years agojavatidy
jprocter [Thu, 7 Jun 2012 10:03:14 +0000 (11:03 +0100)]
javatidy

12 years agoJAL-967, JAL-1114, JAL-1115 - modified render and calculation api to work on bare...
jprocter [Thu, 7 Jun 2012 09:44:43 +0000 (10:44 +0100)]
JAL-967, JAL-1114, JAL-1115 - modified render and calculation api to work on bare array reference for current instance of data rather than via reference to container object, so as to minimise errors arising from race between rendering code and calculations triggered by alignment data edits which create new data arrays.

12 years agoJAL-976 ensure job id gets written out if there's an exception
jprocter [Mon, 4 Jun 2012 16:28:21 +0000 (17:28 +0100)]
JAL-976 ensure job id gets written out if there's an exception

12 years agojavatidy
jprocter [Mon, 4 Jun 2012 16:27:02 +0000 (17:27 +0100)]
javatidy

12 years agojavatidy
jprocter [Thu, 31 May 2012 09:41:48 +0000 (10:41 +0100)]
javatidy

12 years agoformatting
jprocter [Thu, 31 May 2012 09:40:23 +0000 (10:40 +0100)]
formatting

12 years agoJAL-969 - refactor colourscheme machinery from GUI code to core alignment view model
jprocter [Wed, 30 May 2012 18:30:41 +0000 (19:30 +0100)]
JAL-969 - refactor colourscheme machinery from GUI code to core alignment view model

12 years agoJAL-1109 JAL-1065 resolve t-coffee score scheme by name
jprocter [Wed, 30 May 2012 18:28:07 +0000 (19:28 +0100)]
JAL-1109 JAL-1065 resolve t-coffee score scheme by name

12 years agoupdated schema to store and recover belowAlignment and calcId for JAL-1109 and JAL...
jprocter [Wed, 30 May 2012 18:26:19 +0000 (19:26 +0100)]
updated schema to store and recover belowAlignment and calcId for JAL-1109 and JAL-1110

12 years agoJAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...
jprocter [Wed, 30 May 2012 18:21:25 +0000 (19:21 +0100)]
JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and use SequenceCollectionI and AnnotationCollectionI where possible to simplify code.

12 years agoformatting
jprocter [Wed, 30 May 2012 08:21:22 +0000 (09:21 +0100)]
formatting

12 years agoformatting
jprocter [Wed, 30 May 2012 08:02:19 +0000 (09:02 +0100)]
formatting

12 years agoTODO: JAL-1108
jprocter [Thu, 24 May 2012 18:53:22 +0000 (19:53 +0100)]
TODO: JAL-1108

12 years agoJAL-1078 - removed 'Load Score File' menu item and extended annotation file loader...
jprocter [Thu, 24 May 2012 18:53:06 +0000 (19:53 +0100)]
JAL-1078 - removed 'Load Score File' menu item and extended annotation file loader to recognise and load T-COFFEE files.

12 years agoJAL-1065 per sequence and per-alignment scores added to annotation
jprocter [Thu, 24 May 2012 17:52:03 +0000 (18:52 +0100)]
JAL-1065 per sequence and per-alignment scores added to annotation

12 years agoJAL-1065 - ensure null entries in annotation row so T-COFFEE annotation can be reloca...
jprocter [Thu, 24 May 2012 17:51:24 +0000 (18:51 +0100)]
JAL-1065 - ensure null entries in annotation row so T-COFFEE annotation can be relocated as alignment is edited.

12 years agotodo: JAL-1105
jprocter [Thu, 24 May 2012 17:46:16 +0000 (18:46 +0100)]
todo: JAL-1105

12 years agotodo: JAL-1108
jprocter [Thu, 24 May 2012 17:45:22 +0000 (18:45 +0100)]
todo: JAL-1108

12 years agoensure annotation isn't added twice - note - this could cause efficiency problems
jprocter [Thu, 24 May 2012 17:45:03 +0000 (18:45 +0100)]
ensure annotation isn't added twice - note - this could cause efficiency problems

12 years agoJAL-1107 - documentation explaining '*' and '+' in the conservation histogram.
jprocter [Thu, 24 May 2012 10:58:53 +0000 (11:58 +0100)]
JAL-1107 - documentation explaining '*' and '+' in the conservation histogram.

12 years agopatch for occasional NPE when applet is quit
jprocter [Thu, 24 May 2012 10:04:38 +0000 (11:04 +0100)]
patch for occasional NPE when applet is quit

12 years agoJAL-1078 - extend applet cut'n'paste features/annotation to support t-coffee file
jprocter [Wed, 23 May 2012 19:19:17 +0000 (20:19 +0100)]
JAL-1078 - extend applet cut'n'paste features/annotation to support t-coffee file
JAL-1102 - feedback for successful or unsuccessful parsing of annotation files

12 years agoJAL-1067 report any warning messages to user
jprocter [Wed, 23 May 2012 19:15:39 +0000 (20:15 +0100)]
JAL-1067 report any warning messages to user

12 years agoTODO for JAL-976
jprocter [Wed, 23 May 2012 19:09:58 +0000 (20:09 +0100)]
TODO for JAL-976

12 years agotodo for JAL-1106
jprocter [Wed, 23 May 2012 19:09:01 +0000 (20:09 +0100)]
todo for JAL-1106

12 years agoJAL-1066,JAL-1068,JAL-961 - use alignment annotation query api to get t-coffee annotation
jprocter [Wed, 23 May 2012 19:03:14 +0000 (20:03 +0100)]
JAL-1066,JAL-1068,JAL-961 - use alignment annotation query api to get t-coffee annotation

12 years agoJAL-1067, JAL-1105 - refactor parser to fit Jalview's data parsing architecture
jprocter [Wed, 23 May 2012 18:54:44 +0000 (19:54 +0100)]
JAL-1067, JAL-1105 - refactor parser to fit Jalview's data parsing architecture

12 years agoJAL-961 - annotatable datamodel objects can be queried to obtain annotation with...
jprocter [Wed, 23 May 2012 18:36:20 +0000 (19:36 +0100)]
JAL-961 - annotatable datamodel objects can be queried to obtain annotation with a particular calculation ID

12 years agoJAL-1102 todos and status updates when data is added
jprocter [Wed, 23 May 2012 18:29:40 +0000 (19:29 +0100)]
JAL-1102 todos and status updates when data is added

12 years agotodo JAL-1104 : functions to refactor
jprocter [Wed, 23 May 2012 18:25:29 +0000 (19:25 +0100)]
todo JAL-1104 : functions to refactor

12 years agotodo: blocked by JAL-1104
jprocter [Wed, 23 May 2012 18:24:09 +0000 (19:24 +0100)]
todo: blocked by JAL-1104

12 years agoJAL-958 - ensure logo is rendered even if consensus for column is at zero
jprocter [Wed, 23 May 2012 12:06:56 +0000 (13:06 +0100)]
JAL-958 - ensure logo is rendered even if consensus for column is at zero

12 years agoupdate the copy constructor
jprocter [Tue, 22 May 2012 11:33:51 +0000 (12:33 +0100)]
update the copy constructor

12 years agoJAL-1065,JAL-1066 propagated notification of colourscheme when alignment changed...
jprocter [Tue, 22 May 2012 11:33:19 +0000 (12:33 +0100)]
JAL-1065,JAL-1066 propagated notification of colourscheme when alignment changed to refactored code (SHA:677878508a8006cbf7e94e4d4e129ddcf3e3f2c2)

12 years agoJAL-1065,JAL-1066 - propagated 863467bf6c59c0bc5368c8f3a03d9d5a4f10700d to refactored...
jprocter [Tue, 22 May 2012 11:30:25 +0000 (12:30 +0100)]
JAL-1065,JAL-1066 - propagated 863467bf6c59c0bc5368c8f3a03d9d5a4f10700d to refactored renderer code.

12 years agoMerge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
jprocter [Tue, 22 May 2012 11:20:02 +0000 (12:20 +0100)]
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
conflicts due to refactoring according to JAL-972, JAL-968, JAL-968
Conflicts:
.classpath
examples/appletParameters.html
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/jbgui/GAlignFrame.java

12 years agowarning dialog - fixes JAL-1099
jprocter [Wed, 16 May 2012 10:48:55 +0000 (11:48 +0100)]
warning dialog - fixes JAL-1099

12 years agofixed JAL-1086: pass column index so colourscheme profile data is used to calculate...
jprocter [Wed, 16 May 2012 10:08:43 +0000 (11:08 +0100)]
fixed JAL-1086: pass column index so colourscheme profile data is used to calculate symbol colour

12 years agoJAL-958 - don't try to draw all zero profiles
jprocter [Wed, 16 May 2012 10:07:37 +0000 (11:07 +0100)]
JAL-958 - don't try to draw all zero profiles

12 years agoJAL-958 JAL-1086 formatting and remove old code
jprocter [Wed, 16 May 2012 10:06:41 +0000 (11:06 +0100)]
JAL-958 JAL-1086 formatting and remove old code

12 years agopack before displaying splashscreen to ensure its preferred size is correctly calculated
jprocter [Mon, 14 May 2012 16:54:46 +0000 (17:54 +0100)]
pack before displaying splashscreen to ensure its preferred size is correctly calculated

12 years agoformatting
jprocter [Mon, 14 May 2012 16:53:51 +0000 (17:53 +0100)]
formatting

12 years agoJAL-1097 - ensure replace comma for semicolon always disabled for das sources
jprocter [Mon, 14 May 2012 16:10:54 +0000 (17:10 +0100)]
JAL-1097 - ensure replace comma for semicolon always disabled for das sources

12 years agoMerge branch 'JAL-972-jdas' into develop
jprocter [Mon, 14 May 2012 10:37:08 +0000 (11:37 +0100)]
Merge branch 'JAL-972-jdas' into develop

12 years agoJAL-1075
jprocter [Mon, 14 May 2012 10:19:25 +0000 (11:19 +0100)]
JAL-1075
 - introduce flag to disable ability to select multiple sources (for v2.8 release).
 - currently selected database source information panel
 - cancel/ok reverts to last selection or accepts new selection
 - key handlers for escape (cancel) and return (ok).

12 years agoJAL-1061,JAL-1075 - first pass at implementing sequence record fetching across multip...
jprocter [Mon, 14 May 2012 10:12:43 +0000 (11:12 +0100)]
JAL-1061,JAL-1075 - first pass at implementing sequence record fetching across multiple sources.

 Multiple source fetching not yet ready for production use (disabled for v2.8 release)

12 years agoclean up old commented code
jprocter [Mon, 14 May 2012 10:10:57 +0000 (11:10 +0100)]
clean up old commented code

12 years agoJAL-1095 - todo
jprocter [Mon, 14 May 2012 10:10:03 +0000 (11:10 +0100)]
JAL-1095 - todo

12 years agojavadoc
jprocter [Mon, 14 May 2012 09:02:22 +0000 (10:02 +0100)]
javadoc

12 years agoJAL-972 workaround for working out source URL for pre DAS 1.6 sources.
jprocter [Fri, 11 May 2012 13:22:08 +0000 (14:22 +0100)]
JAL-972 workaround for working out source URL for pre DAS 1.6 sources.
note - certain sources currently in registry have invalid URLs in their capability elements (missing '/' between URL and command)

12 years agoformatting
jprocter [Fri, 11 May 2012 13:17:09 +0000 (14:17 +0100)]
formatting

12 years agoJAL-972 migration from dasobert to jdas registry URLs
jprocter [Fri, 11 May 2012 13:16:36 +0000 (14:16 +0100)]
JAL-972 migration from dasobert to jdas registry URLs

12 years agoJAL-972 local do not have a coordsys element with source metadata (JAL-424 would...
jprocter [Fri, 11 May 2012 13:15:56 +0000 (14:15 +0100)]
JAL-972 local do not have a coordsys element with source metadata (JAL-424 would resolve this!)

12 years agoJAL-424 TODO: new method signature for local source creation
jprocter [Fri, 11 May 2012 13:14:14 +0000 (14:14 +0100)]
JAL-424 TODO: new method signature for local source creation

12 years agoJAL-1085 - ensure sequence fetching client waits around until feature retrieval has...
jprocter [Thu, 10 May 2012 16:24:09 +0000 (17:24 +0100)]
JAL-1085 - ensure sequence fetching client waits around until feature retrieval has finished before returning sequences for display.

12 years agoJAL-972 JAL-1084 propagate reference to local authentication provider so it can be...
jprocter [Thu, 10 May 2012 16:14:26 +0000 (17:14 +0100)]
JAL-972 JAL-1084 propagate reference to local authentication provider so it can be passed to JDAS clients when querying sources.

12 years agoJAL-1083 - graceful failover to single ID query mode for fetching features
jprocter [Thu, 10 May 2012 16:06:39 +0000 (17:06 +0100)]
JAL-1083 - graceful failover to single ID query mode for fetching features

12 years agoformatting
jprocter [Thu, 10 May 2012 15:04:35 +0000 (16:04 +0100)]
formatting

12 years agoJAL-1083 graceful failover to one ID per sequences query for sources that fail for...
jprocter [Thu, 10 May 2012 15:04:06 +0000 (16:04 +0100)]
JAL-1083 graceful failover to one ID per sequences query for sources that fail for multiple ID queries

12 years agoJAL-1075 better layout and info box for source browser
jprocter [Thu, 10 May 2012 13:41:52 +0000 (14:41 +0100)]
JAL-1075 better layout and info box for source browser

12 years agoJAL-1075 tweak layout and test display for tree based sequence source browser
jprocter [Tue, 1 May 2012 16:09:06 +0000 (17:09 +0100)]
JAL-1075 tweak layout and test display for tree based sequence source browser

12 years agoJAL-1075, JAL-1061, JAL-1064 - introduced second tier of 'fetch database' menu hierar...
jprocter [Tue, 24 Apr 2012 15:37:28 +0000 (16:37 +0100)]
JAL-1075, JAL-1061, JAL-1064 - introduced second tier of 'fetch database' menu hierarchy for source groups like Ensembl (fetch all or submenu for individual fetch). Also shortened width of menu entries so that user can browse the hierarchy more easily.

12 years agoJAL-1064 sequence database sources are stored and retrieved as lists associated with...
jprocter [Tue, 24 Apr 2012 14:40:37 +0000 (15:40 +0100)]
JAL-1064 sequence database sources are stored and retrieved as lists associated with each canonical database name rather than assuming 1:1 mapping between string and source instance

12 years agoJAL-972 correct das registry default URL (JDAS automatically adds the sources command...
jprocter [Tue, 24 Apr 2012 14:33:45 +0000 (15:33 +0100)]
JAL-972 correct das registry default URL (JDAS automatically adds the sources command to the URL)

12 years agoJAL-972 - test to distinguish sources based on age - used to select one of duplicate...
jprocter [Tue, 24 Apr 2012 14:31:53 +0000 (15:31 +0100)]
JAL-972 - test to distinguish sources based on age - used to select one of duplicate sources in registry

12 years agoJAL-1074 fix - missing tag indicating alignments are retrieved from RFAM.
jprocter [Tue, 24 Apr 2012 13:51:11 +0000 (14:51 +0100)]
JAL-1074 fix - missing tag indicating alignments are retrieved from RFAM.

12 years agoJAL-972, JAL-1072 new default dasregistry.org registry URL for JDAS
jprocter [Fri, 20 Apr 2012 16:06:32 +0000 (17:06 +0100)]
JAL-972, JAL-1072  new default dasregistry.org registry URL for JDAS

12 years agoJAL-1064 JAL-671 - add tree based database dialog as button in sequence fetcher
jprocter [Fri, 20 Apr 2012 15:57:37 +0000 (16:57 +0100)]
JAL-1064 JAL-671 - add tree based database dialog as button in sequence fetcher

12 years agoJAL-1064 - hack to create menu item label for each fetch from DB item (need to review...
jprocter [Fri, 20 Apr 2012 15:54:08 +0000 (16:54 +0100)]
JAL-1064 - hack to create menu item label for each fetch from DB item (need to review this)

12 years agoJAL-1064 - refactor to iterate over many sources associated with a database authority
jprocter [Fri, 20 Apr 2012 15:52:28 +0000 (16:52 +0100)]
JAL-1064 - refactor to iterate over many sources associated with a database authority

12 years agoJAL-972 - correct name when constructing db-source from DAS source
jprocter [Fri, 20 Apr 2012 15:39:42 +0000 (16:39 +0100)]
JAL-972 - correct name when constructing db-source from DAS source

12 years ago(JAL-1071) hacked the square matrix that stores the interacting pairs to allow 36...
jprocter [Fri, 20 Apr 2012 15:04:38 +0000 (16:04 +0100)]
(JAL-1071) hacked the square matrix that stores the interacting pairs to allow 36 types of base pair rather than 25 (so self-pair interactions can be counted too)

12 years agodialog for browsing and selecting datasources hierarchically JAL-671 JAL-1064
jprocter [Wed, 11 Apr 2012 11:02:25 +0000 (12:02 +0100)]
dialog for browsing and selecting datasources hierarchically JAL-671 JAL-1064

12 years agoJAL-1062 - recognise and split off the range qualifier in a DAS sequence fetch query
jprocter [Fri, 30 Mar 2012 15:35:47 +0000 (16:35 +0100)]
JAL-1062 - recognise and split off the range qualifier in a DAS sequence fetch query

12 years ago(JAL-972) format tweak for source information box
jprocter [Fri, 30 Mar 2012 13:59:59 +0000 (14:59 +0100)]
(JAL-972) format tweak for source information box

12 years agoMerge branch 'JAL-972-dasobert-to-jdas' into JAL-972-jdas
jprocter [Fri, 30 Mar 2012 12:29:04 +0000 (13:29 +0100)]
Merge branch 'JAL-972-dasobert-to-jdas' into JAL-972-jdas

Conflicts:
.classpath
src/jalview/ws/dbsources/DasSequenceSource.java
src/jalview/ws/dbsources/das/DasSequenceSourceListener.java

merged jdas switchover into v2.8 development branch

12 years ago(JAL-972) jdas latest build
jprocter [Fri, 30 Mar 2012 12:11:11 +0000 (13:11 +0100)]
(JAL-972) jdas latest build

12 years agologic bug
jprocter [Fri, 30 Mar 2012 10:24:12 +0000 (11:24 +0100)]
logic bug

Signed-off-by: jprocter <jprocter@compbio.dundee.ac.uk>

12 years agoJAL-893 JAL-842 - updated VARNA - fix typo in InstallAnywhere build
jprocter [Wed, 28 Mar 2012 14:19:04 +0000 (15:19 +0100)]
JAL-893 JAL-842 - updated VARNA - fix typo in InstallAnywhere build

12 years agoMerge branch 'JAL-976_jabaws2supp' into develop
jprocter [Wed, 28 Mar 2012 13:57:23 +0000 (14:57 +0100)]
Merge branch 'JAL-976_jabaws2supp' into develop

12 years agoJAL-1060 - prototype GUI with traffic light coding for JABAWS urls that were fine...
jprocter [Wed, 28 Mar 2012 13:30:23 +0000 (14:30 +0100)]
JAL-1060 - prototype GUI with traffic light coding for JABAWS urls that were fine, had some problems or couldn't be contacted.

12 years agoJAL-1060 - record which services are invalid, valid or did not have any services...
jprocter [Wed, 28 Mar 2012 13:29:39 +0000 (14:29 +0100)]
JAL-1060 - record which services are invalid, valid or did not have any services and allow status for URL to be tested

12 years agoformatting
jprocter [Tue, 27 Mar 2012 15:00:04 +0000 (16:00 +0100)]
formatting

12 years agoJAL-976 - tweak web services gui so empty menus don't get shown and included a 'still...
jprocter [Tue, 27 Mar 2012 14:59:39 +0000 (15:59 +0100)]
JAL-976 - tweak web services gui so empty menus don't get shown and included a 'still discovering' menu item when JABAWS discovery is still in progress.

12 years ago(JAL-976) - consistent ordering of services according to server URLs and debugging...
jprocter [Tue, 27 Mar 2012 14:55:16 +0000 (15:55 +0100)]
(JAL-976) - consistent ordering of services according to server URLs and debugging race conditions and menu generation

12 years agoJAL-976 - hack to provide consistent ordering of JABAWS2 service names used when...
jprocter [Tue, 27 Mar 2012 14:54:07 +0000 (15:54 +0100)]
JAL-976 - hack to provide consistent ordering of JABAWS2 service names used when building GUI

12 years ago(JAL-976) refactor JABAWS1 list
jprocter [Tue, 27 Mar 2012 14:53:31 +0000 (15:53 +0100)]
(JAL-976) refactor JABAWS1 list

12 years ago(JAL-942) comment out non-functional buttons in VARNA
jprocter [Mon, 5 Mar 2012 09:49:15 +0000 (10:49 +0100)]
(JAL-942) comment out non-functional buttons in VARNA

12 years ago(JAL-942) clearer view structure menu entry
jprocter [Mon, 5 Mar 2012 09:48:54 +0000 (10:48 +0100)]
(JAL-942) clearer view structure menu entry

12 years agoJAL-942 - sensible name on window
jprocter [Mon, 5 Mar 2012 09:36:29 +0000 (10:36 +0100)]
JAL-942 - sensible name on window

12 years agoJAL-942 - make sure rna structures get a sensible name
jprocter [Mon, 5 Mar 2012 09:16:01 +0000 (10:16 +0100)]
JAL-942 - make sure rna structures get a sensible name