jalview.git
12 years agoJAL-1001 - hack to extract the global URL for a service from the 'MORE INFORMATION...
jprocter [Tue, 28 Aug 2012 13:00:22 +0000 (14:00 +0100)]
JAL-1001 - hack to extract the global URL for a service from the 'MORE INFORMATION' url.

12 years agojavadoc and note about broken semantics for findIndex
jprocter [Tue, 28 Aug 2012 09:46:44 +0000 (10:46 +0100)]
javadoc and note about broken semantics for findIndex

12 years agoJAL-1149 patch
jprocter [Tue, 28 Aug 2012 09:43:13 +0000 (10:43 +0100)]
JAL-1149 patch

12 years agoJAL-1148 reinstate sequence references for annotation regardless of whether they...
jprocter [Tue, 28 Aug 2012 09:31:50 +0000 (10:31 +0100)]
JAL-1148 reinstate sequence references for annotation regardless of whether they are autocalculated or not (patch not checked for regressions!)

12 years agoJAL-1087 skip processing any of the other command line arguments if no alignment...
jprocter [Fri, 24 Aug 2012 15:09:06 +0000 (16:09 +0100)]
JAL-1087 skip processing any of the other command line arguments if no alignment window created
from -open parameter

12 years agoJAL-1143 - ensure we revalidate annotation panel height in all views after pasting...
jprocter [Fri, 24 Aug 2012 15:02:40 +0000 (16:02 +0100)]
JAL-1143 - ensure we revalidate annotation panel height in all views after pasting any annotation rows

12 years agoJAL-975 JAL-951 test class for viewing layout for JABAWS services
jprocter [Thu, 23 Aug 2012 10:38:00 +0000 (11:38 +0100)]
JAL-975 JAL-951 test class for viewing layout for JABAWS services

12 years agoJAL-1137 clean up old-style menu code and look
jprocter [Tue, 7 Aug 2012 15:56:40 +0000 (16:56 +0100)]
JAL-1137 clean up old-style menu code and look

12 years agoJAL-1137 JAL-975 simpler menu for the AACon service - allows user to switch calculati...
jprocter [Tue, 7 Aug 2012 15:46:35 +0000 (16:46 +0100)]
JAL-1137 JAL-975 simpler menu for the AACon service - allows user to switch calculation to different servers for an alignment view.

12 years agoDebug message associated with TODO for JAL-1136 - re-enable dynamic recalculation...
jprocter [Tue, 7 Aug 2012 15:42:01 +0000 (16:42 +0100)]
Debug message associated with TODO for JAL-1136 - re-enable dynamic recalculation when a project with AACon annotation is imported.

12 years agoJAL-975 JAL-1137 debug messages for web service client and discovery code
jprocter [Tue, 7 Aug 2012 11:09:38 +0000 (12:09 +0100)]
JAL-975 JAL-1137 debug messages for web service client and discovery code

12 years agoJAL-1131 - todos for later versions
jprocter [Sun, 5 Aug 2012 17:32:27 +0000 (18:32 +0100)]
JAL-1131 - todos for later versions

12 years agoJAL-1131 ensure new dataset sequence is created if seuqence replacement results in...
jprocter [Sun, 5 Aug 2012 17:28:03 +0000 (18:28 +0100)]
JAL-1131 ensure new dataset sequence is created if seuqence replacement results in different non-gap characters

12 years agoJAL-1136 Ensure asynchronously calculated autoannotation is also added to the alignme...
jprocter [Fri, 3 Aug 2012 16:53:41 +0000 (17:53 +0100)]
JAL-1136 Ensure asynchronously calculated autoannotation is also added to the alignment in the correct order

12 years agoJAL-1136 JAL-811 JAL-812 store/recover autocalc alignment annotation based on calcId...
jprocter [Fri, 3 Aug 2012 16:28:48 +0000 (17:28 +0100)]
JAL-1136 JAL-811 JAL-812 store/recover autocalc alignment annotation based on calcId if present

12 years agoJAL-1136 fix logic for recovering AACons params
jprocter [Fri, 3 Aug 2012 16:26:27 +0000 (17:26 +0100)]
JAL-1136 fix logic for recovering AACons params

12 years agoJAL-1136 store ws-parameter list as XML element content after first escaping newlines...
jprocter [Fri, 3 Aug 2012 16:24:02 +0000 (17:24 +0100)]
JAL-1136 store ws-parameter list as XML element content after first escaping newlines. TODO: consider revising

12 years agoJAL-1136 allow parameter sets to be transferred across different JABAWS servers using...
jprocter [Fri, 3 Aug 2012 16:21:52 +0000 (17:21 +0100)]
JAL-1136 allow parameter sets to be transferred across different JABAWS servers using server-independent JABA service identifier

12 years agoJAL-1136 less code-dependent formula for creating server-independent JABA service...
jprocter [Fri, 3 Aug 2012 16:19:51 +0000 (17:19 +0100)]
JAL-1136 less code-dependent formula for creating server-independent JABA service identifier

12 years agoJAL-1136 - fix abstraction for parameter container class
jprocter [Fri, 3 Aug 2012 16:18:46 +0000 (17:18 +0100)]
JAL-1136 - fix abstraction for parameter container class

12 years agoJAL-1115 reference to List<SequenceI> passed in 'alignment' changeSupport message
jprocter [Fri, 3 Aug 2012 16:08:07 +0000 (17:08 +0100)]
JAL-1115 reference to List<SequenceI> passed in 'alignment' changeSupport message

12 years agoJAL-976 better logging/error reporting for disorder/conservation jobs
jprocter [Thu, 2 Aug 2012 10:21:46 +0000 (11:21 +0100)]
JAL-976 better logging/error reporting for disorder/conservation jobs

12 years agoJAL-976 JAL-958 todo list for release
jprocter [Thu, 2 Aug 2012 10:20:21 +0000 (11:20 +0100)]
JAL-976 JAL-958 todo list for release

12 years agoJAL-976 ensure protein disorder services appears in correct place
jprocter [Wed, 1 Aug 2012 15:58:29 +0000 (16:58 +0100)]
JAL-976 ensure protein disorder services appears in correct place

12 years agoJAL-976 don't clear menu out before adding jabaws services so JPred service still...
jprocter [Wed, 1 Aug 2012 15:57:11 +0000 (16:57 +0100)]
JAL-976 don't clear menu out before adding jabaws services so JPred service still shown

12 years agoJAL-1066 patch regression ac33424148b2a4de29b3ca43f941162e8ba0384c causing exception...
jprocter [Wed, 1 Aug 2012 14:22:44 +0000 (15:22 +0100)]
JAL-1066 patch regression ac33424148b2a4de29b3ca43f941162e8ba0384c causing exception when feature colourschemes are imported

12 years agodocumentation for PCA calculation parameters and reset button.
jprocter [Sun, 8 Jul 2012 15:37:08 +0000 (16:37 +0100)]
documentation for PCA calculation parameters and reset button.

12 years agoa209409239 (JAL-976 - add support for storing service parameter sets in project)
jprocter [Sun, 8 Jul 2012 14:24:05 +0000 (15:24 +0100)]
a209409239 (JAL-976 - add support for storing service parameter sets in project)

12 years agoJAL-976 clean out associated annotation
jprocter [Sun, 8 Jul 2012 14:20:32 +0000 (15:20 +0100)]
JAL-976 clean out associated annotation

12 years agoJAL-976 implement additional calcId method
jprocter [Sun, 8 Jul 2012 14:17:41 +0000 (15:17 +0100)]
JAL-976 implement additional calcId method

12 years agoJAL-976 simpler parameter update model
jprocter [Sun, 8 Jul 2012 14:15:53 +0000 (15:15 +0100)]
JAL-976 simpler parameter update model

12 years agoJAL-961 JAL-976 allow access to service URI for parameter recovery
jprocter [Sun, 8 Jul 2012 14:15:03 +0000 (15:15 +0100)]
JAL-961 JAL-976 allow access to service URI for parameter recovery

12 years agoJAL-961 JAL-976 recover current settings from associated viewport
jprocter [Sun, 8 Jul 2012 14:13:14 +0000 (15:13 +0100)]
JAL-961 JAL-976 recover current settings from associated viewport

12 years agoJAL-976 pick an available instance of a service based on server-independent URI string
jprocter [Sun, 8 Jul 2012 14:11:08 +0000 (15:11 +0100)]
JAL-976 pick an available instance of a service based on server-independent URI string

12 years agobugfix - use currently held parameters
jprocter [Sun, 8 Jul 2012 14:09:13 +0000 (15:09 +0100)]
bugfix - use currently held parameters

12 years agoJAL-976 - storing service parameters on the view model
jprocter [Sun, 8 Jul 2012 14:08:35 +0000 (15:08 +0100)]
JAL-976 - storing service parameters on the view model

12 years agoJAL-976 test if the sliders have been modified from the service default (where no...
jprocter [Fri, 6 Jul 2012 17:32:04 +0000 (18:32 +0100)]
JAL-976 test if the sliders have been modified from the service default (where no preset is selected and no sliders changed)

12 years agounique URI for service type
jprocter [Fri, 6 Jul 2012 17:30:59 +0000 (18:30 +0100)]
unique URI for service type

12 years agoJAL-961 JAL-976 abstracted container for dynamic calculation parameters
jprocter [Fri, 6 Jul 2012 17:29:00 +0000 (18:29 +0100)]
JAL-961 JAL-976 abstracted container for dynamic calculation parameters

12 years agotidy imports
jprocter [Fri, 6 Jul 2012 17:27:49 +0000 (18:27 +0100)]
tidy imports

12 years agoJAL-976 - add support for storing service parameter sets in project
jprocter [Fri, 6 Jul 2012 17:25:54 +0000 (18:25 +0100)]
JAL-976 - add support for storing service parameter sets in project

12 years agoJAL-961 allow calcId to be specified independently of alignment annotation row label
jprocter [Tue, 3 Jul 2012 15:01:26 +0000 (16:01 +0100)]
JAL-961 allow calcId to be specified independently of alignment annotation row label

12 years agoJAL-974 - broken copy of feature settings
jprocter [Tue, 3 Jul 2012 08:55:16 +0000 (09:55 +0100)]
JAL-974 - broken copy of feature settings

12 years agoJAL-1129 progress bar - this patch doesn't provide any indication of whether the...
jprocter [Mon, 2 Jul 2012 07:29:23 +0000 (08:29 +0100)]
JAL-1129 progress bar - this patch doesn't provide any indication of whether the export was successful.

12 years agoJAL-968 incremental - PNG/EPS output has annotation overlapping alignment when annota...
jprocter [Mon, 2 Jul 2012 07:27:48 +0000 (08:27 +0100)]
JAL-968 incremental - PNG/EPS output has annotation overlapping alignment when annotation scroll bar not at top of panel.

12 years agotidy imports
jprocter [Mon, 2 Jul 2012 07:23:41 +0000 (08:23 +0100)]
tidy imports

12 years agoJAL-974 create graduated feature colours for annotation with scores.
jprocter [Mon, 2 Jul 2012 06:40:33 +0000 (07:40 +0100)]
JAL-974 create graduated feature colours for annotation with scores.

12 years agoJAL-974 - use refactored methods on AlignmentPanel
jprocter [Mon, 2 Jul 2012 06:36:24 +0000 (07:36 +0100)]
JAL-974 - use refactored methods on AlignmentPanel

12 years agoJAL-974 - refactor FeatureRenderer constructor to AlignmentPanel (should probably...
jprocter [Mon, 2 Jul 2012 06:35:38 +0000 (07:35 +0100)]
JAL-974 - refactor FeatureRenderer constructor to AlignmentPanel (should probably add to AlignPanel API JAL-966)

12 years agoJAL-1117 alleviate lock starvation
jprocter [Sun, 1 Jul 2012 16:02:51 +0000 (17:02 +0100)]
JAL-1117 alleviate lock starvation

12 years agoensure all annotation dependent rendering gets refreshed
jprocter [Sun, 1 Jul 2012 15:58:21 +0000 (16:58 +0100)]
ensure all annotation dependent rendering gets refreshed

12 years agoJAL-1065 JAL-1066 ensure non-residue based schemes actually override the new findColo...
jprocter [Fri, 29 Jun 2012 15:19:19 +0000 (16:19 +0100)]
JAL-1065 JAL-1066 ensure non-residue based schemes actually override the new findColor methods

12 years agoJAL-1065 JAL-1066 allow different lookup tables for nucleotide or amino acid coloursc...
jprocter [Fri, 29 Jun 2012 15:18:41 +0000 (16:18 +0100)]
JAL-1065 JAL-1066 allow different lookup tables for nucleotide or amino acid colourschemes

12 years agoJAL-899 added groovy support to develop branch
jprocter [Tue, 26 Jun 2012 21:12:50 +0000 (22:12 +0100)]
JAL-899 added groovy support to develop branch

12 years agoformatting
jprocter [Wed, 20 Jun 2012 18:49:27 +0000 (19:49 +0100)]
formatting

12 years agoJAL-976 JAL-975 JAL-1119 - pass on any existing parameters to initialise the service...
jprocter [Tue, 19 Jun 2012 16:33:18 +0000 (17:33 +0100)]
JAL-976 JAL-975 JAL-1119 - pass on any existing parameters to initialise the service parameters dialog box

12 years agoJAL-975 JAL-1119 - prototype adjustable AACons parameters for the currrent alignment...
jprocter [Tue, 19 Jun 2012 16:30:56 +0000 (17:30 +0100)]
JAL-975 JAL-1119 - prototype adjustable AACons parameters for the currrent alignment view

12 years agoJAL-975 - doh! valid result if width matches *ungapped* input data
jprocter [Tue, 19 Jun 2012 16:28:50 +0000 (17:28 +0100)]
JAL-975 - doh! valid result if width matches *ungapped* input data

12 years agoJAL-975 - bespoke AACons settings object to save current service settings for the...
jprocter [Tue, 19 Jun 2012 16:26:57 +0000 (17:26 +0100)]
JAL-975 - bespoke AACons settings object to save current service settings for the AlignViewport

12 years agopatch for JAL-1172 ensure option's default value is set in widget so it gets saved...
jprocter [Tue, 19 Jun 2012 16:25:05 +0000 (17:25 +0100)]
patch for JAL-1172 ensure option's default value is set in widget so it gets saved in paramStore

12 years agoJAL-961 JAL-975 extend api to support removal of workers no-longer required by the...
jprocter [Tue, 19 Jun 2012 16:22:52 +0000 (17:22 +0100)]
JAL-961 JAL-975 extend api to support removal of workers no-longer required by the user

12 years agoJAL-975 - ensure we only submit ungapped, padded alignment data to AACon - otherwise...
jprocter [Tue, 19 Jun 2012 10:49:04 +0000 (11:49 +0100)]
JAL-975 - ensure we only submit ungapped, padded alignment data to AACon - otherwise jobs fail.

12 years agoformatting
jprocter [Fri, 15 Jun 2012 16:52:58 +0000 (17:52 +0100)]
formatting

12 years agoJAL-1125 option to switch between Jalview and SeqSpace PCA calculation modes
jprocter [Fri, 15 Jun 2012 16:52:37 +0000 (17:52 +0100)]
JAL-1125 option to switch between Jalview and SeqSpace PCA calculation modes

12 years agofix JAL-1122
jprocter [Fri, 15 Jun 2012 15:13:20 +0000 (16:13 +0100)]
fix JAL-1122

12 years agoJAL-1123 - make clear where off-by-one error was occuring (patched problem in previou...
jprocter [Fri, 15 Jun 2012 15:08:38 +0000 (16:08 +0100)]
JAL-1123 - make clear where off-by-one error was occuring (patched problem in previous commit)

12 years agoJAL-535 - refactored core PCA viewer code to viewmodel
jprocter [Fri, 15 Jun 2012 14:59:40 +0000 (15:59 +0100)]
JAL-535 - refactored core PCA viewer code to viewmodel
JAL-1013 - port protein/nucleotide settings to applet PCA viewer

12 years agoJAL-535 refactored core code from PCA viewer to viewmodel.
jprocter [Fri, 15 Jun 2012 14:54:28 +0000 (15:54 +0100)]
JAL-535 refactored core code from PCA viewer to viewmodel.

12 years agoJAL-1120 patch for desktop
jprocter [Fri, 15 Jun 2012 10:49:37 +0000 (11:49 +0100)]
JAL-1120 patch for desktop

12 years agopatch for JAL-1121 - reset button and slightly wider default window size
jprocter [Fri, 15 Jun 2012 10:44:21 +0000 (11:44 +0100)]
patch for JAL-1121 - reset button and slightly wider default window size

12 years agoJAL-535 refactoring todo
jprocter [Fri, 15 Jun 2012 10:36:25 +0000 (11:36 +0100)]
JAL-535 refactoring todo

12 years agoExtended IProgressIndicator with method to check if any progress bars are currently...
jprocter [Fri, 15 Jun 2012 10:35:03 +0000 (11:35 +0100)]
Extended IProgressIndicator with method to check if any progress bars are currently displayed.

12 years agoMerge branch 'JAL-1013_pca_rna_dna' into develop
jprocter [Fri, 15 Jun 2012 08:58:07 +0000 (09:58 +0100)]
Merge branch 'JAL-1013_pca_rna_dna' into develop

12 years agoJAL-975 JAL-1002 ensure custom parameters are actually passed to service
jprocter [Thu, 14 Jun 2012 13:59:31 +0000 (14:59 +0100)]
JAL-975 JAL-1002 ensure custom parameters are actually passed to service

12 years agoJAL-1115 - synchronized access to group list
jprocter [Thu, 14 Jun 2012 11:28:38 +0000 (12:28 +0100)]
JAL-1115 - synchronized access to group list

12 years agoJAL-976 - make sure annotation panel is updated to grey out any stale annotation...
jprocter [Thu, 14 Jun 2012 10:48:12 +0000 (11:48 +0100)]
JAL-976 - make sure annotation panel is updated to grey out any stale annotation rows

12 years agoJAL-961 JAL-976 kill any existing AACon job if a new AACon worker is started due...
jprocter [Thu, 14 Jun 2012 10:47:25 +0000 (11:47 +0100)]
JAL-961 JAL-976 kill any existing AACon job if a new AACon worker is started due to an alignment edit or change in parameters

12 years agoJAL-1003 visual delay when running a sequence or alignment annotation job
jprocter [Thu, 14 Jun 2012 10:45:28 +0000 (11:45 +0100)]
JAL-1003 visual delay when running a sequence or alignment annotation job

12 years agoJAL-961 JAL-976 tweaked way that AACons client is registered and started.
jprocter [Thu, 14 Jun 2012 10:44:05 +0000 (11:44 +0100)]
JAL-961 JAL-976 tweaked way that AACons client is registered and started.

12 years agoformatting
jprocter [Thu, 14 Jun 2012 10:41:42 +0000 (11:41 +0100)]
formatting

12 years agoformatting
jprocter [Thu, 14 Jun 2012 10:38:26 +0000 (11:38 +0100)]
formatting

12 years agoJAL-1118 - hack to try and get rid of flicker. consider moving greyed out image rende...
jprocter [Thu, 14 Jun 2012 10:36:03 +0000 (11:36 +0100)]
JAL-1118 - hack to try and get rid of flicker. consider moving greyed out image rendering to after we call the panel renderer.

12 years agoJAL-1118 WIP - flag to mark if image buffer has just been cleared ready for a redraw
jprocter [Thu, 14 Jun 2012 10:34:01 +0000 (11:34 +0100)]
JAL-1118 WIP - flag to mark if image buffer has just been cleared ready for a redraw

12 years agoJAL-1115 trap exception arising from race condition when alignment edited during...
jprocter [Thu, 14 Jun 2012 10:32:08 +0000 (11:32 +0100)]
JAL-1115 trap exception arising from race condition when alignment edited during calculation

12 years agoJAL-968 javadoc and return flag indicating if any of the annotation rows were being...
jprocter [Thu, 14 Jun 2012 10:30:45 +0000 (11:30 +0100)]
JAL-968 javadoc and return flag indicating if any of the annotation rows were being worked on whilst the panel was rendered.

12 years agoJAL-961 ensure we only add one instance of a worker to the registered list of workers...
jprocter [Thu, 14 Jun 2012 10:20:49 +0000 (11:20 +0100)]
JAL-961 ensure we only add one instance of a worker to the registered list of workers for an alignment.

12 years agoJAL-961 potentially helpful println statements when debugging alignment calculation...
jprocter [Thu, 14 Jun 2012 10:18:54 +0000 (11:18 +0100)]
JAL-961 potentially helpful println statements when debugging alignment calculation queue

12 years agoJAL-1115 refactor base collection for Alignment from Vector to locally synchronized...
jprocter [Wed, 13 Jun 2012 09:35:20 +0000 (10:35 +0100)]
JAL-1115 refactor base collection for Alignment from Vector to locally synchronized List<SequenceI>
(missed this one from d6509fcf3a8cc90616e18cb22cec97f85c722bb8)

12 years agoJAL-1116 - location where vamsas sync failure occurs
jprocter [Wed, 13 Jun 2012 09:28:28 +0000 (10:28 +0100)]
JAL-1116 - location where vamsas sync failure occurs

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.