jalview.git
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

12 years ago(JAL-1052) todo for output of RNA consensus lines
jprocter [Fri, 2 Mar 2012 23:01:34 +0000 (23:01 +0000)]
(JAL-1052) todo for output of RNA consensus lines

12 years ago(JAL-1052) basic consensus line parsing to rna structure lines
jprocter [Fri, 2 Mar 2012 23:00:40 +0000 (23:00 +0000)]
(JAL-1052) basic consensus line parsing to rna structure lines

12 years ago(JAL-1052) make RNA secondary structure string parsing code accessible to Clustal...
jprocter [Fri, 2 Mar 2012 22:56:18 +0000 (22:56 +0000)]
(JAL-1052) make RNA secondary structure string parsing code accessible to Clustal class

12 years agoformatting
jprocter [Fri, 2 Mar 2012 16:23:28 +0000 (16:23 +0000)]
formatting

12 years ago(JAL-942) more tweaking mapping between 2-struct and seqs
jprocter [Fri, 2 Mar 2012 16:23:20 +0000 (16:23 +0000)]
(JAL-942) more tweaking mapping between 2-struct and seqs

12 years ago(JAL-842) debug mouseover for sequences that don't start at 1 and ensure varna only...
jprocter [Fri, 2 Mar 2012 12:26:03 +0000 (12:26 +0000)]
(JAL-842) debug mouseover for sequences that don't start at 1 and ensure varna only responds to highlights for its associated alignment panel

12 years ago(JAL-842) todo
jprocter [Fri, 2 Mar 2012 12:24:45 +0000 (12:24 +0000)]
(JAL-842) todo

12 years agoremove unnecessary method
jprocter [Fri, 2 Mar 2012 12:24:35 +0000 (12:24 +0000)]
remove unnecessary method

12 years agoefficiency, and ensure mouseover messages originating from a source are not broadcast...
jprocter [Fri, 2 Mar 2012 12:23:06 +0000 (12:23 +0000)]
efficiency, and ensure mouseover messages originating from a source are not broadcast to itself

12 years ago(JAL-842) ensure deletions are accounted for when highlighting mouseover in alignment...
jprocter [Thu, 1 Mar 2012 21:40:52 +0000 (21:40 +0000)]
(JAL-842) ensure deletions are accounted for when highlighting mouseover in alignment panel on RNA structure, basic selected region highlighting, and broadcast of mouse position in varna window to associated sequence.

12 years ago(JAL-893) update to VARNAv3.9-dev version
jprocter [Thu, 1 Mar 2012 13:47:14 +0000 (13:47 +0000)]
(JAL-893) update to VARNAv3.9-dev version

12 years agoMerge branch 'Release_2_7_Branch' into develop
jprocter [Thu, 1 Mar 2012 12:07:04 +0000 (12:07 +0000)]
Merge branch 'Release_2_7_Branch' into develop

12 years agodebug local source management buttons and formatting
jprocter [Thu, 1 Mar 2012 11:05:17 +0000 (11:05 +0000)]
debug local source management buttons and formatting

12 years agorevised version of Jdas with simpler connectionPropertyProviderI provider interface...
jprocter [Thu, 1 Mar 2012 11:04:45 +0000 (11:04 +0000)]
revised version of Jdas with simpler connectionPropertyProviderI provider interface for multiple thread clients.

12 years agoupdate to latest build
jprocter [Wed, 29 Feb 2012 16:36:43 +0000 (16:36 +0000)]
update to latest build

12 years agomove from dasobert to jdas multithreaded feature fetching - and use jalview das api...
jprocter [Wed, 29 Feb 2012 16:24:50 +0000 (16:24 +0000)]
move from dasobert to jdas multithreaded feature fetching - and use jalview das api where possible (introduces issue JAL-1051)

12 years agotidy imports and switch over to use das source registry API
jprocter [Wed, 29 Feb 2012 16:23:19 +0000 (16:23 +0000)]
tidy imports and switch over to use das source registry API

12 years agotidy imports
jprocter [Wed, 29 Feb 2012 16:22:30 +0000 (16:22 +0000)]
tidy imports

12 years agofallout from refactoring registry datamodel to a sourceRegistry object
jprocter [Wed, 29 Feb 2012 16:21:24 +0000 (16:21 +0000)]
fallout from refactoring registry datamodel to a sourceRegistry object

12 years ago(JAL-972) replaced biodas with jdas sources datastructures - refactored source list...
jprocter [Wed, 29 Feb 2012 16:20:12 +0000 (16:20 +0000)]
(JAL-972) replaced biodas with jdas sources datastructures - refactored source list model to a sourceregistry object

12 years agorefactoring dassequencesource code fallout
jprocter [Wed, 29 Feb 2012 16:18:47 +0000 (16:18 +0000)]
refactoring dassequencesource code fallout

12 years agorefactored das sequence source creation code to the implementor of the das source...
jprocter [Wed, 29 Feb 2012 16:16:58 +0000 (16:16 +0000)]
refactored das sequence source creation code to the implementor of the das source api and das registry api

12 years agoremoved excess imports
jprocter [Wed, 29 Feb 2012 16:13:38 +0000 (16:13 +0000)]
removed excess imports

12 years agoupdated das sequence source for jdas client and refactored to implementation package
jprocter [Wed, 29 Feb 2012 16:13:22 +0000 (16:13 +0000)]
updated das sequence source for jdas client and refactored to implementation package

12 years agoJAL-972 - refactored local source builder to registry implementation and made Cache...
jprocter [Wed, 29 Feb 2012 16:03:02 +0000 (16:03 +0000)]
JAL-972 - refactored local source builder to registry implementation and made Cache the holder of the registry singleton

12 years agoJAL-966 todo for jalview 3 api
jprocter [Wed, 29 Feb 2012 16:01:01 +0000 (16:01 +0000)]
JAL-966 todo for jalview 3 api

12 years agojalview das registry and source api and jdas specific implementations
jprocter [Wed, 29 Feb 2012 16:00:08 +0000 (16:00 +0000)]
jalview das registry and source api and jdas specific implementations

12 years agojdas runtime dependencies
jprocter [Wed, 29 Feb 2012 15:58:08 +0000 (15:58 +0000)]
jdas runtime dependencies

12 years agoupdated build of jdas
jprocter [Wed, 29 Feb 2012 15:50:32 +0000 (15:50 +0000)]
updated build of jdas

12 years agojdas doesn't need a listener for das sequence retrieval events
jprocter [Wed, 29 Feb 2012 15:50:11 +0000 (15:50 +0000)]
jdas doesn't need a listener for das sequence retrieval events

12 years agogroovy nature not needed in project
jprocter [Mon, 13 Feb 2012 08:52:52 +0000 (08:52 +0000)]
groovy nature not needed in project

12 years agoremove dead imports
jprocter [Mon, 13 Feb 2012 08:50:53 +0000 (08:50 +0000)]
remove dead imports

12 years ago(JAL-972) relative refs for libraries and some additional eclipse 3.7.2 decorators...
jprocter [Fri, 20 Jan 2012 13:35:15 +0000 (13:35 +0000)]
(JAL-972) relative refs for libraries and some additional eclipse 3.7.2 decorators for updated groovy projects

12 years ago(JAL-972) jdas source retrieval and use of jdas structures for local sources
jprocter [Wed, 18 Jan 2012 11:14:06 +0000 (11:14 +0000)]
(JAL-972) jdas source retrieval and use of jdas structures for local sources

12 years ago(JAL-972) updated jdas to latest version includign concurrent DAS request api
jprocter [Wed, 18 Jan 2012 11:10:00 +0000 (11:10 +0000)]
(JAL-972) updated jdas to latest version includign concurrent DAS request api