jalview.git
15 years agoexplicitly grab all permissions for application execution (need feedback on the effec...
jprocter [Fri, 24 Jul 2009 15:27:37 +0000 (15:27 +0000)]
explicitly grab all permissions for application execution (need feedback on the effect of this on javaws security exceptions)

15 years agoupdate annotation when group state is changed
jprocter [Fri, 24 Jul 2009 15:26:54 +0000 (15:26 +0000)]
update annotation when group state is changed

15 years agoshow group annotation menu entries
jprocter [Fri, 24 Jul 2009 15:26:37 +0000 (15:26 +0000)]
show group annotation menu entries

15 years agocolour by label prototype flag
jprocter [Fri, 24 Jul 2009 15:26:23 +0000 (15:26 +0000)]
colour by label prototype flag

15 years agocatch null pointer exception in headless context
jprocter [Fri, 24 Jul 2009 15:25:56 +0000 (15:25 +0000)]
catch null pointer exception in headless context

15 years agoget consensus sequence and set ignore gaps flag for group consensus row
jprocter [Fri, 24 Jul 2009 15:25:40 +0000 (15:25 +0000)]
get consensus sequence and set ignore gaps flag for group consensus row

15 years agoannotation update method synchronises group annotation
jprocter [Fri, 24 Jul 2009 15:24:45 +0000 (15:24 +0000)]
annotation update method synchronises group annotation

15 years agoheadless warning messages, prototype group annotation and annotation update method
jprocter [Fri, 24 Jul 2009 15:24:10 +0000 (15:24 +0000)]
headless warning messages, prototype group annotation and annotation update method

15 years agorefactored conservation thread, added showgroupannotation flags
jprocter [Fri, 24 Jul 2009 15:23:01 +0000 (15:23 +0000)]
refactored conservation thread, added showgroupannotation flags

15 years agoconservation thread refactored from AlignViewport
jprocter [Fri, 24 Jul 2009 15:22:31 +0000 (15:22 +0000)]
conservation thread refactored from AlignViewport

15 years agofeature colour by label flag/style
jprocter [Fri, 24 Jul 2009 15:13:34 +0000 (15:13 +0000)]
feature colour by label flag/style

15 years agoheadless test
jprocter [Fri, 24 Jul 2009 15:11:57 +0000 (15:11 +0000)]
headless test

15 years agotodo
jprocter [Fri, 24 Jul 2009 15:10:39 +0000 (15:10 +0000)]
todo

15 years agoimplement new insert annotation row method and ensure group annotation rows are remov...
jprocter [Fri, 24 Jul 2009 15:10:05 +0000 (15:10 +0000)]
implement new insert annotation row method and ensure group annotation rows are removed when groups are removed

15 years agoinsert annotation at specific position
jprocter [Fri, 24 Jul 2009 15:09:08 +0000 (15:09 +0000)]
insert annotation at specific position

15 years agooptional sequencegroup ref for annotation row
jprocter [Fri, 24 Jul 2009 15:07:35 +0000 (15:07 +0000)]
optional sequencegroup ref for annotation row

15 years agosequence groups carry their own conservation and consensus annotation rows
jprocter [Fri, 24 Jul 2009 15:07:10 +0000 (15:07 +0000)]
sequence groups carry their own conservation and consensus annotation rows

15 years agocomplete alignment annotation row procedure
jprocter [Fri, 24 Jul 2009 14:42:26 +0000 (14:42 +0000)]
complete alignment annotation row procedure

15 years agoensure annotation row height is honoured for new VAMSAS annotation
jprocter [Wed, 24 Jun 2009 08:31:44 +0000 (08:31 +0000)]
ensure annotation row height is honoured for new VAMSAS annotation

15 years agoall alignment sequences associated with a dataset sequence must have start-end update...
jprocter [Wed, 24 Jun 2009 08:28:23 +0000 (08:28 +0000)]
all alignment sequences associated with a dataset sequence must have start-end updated (and any mappings adjusted - see TODO)

15 years agocan use whitespace, comma or semicolon to separate IDs
jprocter [Wed, 24 Jun 2009 08:24:33 +0000 (08:24 +0000)]
can use whitespace, comma or semicolon to separate IDs

15 years agofix to cope with EMBL records containing a CDS fragment (proper start/end codon posit...
jprocter [Wed, 24 Jun 2009 08:24:00 +0000 (08:24 +0000)]
fix to cope with EMBL records containing a CDS fragment (proper start/end codon positioning and trimming)

15 years agotake the average of the three consecutive codon sites when translating annotation...
jprocter [Wed, 24 Jun 2009 08:22:47 +0000 (08:22 +0000)]
take the average of the three consecutive codon sites when translating annotation row scores from cDNA to protein.

15 years agoimplementation error warning todo
jprocter [Fri, 19 Jun 2009 10:11:43 +0000 (10:11 +0000)]
implementation error warning todo

15 years agodebug and cyclefix for dbrefs with embedded sequences
jprocter [Fri, 19 Jun 2009 10:10:46 +0000 (10:10 +0000)]
debug and cyclefix for dbrefs with embedded sequences

15 years agojavadoc and datastoreitem registry support for binding/rebinding methods
jprocter [Fri, 19 Jun 2009 10:09:56 +0000 (10:09 +0000)]
javadoc and datastoreitem registry support for binding/rebinding methods

15 years agomore efficient synchronized methods
jprocter [Fri, 19 Jun 2009 10:09:19 +0000 (10:09 +0000)]
more efficient synchronized methods

15 years agobugfix mapped reference transfer and made picr ID retrieval optional
jprocter [Fri, 19 Jun 2009 10:01:09 +0000 (10:01 +0000)]
bugfix mapped reference transfer and made picr ID retrieval optional

15 years agoselection handler and sender bugfix
jprocter [Fri, 19 Jun 2009 09:59:46 +0000 (09:59 +0000)]
selection handler and sender bugfix

15 years agotodo
jprocter [Fri, 19 Jun 2009 09:58:50 +0000 (09:58 +0000)]
todo

15 years agoselections sent when mouse is released (drags on ID panel)
jprocter [Fri, 19 Jun 2009 09:58:33 +0000 (09:58 +0000)]
selections sent when mouse is released (drags on ID panel)

15 years agoprogress bars (still need to be threaded properly) and URI drag'n'dropping
jprocter [Fri, 19 Jun 2009 09:57:42 +0000 (09:57 +0000)]
progress bars (still need to be threaded properly) and URI drag'n'dropping

15 years agosmoother scroll-to-position action
jprocter [Fri, 19 Jun 2009 09:56:12 +0000 (09:56 +0000)]
smoother scroll-to-position action

15 years agodrag'n'drop a URL on to an alignment
jprocter [Fri, 19 Jun 2009 09:55:34 +0000 (09:55 +0000)]
drag'n'drop a URL on to an alignment

15 years agoparent db references and mappings added to retrieved sequences, debugging of codon_st...
jprocter [Fri, 19 Jun 2009 09:54:59 +0000 (09:54 +0000)]
parent db references and mappings added to retrieved sequences, debugging of codon_start>1 for coding region and stop codon inclusion/exclusion detection

15 years agointersect did not intersect (used in selection listener)
jprocter [Fri, 19 Jun 2009 09:53:27 +0000 (09:53 +0000)]
intersect did not intersect (used in selection listener)

15 years agoregex validator for uniprot
jprocter [Fri, 19 Jun 2009 09:49:37 +0000 (09:49 +0000)]
regex validator for uniprot

15 years agousepicr config property
jprocter [Fri, 19 Jun 2009 09:49:14 +0000 (09:49 +0000)]
usepicr config property

15 years agodebug
jprocter [Fri, 19 Jun 2009 09:48:55 +0000 (09:48 +0000)]
debug

15 years agodebug comments
jprocter [Fri, 19 Jun 2009 09:41:04 +0000 (09:41 +0000)]
debug comments

15 years agonew coverage comparison - no test case in main method yet
jprocter [Fri, 19 Jun 2009 09:40:18 +0000 (09:40 +0000)]
new coverage comparison - no test case in main method yet

15 years agoupdated Iclientfactory interface, XMl viewer tests - not properly released source...
jprocter [Fri, 12 Jun 2009 16:02:39 +0000 (16:02 +0000)]
updated Iclientfactory interface, XMl viewer tests - not properly released source yet...

15 years agosynching of all db references and sequence features
jprocter [Fri, 12 Jun 2009 15:57:44 +0000 (15:57 +0000)]
synching of all db references and sequence features

15 years agoprevent dbref->map->to->datasetsequence->dbref-> type cycles
jprocter [Fri, 12 Jun 2009 15:57:08 +0000 (15:57 +0000)]
prevent dbref->map->to->datasetsequence->dbref-> type cycles

15 years agoreinstate links on features
jprocter [Fri, 12 Jun 2009 15:56:21 +0000 (15:56 +0000)]
reinstate links on features

15 years agodatastore registration and class cast exception fix
jprocter [Fri, 12 Jun 2009 15:55:32 +0000 (15:55 +0000)]
datastore registration and class cast exception fix

15 years agoprevent and keep track of which objects handling element/jv obj synchronizations.
jprocter [Fri, 12 Jun 2009 15:54:53 +0000 (15:54 +0000)]
prevent and keep track of which objects handling element/jv obj synchronizations.

15 years agonumerous bugfixs (tree panel synchs) and DatastoreRegistry clas.
jprocter [Fri, 12 Jun 2009 15:54:09 +0000 (15:54 +0000)]
numerous bugfixs (tree panel synchs) and DatastoreRegistry clas.

15 years agomethods for importing anonymous vamsas documents into explicitly named sessions ...
jprocter [Fri, 12 Jun 2009 15:51:54 +0000 (15:51 +0000)]
methods for importing anonymous vamsas documents into explicitly named sessions (e.g. temp file from URL). Suppress implementation Error messages if session update fails on first update.

15 years agonullpointer bugfix (possibly not needed - was an error in closing of alignment panels)
jprocter [Fri, 12 Jun 2009 15:49:54 +0000 (15:49 +0000)]
nullpointer bugfix (possibly not needed - was an error in closing of alignment panels)

15 years agorecover pdb from jalview-xml in vamsas doc
jprocter [Fri, 12 Jun 2009 15:49:17 +0000 (15:49 +0000)]
recover pdb from jalview-xml in vamsas doc

15 years agosend selection on drag over sequence ids
jprocter [Fri, 12 Jun 2009 15:48:21 +0000 (15:48 +0000)]
send selection on drag over sequence ids

15 years agoretrieve and init vamsas session from vdoc at URL
jprocter [Fri, 12 Jun 2009 15:47:50 +0000 (15:47 +0000)]
retrieve and init vamsas session from vdoc at URL

15 years agoreinstated blind querying of datasources. Transfer references to alignment from Map...
jprocter [Fri, 12 Jun 2009 15:46:22 +0000 (15:46 +0000)]
reinstated blind querying of datasources. Transfer references to alignment from Map.To sequences on retrieved entries (e.g. protein product from EMBLCDS record)

15 years agomore ID validation
jprocter [Fri, 12 Jun 2009 15:43:42 +0000 (15:43 +0000)]
more ID validation

15 years agojavadoc
jprocter [Fri, 12 Jun 2009 15:43:12 +0000 (15:43 +0000)]
javadoc

15 years agocom.boxysystems.jgogleanalytics is now an optional dependency
jprocter [Wed, 10 Jun 2009 12:04:12 +0000 (12:04 +0000)]
com.boxysystems.jgogleanalytics is now an optional dependency

15 years agofix null pointer when new view is created then closed after a vamsas sync of stored...
jprocter [Tue, 9 Jun 2009 15:16:59 +0000 (15:16 +0000)]
fix null pointer when new view is created then closed after a vamsas sync of stored views

15 years agofix null pointer when new view created on alignment with existing sequence mappings...
jprocter [Tue, 9 Jun 2009 15:14:59 +0000 (15:14 +0000)]
fix null pointer when new view created on alignment with existing sequence mappings (cDNA list is null)

15 years agouse structured UA naming for googleanalytics client
jprocter [Mon, 8 Jun 2009 14:38:06 +0000 (14:38 +0000)]
use structured UA naming for googleanalytics client

15 years agoupgrade to simple vamsas client version 0.2 (not runtime compatible)
jprocter [Mon, 8 Jun 2009 14:07:40 +0000 (14:07 +0000)]
upgrade to simple vamsas client version 0.2 (not runtime compatible)

15 years agotrial of jGA with proper useragent info
jprocter [Mon, 8 Jun 2009 14:06:53 +0000 (14:06 +0000)]
trial of jGA with proper useragent info

15 years ago*experimental use of picr* apply gpl development license
jprocter [Mon, 8 Jun 2009 11:20:50 +0000 (11:20 +0000)]
*experimental use of picr* apply gpl development license

15 years agoclargs documentation, new vamsas session import and join args. apply gpl development...
jprocter [Mon, 8 Jun 2009 11:19:28 +0000 (11:19 +0000)]
clargs documentation, new vamsas session import and join args. apply gpl development license

15 years agorefactored public methods for non-interactive import and initiation of vamsas session...
jprocter [Mon, 8 Jun 2009 11:18:07 +0000 (11:18 +0000)]
refactored public methods for non-interactive import and initiation of vamsas sessions. apply gpl development license

15 years agorefactored for non-interactive import and initiation of sessions. apply gpl developme...
jprocter [Mon, 8 Jun 2009 11:17:06 +0000 (11:17 +0000)]
refactored for non-interactive import and initiation of sessions. apply gpl development license

15 years agosequence scores only shown if they vary. shift stops tooltip moving with mouse pointe...
jprocter [Mon, 8 Jun 2009 11:14:57 +0000 (11:14 +0000)]
sequence scores only shown if they vary. shift stops tooltip moving with mouse pointer. bugfix selection sharing. apply gpl development license

15 years agodebug messages and graceful recovery when structure state is corrupted. apply gpl...
jprocter [Mon, 8 Jun 2009 11:11:41 +0000 (11:11 +0000)]
debug messages and graceful recovery when structure state is corrupted. apply gpl development license

15 years agobetter thread safety for tooltip. apply gpl development license
jprocter [Mon, 8 Jun 2009 11:10:47 +0000 (11:10 +0000)]
better thread safety for tooltip. apply gpl development license

15 years agoensure listeners are deregistered when panel is closed. apply gpl development license
jprocter [Mon, 8 Jun 2009 11:08:32 +0000 (11:08 +0000)]
ensure listeners are deregistered when panel is closed. apply gpl development license

15 years agoensure listeners are deregistered when panel is closed. Fix a scrolling bug and apply...
jprocter [Mon, 8 Jun 2009 11:08:06 +0000 (11:08 +0000)]
ensure listeners are deregistered when panel is closed. Fix a scrolling bug and apply gpl development license

15 years agoga tracker option and apply gpl development license
jprocter [Mon, 8 Jun 2009 11:00:34 +0000 (11:00 +0000)]
ga tracker option and apply gpl development license

15 years agoapply gpl development license
jprocter [Mon, 8 Jun 2009 10:58:52 +0000 (10:58 +0000)]
apply gpl development license

15 years agominor optimization. apply gpl development license
jprocter [Mon, 8 Jun 2009 10:53:26 +0000 (10:53 +0000)]
minor optimization. apply gpl development license

15 years agopatch for wierd format header lines and apply gpl development license
jprocter [Mon, 8 Jun 2009 10:40:37 +0000 (10:40 +0000)]
patch for wierd format header lines and apply gpl development license

15 years agoga in 2.4.0b2 release
jprocter [Mon, 8 Jun 2009 10:31:54 +0000 (10:31 +0000)]
ga in 2.4.0b2 release

15 years agonousagestats cli
jprocter [Mon, 8 Jun 2009 10:31:26 +0000 (10:31 +0000)]
nousagestats cli

15 years agoapply gpl development license and new donotobfuscate flag
jprocter [Mon, 8 Jun 2009 10:29:47 +0000 (10:29 +0000)]
apply gpl development license and new donotobfuscate flag

15 years agofull reference added.
jprocter [Thu, 4 Jun 2009 09:11:35 +0000 (09:11 +0000)]
full reference added.

15 years agospelling
jprocter [Thu, 4 Jun 2009 09:08:52 +0000 (09:08 +0000)]
spelling

15 years agoscript goes at beginning of body to allow linkthrus to be embedded.
jprocter [Thu, 4 Jun 2009 08:38:04 +0000 (08:38 +0000)]
script goes at beginning of body to allow linkthrus to be embedded.

15 years agoupdate minor version of release branch
jprocter [Tue, 2 Jun 2009 12:20:39 +0000 (12:20 +0000)]
update minor version of release branch

15 years agograduated feature colour documentation
jprocter [Mon, 1 Jun 2009 15:54:54 +0000 (15:54 +0000)]
graduated feature colour documentation

15 years agoGA appender script
jprocter [Mon, 1 Jun 2009 15:54:32 +0000 (15:54 +0000)]
GA appender script

15 years agogoogle tracking for index document
jprocter [Mon, 1 Jun 2009 15:54:07 +0000 (15:54 +0000)]
google tracking for index document

15 years agomore graduated feature support
jprocter [Mon, 1 Jun 2009 15:53:43 +0000 (15:53 +0000)]
more graduated feature support

15 years agoproperly export graduated colour features
jprocter [Mon, 1 Jun 2009 15:53:18 +0000 (15:53 +0000)]
properly export graduated colour features

15 years agoprototype function for relabelling treenodes with different accession/labels
jprocter [Mon, 1 Jun 2009 15:52:28 +0000 (15:52 +0000)]
prototype function for relabelling treenodes with different accession/labels

15 years agobetter tooltip placement in alignment window
jprocter [Mon, 1 Jun 2009 15:51:46 +0000 (15:51 +0000)]
better tooltip placement in alignment window

15 years agoadded graduated colourscheme support for feature file
jprocter [Mon, 1 Jun 2009 15:48:43 +0000 (15:48 +0000)]
added graduated colourscheme support for feature file

15 years agobetter decoupling of data loading routines for AJAX
jprocter [Mon, 1 Jun 2009 15:47:42 +0000 (15:47 +0000)]
better decoupling of data loading routines for AJAX

15 years agofirst experiment with GA application use tracking
jprocter [Mon, 1 Jun 2009 15:46:54 +0000 (15:46 +0000)]
first experiment with GA application use tracking

15 years agolook in database references for more ID strings to match against node labels
jprocter [Mon, 1 Jun 2009 15:45:56 +0000 (15:45 +0000)]
look in database references for more ID strings to match against node labels

15 years agoapply method for a NodeTransform to nodes in a tree
jprocter [Mon, 1 Jun 2009 15:45:29 +0000 (15:45 +0000)]
apply method for a NodeTransform to nodes in a tree

15 years agojavadoc
jprocter [Mon, 1 Jun 2009 15:45:07 +0000 (15:45 +0000)]
javadoc

15 years agoonly make a link menu when there are links
jprocter [Mon, 1 Jun 2009 15:44:42 +0000 (15:44 +0000)]
only make a link menu when there are links

15 years agomaxcolour is default colour for no-score features
jprocter [Mon, 1 Jun 2009 15:44:27 +0000 (15:44 +0000)]
maxcolour is default colour for no-score features

15 years agobugfix autobuild of release branch
jprocter [Tue, 14 Apr 2009 12:39:13 +0000 (12:39 +0000)]
bugfix autobuild of release branch

15 years agobugfix autobuild of release branch
jprocter [Tue, 14 Apr 2009 12:32:43 +0000 (12:32 +0000)]
bugfix autobuild of release branch

15 years agopatch to fix occasional arrayoutofbounds exception when working with hidden columns...
jprocter [Tue, 14 Apr 2009 12:32:14 +0000 (12:32 +0000)]
patch to fix occasional arrayoutofbounds exception when working with hidden columns and ragged annotation rows