jalview.git
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

15 years agodocumented fix to sequencefetcher for multiple ID retrieval
jprocter [Tue, 7 Apr 2009 11:39:54 +0000 (11:39 +0000)]
documented fix to sequencefetcher for multiple ID retrieval

15 years agorejigged jmol check thread to run prior to data loading thread to avoid classloader...
jprocter [Sat, 4 Apr 2009 11:35:24 +0000 (11:35 +0000)]
rejigged jmol check thread to run prior to data loading thread to avoid classloader race condition in java 1.6_10 (Sillitoe/Clegg/CATH issue)

15 years agorejigged jmol check thread to run prior to data loading thread to avoid classloader...
jprocter [Sat, 4 Apr 2009 11:17:16 +0000 (11:17 +0000)]
rejigged jmol check thread to run prior to data loading thread to avoid classloader race condition in java 1.6_10 (Sillitoe/Clegg/CATH issue)

15 years agonote on new popup menu in feature settings dialog
jprocter [Tue, 31 Mar 2009 16:42:31 +0000 (16:42 +0000)]
note on new popup menu in feature settings dialog

15 years agoadded feature gradient colours and sortby feature score/density to feature settings...
jprocter [Tue, 31 Mar 2009 16:40:22 +0000 (16:40 +0000)]
added feature gradient colours and sortby feature score/density to feature settings dialog.

15 years agoprototype for store/restore of feature colour gradient settings
jprocter [Tue, 31 Mar 2009 16:39:56 +0000 (16:39 +0000)]
prototype for store/restore of feature colour gradient settings

15 years agotodo
jprocter [Tue, 31 Mar 2009 16:39:14 +0000 (16:39 +0000)]
todo

15 years agoallow configuration of graduated colour
jprocter [Tue, 17 Mar 2009 17:00:37 +0000 (17:00 +0000)]
allow configuration of graduated colour

15 years agoquantitative shading of features by GraduatedColor
jprocter [Tue, 17 Mar 2009 17:00:20 +0000 (17:00 +0000)]
quantitative shading of features by GraduatedColor

15 years agoprototype dialog for setting feature display shading and threshold
jprocter [Tue, 17 Mar 2009 16:59:45 +0000 (16:59 +0000)]
prototype dialog for setting feature display shading and threshold

15 years agoholds shading and range parameters rendering a feature colour
jprocter [Tue, 17 Mar 2009 16:58:35 +0000 (16:58 +0000)]
holds shading and range parameters rendering a feature colour

15 years agosortbytree view setting and action added - setting is not yet stored in the jalview xml
jprocter [Tue, 17 Mar 2009 16:57:34 +0000 (16:57 +0000)]
sortbytree view setting and action added - setting is not yet stored in the jalview xml

15 years agosortbytree/nosortbytree and defprop arguments. (defprop disabled for moment)
jprocter [Tue, 17 Mar 2009 16:56:05 +0000 (16:56 +0000)]
sortbytree/nosortbytree and defprop arguments. (defprop disabled for moment)

15 years agonew sortbytree default config property
jprocter [Tue, 17 Mar 2009 16:55:42 +0000 (16:55 +0000)]
new sortbytree default config property

15 years agosortbytree parameter added and undo re-instated for sort by tree and sort by id
jprocter [Tue, 17 Mar 2009 16:54:30 +0000 (16:54 +0000)]
sortbytree parameter added and undo re-instated for sort by tree and sort by id

15 years agofixes launchApp bug where user defined colourscheme defined in applet parameter does...
jprocter [Tue, 17 Mar 2009 16:50:48 +0000 (16:50 +0000)]
fixes launchApp bug where user defined colourscheme defined in applet parameter does not get passed to application

15 years agobetter tooltip display and placement, cope with linkOnly features (hack) and safer...
jprocter [Tue, 24 Feb 2009 17:56:51 +0000 (17:56 +0000)]
better tooltip display and placement, cope with linkOnly features (hack) and safer method for send/receive selections

15 years agodebugging selection message send/receive
jprocter [Tue, 24 Feb 2009 17:55:18 +0000 (17:55 +0000)]
debugging selection message send/receive

15 years agoonly display unique url links (both in label and in destination)
jprocter [Tue, 24 Feb 2009 17:54:20 +0000 (17:54 +0000)]
only display unique url links (both in label and in destination)

15 years agobugfix for occasional nullpointer exceptions when selecting menu items that operate...
jprocter [Tue, 24 Feb 2009 17:53:27 +0000 (17:53 +0000)]
bugfix for occasional nullpointer exceptions when selecting menu items that operate on the current selection

15 years agochange method signature to allow caller to test if panel actually scrolled or not
jprocter [Tue, 24 Feb 2009 17:52:48 +0000 (17:52 +0000)]
change method signature to allow caller to test if panel actually scrolled or not

15 years agobugfix the bugfix
jprocter [Tue, 24 Feb 2009 17:52:10 +0000 (17:52 +0000)]
bugfix the bugfix

15 years agoallow label to be set independently of parsed input string
jprocter [Tue, 24 Feb 2009 17:28:22 +0000 (17:28 +0000)]
allow label to be set independently of parsed input string

15 years agobug fixes (infinite loop when fetcher given same sequence several times, race conditi...
jprocter [Tue, 24 Feb 2009 17:27:33 +0000 (17:27 +0000)]
bug fixes (infinite loop when fetcher given same sequence several times, race conditions when fetching features immediatly after fetching sequences) and enhanced parsing of protein_name dbref types and URL link handling for features with no label.

15 years agoupdated jalview reference
jprocter [Fri, 6 Feb 2009 14:57:06 +0000 (14:57 +0000)]
updated jalview reference

15 years agoupdated binding
jprocter [Fri, 6 Feb 2009 14:56:52 +0000 (14:56 +0000)]
updated binding

15 years agofix occasional nullpointer ref when seq ID retrieval doesn't resolve to a sequence...
jprocter [Fri, 6 Feb 2009 14:56:21 +0000 (14:56 +0000)]
fix occasional nullpointer ref when seq ID retrieval doesn't resolve to a sequence object

15 years agoshowUnconserved and updated reference
jprocter [Fri, 6 Feb 2009 14:55:41 +0000 (14:55 +0000)]
showUnconserved and updated reference

15 years agoshowunconserved preference
jprocter [Fri, 6 Feb 2009 14:55:06 +0000 (14:55 +0000)]
showunconserved preference

15 years agoshowUnconserved group attribute
jprocter [Fri, 6 Feb 2009 14:54:46 +0000 (14:54 +0000)]
showUnconserved group attribute

15 years agoshowUnconserved IO
jprocter [Fri, 6 Feb 2009 14:54:03 +0000 (14:54 +0000)]
showUnconserved IO

15 years agoshowUnconserved view and group setting
jprocter [Fri, 6 Feb 2009 14:53:55 +0000 (14:53 +0000)]
showUnconserved view and group setting

15 years agoshow unconserved gui and annotation file attribute
jprocter [Fri, 6 Feb 2009 14:51:48 +0000 (14:51 +0000)]
show unconserved gui and annotation file attribute

15 years agoadded showUnconserved property to group and view attributes
jprocter [Fri, 6 Feb 2009 14:51:06 +0000 (14:51 +0000)]
added showUnconserved property to group and view attributes

15 years agohack to completely disable calculation of consensus and conservation if autocalculate...
jprocter [Fri, 9 Jan 2009 15:11:33 +0000 (15:11 +0000)]
hack to completely disable calculation of consensus and conservation if autocalculate is not enabled

15 years agobugfix
jprocter [Fri, 9 Jan 2009 10:30:23 +0000 (10:30 +0000)]
bugfix

15 years agofix broken parsing of non-positional features in GFF files
jprocter [Thu, 8 Jan 2009 16:01:03 +0000 (16:01 +0000)]
fix broken parsing of non-positional features in GFF files

15 years agostructure ids are not IDs, but simply references
jprocter [Thu, 8 Jan 2009 16:00:17 +0000 (16:00 +0000)]
structure ids are not IDs, but simply references

15 years agorefactor
jprocter [Thu, 8 Jan 2009 15:59:40 +0000 (15:59 +0000)]
refactor

15 years agoadded links to the das settings help, and explanation of how to actually open the...
jprocter [Wed, 7 Jan 2009 14:32:11 +0000 (14:32 +0000)]
added links to the das settings help, and explanation of how to actually open the DAS Settings dialog

15 years agoensure that the DAS sequence source checkbox is checked when a local sequence source...
jprocter [Wed, 7 Jan 2009 14:30:39 +0000 (14:30 +0000)]
ensure that the DAS sequence source checkbox is checked when a local sequence source is edited.

15 years agocheck for features on the retrieved sequences
jprocter [Wed, 7 Jan 2009 14:30:07 +0000 (14:30 +0000)]
check for features on the retrieved sequences