jalview.git
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

15 years agorefactor
jprocter [Wed, 7 Jan 2009 14:29:40 +0000 (14:29 +0000)]
refactor

15 years agoadded higher level method to enable the display of sequence features
jprocter [Wed, 7 Jan 2009 14:29:14 +0000 (14:29 +0000)]
added higher level method to enable the display of sequence features

15 years agojustify cannot be undone - commented out menu items for moment
jprocter [Fri, 19 Dec 2008 16:10:07 +0000 (16:10 +0000)]
justify cannot be undone - commented out menu items for moment

15 years agoexperimental: sort by feature UI in feature settings and variable height rendering...
jprocter [Fri, 19 Dec 2008 15:39:12 +0000 (15:39 +0000)]
experimental: sort by feature UI in feature settings and variable height rendering of features by score

15 years agonew sort by length method, justify edit menu entries and experimental support for...
jprocter [Fri, 19 Dec 2008 15:37:49 +0000 (15:37 +0000)]
new sort by length method, justify edit menu entries and experimental support for variable height sequence feature rendering

15 years agocatch null pointer exception when no colourscheme is active
jprocter [Fri, 19 Dec 2008 15:36:30 +0000 (15:36 +0000)]
catch null pointer exception when no colourscheme is active

15 years agosimple transformation of feature types like dbref and dbxref into database references
jprocter [Fri, 19 Dec 2008 15:36:08 +0000 (15:36 +0000)]
simple transformation of feature types like dbref and dbxref into database references

15 years agotodo
jprocter [Fri, 19 Dec 2008 15:35:15 +0000 (15:35 +0000)]
todo

15 years agowsdbfetch parameter change again (uniprotkb is dbname for uniprot)
jprocter [Fri, 19 Dec 2008 15:34:58 +0000 (15:34 +0000)]
wsdbfetch parameter change again (uniprotkb is dbname for uniprot)

15 years agoavoid null pointer exception when no features visible
jprocter [Fri, 19 Dec 2008 15:34:33 +0000 (15:34 +0000)]
avoid null pointer exception when no features visible

15 years agoavoid null pointer exception when groupName is not set
jprocter [Fri, 19 Dec 2008 15:34:07 +0000 (15:34 +0000)]
avoid null pointer exception when groupName is not set

15 years agoleft and right justify method
jprocter [Fri, 19 Dec 2008 15:33:39 +0000 (15:33 +0000)]
left and right justify method

15 years agosort by length
jprocter [Fri, 19 Dec 2008 15:33:08 +0000 (15:33 +0000)]
sort by length

15 years agoadded (and enabled) switch to store gff source string as sequencefeature.group rather...
jprocter [Mon, 15 Dec 2008 10:35:09 +0000 (10:35 +0000)]
added (and enabled) switch to store gff source string as sequencefeature.group rather than add it to description

15 years agotemporary fix and note about null feature group mucking up selection of features...
jprocter [Mon, 15 Dec 2008 10:34:19 +0000 (10:34 +0000)]
temporary fix and note about null feature group mucking up selection of features to be sorted on

15 years agowarning for failed parsing of newick strings
jprocter [Mon, 15 Dec 2008 10:33:26 +0000 (10:33 +0000)]
warning for failed parsing of newick strings

15 years agonew callback handler allowing threads that request a progress bar to be cancelled...
jprocter [Mon, 15 Dec 2008 10:32:52 +0000 (10:32 +0000)]
new callback handler allowing threads that request a progress bar to be cancelled (this is untested!)

15 years agostructureState element to structure view Id is a many to one relationship - so viewId...
jprocter [Mon, 15 Dec 2008 10:31:38 +0000 (10:31 +0000)]
structureState element to structure view Id is a many to one relationship - so viewId cannot be an XML element ID.

15 years agoDAS feature scores are parsed into floats on sequence features
jprocter [Mon, 8 Dec 2008 13:03:22 +0000 (13:03 +0000)]
DAS feature scores are parsed into floats on sequence features

15 years agooutput average score to stdout
jprocter [Mon, 8 Dec 2008 13:02:53 +0000 (13:02 +0000)]
output average score to stdout

15 years agodisplay feature score in tooltip
jprocter [Mon, 8 Dec 2008 13:02:02 +0000 (13:02 +0000)]
display feature score in tooltip

15 years agoorder by feature documentation
jprocter [Mon, 8 Dec 2008 12:44:07 +0000 (12:44 +0000)]
order by feature documentation

15 years agoexperimental buttons for sort on score/density and popup menu to sort by score/densit...
jprocter [Mon, 8 Dec 2008 12:38:32 +0000 (12:38 +0000)]
experimental buttons for sort on score/density and popup menu to sort by score/density for a specific feature type

15 years agonew sort functions for ordering sequence by annotated features (probably still buggy...
jprocter [Mon, 8 Dec 2008 12:37:40 +0000 (12:37 +0000)]
new sort functions for ordering sequence by annotated features (probably still buggy) - sorts on distribution and score

15 years agoadded location of menu option and keystroke
jprocter [Fri, 5 Dec 2008 13:19:00 +0000 (13:19 +0000)]
added location of menu option and keystroke

15 years agosupport for multiple accession retrieval from a database source
jprocter [Fri, 5 Dec 2008 13:09:46 +0000 (13:09 +0000)]
support for multiple accession retrieval from a database source

15 years agoadded local das sequence source CLI and documentation
jprocter [Thu, 4 Dec 2008 10:46:43 +0000 (10:46 +0000)]
added local das sequence source CLI and documentation

15 years agofetch database references for all EBI db + selected das sequence sources or a specifi...
jprocter [Thu, 4 Dec 2008 10:28:02 +0000 (10:28 +0000)]
fetch database references for all EBI db + selected das sequence sources or a specific list of named sources

15 years agosequence fetchers generated for local das sequence sources
jprocter [Thu, 4 Dec 2008 10:27:03 +0000 (10:27 +0000)]
sequence fetchers generated for local das sequence sources

15 years agodas source browser uses local source method from jalview.bin.Cache and methods refact...
jprocter [Thu, 4 Dec 2008 10:25:43 +0000 (10:25 +0000)]
das source browser uses local source method from jalview.bin.Cache and methods refactored to allow headless access to list of selected das sources