jalview.git
14 years agothread off a Filechooser instance on startup to make the dialog open quicker later on.
jprocter [Fri, 23 Apr 2010 14:20:46 +0000 (14:20 +0000)]
thread off a Filechooser instance on startup to make the dialog open quicker later on.

14 years agodefault value boolean parameter getter
jprocter [Fri, 23 Apr 2010 12:20:56 +0000 (12:20 +0000)]
default value boolean parameter getter

14 years agofix for bug #8333
jprocter [Fri, 23 Apr 2010 12:20:42 +0000 (12:20 +0000)]
fix for bug #8333

14 years agofix for bug #62456
jprocter [Fri, 23 Apr 2010 12:19:24 +0000 (12:19 +0000)]
fix for bug #62456

14 years agoported logo rendering and label fit to column width - but disabled due to 1.1 incompa...
jprocter [Fri, 23 Apr 2010 10:56:28 +0000 (10:56 +0000)]
ported logo rendering and label fit to column width - but disabled due to 1.1 incompatibility.

14 years agoported basic elements of logo and group annotation display, but disabled due to 1...
jprocter [Fri, 23 Apr 2010 10:55:31 +0000 (10:55 +0000)]
ported basic elements of logo and group annotation display, but disabled due to 1.1 incompatibility.

14 years agorefresh table method
jprocter [Fri, 23 Apr 2010 10:54:36 +0000 (10:54 +0000)]
refresh table method

14 years ago1.1 compatibility
jprocter [Fri, 23 Apr 2010 10:53:24 +0000 (10:53 +0000)]
1.1 compatibility

14 years ago1.1 compatibility and refresh table method
jprocter [Fri, 23 Apr 2010 10:51:00 +0000 (10:51 +0000)]
1.1 compatibility and refresh table method

14 years agonon-positional feature export in gff and features file: bug #54325
jprocter [Thu, 22 Apr 2010 14:15:54 +0000 (14:15 +0000)]
non-positional feature export in gff and features file: bug #54325

14 years agofeature settings is updated if new features are added and dialog is refreshed on...
jprocter [Thu, 22 Apr 2010 12:01:14 +0000 (12:01 +0000)]
feature settings is updated if new features are added and dialog is refreshed on a reload

14 years agodoc and todo about setting position of new internal frames
jprocter [Thu, 22 Apr 2010 12:00:45 +0000 (12:00 +0000)]
doc and todo about setting position of new internal frames

14 years agoensure there's always a space between ID and feature/descr/dbref list.
jprocter [Thu, 22 Apr 2010 12:00:20 +0000 (12:00 +0000)]
ensure there's always a space between ID and feature/descr/dbref list.

14 years agopatch for bug #36198 - more to follow on Monday.
jprocter [Fri, 16 Apr 2010 16:43:38 +0000 (16:43 +0000)]
patch for bug #36198 - more to follow on Monday.

14 years agograduated feature color editing
jprocter [Fri, 16 Apr 2010 14:32:29 +0000 (14:32 +0000)]
graduated feature color editing

14 years agoexport graduated feature colors
jprocter [Fri, 16 Apr 2010 14:31:55 +0000 (14:31 +0000)]
export graduated feature colors

14 years agotodo javadoc
jprocter [Fri, 16 Apr 2010 14:31:33 +0000 (14:31 +0000)]
todo javadoc

14 years agodefault for colourBylabel is false
jprocter [Fri, 16 Apr 2010 14:31:23 +0000 (14:31 +0000)]
default for colourBylabel is false

14 years agonullpointer bugfix (another repaint racecondition)
jprocter [Thu, 15 Apr 2010 09:20:28 +0000 (09:20 +0000)]
nullpointer bugfix (another repaint racecondition)

14 years agoID tooltip preference settings and doc
jprocter [Thu, 15 Apr 2010 09:17:26 +0000 (09:17 +0000)]
ID tooltip preference settings and doc

14 years agodialog box appears in centre of desktop window
jprocter [Wed, 14 Apr 2010 14:39:33 +0000 (14:39 +0000)]
dialog box appears in centre of desktop window

14 years agotodo and disable selection sharing between views on same alignment
jprocter [Wed, 14 Apr 2010 14:39:18 +0000 (14:39 +0000)]
todo and disable selection sharing between views on same alignment

14 years agoremove debug messages. fix order/reverse order issue for sortByFeature
jprocter [Wed, 14 Apr 2010 14:39:08 +0000 (14:39 +0000)]
remove debug messages. fix order/reverse order issue for sortByFeature

14 years agoprofile visualizations are now logos
jprocter [Wed, 14 Apr 2010 14:37:55 +0000 (14:37 +0000)]
profile visualizations are now logos

14 years agofix order/reverse order issue for sortByFeature
jprocter [Wed, 14 Apr 2010 14:35:51 +0000 (14:35 +0000)]
fix order/reverse order issue for sortByFeature

14 years agoensure console contains build details in header
jprocter [Mon, 5 Apr 2010 15:56:59 +0000 (15:56 +0000)]
ensure console contains build details in header

14 years agoregenerated binding for extensions to XML for 2.5
jprocter [Mon, 5 Apr 2010 15:39:39 +0000 (15:39 +0000)]
regenerated binding for extensions to XML for 2.5

14 years agojavadoc, and unimplemented warning for group associated annotation (not shared to...
jprocter [Mon, 5 Apr 2010 15:38:53 +0000 (15:38 +0000)]
javadoc, and unimplemented warning for group associated annotation (not shared to vamsas session in 2.5)

14 years agounnecessary code
jprocter [Mon, 5 Apr 2010 15:38:06 +0000 (15:38 +0000)]
unnecessary code

14 years agojavadoc
jprocter [Mon, 5 Apr 2010 15:36:39 +0000 (15:36 +0000)]
javadoc

14 years agoExtend XML model for graduated feature colours, group associated manual/auto annotati...
jprocter [Mon, 5 Apr 2010 15:36:25 +0000 (15:36 +0000)]
Extend XML model for graduated feature colours, group associated manual/auto annotation, consensus profile/histograms, annotation label formatting, viewport highlight follow/select message receive settings. Fix group+ucs recovery bug #0061271

14 years agoextend XML model for graduated feature colours, group associated manual/auto annotati...
jprocter [Mon, 5 Apr 2010 15:34:09 +0000 (15:34 +0000)]
extend XML model for graduated feature colours, group associated manual/auto annotation, consensus profile/histograms, annotation label formatting, viewport highlight follow/select message receive settings

14 years agodocument XML extension
jprocter [Fri, 2 Apr 2010 14:46:13 +0000 (14:46 +0000)]
document XML extension

14 years agojavadoc
jprocter [Fri, 2 Apr 2010 14:43:02 +0000 (14:43 +0000)]
javadoc

14 years agomade threshold type enumaration into set of constants
jprocter [Fri, 2 Apr 2010 14:42:32 +0000 (14:42 +0000)]
made threshold type enumaration into set of constants

14 years agoload and save graduated feature colours in XML
jprocter [Fri, 2 Apr 2010 14:41:39 +0000 (14:41 +0000)]
load and save graduated feature colours in XML

14 years agoextended Colour element with additional optional attributes for graduated colour
jprocter [Fri, 2 Apr 2010 14:41:11 +0000 (14:41 +0000)]
extended Colour element with additional optional attributes for graduated colour

14 years agoindicate the database id source associated with the sequences being submitted.
jprocter [Fri, 2 Apr 2010 10:35:13 +0000 (10:35 +0000)]
indicate the database id source associated with the sequences being submitted.

14 years agocli length limit
jprocter [Fri, 2 Apr 2010 10:34:08 +0000 (10:34 +0000)]
cli length limit

14 years agourllength limit and more efficient url construction
jprocter [Fri, 2 Apr 2010 10:33:54 +0000 (10:33 +0000)]
urllength limit and more efficient url construction

14 years agoavoid occasional null exception
jprocter [Fri, 2 Apr 2010 09:39:51 +0000 (09:39 +0000)]
avoid occasional null exception

14 years agobetter truncation mechanism
jprocter [Fri, 2 Apr 2010 09:38:52 +0000 (09:38 +0000)]
better truncation mechanism

14 years agoprevent duplicate service submission links
jprocter [Thu, 1 Apr 2010 16:30:36 +0000 (16:30 +0000)]
prevent duplicate service submission links

14 years agoreinstate submission of database Ids as well as sequence Id strings.
jprocter [Thu, 1 Apr 2010 16:05:03 +0000 (16:05 +0000)]
reinstate submission of database Ids as well as sequence Id strings.

14 years agorefactored copy of groupURL mechanism into new Envision service discovery class.
jprocter [Thu, 1 Apr 2010 14:19:25 +0000 (14:19 +0000)]
refactored copy of groupURL mechanism into new Envision service discovery class.

14 years agosay which url was a problem when exceptions are raised.
jprocter [Thu, 1 Apr 2010 14:18:35 +0000 (14:18 +0000)]
say which url was a problem when exceptions are raised.

14 years agonew interface
jprocter [Thu, 1 Apr 2010 14:18:19 +0000 (14:18 +0000)]
new interface

14 years agotodo
jprocter [Thu, 1 Apr 2010 14:17:39 +0000 (14:17 +0000)]
todo

14 years agogroup autoannotation and consensus display, annotation label scale to width, etc.
jprocter [Tue, 30 Mar 2010 17:49:49 +0000 (17:49 +0000)]
group autoannotation and consensus display, annotation label scale to width, etc.

14 years agodocumenting histogram colour spec
jprocter [Tue, 30 Mar 2010 17:48:43 +0000 (17:48 +0000)]
documenting histogram colour spec

14 years agogroup autoannotation and consensus display settings
jprocter [Tue, 30 Mar 2010 17:48:15 +0000 (17:48 +0000)]
group autoannotation and consensus display settings

14 years agobugfix for redraw when AlignPanel partially constructed. group autoannotation and...
jprocter [Tue, 30 Mar 2010 17:46:55 +0000 (17:46 +0000)]
bugfix for redraw when AlignPanel partially constructed. group autoannotation and consensus display settings

14 years agoname update for group autoannotation and consensus display settings
jprocter [Tue, 30 Mar 2010 17:45:22 +0000 (17:45 +0000)]
name update for group autoannotation and consensus display settings

14 years agosync for cvs wierdness
jprocter [Fri, 26 Mar 2010 14:31:59 +0000 (14:31 +0000)]
sync for cvs wierdness

14 years agosync for cvs wierdness
jprocter [Fri, 26 Mar 2010 13:33:55 +0000 (13:33 +0000)]
sync for cvs wierdness

14 years agoFeatureColourI removed
jprocter [Fri, 26 Mar 2010 13:33:31 +0000 (13:33 +0000)]
FeatureColourI removed

14 years agogui/debug: integrate graduated feature colour editor into amend feature and feature...
jprocter [Fri, 26 Mar 2010 12:27:17 +0000 (12:27 +0000)]
gui/debug: integrate graduated feature colour editor into amend feature and feature settings dialog box.

14 years agogroup autocalc annotation update logic (still broken)
jprocter [Fri, 26 Mar 2010 12:26:36 +0000 (12:26 +0000)]
group autocalc annotation update logic (still broken)

14 years agoconsole output to stderr and stdout, and console buffer stays constant size (needs...
jprocter [Fri, 26 Mar 2010 12:23:50 +0000 (12:23 +0000)]
console output to stderr and stdout, and console buffer stays constant size (needs optimising)

14 years agoprofiles only shown for consensus row
jprocter [Fri, 26 Mar 2010 12:23:10 +0000 (12:23 +0000)]
profiles only shown for consensus row

14 years agofix logic for annotation label popup (still outstanding todo)
jprocter [Fri, 26 Mar 2010 12:22:33 +0000 (12:22 +0000)]
fix logic for annotation label popup (still outstanding todo)

14 years agoenable feature display when feature settings is opened.
jprocter [Fri, 26 Mar 2010 12:21:10 +0000 (12:21 +0000)]
enable feature display when feature settings is opened.

14 years agocomments
jprocter [Fri, 26 Mar 2010 12:20:41 +0000 (12:20 +0000)]
comments

14 years agotodo for graduated feature colours
jprocter [Fri, 26 Mar 2010 12:19:56 +0000 (12:19 +0000)]
todo for graduated feature colours

14 years agocommented out for release
jprocter [Fri, 26 Mar 2010 12:19:28 +0000 (12:19 +0000)]
commented out for release

14 years agoindicate which registry timed out.
jprocter [Fri, 26 Mar 2010 12:18:56 +0000 (12:18 +0000)]
indicate which registry timed out.

14 years agomore efficient group URL generation.
jprocter [Fri, 26 Mar 2010 12:18:16 +0000 (12:18 +0000)]
more efficient group URL generation.

14 years agoonly do scaletofit for annotation labels
jprocter [Mon, 22 Mar 2010 17:17:39 +0000 (17:17 +0000)]
only do scaletofit for annotation labels

14 years agoensure that all bits of annotation panel (slider, annotation labels) get updated
jprocter [Mon, 22 Mar 2010 17:17:06 +0000 (17:17 +0000)]
ensure that all bits of annotation panel (slider, annotation labels) get updated

14 years agonote to callers of adjustPanelHeight
jprocter [Mon, 22 Mar 2010 17:16:30 +0000 (17:16 +0000)]
note to callers of adjustPanelHeight

14 years agotodo and sensible default setting of min/max for histograms and line graphs to include 0
jprocter [Mon, 22 Mar 2010 17:14:51 +0000 (17:14 +0000)]
todo and sensible default setting of min/max for histograms and line graphs to include 0

14 years agoSee note in Mantis bug #55537 : inconsistency between loading in exported histogram...
jprocter [Mon, 22 Mar 2010 17:13:12 +0000 (17:13 +0000)]
See note in Mantis bug #55537 : inconsistency between loading in exported histogram annotation and annotation row type dependent parsing of the column annotation fields.

14 years agodisabled simple blast parser for 2.4.1 release
jprocter [Thu, 18 Mar 2010 10:38:13 +0000 (10:38 +0000)]
disabled simple blast parser for 2.4.1 release

14 years agosimple query anchored blast report parser (shh!)
jprocter [Wed, 17 Mar 2010 17:39:58 +0000 (17:39 +0000)]
simple query anchored blast report parser (shh!)
main method tester: also tries to output imported alignment as FASTA

14 years agosimple query anchored blast report parser (shh!)
jprocter [Wed, 17 Mar 2010 17:39:02 +0000 (17:39 +0000)]
simple query anchored blast report parser (shh!)

14 years ago1.1 compatibility
jprocter [Fri, 12 Mar 2010 12:08:32 +0000 (12:08 +0000)]
1.1 compatibility

14 years agofiner column label format control and new 'scale label to column' format for annotati...
jprocter [Thu, 11 Mar 2010 18:02:12 +0000 (18:02 +0000)]
finer column label format control and new 'scale label to column' format for annotation rows.

14 years agodocumented new ROWPROPERTIES keyword.
jprocter [Thu, 11 Mar 2010 18:01:02 +0000 (18:01 +0000)]
documented new ROWPROPERTIES keyword.

14 years agowarning for unresolvable database source strings (or ones which apparently have no...
jprocter [Thu, 11 Mar 2010 17:18:40 +0000 (17:18 +0000)]
warning for unresolvable database source strings (or ones which apparently have no cross references)

14 years agofeature settings type popup menu
jprocter [Thu, 11 Mar 2010 17:12:45 +0000 (17:12 +0000)]
feature settings type popup menu

14 years agogroup links menu documentation
jprocter [Thu, 11 Mar 2010 17:12:02 +0000 (17:12 +0000)]
group links menu documentation

14 years agofiner column label format control and new 'scale label to column' format for annotati...
jprocter [Thu, 11 Mar 2010 17:10:45 +0000 (17:10 +0000)]
finer column label format control and new 'scale label to column' format for annotation rows.

14 years agonew ROWPROPERTIES statement for setting an individual row's label format
jprocter [Thu, 11 Mar 2010 17:08:15 +0000 (17:08 +0000)]
new ROWPROPERTIES statement for setting an individual row's label format

14 years agopass any warning messages to StdErr - also todo to allow caller to check for any...
jprocter [Thu, 11 Mar 2010 17:06:16 +0000 (17:06 +0000)]
pass any warning messages to StdErr - also todo to allow caller to check for any output warnings.

14 years agoraise a warning if column annotation gets truncated.
jprocter [Thu, 11 Mar 2010 17:04:54 +0000 (17:04 +0000)]
raise a warning if column annotation gets truncated.

14 years agoindividual label format settings for each annotation row. Removed excess term in...
jprocter [Thu, 11 Mar 2010 17:04:40 +0000 (17:04 +0000)]
individual label format settings for each annotation row. Removed excess term in conditional.

14 years agotodos re adding groupUrl menu item code
jprocter [Wed, 10 Feb 2010 14:48:55 +0000 (14:48 +0000)]
todos re adding groupUrl menu item code

14 years agodas feature fetch followed by png output fixed (bug #0059977). Trial of utf8 decoding...
jprocter [Wed, 10 Feb 2010 14:48:27 +0000 (14:48 +0000)]
das feature fetch followed by png output fixed (bug #0059977). Trial of utf8 decoding of command line arguments to fix applet-application parameter transfer problems.

14 years agoonly need to remove progress bar if fetch wasn't cancelled (bug #0059977)
jprocter [Wed, 10 Feb 2010 14:46:41 +0000 (14:46 +0000)]
only need to remove progress bar if fetch wasn't cancelled (bug #0059977)

14 years agocommented out enfin/envision2 sequence submission URL - mechanism is not yet efficient
jprocter [Wed, 10 Feb 2010 14:45:46 +0000 (14:45 +0000)]
commented out enfin/envision2 sequence submission URL - mechanism is not yet efficient

14 years agoallow das fetch to be blocking or non-blocking (bug #0059977)
jprocter [Wed, 10 Feb 2010 14:45:03 +0000 (14:45 +0000)]
allow das fetch to be blocking or non-blocking (bug #0059977)

14 years agoprogress bar hashtable entry was not being removed (bug #0059977)
jprocter [Wed, 10 Feb 2010 14:44:06 +0000 (14:44 +0000)]
progress bar hashtable entry was not being removed (bug #0059977)

14 years agogroupURL link prototype
jprocter [Tue, 9 Feb 2010 17:37:02 +0000 (17:37 +0000)]
groupURL link prototype

14 years agogroupURL link preference variables
jprocter [Tue, 9 Feb 2010 17:36:37 +0000 (17:36 +0000)]
groupURL link preference variables

14 years agotodo
jprocter [Tue, 9 Feb 2010 17:36:13 +0000 (17:36 +0000)]
todo

14 years agotoken replacement engine for generation of urls for a group of sequences
jprocter [Tue, 9 Feb 2010 17:31:14 +0000 (17:31 +0000)]
token replacement engine for generation of urls for a group of sequences

14 years agoqsort objects on integers
jprocter [Tue, 9 Feb 2010 17:30:00 +0000 (17:30 +0000)]
qsort objects on integers

14 years agoquick fix for very broken checkin - see Mantis bug #55537
jprocter [Thu, 28 Jan 2010 15:36:17 +0000 (15:36 +0000)]
quick fix for very broken checkin - see Mantis bug #55537

14 years agotodo for bug #0058199
jprocter [Thu, 28 Jan 2010 12:28:14 +0000 (12:28 +0000)]
todo for bug #0058199

14 years agomore rigorous annotation row content check to limit fields output in annotation file...
jprocter [Thu, 28 Jan 2010 12:27:25 +0000 (12:27 +0000)]
more rigorous annotation row content check to limit fields output in annotation file. Needs testing further. See Mantis bug #55537