jalview.git
14 years agoremoved vamsas deps
jprocter [Tue, 1 Jun 2010 09:06:29 +0000 (09:06 +0000)]
removed vamsas deps

14 years agoquick workaround for JAL-537.
jprocter [Fri, 21 May 2010 09:43:24 +0000 (09:43 +0000)]
quick workaround for JAL-537.

14 years agopartial patch for * JAL-466
jprocter [Fri, 14 May 2010 14:37:23 +0000 (14:37 +0000)]
partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.

14 years agopartial patch for * JAL-466
jprocter [Fri, 14 May 2010 14:34:06 +0000 (14:34 +0000)]
partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.

14 years agofix for JAL-533
jprocter [Fri, 14 May 2010 11:47:38 +0000 (11:47 +0000)]
fix for JAL-533

14 years agopatch for JAL-528
jprocter [Wed, 12 May 2010 09:36:39 +0000 (09:36 +0000)]
patch for JAL-528

14 years agofix for JAL-527
jprocter [Wed, 12 May 2010 08:46:30 +0000 (08:46 +0000)]
fix for JAL-527

14 years agojalview 2.5 documentation (still)
jprocter [Sat, 1 May 2010 17:29:14 +0000 (17:29 +0000)]
jalview 2.5 documentation (still)

14 years agocorrect branch
jprocter [Sat, 1 May 2010 16:17:40 +0000 (16:17 +0000)]
correct branch

14 years agorelocatable reference to build file and dropped groovy library from classpath Root_Release_2_5_Branch
jprocter [Sat, 1 May 2010 15:40:30 +0000 (15:40 +0000)]
relocatable reference to build file and dropped groovy library from classpath

14 years agohref for version
jprocter [Sat, 1 May 2010 15:25:29 +0000 (15:25 +0000)]
href for version

14 years ago2.5 release details Release_2_5 Release_2_5_branch
jprocter [Fri, 30 Apr 2010 16:05:04 +0000 (16:05 +0000)]
2.5 release details

14 years ago2.5 release notes
jprocter [Fri, 30 Apr 2010 15:51:33 +0000 (15:51 +0000)]
2.5 release notes

14 years agoget the html header comment right!
jprocter [Fri, 30 Apr 2010 15:11:37 +0000 (15:11 +0000)]
get the html header comment right!

14 years agoget the html header comment right!
jprocter [Fri, 30 Apr 2010 14:11:06 +0000 (14:11 +0000)]
get the html header comment right!

14 years agotidying for 2.5 release
jprocter [Fri, 30 Apr 2010 14:10:29 +0000 (14:10 +0000)]
tidying for 2.5 release

14 years agopatch for bug #59999
jprocter [Fri, 30 Apr 2010 13:19:37 +0000 (13:19 +0000)]
patch for bug #59999

14 years agodoc
jprocter [Fri, 30 Apr 2010 11:52:50 +0000 (11:52 +0000)]
doc

14 years agosort by length
jprocter [Fri, 30 Apr 2010 11:52:23 +0000 (11:52 +0000)]
sort by length

14 years agojalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:39:12 +0000 (09:39 +0000)]
jalview 2.5 release banner

14 years agojalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:30:38 +0000 (09:30 +0000)]
jalview 2.5 release banner

14 years agoclasspath for eclipse is shared
jprocter [Fri, 30 Apr 2010 09:16:48 +0000 (09:16 +0000)]
classpath for eclipse is shared

14 years ago2.5 doc
jprocter [Fri, 30 Apr 2010 07:03:41 +0000 (07:03 +0000)]
2.5 doc

14 years ago2.5 hidden capabilities
jprocter [Fri, 30 Apr 2010 07:02:49 +0000 (07:02 +0000)]
2.5 hidden capabilities

14 years agovamsas 0.2 client capabilities
jprocter [Fri, 30 Apr 2010 07:02:32 +0000 (07:02 +0000)]
vamsas 0.2 client capabilities

14 years agomake sure references are intact when group annotation is accessed
jprocter [Thu, 29 Apr 2010 16:09:07 +0000 (16:09 +0000)]
make sure references are intact when group annotation is accessed

14 years agohighlighting/selecting is application only for 2.5.0 release
jprocter [Thu, 29 Apr 2010 15:12:10 +0000 (15:12 +0000)]
highlighting/selecting is application only for 2.5.0 release

14 years ago2.5 release doc
jprocter [Thu, 29 Apr 2010 15:03:44 +0000 (15:03 +0000)]
2.5 release doc

14 years agoisAligned assertion (bug 0008144)
jprocter [Thu, 29 Apr 2010 15:03:07 +0000 (15:03 +0000)]
isAligned assertion (bug 0008144)

14 years agoproperty change race condition (bug 0062693) and isAligned assertion (bug 0008144)
jprocter [Thu, 29 Apr 2010 15:02:42 +0000 (15:02 +0000)]
property change race condition (bug 0062693) and isAligned assertion (bug 0008144)

14 years agohide/show selected region menu entries and key bindings
jprocter [Thu, 29 Apr 2010 11:13:01 +0000 (11:13 +0000)]
hide/show selected region menu entries and key bindings

14 years agonew selection manipulation method
jprocter [Thu, 29 Apr 2010 11:12:16 +0000 (11:12 +0000)]
new selection manipulation method

14 years agopopup menu toggles between graduated colour and single colour feature style
jprocter [Thu, 29 Apr 2010 08:51:30 +0000 (08:51 +0000)]
popup menu toggles between graduated colour and single colour feature style

14 years agoosx pixel tweak
jprocter [Thu, 29 Apr 2010 08:50:54 +0000 (08:50 +0000)]
osx pixel tweak

14 years agoeclipse source code formatting
jprocter [Thu, 29 Apr 2010 08:45:48 +0000 (08:45 +0000)]
eclipse source code formatting

14 years agoshare eclipse settings
jprocter [Thu, 29 Apr 2010 08:38:54 +0000 (08:38 +0000)]
share eclipse settings

14 years agojog pixels for OSX
jprocter [Wed, 28 Apr 2010 17:01:27 +0000 (17:01 +0000)]
jog pixels for OSX

14 years agoosx button colouring issue
jprocter [Wed, 28 Apr 2010 17:01:17 +0000 (17:01 +0000)]
osx button colouring issue

14 years agojog pixels for OSX
jprocter [Wed, 28 Apr 2010 14:23:18 +0000 (14:23 +0000)]
jog pixels for OSX

14 years agofind incrementally searches ID then subsequence matches. Dialog reports number of...
jprocter [Wed, 28 Apr 2010 14:03:51 +0000 (14:03 +0000)]
find incrementally searches ID then subsequence matches. Dialog reports number of ID and subsequence matches correctly (bugfix)

14 years agofind incrementally searches ID then subsequence matches.
jprocter [Wed, 28 Apr 2010 14:03:21 +0000 (14:03 +0000)]
find incrementally searches ID then subsequence matches.

14 years agoexcludes
jprocter [Wed, 28 Apr 2010 10:25:44 +0000 (10:25 +0000)]
excludes

14 years agocheck class versions
jprocter [Wed, 28 Apr 2010 10:25:37 +0000 (10:25 +0000)]
check class versions

14 years ago2.5 updates...
jprocter [Wed, 28 Apr 2010 10:23:26 +0000 (10:23 +0000)]
2.5 updates...

14 years agograduated feature schemes
jprocter [Wed, 28 Apr 2010 10:23:07 +0000 (10:23 +0000)]
graduated feature schemes

14 years agotypo
jprocter [Wed, 28 Apr 2010 10:22:37 +0000 (10:22 +0000)]
typo

14 years agoenvision2 service
jprocter [Wed, 28 Apr 2010 10:22:27 +0000 (10:22 +0000)]
envision2 service

14 years agobetter ui description
jprocter [Wed, 28 Apr 2010 10:21:56 +0000 (10:21 +0000)]
better ui description

14 years agomake groups function
jprocter [Wed, 28 Apr 2010 10:21:33 +0000 (10:21 +0000)]
make groups function

14 years agograduated feature schemes (with visual indication of thresholding)
jprocter [Wed, 28 Apr 2010 10:21:20 +0000 (10:21 +0000)]
graduated feature schemes (with visual indication of thresholding)

14 years agogroup/annotation association, logos, autocalc group annotation and sequence id tooltip
jprocter [Wed, 28 Apr 2010 10:21:05 +0000 (10:21 +0000)]
group/annotation association, logos, autocalc group annotation and sequence id tooltip

14 years agonull pointer when double click event occurs without an existing selection (happens...
jprocter [Wed, 28 Apr 2010 10:18:56 +0000 (10:18 +0000)]
null pointer when double click event occurs without an existing selection (happens when tooltip position has been locked using shift key, and then user double clicks).

14 years agomake groups from selection
jprocter [Wed, 28 Apr 2010 10:17:09 +0000 (10:17 +0000)]
make groups from selection

14 years agogroup/annotation association
jprocter [Wed, 28 Apr 2010 10:16:32 +0000 (10:16 +0000)]
group/annotation association

14 years agogroup/annotation association housekeeping
jprocter [Wed, 28 Apr 2010 10:15:51 +0000 (10:15 +0000)]
group/annotation association housekeeping

14 years agonew applet parameters: heightScale and widthScale
jprocter [Mon, 26 Apr 2010 10:00:53 +0000 (10:00 +0000)]
new applet parameters: heightScale and widthScale

14 years agobuild date output in the About box, and build details output on startup when debug...
jprocter [Mon, 26 Apr 2010 09:32:15 +0000 (09:32 +0000)]
build date output in the About box, and build details output on startup when debug flag is set.

14 years agodisabled the justify functions for 2.5 release (see bug # 62495 )
jprocter [Mon, 26 Apr 2010 09:31:33 +0000 (09:31 +0000)]
disabled the justify functions for 2.5 release (see bug # 62495 )

14 years agoupgrade to Vamsas client 0.2
jprocter [Fri, 23 Apr 2010 16:17:00 +0000 (16:17 +0000)]
upgrade to  Vamsas client 0.2

14 years agoskips any annotation that appears to be identical to existing autogenerated annotatio...
jprocter [Fri, 23 Apr 2010 15:59:56 +0000 (15:59 +0000)]
skips any annotation that appears to be identical to existing autogenerated annotation on the alignment.

14 years agonext attempt for Bug #36198 - appears to work reproducibly
jprocter [Fri, 23 Apr 2010 15:11:10 +0000 (15:11 +0000)]
next attempt for Bug #36198 - appears to work reproducibly

14 years agotooltip is not shown for Annotation elements with zero length description
jprocter [Fri, 23 Apr 2010 15:10:22 +0000 (15:10 +0000)]
tooltip is not shown for Annotation elements with zero length description

14 years agojavadoc
jprocter [Fri, 23 Apr 2010 15:09:40 +0000 (15:09 +0000)]
javadoc

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