jprocter [Fri, 9 Feb 2007 18:02:18 +0000 (18:02 +0000)]
This commit was manufactured by cvs2svn to create tag 'Release_2_1_1'.
Sprout from master 2006-09-12 10:01:52 UTC andrew 'Copy consensus'
Cherrypick from master 2007-02-09 18:02:17 UTC jprocter 'running jalview from the command line.':
doc/AddingGroovySupport.html
help/html/align.jpg
help/html/colourSchemes/textcolour.gif
help/html/colourSchemes/textcolour.html
help/html/features/amendfeature.gif
help/html/features/clarguments.html
help/html/features/codingfeatures.html
help/html/features/commandline.html
help/html/features/creatinFeatures.html
help/html/features/crnewfeature.gif
help/html/features/das.gif
help/html/features/editingFeatures.html
help/html/features/multipleViews.html
help/html/features/newkeystrokes.html
help/html/features/seqmappings.html
help/html/menus/alwformat.html
help/html/menus/alwselect.html
lib/vamsas-client.jar
src/jalview/analysis/Finder.java
src/jalview/appletgui/EditNameDialog.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/CommandI.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
src/jalview/commands/RemoveGapColCommand.java
src/jalview/commands/RemoveGapsCommand.java
src/jalview/commands/TrimRegionCommand.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasClient.java
src/jalview/io/AMSAFile.java
src/jalview/io/VamsasDatastore.java
src/jalview/schemes/ScoreMatrix.java
src/jalview/util/MapList.java
src/jalview/ws/JPredThread.java
amwaterhouse [Tue, 12 Sep 2006 10:01:52 +0000 (10:01 +0000)]
Copy consensus
amwaterhouse [Tue, 12 Sep 2006 09:32:17 +0000 (09:32 +0000)]
2.1.1 bug fix
amwaterhouse [Tue, 12 Sep 2006 09:31:04 +0000 (09:31 +0000)]
2.1.1 bug fix
amwaterhouse [Tue, 12 Sep 2006 09:24:00 +0000 (09:24 +0000)]
Add copy consensus sequence
amwaterhouse [Tue, 12 Sep 2006 09:20:18 +0000 (09:20 +0000)]
Allow alt for group editing
amwaterhouse [Tue, 12 Sep 2006 09:19:45 +0000 (09:19 +0000)]
For now ignore middle mouse font resize on Mac applet
amwaterhouse [Tue, 12 Sep 2006 09:19:18 +0000 (09:19 +0000)]
Allow alt button for Mac applet group editing
amwaterhouse [Mon, 11 Sep 2006 16:24:41 +0000 (16:24 +0000)]
Comment out lower case colouring for bug fix release
amwaterhouse [Mon, 11 Sep 2006 15:43:31 +0000 (15:43 +0000)]
Remove system.outs
amwaterhouse [Mon, 11 Sep 2006 15:42:43 +0000 (15:42 +0000)]
get idWidth should use italic font when getting size
amwaterhouse [Mon, 11 Sep 2006 15:28:53 +0000 (15:28 +0000)]
Error message if file not found moved for headless state
amwaterhouse [Mon, 11 Sep 2006 15:27:34 +0000 (15:27 +0000)]
visWidth allows borders to be drawn around offscreen images when making images
amwaterhouse [Mon, 11 Sep 2006 14:44:48 +0000 (14:44 +0000)]
Remove system.out
amwaterhouse [Mon, 11 Sep 2006 11:30:23 +0000 (11:30 +0000)]
getVisibleIdWidth() for making images
jprocter [Thu, 7 Sep 2006 11:39:36 +0000 (11:39 +0000)]
added copy consensus sequence to consensus annotation popup menu
jprocter [Tue, 5 Sep 2006 13:36:07 +0000 (13:36 +0000)]
getVisibleContigs() returns start and end positions of visible regions of an alignmentView.
jprocter [Tue, 5 Sep 2006 13:03:19 +0000 (13:03 +0000)]
javadoc on contigs
amwaterhouse [Fri, 1 Sep 2006 12:30:07 +0000 (12:30 +0000)]
Dont look for middle mouse on the Mac
amwaterhouse [Fri, 1 Sep 2006 12:25:34 +0000 (12:25 +0000)]
MAC moved to viewport
amwaterhouse [Fri, 1 Sep 2006 11:23:03 +0000 (11:23 +0000)]
feature settings
amwaterhouse [Fri, 1 Sep 2006 11:22:33 +0000 (11:22 +0000)]
Feature Settings
amwaterhouse [Wed, 30 Aug 2006 16:10:07 +0000 (16:10 +0000)]
GraphHeight might be zero
amwaterhouse [Wed, 30 Aug 2006 16:09:47 +0000 (16:09 +0000)]
jnet file is 1 to 1 mapping
amwaterhouse [Wed, 30 Aug 2006 16:09:25 +0000 (16:09 +0000)]
Remove unnecessary separotor
amwaterhouse [Wed, 30 Aug 2006 16:08:58 +0000 (16:08 +0000)]
Gap added to aa3Hash
amwaterhouse [Wed, 30 Aug 2006 16:08:36 +0000 (16:08 +0000)]
User colours are case sensitive
amwaterhouse [Tue, 29 Aug 2006 15:31:04 +0000 (15:31 +0000)]
Can shrink graph to zero
amwaterhouse [Tue, 29 Aug 2006 15:24:40 +0000 (15:24 +0000)]
No stacktrace
amwaterhouse [Tue, 29 Aug 2006 15:24:22 +0000 (15:24 +0000)]
createMapping alreadyMapped
amwaterhouse [Tue, 29 Aug 2006 15:22:59 +0000 (15:22 +0000)]
Additional repaint
amwaterhouse [Tue, 29 Aug 2006 15:22:15 +0000 (15:22 +0000)]
jnetfile can be loaded onto alignment
amwaterhouse [Tue, 29 Aug 2006 15:21:39 +0000 (15:21 +0000)]
SequenceMapping updated
amwaterhouse [Tue, 29 Aug 2006 15:15:25 +0000 (15:15 +0000)]
Jnet files sent to servlet as annotations
amwaterhouse [Thu, 24 Aug 2006 13:03:23 +0000 (13:03 +0000)]
unbalanced head tag
amwaterhouse [Wed, 23 Aug 2006 08:03:04 +0000 (08:03 +0000)]
volume 20
amwaterhouse [Tue, 22 Aug 2006 16:54:40 +0000 (16:54 +0000)]
2.1 updates
amwaterhouse [Tue, 22 Aug 2006 16:25:21 +0000 (16:25 +0000)]
add link.gif
amwaterhouse [Tue, 22 Aug 2006 15:31:31 +0000 (15:31 +0000)]
2.1 update
amwaterhouse [Tue, 22 Aug 2006 14:29:10 +0000 (14:29 +0000)]
To uppercase only visible
jprocter [Tue, 22 Aug 2006 13:47:47 +0000 (13:47 +0000)]
documentation - adding new Input data menu entries.
jprocter [Tue, 22 Aug 2006 13:25:47 +0000 (13:25 +0000)]
added note on column-separability
jprocter [Tue, 22 Aug 2006 13:13:23 +0000 (13:13 +0000)]
documentation
jprocter [Tue, 22 Aug 2006 13:01:50 +0000 (13:01 +0000)]
getSequenceStrings() bug fixed.
amwaterhouse [Tue, 22 Aug 2006 10:39:03 +0000 (10:39 +0000)]
Remove group when hiding cols from scalePanel
amwaterhouse [Tue, 22 Aug 2006 09:11:05 +0000 (09:11 +0000)]
2006
amwaterhouse [Tue, 22 Aug 2006 09:10:48 +0000 (09:10 +0000)]
Put transparency back
amwaterhouse [Tue, 22 Aug 2006 09:10:28 +0000 (09:10 +0000)]
make 1.1 compatible
jprocter [Tue, 22 Aug 2006 08:34:04 +0000 (08:34 +0000)]
hidden region recovery in JPred and new hidden region pruning function
jprocter [Tue, 22 Aug 2006 08:32:40 +0000 (08:32 +0000)]
off by one bug in hiden column unmarshalling
amwaterhouse [Mon, 21 Aug 2006 15:36:21 +0000 (15:36 +0000)]
header updated
amwaterhouse [Mon, 21 Aug 2006 15:29:26 +0000 (15:29 +0000)]
header updated
amwaterhouse [Mon, 21 Aug 2006 14:48:49 +0000 (14:48 +0000)]
validate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:39:50 +0000 (14:39 +0000)]
validate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:39:36 +0000 (14:39 +0000)]
Add uniprot DBref
amwaterhouse [Mon, 21 Aug 2006 14:14:07 +0000 (14:14 +0000)]
Remove system.out
amwaterhouse [Mon, 21 Aug 2006 14:13:49 +0000 (14:13 +0000)]
1.1 compatible
jprocter [Mon, 21 Aug 2006 13:41:41 +0000 (13:41 +0000)]
Refactored Jnet and added hidden columns support.
fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo.
jprocter [Mon, 21 Aug 2006 13:40:54 +0000 (13:40 +0000)]
fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo
jprocter [Mon, 21 Aug 2006 13:03:28 +0000 (13:03 +0000)]
removeGaps method can record changes in alignment columns to pass to ColumnSelection
jprocter [Mon, 21 Aug 2006 12:51:46 +0000 (12:51 +0000)]
fix for truncation of sequence associated annotation mapped onto alignment
jprocter [Mon, 21 Aug 2006 12:46:32 +0000 (12:46 +0000)]
added shiftList to record changes in alignment column positions.
jprocter [Mon, 21 Aug 2006 12:45:09 +0000 (12:45 +0000)]
remove gaps method from AlignFrame.remove_gaps_actionPerformed
jprocter [Mon, 21 Aug 2006 12:43:39 +0000 (12:43 +0000)]
inverse ShiftList and SequenceI.gapMap->ShiftList methods.
jprocter [Mon, 21 Aug 2006 12:42:25 +0000 (12:42 +0000)]
avoid null pointer exceptions
jprocter [Sun, 20 Aug 2006 12:00:35 +0000 (12:00 +0000)]
javadoc
amwaterhouse [Fri, 18 Aug 2006 16:54:54 +0000 (16:54 +0000)]
Check colourScheme is not null - jalview prior 2.5 incompatibility
amwaterhouse [Fri, 18 Aug 2006 14:02:52 +0000 (14:02 +0000)]
dont remove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 13:57:14 +0000 (13:57 +0000)]
remove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 09:23:25 +0000 (09:23 +0000)]
treeFile = treeFile
amwaterhouse [Fri, 18 Aug 2006 08:53:07 +0000 (08:53 +0000)]
Only discover DAS sources if panel shown
amwaterhouse [Fri, 18 Aug 2006 08:52:28 +0000 (08:52 +0000)]
only set new layout if 2 buttons visible
amwaterhouse [Fri, 18 Aug 2006 08:51:58 +0000 (08:51 +0000)]
Jalview features format adds links as hrefs
amwaterhouse [Thu, 17 Aug 2006 14:06:02 +0000 (14:06 +0000)]
H key updates
amwaterhouse [Thu, 17 Aug 2006 13:51:56 +0000 (13:51 +0000)]
OptionPane invokeLater
amwaterhouse [Thu, 17 Aug 2006 13:41:37 +0000 (13:41 +0000)]
If no annotation exists
amwaterhouse [Thu, 17 Aug 2006 13:41:10 +0000 (13:41 +0000)]
Set bg white
amwaterhouse [Thu, 17 Aug 2006 13:40:57 +0000 (13:40 +0000)]
Hold onto selected region when hiding all columns only
jprocter [Thu, 17 Aug 2006 13:33:59 +0000 (13:33 +0000)]
moved visible sub-alignment extraction and update from MsaWSThread to
an AlignmentView method, refactored JPredClient to new abstraction and
added flags for canMergeResults and openResultsImmediatly to web
service gui.
jprocter [Thu, 17 Aug 2006 13:31:23 +0000 (13:31 +0000)]
javadoc
amwaterhouse [Thu, 17 Aug 2006 12:34:07 +0000 (12:34 +0000)]
Monospace check
amwaterhouse [Thu, 17 Aug 2006 12:33:55 +0000 (12:33 +0000)]
1 more pixel allowed between chars and graph
amwaterhouse [Thu, 17 Aug 2006 10:14:00 +0000 (10:14 +0000)]
Keys update
amwaterhouse [Thu, 17 Aug 2006 10:11:48 +0000 (10:11 +0000)]
control and shift
amwaterhouse [Thu, 17 Aug 2006 10:08:46 +0000 (10:08 +0000)]
Dont set group null hideCOls
amwaterhouse [Thu, 17 Aug 2006 10:08:18 +0000 (10:08 +0000)]
OptionPanes invokeLater
amwaterhouse [Thu, 17 Aug 2006 10:08:02 +0000 (10:08 +0000)]
Control and alt for toggle hide
amwaterhouse [Wed, 16 Aug 2006 08:05:35 +0000 (08:05 +0000)]
Fire alignment changed if seqs hidden / revealed
amwaterhouse [Tue, 15 Aug 2006 12:47:04 +0000 (12:47 +0000)]
Correct title for sequence parameter applets
amwaterhouse [Tue, 15 Aug 2006 12:36:11 +0000 (12:36 +0000)]
Sequences can be added as parameter
amwaterhouse [Tue, 15 Aug 2006 11:14:25 +0000 (11:14 +0000)]
H key added
jprocter [Tue, 15 Aug 2006 11:10:03 +0000 (11:10 +0000)]
make annotation label font size follow alignment font size.
jprocter [Tue, 15 Aug 2006 10:59:31 +0000 (10:59 +0000)]
first stage of adapting JNet client to hidden regions and new WSClient
structure.
jprocter [Tue, 15 Aug 2006 10:57:59 +0000 (10:57 +0000)]
fixed alignment ordering name.
jprocter [Tue, 15 Aug 2006 10:57:32 +0000 (10:57 +0000)]
ensure that close widget is available for jobs that cannot be
cancelled.
amwaterhouse [Tue, 15 Aug 2006 10:35:37 +0000 (10:35 +0000)]
Acknowledgement
amwaterhouse [Tue, 15 Aug 2006 10:35:09 +0000 (10:35 +0000)]
Setselectiongroup null on hide
amwaterhouse [Tue, 15 Aug 2006 10:34:56 +0000 (10:34 +0000)]
H key to hide / reveal
amwaterhouse [Tue, 15 Aug 2006 10:34:29 +0000 (10:34 +0000)]
Add key listener to scalePanel and annotationPanel
amwaterhouse [Tue, 15 Aug 2006 10:34:11 +0000 (10:34 +0000)]
Select revealed seqs
git://source.jalview.org / jalview.git / log