jprocter [Mon, 12 Dec 2005 15:53:11 +0000 (15:53 +0000)]
This commit was manufactured by cvs2svn to create tag 'Release_2_07'.
Sprout from master 2005-12-12 15:53:10 UTC andrew 'Change dataset name'
Delete:
src/uk/ac/ebi/www/Data.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/WSFile.java
src/uk/ac/ebi/www/WSWUBlast.java
src/uk/ac/ebi/www/WSWUBlastService.java
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
src/vamsas/IMsaWS.java
src/vamsas/objects/simple/Alignment.java
src/vamsas/objects/simple/Alignment_Helper.java
src/vamsas/objects/simple/JpredResult.java
src/vamsas/objects/simple/JpredResult_Helper.java
src/vamsas/objects/simple/MsaResult.java
src/vamsas/objects/simple/MsaResult_Helper.java
src/vamsas/objects/simple/Msfalignment.java
src/vamsas/objects/simple/Msfalignment_Helper.java
src/vamsas/objects/simple/Object.java
src/vamsas/objects/simple/Object_Helper.java
src/vamsas/objects/simple/Result.java
src/vamsas/objects/simple/Result_Helper.java
src/vamsas/objects/simple/Secstructpred.java
src/vamsas/objects/simple/Secstructpred_Helper.java
src/vamsas/objects/simple/Sequence.java
src/vamsas/objects/simple/SequenceSet.java
src/vamsas/objects/simple/SequenceSet_Helper.java
src/vamsas/objects/simple/Sequence_Helper.java
src/vamsas/objects/simple/WsJobId.java
src/vamsas/objects/simple/WsJobId_Helper.java
utils/InstallAnywhere/Jalview.iap_xml
utils/InstallAnywhere/README_IA
utils/InstallAnywhere/align.gif
utils/InstallAnywhere/bartonGroup.gif
utils/InstallAnywhere/jalview.gif
utils/InstallAnywhere/mac_logo.icns
utils/axis-ant.jar
utils/jalopy/bin/lcp.bat
utils/jalopy/bin/preferences.bat
utils/jalopy/bin/preferences.sh
utils/jalopy/docs/acknowledge.html
utils/jalopy/docs/bi01.html
utils/jalopy/docs/build.html
utils/jalopy/docs/comments.html
utils/jalopy/docs/contact.html
utils/jalopy/docs/contributors.html
utils/jalopy/docs/dedication.html
utils/jalopy/docs/dependencies.html
utils/jalopy/docs/docs.html
utils/jalopy/docs/download.html
utils/jalopy/docs/environment.html
utils/jalopy/docs/faq.html
utils/jalopy/docs/features.html
utils/jalopy/docs/footer.html
utils/jalopy/docs/header.html
utils/jalopy/docs/history.html
utils/jalopy/docs/imports.html
utils/jalopy/docs/indentation.html
utils/jalopy/docs/index.html
utils/jalopy/docs/inspector-naming.html
utils/jalopy/docs/inspector.html
utils/jalopy/docs/installation.html
utils/jalopy/docs/introduction.html
utils/jalopy/docs/ix01.html
utils/jalopy/docs/javadoc.html
utils/jalopy/docs/license-antlr.html
utils/jalopy/docs/license-apache.html
utils/jalopy/docs/license-bsd.html
utils/jalopy/docs/license-common-public.html
utils/jalopy/docs/license-gnu-doc.html
utils/jalopy/docs/license-gnu.html
utils/jalopy/docs/license-sun-public.html
utils/jalopy/docs/links.html
utils/jalopy/docs/manual.html
utils/jalopy/docs/messages.html
utils/jalopy/docs/misc.html
utils/jalopy/docs/part-core.html
utils/jalopy/docs/part-plugins.html
utils/jalopy/docs/plugin-ant-config.html
utils/jalopy/docs/plugin-ant-license.html
utils/jalopy/docs/plugin-ant-usage.html
utils/jalopy/docs/plugin-ant.html
utils/jalopy/docs/plugin-console-license.html
utils/jalopy/docs/plugin-console-usage.html
utils/jalopy/docs/plugin-console.html
utils/jalopy/docs/plugin-eclipse-integration.html
utils/jalopy/docs/plugin-eclipse-license.html
utils/jalopy/docs/plugin-eclipse.html
utils/jalopy/docs/plugin-jbuilder-integration.html
utils/jalopy/docs/plugin-jbuilder-license.html
utils/jalopy/docs/plugin-jbuilder.html
utils/jalopy/docs/plugin-jdev-integration.html
utils/jalopy/docs/plugin-jdev-license.html
utils/jalopy/docs/plugin-jdev.html
utils/jalopy/docs/plugin-jedit-integration.html
utils/jalopy/docs/plugin-jedit-license.html
utils/jalopy/docs/plugin-jedit.html
utils/jalopy/docs/plugin-netbeans-integration.html
utils/jalopy/docs/plugin-netbeans-license.html
utils/jalopy/docs/plugin-netbeans.html
utils/jalopy/docs/plugins.html
utils/jalopy/docs/printer.html
utils/jalopy/docs/project.html
utils/jalopy/docs/separation.html
utils/jalopy/docs/settings.html
utils/jalopy/docs/site.css
utils/jalopy/docs/sorting.html
utils/jalopy/docs/usage.html
utils/jalopy/docs/whitespace.html
utils/jalopy/docs/wrapping.html
utils/jalopy/lib/aelfred-1.2.jar
utils/jalopy/lib/jalopy-1.0b11.jar
utils/jalopy/lib/jalopy-ant-0.6.2.jar
utils/jalopy/lib/jaxp-1.2.jar
utils/jalopy/lib/jdom-1.0b8.jar
utils/jalopy/lib/log4j-1.2.6.jar
utils/jalopy/lib/oro-2.0.6.jar
utils/jalopy/lib/sax-2.0.1.jar
utils/jalopy/readme.html
utils/jarunsigner.pl
utils/jhall.jar
utils/jhindexer
utils/jhindexer.jar
utils/proguard.jar
utils/roxes-ant-tasks-1.2-2004-01-30.jar
utils/wsdl4j.jar
amwaterhouse [Mon, 12 Dec 2005 15:53:10 +0000 (15:53 +0000)]
Change dataset name
amwaterhouse [Mon, 12 Dec 2005 15:51:48 +0000 (15:51 +0000)]
Change title
amwaterhouse [Mon, 12 Dec 2005 14:47:52 +0000 (14:47 +0000)]
Release date
amwaterhouse [Mon, 12 Dec 2005 14:47:41 +0000 (14:47 +0000)]
DOnt mention WSWublast for now
amwaterhouse [Mon, 12 Dec 2005 14:20:09 +0000 (14:20 +0000)]
Jbinit
amwaterhouse [Mon, 12 Dec 2005 14:15:03 +0000 (14:15 +0000)]
Font size label
amwaterhouse [Mon, 12 Dec 2005 14:14:28 +0000 (14:14 +0000)]
Dont bother with WSWUBlast for now
amwaterhouse [Mon, 12 Dec 2005 13:31:49 +0000 (13:31 +0000)]
FOnt size -3 for labels
amwaterhouse [Mon, 12 Dec 2005 13:31:29 +0000 (13:31 +0000)]
Check if user cancelled before making image
amwaterhouse [Mon, 12 Dec 2005 12:24:57 +0000 (12:24 +0000)]
Set font italic
amwaterhouse [Mon, 12 Dec 2005 12:24:24 +0000 (12:24 +0000)]
Font changes on export png/eps
amwaterhouse [Mon, 12 Dec 2005 10:45:39 +0000 (10:45 +0000)]
Getmask is slightly wider
jprocter [Fri, 9 Dec 2005 18:48:09 +0000 (18:48 +0000)]
added description of how PDB structures can be associated with
sequences (and so viewed in the PDB viewer).
jprocter [Fri, 9 Dec 2005 18:47:23 +0000 (18:47 +0000)]
Rearranged 'What's new' and debugged/verified the sequence fetcher and
pdbviewer/viewingpdbs entries.
jprocter [Fri, 9 Dec 2005 16:02:40 +0000 (16:02 +0000)]
fixed pdbentry creation and multiple uniprot or pdb entry retrieval.
amwaterhouse [Fri, 9 Dec 2005 14:25:10 +0000 (14:25 +0000)]
Change order of repaint if wrapped
amwaterhouse [Fri, 9 Dec 2005 14:10:59 +0000 (14:10 +0000)]
Applet Structure viewer has all colours available
amwaterhouse [Fri, 9 Dec 2005 13:35:03 +0000 (13:35 +0000)]
Can be used by PDBViewer
amwaterhouse [Fri, 9 Dec 2005 13:34:46 +0000 (13:34 +0000)]
All colours added to Structure viewer
amwaterhouse [Fri, 9 Dec 2005 11:13:18 +0000 (11:13 +0000)]
Only load the tree file once, for first alignment
amwaterhouse [Fri, 9 Dec 2005 11:12:56 +0000 (11:12 +0000)]
Keylistener added to frame and seqcanvas
jprocter [Thu, 8 Dec 2005 16:45:04 +0000 (16:45 +0000)]
context dependent title for when called from desktop or alignment window menu
jprocter [Thu, 8 Dec 2005 16:19:51 +0000 (16:19 +0000)]
changed WhatsNew to a folder and modified preferences and seqfetcher
entries.
amwaterhouse [Thu, 8 Dec 2005 16:18:10 +0000 (16:18 +0000)]
If dataset seq exists for paste to existing alignment, make a ref
jprocter [Thu, 8 Dec 2005 16:10:39 +0000 (16:10 +0000)]
added some error checking and instruction dialogs
amwaterhouse [Thu, 8 Dec 2005 15:39:46 +0000 (15:39 +0000)]
Should call deselectAll when escape pressed
amwaterhouse [Thu, 8 Dec 2005 15:34:59 +0000 (15:34 +0000)]
Dont repaint if component has been removed
amwaterhouse [Thu, 8 Dec 2005 15:34:29 +0000 (15:34 +0000)]
SeqColoursReady
jprocter [Thu, 8 Dec 2005 14:09:17 +0000 (14:09 +0000)]
modified jnet parsing exception report string.
jprocter [Thu, 8 Dec 2005 14:08:22 +0000 (14:08 +0000)]
exception checks for (de)uniquify
amwaterhouse [Thu, 8 Dec 2005 13:42:00 +0000 (13:42 +0000)]
Clustal colour added to table
amwaterhouse [Thu, 8 Dec 2005 12:04:29 +0000 (12:04 +0000)]
SeqColoursReady boolean added
amwaterhouse [Thu, 8 Dec 2005 12:04:14 +0000 (12:04 +0000)]
UnknownSequences.remove moved out of loop
amwaterhouse [Thu, 8 Dec 2005 11:54:51 +0000 (11:54 +0000)]
showAnnotation state loaded
amwaterhouse [Thu, 8 Dec 2005 11:54:24 +0000 (11:54 +0000)]
null pointer in wrapped mode, click near sequence
amwaterhouse [Thu, 8 Dec 2005 10:58:27 +0000 (10:58 +0000)]
new help
amwaterhouse [Thu, 8 Dec 2005 10:57:52 +0000 (10:57 +0000)]
Updated help
amwaterhouse [Thu, 8 Dec 2005 09:25:26 +0000 (09:25 +0000)]
Revert to version 1.25
amwaterhouse [Thu, 8 Dec 2005 09:18:08 +0000 (09:18 +0000)]
After merge
amwaterhouse [Thu, 8 Dec 2005 09:17:41 +0000 (09:17 +0000)]
EqualsignoreCase
amwaterhouse [Wed, 7 Dec 2005 15:08:07 +0000 (15:08 +0000)]
License added to new files
amwaterhouse [Tue, 6 Dec 2005 18:07:33 +0000 (18:07 +0000)]
View menu added to TOC
amwaterhouse [Tue, 6 Dec 2005 18:06:56 +0000 (18:06 +0000)]
Slightly larger
amwaterhouse [Tue, 6 Dec 2005 17:42:28 +0000 (17:42 +0000)]
Allow for DNA alignments in imgMap
amwaterhouse [Tue, 6 Dec 2005 17:14:57 +0000 (17:14 +0000)]
Make ImageMap for features as well as groups
amwaterhouse [Tue, 6 Dec 2005 17:14:36 +0000 (17:14 +0000)]
Add features to dataset
amwaterhouse [Tue, 6 Dec 2005 12:19:44 +0000 (12:19 +0000)]
Add internalFrameActivated listener
amwaterhouse [Tue, 6 Dec 2005 12:08:56 +0000 (12:08 +0000)]
After merge
amwaterhouse [Tue, 6 Dec 2005 12:08:29 +0000 (12:08 +0000)]
Readded
amwaterhouse [Tue, 6 Dec 2005 12:07:06 +0000 (12:07 +0000)]
hasDistances added
amwaterhouse [Tue, 6 Dec 2005 12:03:46 +0000 (12:03 +0000)]
After merge
amwaterhouse [Tue, 6 Dec 2005 11:51:36 +0000 (11:51 +0000)]
after merge
amwaterhouse [Tue, 6 Dec 2005 11:46:19 +0000 (11:46 +0000)]
after merge
amwaterhouse [Tue, 6 Dec 2005 11:42:19 +0000 (11:42 +0000)]
After merge
amwaterhouse [Tue, 6 Dec 2005 11:41:09 +0000 (11:41 +0000)]
After branch merge
amwaterhouse [Tue, 6 Dec 2005 11:40:04 +0000 (11:40 +0000)]
PDB structure viewer updated
amwaterhouse [Tue, 6 Dec 2005 11:38:11 +0000 (11:38 +0000)]
Saves features
amwaterhouse [Tue, 6 Dec 2005 11:37:08 +0000 (11:37 +0000)]
New help files
jprocter [Fri, 18 Nov 2005 16:07:41 +0000 (16:07 +0000)]
Fixed bug dragonfly.compbio.dundee.ac.uk/mantis/view.php?id=9326 for viewing trees without explicit distances. made sure trees output from treeviewer contain only as much information (distance, bootstraps, etc) as was read in from original tree file (or algorithm).
jprocter [Fri, 18 Nov 2005 13:30:08 +0000 (13:30 +0000)]
added 3 letter IUB codes for ambiguous residues/bases
amwaterhouse [Fri, 7 Oct 2005 10:24:56 +0000 (10:24 +0000)]
comma separated rgb values
amwaterhouse [Fri, 7 Oct 2005 10:24:23 +0000 (10:24 +0000)]
getalignment method added
amwaterhouse [Fri, 7 Oct 2005 10:23:28 +0000 (10:23 +0000)]
Quick fix for reading sequence
amwaterhouse [Fri, 7 Oct 2005 10:22:57 +0000 (10:22 +0000)]
Select all cutandpaste
amwaterhouse [Fri, 7 Oct 2005 10:20:49 +0000 (10:20 +0000)]
Don't exit if file not found and not headless
amwaterhouse [Wed, 5 Oct 2005 12:34:32 +0000 (12:34 +0000)]
Sequence start end added for the time being
amwaterhouse [Mon, 3 Oct 2005 16:14:54 +0000 (16:14 +0000)]
Remove float width
amwaterhouse [Mon, 3 Oct 2005 11:08:22 +0000 (11:08 +0000)]
Request focus for new frames
amwaterhouse [Mon, 3 Oct 2005 11:07:55 +0000 (11:07 +0000)]
Return if no searchString
amwaterhouse [Mon, 3 Oct 2005 11:07:40 +0000 (11:07 +0000)]
Keylistener added to internalFrame
amwaterhouse [Mon, 3 Oct 2005 10:30:04 +0000 (10:30 +0000)]
Remove development code
amwaterhouse [Mon, 3 Oct 2005 08:33:08 +0000 (08:33 +0000)]
Remove redundancy from eclipse
amwaterhouse [Fri, 30 Sep 2005 17:18:41 +0000 (17:18 +0000)]
Remove redundancy from Eclipse
amwaterhouse [Fri, 30 Sep 2005 17:18:22 +0000 (17:18 +0000)]
Restore file before eclipse changes
amwaterhouse [Fri, 30 Sep 2005 17:03:03 +0000 (17:03 +0000)]
Remove redundancy in Eclipse
amwaterhouse [Thu, 29 Sep 2005 16:11:50 +0000 (16:11 +0000)]
Take into account scroll value
amwaterhouse [Wed, 28 Sep 2005 16:54:08 +0000 (16:54 +0000)]
use lower case home.png
amwaterhouse [Wed, 28 Sep 2005 16:53:46 +0000 (16:53 +0000)]
Applet frame name
amwaterhouse [Wed, 28 Sep 2005 16:13:09 +0000 (16:13 +0000)]
Set frame size each applet
amwaterhouse [Wed, 28 Sep 2005 15:42:18 +0000 (15:42 +0000)]
Remove latestVersion if null
amwaterhouse [Wed, 28 Sep 2005 15:39:51 +0000 (15:39 +0000)]
Remove latestVersion if null
amwaterhouse [Wed, 28 Sep 2005 15:08:50 +0000 (15:08 +0000)]
2.06
amwaterhouse [Wed, 28 Sep 2005 15:07:04 +0000 (15:07 +0000)]
Put clip back in
amwaterhouse [Wed, 28 Sep 2005 14:55:06 +0000 (14:55 +0000)]
Change font
amwaterhouse [Wed, 28 Sep 2005 14:54:23 +0000 (14:54 +0000)]
More features for PCA
amwaterhouse [Wed, 28 Sep 2005 14:54:03 +0000 (14:54 +0000)]
Wrap alignment with annotations
amwaterhouse [Wed, 28 Sep 2005 14:53:45 +0000 (14:53 +0000)]
New params
amwaterhouse [Tue, 27 Sep 2005 14:16:59 +0000 (14:16 +0000)]
Show labels in wrapped view
amwaterhouse [Fri, 23 Sep 2005 16:18:02 +0000 (16:18 +0000)]
Draw labels, anti alias
amwaterhouse [Fri, 23 Sep 2005 16:17:33 +0000 (16:17 +0000)]
Capture output as details
amwaterhouse [Fri, 23 Sep 2005 16:17:12 +0000 (16:17 +0000)]
Right click copy/paste popup
amwaterhouse [Fri, 23 Sep 2005 16:16:53 +0000 (16:16 +0000)]
Now an InternalFrame with menus
amwaterhouse [Thu, 22 Sep 2005 16:04:51 +0000 (16:04 +0000)]
SetAnnotationVisible - ignore if wrapped
amwaterhouse [Thu, 22 Sep 2005 15:53:18 +0000 (15:53 +0000)]
Create Instance of FormatAdapter
amwaterhouse [Thu, 22 Sep 2005 15:52:52 +0000 (15:52 +0000)]
Dont calculate conservation for nucleotides
amwaterhouse [Thu, 22 Sep 2005 15:50:47 +0000 (15:50 +0000)]
isNucleotide
amwaterhouse [Thu, 22 Sep 2005 15:49:51 +0000 (15:49 +0000)]
Create instance of FormatAdapter
amwaterhouse [Thu, 22 Sep 2005 15:49:21 +0000 (15:49 +0000)]
Add nucleotide names
amwaterhouse [Thu, 22 Sep 2005 15:49:05 +0000 (15:49 +0000)]
Display nucleotides
git://source.jalview.org / jalview.git / log