jprocter [Tue, 8 Feb 2005 16:04:44 +0000 (16:04 +0000)]
formatting imports.
amwaterhouse [Mon, 7 Feb 2005 17:40:27 +0000 (17:40 +0000)]
Properties bug fixed
amwaterhouse [Mon, 7 Feb 2005 17:09:57 +0000 (17:09 +0000)]
New class
amwaterhouse [Mon, 7 Feb 2005 17:09:19 +0000 (17:09 +0000)]
Use Cache.getProperty
amwaterhouse [Mon, 7 Feb 2005 17:08:14 +0000 (17:08 +0000)]
Settooltip for sequence feature
amwaterhouse [Mon, 7 Feb 2005 17:06:34 +0000 (17:06 +0000)]
load properties on startup
amwaterhouse [Mon, 7 Feb 2005 17:06:17 +0000 (17:06 +0000)]
Properties added
amwaterhouse [Mon, 7 Feb 2005 17:05:18 +0000 (17:05 +0000)]
Now displays sequence features
amwaterhouse [Mon, 7 Feb 2005 17:05:01 +0000 (17:05 +0000)]
New class for fetching sequence features
amwaterhouse [Fri, 4 Feb 2005 18:29:43 +0000 (18:29 +0000)]
SequenceFeature display added
amwaterhouse [Wed, 2 Feb 2005 17:17:07 +0000 (17:17 +0000)]
Modified for wrapAlignement
amwaterhouse [Wed, 2 Feb 2005 16:14:01 +0000 (16:14 +0000)]
Remove test image
amwaterhouse [Wed, 2 Feb 2005 16:12:55 +0000 (16:12 +0000)]
Modified for wrappingAlignment
amwaterhouse [Tue, 1 Feb 2005 19:04:14 +0000 (19:04 +0000)]
Apply to all groups method added
amwaterhouse [Tue, 1 Feb 2005 19:03:56 +0000 (19:03 +0000)]
Update PID or conservationSlider if necessary
amwaterhouse [Tue, 1 Feb 2005 19:03:32 +0000 (19:03 +0000)]
Bugs in column selection fixed
amwaterhouse [Tue, 1 Feb 2005 19:03:04 +0000 (19:03 +0000)]
Conservation and PID colouring methods updated, also remove group added
amwaterhouse [Tue, 1 Feb 2005 19:02:28 +0000 (19:02 +0000)]
Conservation and PID colouring methods updated
amwaterhouse [Tue, 1 Feb 2005 19:01:20 +0000 (19:01 +0000)]
Secondary panel is hidden for the moment
amwaterhouse [Tue, 1 Feb 2005 19:00:48 +0000 (19:00 +0000)]
Enable wrap menu item
amwaterhouse [Tue, 1 Feb 2005 19:00:12 +0000 (19:00 +0000)]
Ability to apply to all groups added
amwaterhouse [Tue, 1 Feb 2005 18:59:47 +0000 (18:59 +0000)]
No need for drawableSequence
amwaterhouse [Tue, 1 Feb 2005 18:58:40 +0000 (18:58 +0000)]
Clustal colours now work
amwaterhouse [Fri, 28 Jan 2005 16:27:01 +0000 (16:27 +0000)]
New layout, works 1.4 and 1.5
amwaterhouse [Thu, 27 Jan 2005 18:43:33 +0000 (18:43 +0000)]
correct border width
amwaterhouse [Thu, 27 Jan 2005 18:41:17 +0000 (18:41 +0000)]
JavaHelp files added
amwaterhouse [Thu, 27 Jan 2005 18:34:38 +0000 (18:34 +0000)]
ColourSchemeKey now in documentation
amwaterhouse [Tue, 25 Jan 2005 17:11:52 +0000 (17:11 +0000)]
system.exit or destroy if applet or app
amwaterhouse [Tue, 25 Jan 2005 17:08:00 +0000 (17:08 +0000)]
change order of menuitems
amwaterhouse [Tue, 25 Jan 2005 17:07:13 +0000 (17:07 +0000)]
don't system.ext
amwaterhouse [Tue, 25 Jan 2005 17:06:40 +0000 (17:06 +0000)]
now has key listener
amwaterhouse [Tue, 25 Jan 2005 17:06:09 +0000 (17:06 +0000)]
clustalColour bug fixed, clear selection
amwaterhouse [Tue, 25 Jan 2005 17:05:33 +0000 (17:05 +0000)]
extends Applet
amwaterhouse [Mon, 24 Jan 2005 17:38:39 +0000 (17:38 +0000)]
Adds regex.jar to classpath
amwaterhouse [Mon, 24 Jan 2005 17:31:20 +0000 (17:31 +0000)]
warning! this is obfuscated
amwaterhouse [Mon, 24 Jan 2005 17:27:36 +0000 (17:27 +0000)]
bug in compare fixed
amwaterhouse [Mon, 24 Jan 2005 17:27:00 +0000 (17:27 +0000)]
returns color.white if the underlying colourscheme is null
amwaterhouse [Mon, 24 Jan 2005 17:26:15 +0000 (17:26 +0000)]
creates new groups when selecting branches of the tree
amwaterhouse [Mon, 24 Jan 2005 17:25:31 +0000 (17:25 +0000)]
now uses 1.1 friendly regex
amwaterhouse [Mon, 24 Jan 2005 17:24:52 +0000 (17:24 +0000)]
Clear selection when deleting all groups
amwaterhouse [Mon, 24 Jan 2005 17:24:16 +0000 (17:24 +0000)]
Allow removal of colour when deleting groups
amwaterhouse [Fri, 21 Jan 2005 18:34:34 +0000 (18:34 +0000)]
remove a few imports
amwaterhouse [Fri, 21 Jan 2005 18:34:06 +0000 (18:34 +0000)]
Nucleotide colours added
amwaterhouse [Fri, 21 Jan 2005 18:33:37 +0000 (18:33 +0000)]
New colourScheme
amwaterhouse [Fri, 21 Jan 2005 18:33:07 +0000 (18:33 +0000)]
Create group from search added
amwaterhouse [Fri, 21 Jan 2005 18:32:49 +0000 (18:32 +0000)]
Delete groups added, nucleotide color added
amwaterhouse [Fri, 21 Jan 2005 18:32:14 +0000 (18:32 +0000)]
ForegroundColor is darker.darker.darker
amwaterhouse [Fri, 21 Jan 2005 18:31:40 +0000 (18:31 +0000)]
if stretchGroup is null, set avRubberbandGroup new group
amwaterhouse [Fri, 21 Jan 2005 18:30:59 +0000 (18:30 +0000)]
<= y2 is now < y2
amwaterhouse [Fri, 21 Jan 2005 18:30:06 +0000 (18:30 +0000)]
Commented out code removed
amwaterhouse [Fri, 21 Jan 2005 18:29:34 +0000 (18:29 +0000)]
Fill rect white
amwaterhouse [Fri, 21 Jan 2005 18:29:07 +0000 (18:29 +0000)]
Check if graphics is null in labelSize
amwaterhouse [Fri, 21 Jan 2005 18:28:31 +0000 (18:28 +0000)]
False changed to true
amwaterhouse [Fri, 21 Jan 2005 18:28:00 +0000 (18:28 +0000)]
SuperGroup added
amwaterhouse [Fri, 21 Jan 2005 18:27:41 +0000 (18:27 +0000)]
System.out removed
amwaterhouse [Fri, 21 Jan 2005 18:27:11 +0000 (18:27 +0000)]
SuperGroups added
amwaterhouse [Mon, 17 Jan 2005 18:14:25 +0000 (18:14 +0000)]
new images
amwaterhouse [Mon, 17 Jan 2005 18:08:25 +0000 (18:08 +0000)]
Clustal align DNA spinner added
amwaterhouse [Mon, 17 Jan 2005 16:12:55 +0000 (16:12 +0000)]
Fix overviewPanel bugs
amwaterhouse [Mon, 17 Jan 2005 16:12:06 +0000 (16:12 +0000)]
RefreshPanels after a colour change
amwaterhouse [Mon, 17 Jan 2005 16:03:28 +0000 (16:03 +0000)]
Dont use addToDesktop for splashscreen
amwaterhouse [Mon, 17 Jan 2005 14:17:57 +0000 (14:17 +0000)]
ClustalX added to ColourProperties
amwaterhouse [Mon, 17 Jan 2005 14:17:22 +0000 (14:17 +0000)]
SetSecondaryPanel
amwaterhouse [Mon, 17 Jan 2005 14:16:51 +0000 (14:16 +0000)]
SetSecondaryPanel visible
amwaterhouse [Mon, 17 Jan 2005 14:16:19 +0000 (14:16 +0000)]
Works out exisiting colur of a group
amwaterhouse [Mon, 17 Jan 2005 14:15:30 +0000 (14:15 +0000)]
New class
jprocter [Sat, 15 Jan 2005 15:17:37 +0000 (15:17 +0000)]
JBuilder Project file update
jprocter [Sat, 15 Jan 2005 15:14:42 +0000 (15:14 +0000)]
Jemboss(emboss 2.9.0) classes to provide client functionality to
Jalview.
jprocter [Sat, 15 Jan 2005 15:12:21 +0000 (15:12 +0000)]
first jemboss clustalw client for jalview.
jprocter [Sat, 15 Jan 2005 15:11:38 +0000 (15:11 +0000)]
support for jemboss server interaction.
jprocter [Sat, 15 Jan 2005 15:05:23 +0000 (15:05 +0000)]
bugfix for writing fasta file without gap characters.
jprocter [Sat, 15 Jan 2005 15:04:16 +0000 (15:04 +0000)]
Implemented clustal alignment via jemboss.
amwaterhouse [Fri, 14 Jan 2005 15:47:19 +0000 (15:47 +0000)]
Spaces
amwaterhouse [Fri, 14 Jan 2005 15:46:53 +0000 (15:46 +0000)]
Various color bugs sorted out
amwaterhouse [Fri, 14 Jan 2005 15:46:32 +0000 (15:46 +0000)]
Dispalys rule along top of output
amwaterhouse [Fri, 14 Jan 2005 15:46:04 +0000 (15:46 +0000)]
Hscrollbar is shortened
amwaterhouse [Fri, 14 Jan 2005 15:44:37 +0000 (15:44 +0000)]
Return color.white if a gap char is detected
amwaterhouse [Thu, 13 Jan 2005 18:11:59 +0000 (18:11 +0000)]
getValue method added
amwaterhouse [Thu, 13 Jan 2005 18:11:16 +0000 (18:11 +0000)]
Maintain PID or conservation status when changing colour
amwaterhouse [Thu, 13 Jan 2005 18:10:06 +0000 (18:10 +0000)]
SequenceGroup is now an array
amwaterhouse [Thu, 13 Jan 2005 18:08:41 +0000 (18:08 +0000)]
Send array of groups to renderer
amwaterhouse [Thu, 13 Jan 2005 18:07:42 +0000 (18:07 +0000)]
Initial selection bug fixed
amwaterhouse [Thu, 13 Jan 2005 18:06:55 +0000 (18:06 +0000)]
FindAllGroups added
amwaterhouse [Thu, 13 Jan 2005 18:05:57 +0000 (18:05 +0000)]
Scrollbar at bottom of screen
amwaterhouse [Thu, 13 Jan 2005 12:05:10 +0000 (12:05 +0000)]
GetResidueBoxColour altered for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:04:28 +0000 (12:04 +0000)]
Renderer already has graphics context
amwaterhouse [Thu, 13 Jan 2005 12:03:41 +0000 (12:03 +0000)]
getResidueBoxColour has been removed for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:02:50 +0000 (12:02 +0000)]
Ignores gaps when searching
jprocter [Wed, 12 Jan 2005 19:01:32 +0000 (19:01 +0000)]
random change 3
jprocter [Wed, 12 Jan 2005 18:32:34 +0000 (18:32 +0000)]
another dummy.
amwaterhouse [Wed, 12 Jan 2005 18:15:35 +0000 (18:15 +0000)]
Group editing is done by control and alt key down
amwaterhouse [Wed, 12 Jan 2005 18:14:44 +0000 (18:14 +0000)]
regular expression added
amwaterhouse [Wed, 12 Jan 2005 18:14:27 +0000 (18:14 +0000)]
delete gaps bug fixed
amwaterhouse [Wed, 12 Jan 2005 18:13:54 +0000 (18:13 +0000)]
must append file:/// at beginning of file launch
jprocter [Wed, 12 Jan 2005 17:57:58 +0000 (17:57 +0000)]
irrelevant comment.
amwaterhouse [Mon, 10 Jan 2005 17:39:32 +0000 (17:39 +0000)]
Displays number of matches found in search
amwaterhouse [Fri, 17 Dec 2004 15:39:39 +0000 (15:39 +0000)]
jalview URL updated and authors in about file
amwaterhouse [Fri, 17 Dec 2004 15:15:04 +0000 (15:15 +0000)]
Mac osX doesnt like isControlDown, use alt instead
amwaterhouse [Fri, 17 Dec 2004 15:14:22 +0000 (15:14 +0000)]
All optionpane messages must be added to Desktop.desktop
amwaterhouse [Fri, 17 Dec 2004 14:20:46 +0000 (14:20 +0000)]
If screensize is small, setSize to be the screenSize