jalview.git
19 years agonote of user_defined_colours added
amwaterhouse [Mon, 21 Feb 2005 17:08:42 +0000 (17:08 +0000)]
note of user_defined_colours added

19 years agoimage moved
amwaterhouse [Mon, 21 Feb 2005 17:02:08 +0000 (17:02 +0000)]
image moved

19 years agoSets USER_DEFINED_COLOUR as property
amwaterhouse [Mon, 21 Feb 2005 17:01:41 +0000 (17:01 +0000)]
Sets USER_DEFINED_COLOUR as property

19 years agoimages in image folder
amwaterhouse [Mon, 21 Feb 2005 17:00:39 +0000 (17:00 +0000)]
images in image folder

19 years agoUpdated help pages
amwaterhouse [Mon, 21 Feb 2005 16:59:02 +0000 (16:59 +0000)]
Updated help pages

19 years agotreepanel is now internalframe, has a menu
amwaterhouse [Fri, 18 Feb 2005 12:28:36 +0000 (12:28 +0000)]
treepanel is now internalframe, has a menu

19 years agoshow sequence features is false by default
amwaterhouse [Fri, 18 Feb 2005 12:28:11 +0000 (12:28 +0000)]
show sequence features is false by default

19 years agotree is printable
amwaterhouse [Fri, 18 Feb 2005 12:27:04 +0000 (12:27 +0000)]
tree is printable

19 years agotreepanel is now internalframe
amwaterhouse [Fri, 18 Feb 2005 12:26:49 +0000 (12:26 +0000)]
treepanel is now internalframe

19 years agofeaturesAdded = false
amwaterhouse [Fri, 18 Feb 2005 12:25:11 +0000 (12:25 +0000)]
featuresAdded = false

19 years agowrap alignment id drawing bug fixed
amwaterhouse [Wed, 16 Feb 2005 17:56:53 +0000 (17:56 +0000)]
wrap alignment id drawing bug fixed

19 years agoSave as jpg added
amwaterhouse [Wed, 16 Feb 2005 17:56:33 +0000 (17:56 +0000)]
Save as jpg added

19 years agoFix bug when creating treepanel
amwaterhouse [Tue, 15 Feb 2005 11:19:59 +0000 (11:19 +0000)]
Fix bug when creating treepanel

19 years agoabovePIDThreshold added to viewport
amwaterhouse [Tue, 15 Feb 2005 10:46:52 +0000 (10:46 +0000)]
abovePIDThreshold added to viewport

19 years agono action if supplied colour isnull
amwaterhouse [Tue, 15 Feb 2005 10:46:29 +0000 (10:46 +0000)]
no action if supplied colour isnull

19 years agocatch any pid or conservation related bugs here
amwaterhouse [Tue, 15 Feb 2005 10:46:08 +0000 (10:46 +0000)]
catch any pid or conservation related bugs here

19 years agoadd applytoallgroups colouring option
amwaterhouse [Tue, 15 Feb 2005 10:45:46 +0000 (10:45 +0000)]
add applytoallgroups colouring option

19 years agomust add all features even if start and end res are beyond sequence length
amwaterhouse [Fri, 11 Feb 2005 14:07:49 +0000 (14:07 +0000)]
must add all features even if start and end res are beyond sequence length

19 years agomove sequences up and down
amwaterhouse [Fri, 11 Feb 2005 12:44:39 +0000 (12:44 +0000)]
move sequences up and down

19 years agoadd VK_F key, up down
amwaterhouse [Fri, 11 Feb 2005 12:44:21 +0000 (12:44 +0000)]
add VK_F key, up down

19 years agoend of seq adjustments
amwaterhouse [Fri, 11 Feb 2005 12:43:58 +0000 (12:43 +0000)]
end of seq adjustments

19 years agodont add new seqs to group
amwaterhouse [Fri, 11 Feb 2005 12:43:31 +0000 (12:43 +0000)]
dont add new seqs to group

19 years agowatch out for end of seq in findposition
amwaterhouse [Fri, 11 Feb 2005 11:04:31 +0000 (11:04 +0000)]
watch out for end of seq in findposition

19 years agoupdate start and end res when copying
amwaterhouse [Fri, 11 Feb 2005 11:03:47 +0000 (11:03 +0000)]
update start and end res when copying

19 years agoadd control a key to select all
amwaterhouse [Fri, 11 Feb 2005 10:47:49 +0000 (10:47 +0000)]
add control a key to select all

19 years agobug fixed if featureEnd is beyond end of sequence
amwaterhouse [Fri, 11 Feb 2005 10:39:20 +0000 (10:39 +0000)]
bug fixed if featureEnd is beyond end of sequence

19 years agowatch end of sequence when asking for (start, end)
amwaterhouse [Thu, 10 Feb 2005 18:12:50 +0000 (18:12 +0000)]
watch end of sequence when asking for (start, end)

19 years agodont add new sequences to null groups!
amwaterhouse [Thu, 10 Feb 2005 18:12:22 +0000 (18:12 +0000)]
dont add new sequences to null groups!

19 years agochange of label text
amwaterhouse [Thu, 10 Feb 2005 17:59:50 +0000 (17:59 +0000)]
change of label text

19 years agocut and paste now in main menu
amwaterhouse [Thu, 10 Feb 2005 17:54:13 +0000 (17:54 +0000)]
cut and paste now in main menu

19 years agotrimmed down
amwaterhouse [Thu, 10 Feb 2005 17:53:20 +0000 (17:53 +0000)]
trimmed down

19 years agoKey listener works!!
amwaterhouse [Thu, 10 Feb 2005 17:52:53 +0000 (17:52 +0000)]
Key listener works!!

19 years agoCut and paste implemented
amwaterhouse [Thu, 10 Feb 2005 17:52:35 +0000 (17:52 +0000)]
Cut and paste implemented

19 years agocheck that we're not off the end of a sequence
amwaterhouse [Thu, 10 Feb 2005 13:26:25 +0000 (13:26 +0000)]
check that we're not off the end of a sequence

19 years agocheck that mouse is over sequence if unaligned
amwaterhouse [Thu, 10 Feb 2005 13:23:09 +0000 (13:23 +0000)]
check that mouse is over sequence if unaligned

19 years agoedit sequence name method
amwaterhouse [Thu, 10 Feb 2005 13:21:56 +0000 (13:21 +0000)]
edit sequence name method

19 years agoremove try catch loop
amwaterhouse [Thu, 10 Feb 2005 13:21:29 +0000 (13:21 +0000)]
remove try catch loop

19 years agoisAligned method added, check before making tree
amwaterhouse [Thu, 10 Feb 2005 13:20:58 +0000 (13:20 +0000)]
isAligned method added, check before making tree

19 years agoisAligned method added
amwaterhouse [Thu, 10 Feb 2005 13:20:33 +0000 (13:20 +0000)]
isAligned method added

19 years agoremoved
amwaterhouse [Thu, 10 Feb 2005 13:19:30 +0000 (13:19 +0000)]
removed

19 years agoStart the thread
amwaterhouse [Wed, 9 Feb 2005 16:07:07 +0000 (16:07 +0000)]
Start the thread

19 years agoDisplay tooltip updated
amwaterhouse [Wed, 9 Feb 2005 15:31:12 +0000 (15:31 +0000)]
Display tooltip updated

19 years agoCorrect number of ids is drawn
amwaterhouse [Wed, 9 Feb 2005 15:30:53 +0000 (15:30 +0000)]
Correct number of ids is drawn

19 years agoFixed display bugs when feature is off the screen
amwaterhouse [Wed, 9 Feb 2005 15:30:33 +0000 (15:30 +0000)]
Fixed display bugs when feature is off the screen

19 years agoBlasts asynchronously
amwaterhouse [Wed, 9 Feb 2005 15:29:57 +0000 (15:29 +0000)]
Blasts asynchronously

19 years agoSet property returns key
amwaterhouse [Tue, 8 Feb 2005 18:40:54 +0000 (18:40 +0000)]
Set property returns key

19 years agoLooks for missing ids using BlastClient
amwaterhouse [Tue, 8 Feb 2005 18:40:35 +0000 (18:40 +0000)]
Looks for missing ids using BlastClient

19 years agonew class
amwaterhouse [Tue, 8 Feb 2005 18:39:50 +0000 (18:39 +0000)]
new class

19 years agoformatting imports.
jprocter [Tue, 8 Feb 2005 16:04:44 +0000 (16:04 +0000)]
formatting imports.

19 years agoProperties bug fixed
amwaterhouse [Mon, 7 Feb 2005 17:40:27 +0000 (17:40 +0000)]
Properties bug fixed

19 years agoNew class
amwaterhouse [Mon, 7 Feb 2005 17:09:57 +0000 (17:09 +0000)]
New class

19 years agoUse Cache.getProperty
amwaterhouse [Mon, 7 Feb 2005 17:09:19 +0000 (17:09 +0000)]
Use Cache.getProperty

19 years agoSettooltip for sequence feature
amwaterhouse [Mon, 7 Feb 2005 17:08:14 +0000 (17:08 +0000)]
Settooltip for sequence feature

19 years agoload properties on startup
amwaterhouse [Mon, 7 Feb 2005 17:06:34 +0000 (17:06 +0000)]
load properties on startup

19 years agoProperties added
amwaterhouse [Mon, 7 Feb 2005 17:06:17 +0000 (17:06 +0000)]
Properties added

19 years agoNow displays sequence features
amwaterhouse [Mon, 7 Feb 2005 17:05:18 +0000 (17:05 +0000)]
Now displays sequence features

19 years agoNew class for fetching sequence features
amwaterhouse [Mon, 7 Feb 2005 17:05:01 +0000 (17:05 +0000)]
New class for fetching sequence features

19 years agoSequenceFeature display added
amwaterhouse [Fri, 4 Feb 2005 18:29:43 +0000 (18:29 +0000)]
SequenceFeature display added

19 years agoModified for wrapAlignement
amwaterhouse [Wed, 2 Feb 2005 17:17:07 +0000 (17:17 +0000)]
Modified for wrapAlignement

19 years agoRemove test image
amwaterhouse [Wed, 2 Feb 2005 16:14:01 +0000 (16:14 +0000)]
Remove test image

19 years agoModified for wrappingAlignment
amwaterhouse [Wed, 2 Feb 2005 16:12:55 +0000 (16:12 +0000)]
Modified for wrappingAlignment

19 years agoApply to all groups method added
amwaterhouse [Tue, 1 Feb 2005 19:04:14 +0000 (19:04 +0000)]
Apply to all groups method added

19 years agoUpdate PID or conservationSlider if necessary
amwaterhouse [Tue, 1 Feb 2005 19:03:56 +0000 (19:03 +0000)]
Update PID or conservationSlider if necessary

19 years agoBugs in column selection fixed
amwaterhouse [Tue, 1 Feb 2005 19:03:32 +0000 (19:03 +0000)]
Bugs in column selection fixed

19 years agoConservation and PID colouring methods updated, also remove group added
amwaterhouse [Tue, 1 Feb 2005 19:03:04 +0000 (19:03 +0000)]
Conservation and PID colouring methods updated, also remove group added

19 years agoConservation and PID colouring methods updated
amwaterhouse [Tue, 1 Feb 2005 19:02:28 +0000 (19:02 +0000)]
Conservation and PID colouring methods updated

19 years agoSecondary panel is hidden for the moment
amwaterhouse [Tue, 1 Feb 2005 19:01:20 +0000 (19:01 +0000)]
Secondary panel is hidden for the moment

19 years agoEnable wrap menu item
amwaterhouse [Tue, 1 Feb 2005 19:00:48 +0000 (19:00 +0000)]
Enable wrap menu item

19 years agoAbility to apply to all groups added
amwaterhouse [Tue, 1 Feb 2005 19:00:12 +0000 (19:00 +0000)]
Ability to apply to all groups added

19 years agoNo need for drawableSequence
amwaterhouse [Tue, 1 Feb 2005 18:59:47 +0000 (18:59 +0000)]
No need for drawableSequence

19 years agoClustal colours now work
amwaterhouse [Tue, 1 Feb 2005 18:58:40 +0000 (18:58 +0000)]
Clustal colours now work

19 years agoNew layout, works 1.4 and 1.5
amwaterhouse [Fri, 28 Jan 2005 16:27:01 +0000 (16:27 +0000)]
New layout, works 1.4 and 1.5

19 years agocorrect border width
amwaterhouse [Thu, 27 Jan 2005 18:43:33 +0000 (18:43 +0000)]
correct border width

19 years agoJavaHelp files added
amwaterhouse [Thu, 27 Jan 2005 18:41:17 +0000 (18:41 +0000)]
JavaHelp files added

19 years agoColourSchemeKey now in documentation
amwaterhouse [Thu, 27 Jan 2005 18:34:38 +0000 (18:34 +0000)]
ColourSchemeKey now in documentation

19 years agosystem.exit or destroy if applet or app
amwaterhouse [Tue, 25 Jan 2005 17:11:52 +0000 (17:11 +0000)]
system.exit or destroy if applet or app

19 years agochange order of menuitems
amwaterhouse [Tue, 25 Jan 2005 17:08:00 +0000 (17:08 +0000)]
change order of menuitems

19 years agodon't system.ext
amwaterhouse [Tue, 25 Jan 2005 17:07:13 +0000 (17:07 +0000)]
don't system.ext

19 years agonow has key listener
amwaterhouse [Tue, 25 Jan 2005 17:06:40 +0000 (17:06 +0000)]
now has key listener

19 years agoclustalColour bug fixed, clear selection
amwaterhouse [Tue, 25 Jan 2005 17:06:09 +0000 (17:06 +0000)]
clustalColour bug fixed, clear selection

19 years agoextends Applet
amwaterhouse [Tue, 25 Jan 2005 17:05:33 +0000 (17:05 +0000)]
extends Applet

19 years agoAdds regex.jar to classpath
amwaterhouse [Mon, 24 Jan 2005 17:38:39 +0000 (17:38 +0000)]
Adds regex.jar to classpath

19 years agowarning! this is obfuscated
amwaterhouse [Mon, 24 Jan 2005 17:31:20 +0000 (17:31 +0000)]
warning! this is obfuscated

19 years agobug in compare fixed
amwaterhouse [Mon, 24 Jan 2005 17:27:36 +0000 (17:27 +0000)]
bug in compare fixed

19 years agoreturns color.white if the underlying colourscheme is null
amwaterhouse [Mon, 24 Jan 2005 17:27:00 +0000 (17:27 +0000)]
returns color.white if the underlying colourscheme is null

19 years agocreates new groups when selecting branches of the tree
amwaterhouse [Mon, 24 Jan 2005 17:26:15 +0000 (17:26 +0000)]
creates new groups when selecting branches of the tree

19 years agonow uses 1.1 friendly regex
amwaterhouse [Mon, 24 Jan 2005 17:25:31 +0000 (17:25 +0000)]
now uses 1.1 friendly regex

19 years agoClear selection when deleting all groups
amwaterhouse [Mon, 24 Jan 2005 17:24:52 +0000 (17:24 +0000)]
Clear selection when deleting all groups

19 years agoAllow removal of colour when deleting groups
amwaterhouse [Mon, 24 Jan 2005 17:24:16 +0000 (17:24 +0000)]
Allow removal of colour when deleting groups

19 years agoremove a few imports
amwaterhouse [Fri, 21 Jan 2005 18:34:34 +0000 (18:34 +0000)]
remove a few imports

19 years agoNucleotide colours added
amwaterhouse [Fri, 21 Jan 2005 18:34:06 +0000 (18:34 +0000)]
Nucleotide colours added

19 years agoNew colourScheme
amwaterhouse [Fri, 21 Jan 2005 18:33:37 +0000 (18:33 +0000)]
New colourScheme

19 years agoCreate group from search added
amwaterhouse [Fri, 21 Jan 2005 18:33:07 +0000 (18:33 +0000)]
Create group from search added

19 years agoDelete groups added, nucleotide color added
amwaterhouse [Fri, 21 Jan 2005 18:32:49 +0000 (18:32 +0000)]
Delete groups added, nucleotide color added

19 years agoForegroundColor is darker.darker.darker
amwaterhouse [Fri, 21 Jan 2005 18:32:14 +0000 (18:32 +0000)]
ForegroundColor is darker.darker.darker

19 years agoif stretchGroup is null, set avRubberbandGroup new group
amwaterhouse [Fri, 21 Jan 2005 18:31:40 +0000 (18:31 +0000)]
if stretchGroup is null, set avRubberbandGroup new group

19 years ago<= y2 is now < y2
amwaterhouse [Fri, 21 Jan 2005 18:30:59 +0000 (18:30 +0000)]
<= y2 is now < y2

19 years agoCommented out code removed
amwaterhouse [Fri, 21 Jan 2005 18:30:06 +0000 (18:30 +0000)]
Commented out code removed

19 years agoFill rect white
amwaterhouse [Fri, 21 Jan 2005 18:29:34 +0000 (18:29 +0000)]
Fill rect white

19 years agoCheck if graphics is null in labelSize
amwaterhouse [Fri, 21 Jan 2005 18:29:07 +0000 (18:29 +0000)]
Check if graphics is null in labelSize