jalview.git
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

19 years agoFalse changed to true
amwaterhouse [Fri, 21 Jan 2005 18:28:31 +0000 (18:28 +0000)]
False changed to true

19 years agoSuperGroup added
amwaterhouse [Fri, 21 Jan 2005 18:28:00 +0000 (18:28 +0000)]
SuperGroup added

19 years agoSystem.out removed
amwaterhouse [Fri, 21 Jan 2005 18:27:41 +0000 (18:27 +0000)]
System.out removed

19 years agoSuperGroups added
amwaterhouse [Fri, 21 Jan 2005 18:27:11 +0000 (18:27 +0000)]
SuperGroups added

19 years agonew images
amwaterhouse [Mon, 17 Jan 2005 18:14:25 +0000 (18:14 +0000)]
new images

19 years agoClustal align DNA spinner added
amwaterhouse [Mon, 17 Jan 2005 18:08:25 +0000 (18:08 +0000)]
Clustal align DNA spinner added

19 years agoFix overviewPanel bugs
amwaterhouse [Mon, 17 Jan 2005 16:12:55 +0000 (16:12 +0000)]
Fix overviewPanel bugs

19 years agoRefreshPanels after a colour change
amwaterhouse [Mon, 17 Jan 2005 16:12:06 +0000 (16:12 +0000)]
RefreshPanels after a colour change

19 years agoDont use addToDesktop for splashscreen
amwaterhouse [Mon, 17 Jan 2005 16:03:28 +0000 (16:03 +0000)]
Dont use addToDesktop for splashscreen

19 years agoClustalX added to ColourProperties
amwaterhouse [Mon, 17 Jan 2005 14:17:57 +0000 (14:17 +0000)]
ClustalX added to ColourProperties

19 years agoSetSecondaryPanel
amwaterhouse [Mon, 17 Jan 2005 14:17:22 +0000 (14:17 +0000)]
SetSecondaryPanel

19 years agoSetSecondaryPanel visible
amwaterhouse [Mon, 17 Jan 2005 14:16:51 +0000 (14:16 +0000)]
SetSecondaryPanel visible

19 years agoWorks out exisiting colur of a group
amwaterhouse [Mon, 17 Jan 2005 14:16:19 +0000 (14:16 +0000)]
Works out exisiting colur of a group

19 years agoNew class
amwaterhouse [Mon, 17 Jan 2005 14:15:30 +0000 (14:15 +0000)]
New class

19 years agoJBuilder Project file update
jprocter [Sat, 15 Jan 2005 15:17:37 +0000 (15:17 +0000)]
JBuilder Project file update

19 years agoJemboss(emboss 2.9.0) classes to provide client functionality to
jprocter [Sat, 15 Jan 2005 15:14:42 +0000 (15:14 +0000)]
Jemboss(emboss 2.9.0) classes to provide client functionality to
Jalview.

19 years agofirst jemboss clustalw client for jalview.
jprocter [Sat, 15 Jan 2005 15:12:21 +0000 (15:12 +0000)]
first jemboss clustalw client for jalview.

19 years agosupport for jemboss server interaction.
jprocter [Sat, 15 Jan 2005 15:11:38 +0000 (15:11 +0000)]
support for jemboss server interaction.

19 years agobugfix for writing fasta file without gap characters.
jprocter [Sat, 15 Jan 2005 15:05:23 +0000 (15:05 +0000)]
bugfix for writing fasta file without gap characters.

19 years agoImplemented clustal alignment via jemboss.
jprocter [Sat, 15 Jan 2005 15:04:16 +0000 (15:04 +0000)]
Implemented clustal alignment via jemboss.

19 years agoSpaces
amwaterhouse [Fri, 14 Jan 2005 15:47:19 +0000 (15:47 +0000)]
Spaces

19 years agoVarious color bugs sorted out
amwaterhouse [Fri, 14 Jan 2005 15:46:53 +0000 (15:46 +0000)]
Various color bugs sorted out

19 years agoDispalys rule along top of output
amwaterhouse [Fri, 14 Jan 2005 15:46:32 +0000 (15:46 +0000)]
Dispalys rule along top of output

19 years agoHscrollbar is shortened
amwaterhouse [Fri, 14 Jan 2005 15:46:04 +0000 (15:46 +0000)]
Hscrollbar is shortened

19 years agoReturn color.white if a gap char is detected
amwaterhouse [Fri, 14 Jan 2005 15:44:37 +0000 (15:44 +0000)]
Return color.white if a gap char is detected

19 years agogetValue method added
amwaterhouse [Thu, 13 Jan 2005 18:11:59 +0000 (18:11 +0000)]
getValue method added

19 years agoMaintain PID or conservation status when changing colour
amwaterhouse [Thu, 13 Jan 2005 18:11:16 +0000 (18:11 +0000)]
Maintain PID or conservation status when changing colour

19 years agoSequenceGroup is now an array
amwaterhouse [Thu, 13 Jan 2005 18:10:06 +0000 (18:10 +0000)]
SequenceGroup is now an array

19 years agoSend array of groups to renderer
amwaterhouse [Thu, 13 Jan 2005 18:08:41 +0000 (18:08 +0000)]
Send array of groups to renderer

19 years agoInitial selection bug fixed
amwaterhouse [Thu, 13 Jan 2005 18:07:42 +0000 (18:07 +0000)]
Initial selection bug fixed

19 years agoFindAllGroups added
amwaterhouse [Thu, 13 Jan 2005 18:06:55 +0000 (18:06 +0000)]
FindAllGroups added

19 years agoScrollbar at bottom of screen
amwaterhouse [Thu, 13 Jan 2005 18:05:57 +0000 (18:05 +0000)]
Scrollbar at bottom of screen

19 years agoGetResidueBoxColour altered for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:05:10 +0000 (12:05 +0000)]
GetResidueBoxColour altered for faster rendering

19 years agoRenderer already has graphics context
amwaterhouse [Thu, 13 Jan 2005 12:04:28 +0000 (12:04 +0000)]
Renderer already has graphics context

19 years agogetResidueBoxColour has been removed for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:03:41 +0000 (12:03 +0000)]
getResidueBoxColour has been removed for faster rendering

19 years agoIgnores gaps when searching
amwaterhouse [Thu, 13 Jan 2005 12:02:50 +0000 (12:02 +0000)]
Ignores gaps when searching

19 years agorandom change 3
jprocter [Wed, 12 Jan 2005 19:01:32 +0000 (19:01 +0000)]
random change 3

19 years agoanother dummy.
jprocter [Wed, 12 Jan 2005 18:32:34 +0000 (18:32 +0000)]
another dummy.

19 years agoGroup editing is done by control and alt key down
amwaterhouse [Wed, 12 Jan 2005 18:15:35 +0000 (18:15 +0000)]
Group editing is done by control and alt key down

19 years agoregular expression added
amwaterhouse [Wed, 12 Jan 2005 18:14:44 +0000 (18:14 +0000)]
regular expression added

19 years agodelete gaps bug fixed
amwaterhouse [Wed, 12 Jan 2005 18:14:27 +0000 (18:14 +0000)]
delete gaps bug fixed

19 years agomust append file:/// at beginning of file launch
amwaterhouse [Wed, 12 Jan 2005 18:13:54 +0000 (18:13 +0000)]
must append file:/// at beginning of file launch

19 years agoirrelevant comment.
jprocter [Wed, 12 Jan 2005 17:57:58 +0000 (17:57 +0000)]
irrelevant comment.

19 years agoDisplays number of matches found in search
amwaterhouse [Mon, 10 Jan 2005 17:39:32 +0000 (17:39 +0000)]
Displays number of matches found in search

19 years agojalview URL updated and authors in about file
amwaterhouse [Fri, 17 Dec 2004 15:39:39 +0000 (15:39 +0000)]
jalview URL updated and authors in about file

19 years agoMac osX doesnt like isControlDown, use alt instead
amwaterhouse [Fri, 17 Dec 2004 15:15:04 +0000 (15:15 +0000)]
Mac osX doesnt like isControlDown, use alt instead

19 years agoAll optionpane messages must be added to Desktop.desktop
amwaterhouse [Fri, 17 Dec 2004 15:14:22 +0000 (15:14 +0000)]
All optionpane messages must be added to Desktop.desktop

19 years agoIf screensize is small, setSize to be the screenSize
amwaterhouse [Fri, 17 Dec 2004 14:20:46 +0000 (14:20 +0000)]
If screensize is small, setSize to be the screenSize

19 years agoDoesn't draw the white box at the end of a line
amwaterhouse [Fri, 17 Dec 2004 14:20:04 +0000 (14:20 +0000)]
Doesn't draw the white box at the end of a line

19 years agoFixed bug in editing by group
amwaterhouse [Fri, 17 Dec 2004 14:19:17 +0000 (14:19 +0000)]
Fixed bug in editing by group

19 years agoHide apply and undo buttons
amwaterhouse [Fri, 17 Dec 2004 14:18:43 +0000 (14:18 +0000)]
Hide apply and undo buttons

19 years agoUse the isGap method in utils
amwaterhouse [Fri, 17 Dec 2004 14:18:13 +0000 (14:18 +0000)]
Use the isGap method in utils

19 years agoOutput new alignment bug fixed
amwaterhouse [Thu, 16 Dec 2004 15:45:38 +0000 (15:45 +0000)]
Output new alignment bug fixed

19 years agoilen and jlen no longer +1
amwaterhouse [Thu, 16 Dec 2004 13:19:57 +0000 (13:19 +0000)]
ilen and jlen no longer +1

19 years agoRemove redundancy implemented
amwaterhouse [Thu, 16 Dec 2004 13:19:14 +0000 (13:19 +0000)]
Remove redundancy implemented

19 years agocolours are right, but not the conservation bit!!
amwaterhouse [Wed, 15 Dec 2004 17:29:19 +0000 (17:29 +0000)]
colours are right, but not the conservation bit!!

19 years agono need to send sequence to determine residue colour
amwaterhouse [Wed, 15 Dec 2004 17:28:54 +0000 (17:28 +0000)]
no need to send sequence to determine residue colour

19 years agoAdded for the moment, only used by ClustalxColourScheme
amwaterhouse [Wed, 15 Dec 2004 17:28:07 +0000 (17:28 +0000)]
Added for the moment, only used by ClustalxColourScheme