jalview.git
19 years agouse the fileview
amwaterhouse [Tue, 15 Mar 2005 16:12:00 +0000 (16:12 +0000)]
use the fileview

19 years agonew class
amwaterhouse [Tue, 15 Mar 2005 16:08:15 +0000 (16:08 +0000)]
new class

19 years agotry system look and feel for a change
amwaterhouse [Tue, 15 Mar 2005 16:07:24 +0000 (16:07 +0000)]
try system look and feel for a change

19 years agoselection removed, now SelectionGroup does same job as id select and residue select
amwaterhouse [Tue, 15 Mar 2005 16:06:54 +0000 (16:06 +0000)]
selection removed, now SelectionGroup does same job as id select and residue select

19 years agonew file image
amwaterhouse [Tue, 15 Mar 2005 16:05:35 +0000 (16:05 +0000)]
new file image

19 years agofonts added to properties
amwaterhouse [Thu, 10 Mar 2005 10:13:48 +0000 (10:13 +0000)]
fonts added to properties

19 years agoactionlisteners added
amwaterhouse [Thu, 10 Mar 2005 10:13:18 +0000 (10:13 +0000)]
actionlisteners added

19 years agosearch and font frames are now internalframes
amwaterhouse [Thu, 10 Mar 2005 10:12:48 +0000 (10:12 +0000)]
search and font frames are now internalframes

19 years agoresized scale panel
amwaterhouse [Thu, 10 Mar 2005 10:12:16 +0000 (10:12 +0000)]
resized scale panel

19 years agofonts changed as selection made
amwaterhouse [Thu, 10 Mar 2005 10:12:01 +0000 (10:12 +0000)]
fonts changed as selection made

19 years agoScale canvas not needed
amwaterhouse [Thu, 10 Mar 2005 10:11:42 +0000 (10:11 +0000)]
Scale canvas not needed

19 years agoclear selection once group defined
amwaterhouse [Wed, 9 Mar 2005 18:40:15 +0000 (18:40 +0000)]
clear selection once group defined

19 years agoclear selection
amwaterhouse [Wed, 9 Mar 2005 18:39:45 +0000 (18:39 +0000)]
clear selection

19 years agodelete chars added
amwaterhouse [Wed, 9 Mar 2005 18:38:50 +0000 (18:38 +0000)]
delete chars added

19 years agoclear selection with escape key
amwaterhouse [Wed, 9 Mar 2005 18:37:50 +0000 (18:37 +0000)]
clear selection with escape key

19 years agofont chooser added
amwaterhouse [Wed, 9 Mar 2005 18:37:09 +0000 (18:37 +0000)]
font chooser added

19 years agoallows deletion of chars, font chooser added
amwaterhouse [Wed, 9 Mar 2005 18:36:17 +0000 (18:36 +0000)]
allows deletion of chars, font chooser added

19 years agoallows deletion of chars
amwaterhouse [Wed, 9 Mar 2005 18:35:46 +0000 (18:35 +0000)]
allows deletion of chars

19 years agodont perform blast search at present
amwaterhouse [Wed, 9 Mar 2005 18:35:03 +0000 (18:35 +0000)]
dont perform blast search at present

19 years agoadd lower case residue props
amwaterhouse [Tue, 8 Mar 2005 18:12:13 +0000 (18:12 +0000)]
add lower case residue props

19 years agofixed interface for PID method.
jprocter [Tue, 8 Mar 2005 16:45:22 +0000 (16:45 +0000)]
fixed interface for PID method.

19 years agofixed so that alignment percentage ID is used for distance calculation
jprocter [Tue, 8 Mar 2005 16:44:11 +0000 (16:44 +0000)]
fixed so that alignment percentage ID is used for distance calculation

19 years agofixed signing bug (also updated to latest javahelp library)
jprocter [Tue, 8 Mar 2005 16:43:05 +0000 (16:43 +0000)]
fixed signing bug (also updated to latest javahelp library)

19 years agomore precise methods information in help description.
jprocter [Tue, 8 Mar 2005 16:42:01 +0000 (16:42 +0000)]
more precise methods information in help description.

19 years agofixed some of the jar/wsdl deployment problems.
jprocter [Tue, 8 Mar 2005 16:40:45 +0000 (16:40 +0000)]
fixed some of the jar/wsdl deployment problems.

19 years agoremoved conservation calculation from calculations.
jprocter [Tue, 8 Mar 2005 16:40:11 +0000 (16:40 +0000)]
removed conservation calculation from calculations.

19 years agoTree fits to window by default
amwaterhouse [Tue, 8 Mar 2005 16:36:48 +0000 (16:36 +0000)]
Tree fits to window by default

19 years agogetCharwidth directly
amwaterhouse [Tue, 8 Mar 2005 14:49:41 +0000 (14:49 +0000)]
getCharwidth directly

19 years agoDont set paintFlags
amwaterhouse [Tue, 8 Mar 2005 14:41:51 +0000 (14:41 +0000)]
Dont set paintFlags

19 years agodont set seqPanel paint flag
amwaterhouse [Tue, 8 Mar 2005 14:35:26 +0000 (14:35 +0000)]
dont set seqPanel paint flag

19 years agoonly set graphics black once at beginning of text
amwaterhouse [Tue, 8 Mar 2005 14:34:10 +0000 (14:34 +0000)]
only set graphics black once at beginning of text

19 years agodont color gaps in sequence features
amwaterhouse [Tue, 8 Mar 2005 14:32:21 +0000 (14:32 +0000)]
dont color gaps in sequence features

19 years agoif resIndex > 19 return color.white
amwaterhouse [Tue, 8 Mar 2005 14:31:40 +0000 (14:31 +0000)]
if resIndex > 19 return color.white

19 years agoObsolete. Explanation within the conservation colourscheme entry.
jprocter [Tue, 1 Mar 2005 16:51:50 +0000 (16:51 +0000)]
Obsolete. Explanation within the conservation colourscheme entry.

19 years agoadded uniquify sequence id assertion.
jprocter [Mon, 28 Feb 2005 10:47:32 +0000 (10:47 +0000)]
added uniquify sequence id assertion.

19 years agopartial implementation of JNet server prediction.
jprocter [Mon, 28 Feb 2005 10:45:52 +0000 (10:45 +0000)]
partial implementation of JNet server prediction.

19 years agofirst stab at a JPredClient.
jprocter [Mon, 28 Feb 2005 10:43:43 +0000 (10:43 +0000)]
first stab at a JPredClient.

19 years agobasic jpred concise prediction reader.
jprocter [Wed, 23 Feb 2005 15:57:04 +0000 (15:57 +0000)]
basic jpred concise prediction reader.

19 years agonew resources location.
jprocter [Wed, 23 Feb 2005 15:53:19 +0000 (15:53 +0000)]
new resources location.

19 years agorearranged project structure
jprocter [Wed, 23 Feb 2005 15:51:59 +0000 (15:51 +0000)]
rearranged project structure

19 years agomaking Jemboss client more configurable.
jprocter [Wed, 23 Feb 2005 15:51:44 +0000 (15:51 +0000)]
making Jemboss client more configurable.

19 years agobug fix for unaligned sequence sets and clustal colours (obviated by
jprocter [Wed, 23 Feb 2005 15:48:40 +0000 (15:48 +0000)]
bug fix for unaligned sequence sets and clustal colours (obviated by
'aligned' test).

19 years agorearranged project structure
jprocter [Wed, 23 Feb 2005 15:47:56 +0000 (15:47 +0000)]
rearranged project structure

19 years agonew ant build for Jalview.
jprocter [Wed, 23 Feb 2005 11:57:11 +0000 (11:57 +0000)]
new ant build for Jalview.

19 years agoadd titles
amwaterhouse [Tue, 22 Feb 2005 12:20:21 +0000 (12:20 +0000)]
add titles

19 years agoadd history for cut and paste
amwaterhouse [Tue, 22 Feb 2005 11:46:46 +0000 (11:46 +0000)]
add history for cut and paste

19 years agoupdated help files
amwaterhouse [Tue, 22 Feb 2005 11:46:00 +0000 (11:46 +0000)]
updated help files

19 years agoimages moved
amwaterhouse [Mon, 21 Feb 2005 17:09:13 +0000 (17:09 +0000)]
images moved

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