jalview.git
19 years agoOptimise graphics copy object
amwaterhouse [Tue, 20 Sep 2005 13:13:49 +0000 (13:13 +0000)]
Optimise graphics copy object

19 years agoUse selectionGroup to find chosen sequences
amwaterhouse [Tue, 20 Sep 2005 13:13:32 +0000 (13:13 +0000)]
Use selectionGroup to find chosen sequences

19 years agoMake sure fontmetrics is not null
amwaterhouse [Tue, 20 Sep 2005 13:13:07 +0000 (13:13 +0000)]
Make sure fontmetrics is not null

19 years agoMake sure fontmetrics exists for headless state
amwaterhouse [Mon, 19 Sep 2005 13:41:25 +0000 (13:41 +0000)]
Make sure fontmetrics exists for headless state

19 years agoDont add ServiceListeners if desktop is null
amwaterhouse [Mon, 19 Sep 2005 13:40:55 +0000 (13:40 +0000)]
Dont add ServiceListeners if desktop is null

19 years agoAlignment of node labels modified
amwaterhouse [Mon, 19 Sep 2005 12:49:39 +0000 (12:49 +0000)]
Alignment of node labels modified

19 years agoShowDistances, placeHolders and bootstraps have their own methods
amwaterhouse [Mon, 19 Sep 2005 12:49:14 +0000 (12:49 +0000)]
ShowDistances, placeHolders and bootstraps have their own methods

19 years agoCheck image is not null in fast paint
amwaterhouse [Fri, 16 Sep 2005 14:34:57 +0000 (14:34 +0000)]
Check image is not null in fast paint

19 years agoSet distanceMenu selected true
amwaterhouse [Fri, 16 Sep 2005 14:34:26 +0000 (14:34 +0000)]
Set distanceMenu selected true

19 years agoMemory settings added to help
amwaterhouse [Thu, 15 Sep 2005 14:09:08 +0000 (14:09 +0000)]
Memory settings added to help

19 years agoCorrect date Release_2_05b
amwaterhouse [Thu, 15 Sep 2005 11:19:55 +0000 (11:19 +0000)]
Correct date

19 years agoFixed so job submission and job failure errors are reported to user and server except...
jprocter [Thu, 15 Sep 2005 11:16:12 +0000 (11:16 +0000)]
Fixed so job submission and job failure errors are reported to user and server exceptions also generate error and log messages.

19 years agoCopy uses fasta format
amwaterhouse [Thu, 15 Sep 2005 10:53:35 +0000 (10:53 +0000)]
Copy uses fasta format

19 years ago2.05b
amwaterhouse [Thu, 15 Sep 2005 10:53:12 +0000 (10:53 +0000)]
2.05b

19 years agoAdd Uracil as X unknown
amwaterhouse [Thu, 15 Sep 2005 10:28:30 +0000 (10:28 +0000)]
Add Uracil as X unknown

19 years agoOptionPane warning for out of memory
amwaterhouse [Thu, 15 Sep 2005 10:08:32 +0000 (10:08 +0000)]
OptionPane warning for out of memory

19 years agoremove system.out
amwaterhouse [Thu, 15 Sep 2005 10:08:15 +0000 (10:08 +0000)]
remove system.out

19 years agoRemove key listener
amwaterhouse [Thu, 15 Sep 2005 10:07:56 +0000 (10:07 +0000)]
Remove key listener

19 years agoDont add time to build date
amwaterhouse [Thu, 15 Sep 2005 09:39:30 +0000 (09:39 +0000)]
Dont add time to build date

19 years agoAdd main-class to jar files
amwaterhouse [Thu, 15 Sep 2005 09:11:58 +0000 (09:11 +0000)]
Add main-class to jar files

19 years agoUse equalsIgnoreCase
amwaterhouse [Thu, 15 Sep 2005 09:09:35 +0000 (09:09 +0000)]
Use equalsIgnoreCase

19 years agoApplet has main method, excutable
amwaterhouse [Thu, 15 Sep 2005 09:09:17 +0000 (09:09 +0000)]
Applet has main method, excutable

19 years agoLogger moved to prefs so that class not found error can be handled in main
amwaterhouse [Thu, 15 Sep 2005 09:08:21 +0000 (09:08 +0000)]
Logger moved to prefs so that class not found error can be handled in main

19 years agoPreferences updated
amwaterhouse [Wed, 14 Sep 2005 16:14:02 +0000 (16:14 +0000)]
Preferences updated

19 years agoMove bootStrap/distance settings outside thread
amwaterhouse [Wed, 14 Sep 2005 15:44:27 +0000 (15:44 +0000)]
Move bootStrap/distance settings outside thread

19 years agoAdd end of consensus test for wrapped edit
amwaterhouse [Wed, 14 Sep 2005 15:43:55 +0000 (15:43 +0000)]
Add end of consensus test for wrapped edit

19 years agofullSeqId should follow preference value
amwaterhouse [Wed, 14 Sep 2005 15:43:23 +0000 (15:43 +0000)]
fullSeqId should follow preference value

19 years agoMake new frame selected
amwaterhouse [Wed, 14 Sep 2005 15:42:45 +0000 (15:42 +0000)]
Make new frame selected

19 years agoRemove system out tests
amwaterhouse [Wed, 14 Sep 2005 15:42:26 +0000 (15:42 +0000)]
Remove system out tests

19 years agoCopy and paste uses FASTA format
amwaterhouse [Wed, 14 Sep 2005 15:42:08 +0000 (15:42 +0000)]
Copy and paste uses FASTA format

19 years agoCall methods in treeCanvas on init
amwaterhouse [Wed, 14 Sep 2005 12:41:04 +0000 (12:41 +0000)]
Call methods in treeCanvas on init

19 years agooffy changes
amwaterhouse [Wed, 14 Sep 2005 12:40:49 +0000 (12:40 +0000)]
offy changes

19 years agoOutOfMemory try catch
amwaterhouse [Wed, 14 Sep 2005 12:40:29 +0000 (12:40 +0000)]
OutOfMemory try catch

19 years agoUse font size, not font height
amwaterhouse [Wed, 14 Sep 2005 12:20:48 +0000 (12:20 +0000)]
Use font size, not font height

19 years agoResize for mac
amwaterhouse [Wed, 14 Sep 2005 11:52:23 +0000 (11:52 +0000)]
Resize for mac

19 years agoUse getTreeFont instead of getFont
amwaterhouse [Wed, 14 Sep 2005 11:52:06 +0000 (11:52 +0000)]
Use getTreeFont instead of getFont

19 years agoadd fontname, size and style for trees
amwaterhouse [Wed, 14 Sep 2005 11:25:14 +0000 (11:25 +0000)]
add fontname, size and style for trees

19 years agoFont change instead of font size
amwaterhouse [Wed, 14 Sep 2005 11:24:33 +0000 (11:24 +0000)]
Font change instead of font size

19 years agoAdd Export tab
amwaterhouse [Wed, 14 Sep 2005 11:24:13 +0000 (11:24 +0000)]
Add Export tab

19 years agoMake button protected
amwaterhouse [Wed, 14 Sep 2005 11:23:58 +0000 (11:23 +0000)]
Make button protected

19 years agouse fontchooser to change fonts
amwaterhouse [Wed, 14 Sep 2005 11:23:10 +0000 (11:23 +0000)]
use fontchooser to change fonts

19 years agoCenter labels
amwaterhouse [Wed, 14 Sep 2005 11:22:46 +0000 (11:22 +0000)]
Center labels

19 years agoSave fonts for trees
amwaterhouse [Wed, 14 Sep 2005 11:22:27 +0000 (11:22 +0000)]
Save fonts for trees

19 years agoChange fonts in Treepanel
amwaterhouse [Wed, 14 Sep 2005 11:22:13 +0000 (11:22 +0000)]
Change fonts in Treepanel

19 years agoAdd header
amwaterhouse [Wed, 14 Sep 2005 11:21:48 +0000 (11:21 +0000)]
Add header

19 years agoSystem.gc after outofmemory
amwaterhouse [Wed, 14 Sep 2005 11:20:57 +0000 (11:20 +0000)]
System.gc after outofmemory

19 years agoPCA is in outofmemory try-catch
amwaterhouse [Wed, 14 Sep 2005 11:20:09 +0000 (11:20 +0000)]
PCA is in outofmemory try-catch

19 years agoTreeFont added, binding rebuilt
amwaterhouse [Wed, 14 Sep 2005 11:19:16 +0000 (11:19 +0000)]
TreeFont added, binding rebuilt

19 years agoDont respond to mouse movements if alignment wrapped
amwaterhouse [Tue, 13 Sep 2005 17:45:25 +0000 (17:45 +0000)]
Dont respond to mouse movements if alignment wrapped

19 years agoGive focus to textarea on startup
amwaterhouse [Tue, 13 Sep 2005 17:44:59 +0000 (17:44 +0000)]
Give focus to textarea on startup

19 years agoEPSOptions added
amwaterhouse [Tue, 13 Sep 2005 17:44:32 +0000 (17:44 +0000)]
EPSOptions added

19 years agoWarn if out of memory
amwaterhouse [Tue, 13 Sep 2005 17:44:08 +0000 (17:44 +0000)]
Warn if out of memory

19 years agoRemove gaps in regions, not char by char
amwaterhouse [Mon, 12 Sep 2005 17:00:39 +0000 (17:00 +0000)]
Remove gaps in regions, not char by char

19 years agoAlways return true for directories
amwaterhouse [Mon, 12 Sep 2005 17:00:00 +0000 (17:00 +0000)]
Always return true for directories

19 years agonull pointers removed
amwaterhouse [Mon, 12 Sep 2005 16:59:42 +0000 (16:59 +0000)]
null pointers removed

19 years agoNull pointers removed
amwaterhouse [Mon, 12 Sep 2005 16:56:12 +0000 (16:56 +0000)]
Null pointers removed

19 years agoDont fastpaint if movement is zero
amwaterhouse [Mon, 12 Sep 2005 12:27:08 +0000 (12:27 +0000)]
Dont fastpaint if movement is zero

19 years agoUpdate overview after change
amwaterhouse [Mon, 12 Sep 2005 12:26:25 +0000 (12:26 +0000)]
Update overview after change

19 years agoUpdate overview in alignmentChanged
amwaterhouse [Mon, 12 Sep 2005 12:25:58 +0000 (12:25 +0000)]
Update overview in alignmentChanged

19 years agoSize checking in drawGraph
amwaterhouse [Mon, 12 Sep 2005 12:23:43 +0000 (12:23 +0000)]
Size checking in drawGraph

19 years agoOverview subsamples alignment
amwaterhouse [Mon, 12 Sep 2005 12:23:09 +0000 (12:23 +0000)]
Overview subsamples alignment

19 years agoMove tree property change to treePanel
amwaterhouse [Thu, 8 Sep 2005 16:32:15 +0000 (16:32 +0000)]
Move tree property change to treePanel

19 years agoOnly 1 NJtree
amwaterhouse [Thu, 8 Sep 2005 16:31:49 +0000 (16:31 +0000)]
Only 1 NJtree

19 years agoTreePanel takes viewport
amwaterhouse [Thu, 8 Sep 2005 16:08:23 +0000 (16:08 +0000)]
TreePanel takes viewport

19 years agoREmove unnecessary imports
amwaterhouse [Thu, 8 Sep 2005 16:04:44 +0000 (16:04 +0000)]
REmove unnecessary imports

19 years agoInit PCA in thread
amwaterhouse [Thu, 8 Sep 2005 16:04:11 +0000 (16:04 +0000)]
Init PCA in thread

19 years agoIf no consensus, disable certain colour options
amwaterhouse [Thu, 8 Sep 2005 15:50:42 +0000 (15:50 +0000)]
If no consensus, disable certain colour options

19 years agoupdate consensus and conservation are in try catch for out of memory error
amwaterhouse [Thu, 8 Sep 2005 15:50:11 +0000 (15:50 +0000)]
update consensus and conservation are in try catch for out of memory error

19 years agoOptimise switch to fastPaint
amwaterhouse [Thu, 8 Sep 2005 15:49:27 +0000 (15:49 +0000)]
Optimise switch to fastPaint

19 years agoCorrect mouse pressed bug
amwaterhouse [Thu, 8 Sep 2005 15:48:45 +0000 (15:48 +0000)]
Correct mouse pressed bug

19 years agoOptimised for wide alignments
amwaterhouse [Thu, 8 Sep 2005 15:48:22 +0000 (15:48 +0000)]
Optimised for wide alignments

19 years agoLoad in a thread
amwaterhouse [Thu, 8 Sep 2005 15:47:23 +0000 (15:47 +0000)]
Load in a thread

19 years agoMake menuitems protected
amwaterhouse [Thu, 8 Sep 2005 15:46:36 +0000 (15:46 +0000)]
Make menuitems protected

19 years agoIf vconsensus is null, return
amwaterhouse [Thu, 8 Sep 2005 15:46:02 +0000 (15:46 +0000)]
If vconsensus is null, return

19 years agoAdd lowercase nucleotides to nucleotideHash
amwaterhouse [Thu, 8 Sep 2005 15:45:21 +0000 (15:45 +0000)]
Add lowercase nucleotides to nucleotideHash

19 years agoMore informative error messages.
jprocter [Mon, 5 Sep 2005 15:38:26 +0000 (15:38 +0000)]
More informative error messages.

19 years agoApplet search by residue index fixed
amwaterhouse [Fri, 2 Sep 2005 08:29:13 +0000 (08:29 +0000)]
Applet search by residue index fixed

19 years agoAdd header to file
amwaterhouse [Thu, 1 Sep 2005 16:10:12 +0000 (16:10 +0000)]
Add header to file

19 years agofirePropertyChange if sequences deleted
amwaterhouse [Thu, 1 Sep 2005 13:44:05 +0000 (13:44 +0000)]
firePropertyChange if sequences deleted

19 years agoNeed reference to mainApplet
amwaterhouse [Thu, 1 Sep 2005 13:43:26 +0000 (13:43 +0000)]
Need reference to mainApplet

19 years agoUse propertyListener for alignment edits
amwaterhouse [Thu, 1 Sep 2005 13:20:56 +0000 (13:20 +0000)]
Use propertyListener for alignment edits

19 years agoSort by added to preferences
amwaterhouse [Thu, 1 Sep 2005 13:20:12 +0000 (13:20 +0000)]
Sort by added to preferences

19 years agoNo need to recalculate image for font change
amwaterhouse [Thu, 1 Sep 2005 13:19:28 +0000 (13:19 +0000)]
No need to recalculate image for font change

19 years agoRepaint scale panel after unselect all
amwaterhouse [Wed, 31 Aug 2005 16:54:30 +0000 (16:54 +0000)]
Repaint scale panel after unselect all

19 years agoMust update globalColourScheme with new consensus
amwaterhouse [Wed, 31 Aug 2005 16:53:40 +0000 (16:53 +0000)]
Must update globalColourScheme with new consensus

19 years ago2.05
amwaterhouse [Tue, 30 Aug 2005 16:30:33 +0000 (16:30 +0000)]
2.05

19 years agoUserColour gui modified
amwaterhouse [Tue, 30 Aug 2005 16:07:26 +0000 (16:07 +0000)]
UserColour gui modified

19 years agoMake 24 colours to be sure
amwaterhouse [Tue, 30 Aug 2005 15:26:14 +0000 (15:26 +0000)]
Make 24 colours to be sure

19 years agoValidate buttons and fire on mouse press, not mouse click
amwaterhouse [Tue, 30 Aug 2005 15:25:25 +0000 (15:25 +0000)]
Validate buttons and fire on mouse press, not mouse click

19 years agoSet user colours same as global
amwaterhouse [Tue, 30 Aug 2005 15:24:57 +0000 (15:24 +0000)]
Set user colours same as global

19 years agoRepaint annotations after edit
amwaterhouse [Tue, 30 Aug 2005 14:33:02 +0000 (14:33 +0000)]
Repaint annotations after edit

19 years agoWrapped, getWidth > vconsensus
amwaterhouse [Tue, 30 Aug 2005 14:11:11 +0000 (14:11 +0000)]
Wrapped, getWidth > vconsensus

19 years agoUpdate colours after remove left, cut, paste
amwaterhouse [Tue, 30 Aug 2005 12:46:34 +0000 (12:46 +0000)]
Update colours after remove left, cut, paste

19 years agoKeep mouse drag to 1 block when wrapped
amwaterhouse [Tue, 30 Aug 2005 11:35:55 +0000 (11:35 +0000)]
Keep mouse drag to 1 block when wrapped

19 years agoDont setSelected on new frames
amwaterhouse [Tue, 30 Aug 2005 11:24:44 +0000 (11:24 +0000)]
Dont setSelected on new frames

19 years agoOut of bounds checks
amwaterhouse [Tue, 30 Aug 2005 11:07:46 +0000 (11:07 +0000)]
Out of bounds checks

19 years agoSet startSeq 0 if wrap alignment
amwaterhouse [Tue, 30 Aug 2005 11:07:00 +0000 (11:07 +0000)]
Set startSeq 0 if wrap alignment

19 years agoDont set clip if its not null
amwaterhouse [Tue, 30 Aug 2005 10:34:25 +0000 (10:34 +0000)]
Dont set clip if its not null

19 years agoBounds checking
amwaterhouse [Tue, 30 Aug 2005 10:33:36 +0000 (10:33 +0000)]
Bounds checking

19 years agoIf Mac, dont use fastpaint Release_2_05
amwaterhouse [Tue, 30 Aug 2005 08:59:02 +0000 (08:59 +0000)]
If Mac, dont use fastpaint