jalview.git
19 years agoRemove redundancy from Eclipse
amwaterhouse [Fri, 30 Sep 2005 17:18:41 +0000 (17:18 +0000)]
Remove redundancy from Eclipse

19 years agoRestore file before eclipse changes
amwaterhouse [Fri, 30 Sep 2005 17:18:22 +0000 (17:18 +0000)]
Restore file before eclipse changes

19 years agoRemove redundancy in Eclipse
amwaterhouse [Fri, 30 Sep 2005 17:03:03 +0000 (17:03 +0000)]
Remove redundancy in Eclipse

19 years agoTake into account scroll value
amwaterhouse [Thu, 29 Sep 2005 16:11:50 +0000 (16:11 +0000)]
Take into account scroll value

19 years agouse lower case home.png Release_2_06
amwaterhouse [Wed, 28 Sep 2005 16:54:08 +0000 (16:54 +0000)]
use lower case home.png

19 years agoApplet frame name
amwaterhouse [Wed, 28 Sep 2005 16:53:46 +0000 (16:53 +0000)]
Applet frame name

19 years agoSet frame size each applet
amwaterhouse [Wed, 28 Sep 2005 16:13:09 +0000 (16:13 +0000)]
Set frame size each applet

19 years agoRemove latestVersion if null
amwaterhouse [Wed, 28 Sep 2005 15:42:18 +0000 (15:42 +0000)]
Remove latestVersion if null

19 years agoRemove latestVersion if null
amwaterhouse [Wed, 28 Sep 2005 15:39:51 +0000 (15:39 +0000)]
Remove latestVersion if null

19 years ago2.06
amwaterhouse [Wed, 28 Sep 2005 15:08:50 +0000 (15:08 +0000)]
2.06

19 years agoPut clip back in
amwaterhouse [Wed, 28 Sep 2005 15:07:04 +0000 (15:07 +0000)]
Put clip back in

19 years agoChange font
amwaterhouse [Wed, 28 Sep 2005 14:55:06 +0000 (14:55 +0000)]
Change font

19 years agoMore features for PCA
amwaterhouse [Wed, 28 Sep 2005 14:54:23 +0000 (14:54 +0000)]
More features for PCA

19 years agoWrap alignment with annotations
amwaterhouse [Wed, 28 Sep 2005 14:54:03 +0000 (14:54 +0000)]
Wrap alignment with annotations

19 years agoNew params
amwaterhouse [Wed, 28 Sep 2005 14:53:45 +0000 (14:53 +0000)]
New params

19 years agoShow labels in wrapped view
amwaterhouse [Tue, 27 Sep 2005 14:16:59 +0000 (14:16 +0000)]
Show labels in wrapped view

19 years agoDraw labels, anti alias
amwaterhouse [Fri, 23 Sep 2005 16:18:02 +0000 (16:18 +0000)]
Draw labels, anti alias

19 years agoCapture output as details
amwaterhouse [Fri, 23 Sep 2005 16:17:33 +0000 (16:17 +0000)]
Capture output as details

19 years agoRight click copy/paste popup
amwaterhouse [Fri, 23 Sep 2005 16:17:12 +0000 (16:17 +0000)]
Right click copy/paste popup

19 years agoNow an InternalFrame with menus
amwaterhouse [Fri, 23 Sep 2005 16:16:53 +0000 (16:16 +0000)]
Now an InternalFrame with menus

19 years agoSetAnnotationVisible - ignore if wrapped
amwaterhouse [Thu, 22 Sep 2005 16:04:51 +0000 (16:04 +0000)]
SetAnnotationVisible - ignore if wrapped

19 years agoCreate Instance of FormatAdapter
amwaterhouse [Thu, 22 Sep 2005 15:53:18 +0000 (15:53 +0000)]
Create Instance of FormatAdapter

19 years agoDont calculate conservation for nucleotides
amwaterhouse [Thu, 22 Sep 2005 15:52:52 +0000 (15:52 +0000)]
Dont calculate conservation for nucleotides

19 years agoisNucleotide
amwaterhouse [Thu, 22 Sep 2005 15:50:47 +0000 (15:50 +0000)]
isNucleotide

19 years agoCreate instance of FormatAdapter
amwaterhouse [Thu, 22 Sep 2005 15:49:51 +0000 (15:49 +0000)]
Create instance of FormatAdapter

19 years agoAdd nucleotide names
amwaterhouse [Thu, 22 Sep 2005 15:49:21 +0000 (15:49 +0000)]
Add nucleotide names

19 years agoDisplay nucleotides
amwaterhouse [Thu, 22 Sep 2005 15:49:05 +0000 (15:49 +0000)]
Display nucleotides

19 years agoBreak if regex not found
amwaterhouse [Thu, 22 Sep 2005 15:48:39 +0000 (15:48 +0000)]
Break if regex not found

19 years agoIf Mac user hasnt selected file format, give warning
amwaterhouse [Thu, 22 Sep 2005 13:23:38 +0000 (13:23 +0000)]
If Mac user hasnt selected file format, give warning

19 years agoWrap alignment with annotations
amwaterhouse [Thu, 22 Sep 2005 13:23:07 +0000 (13:23 +0000)]
Wrap alignment with annotations

19 years agoCheck if filefilter is null
amwaterhouse [Thu, 22 Sep 2005 13:21:51 +0000 (13:21 +0000)]
Check if filefilter is null

19 years agoJalview
amwaterhouse [Wed, 21 Sep 2005 17:09:14 +0000 (17:09 +0000)]
Jalview

19 years agoSequences must be aligned before PCA
amwaterhouse [Wed, 21 Sep 2005 17:08:56 +0000 (17:08 +0000)]
Sequences must be aligned before PCA

19 years agoNext active Frame losing focus bug fixed
amwaterhouse [Wed, 21 Sep 2005 17:07:57 +0000 (17:07 +0000)]
Next active Frame losing focus bug fixed

19 years agoUse gtk icons
amwaterhouse [Tue, 20 Sep 2005 14:17:32 +0000 (14:17 +0000)]
Use gtk icons

19 years agoGTK icons
amwaterhouse [Tue, 20 Sep 2005 14:17:15 +0000 (14:17 +0000)]
GTK icons

19 years agoAdd carriage return after memory settings
amwaterhouse [Tue, 20 Sep 2005 14:17:01 +0000 (14:17 +0000)]
Add carriage return after memory settings

19 years agoChecks end of sequence before drawing text
amwaterhouse [Tue, 20 Sep 2005 13:21:39 +0000 (13:21 +0000)]
Checks end of sequence before drawing text

19 years agoFormat label left align
amwaterhouse [Tue, 20 Sep 2005 13:21:13 +0000 (13:21 +0000)]
Format label left align

19 years agoOptimise copy image
amwaterhouse [Tue, 20 Sep 2005 13:20:53 +0000 (13:20 +0000)]
Optimise copy image

19 years agoPCAPanel checks viewport selection group
amwaterhouse [Tue, 20 Sep 2005 13:20:37 +0000 (13:20 +0000)]
PCAPanel checks viewport selection group

19 years agoPCAPanel checks viewport selection
amwaterhouse [Tue, 20 Sep 2005 13:19:33 +0000 (13:19 +0000)]
PCAPanel checks viewport selection

19 years agoPCAPanel just requires viewport
amwaterhouse [Tue, 20 Sep 2005 13:19:07 +0000 (13:19 +0000)]
PCAPanel just requires viewport

19 years agoHelp gets bounds from help map file
amwaterhouse [Tue, 20 Sep 2005 13:17:05 +0000 (13:17 +0000)]
Help gets bounds from help map file

19 years agoNew methods in treePanel
amwaterhouse [Tue, 20 Sep 2005 13:16:09 +0000 (13:16 +0000)]
New methods in treePanel

19 years agoNull pointer if user presses shift before anything else
amwaterhouse [Tue, 20 Sep 2005 13:15:31 +0000 (13:15 +0000)]
Null pointer if user presses shift before anything else

19 years agoAlign labels format left
amwaterhouse [Tue, 20 Sep 2005 13:14:09 +0000 (13:14 +0000)]
Align labels format left

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