jalview.git
18 years agoafter merge
amwaterhouse [Tue, 6 Dec 2005 11:46:19 +0000 (11:46 +0000)]
after merge

18 years agoAfter merge
amwaterhouse [Tue, 6 Dec 2005 11:42:19 +0000 (11:42 +0000)]
After merge

18 years agoAfter branch merge
amwaterhouse [Tue, 6 Dec 2005 11:41:09 +0000 (11:41 +0000)]
After branch merge

18 years agoPDB structure viewer updated
amwaterhouse [Tue, 6 Dec 2005 11:40:04 +0000 (11:40 +0000)]
PDB structure viewer updated

18 years agoSaves features
amwaterhouse [Tue, 6 Dec 2005 11:38:11 +0000 (11:38 +0000)]
Saves features

18 years agoNew help files
amwaterhouse [Tue, 6 Dec 2005 11:37:08 +0000 (11:37 +0000)]
New help files

19 years agoFixed bug http://dragonfly.compbio.dundee.ac.uk/mantis/view.php?id=9326 for viewing...
jprocter [Fri, 18 Nov 2005 16:07:41 +0000 (16:07 +0000)]
Fixed bug dragonfly.compbio.dundee.ac.uk/mantis/view.php?id=9326 for viewing trees without explicit distances. made sure trees output from treeviewer contain only as much information (distance, bootstraps, etc) as was read in from original tree file (or algorithm).

19 years agoadded 3 letter IUB codes for ambiguous residues/bases
jprocter [Fri, 18 Nov 2005 13:30:08 +0000 (13:30 +0000)]
added 3 letter IUB codes for ambiguous residues/bases

19 years agocomma separated rgb values
amwaterhouse [Fri, 7 Oct 2005 10:24:56 +0000 (10:24 +0000)]
comma separated rgb values

19 years agogetalignment method added
amwaterhouse [Fri, 7 Oct 2005 10:24:23 +0000 (10:24 +0000)]
getalignment method added

19 years agoQuick fix for reading sequence
amwaterhouse [Fri, 7 Oct 2005 10:23:28 +0000 (10:23 +0000)]
Quick fix for reading sequence

19 years agoSelect all cutandpaste
amwaterhouse [Fri, 7 Oct 2005 10:22:57 +0000 (10:22 +0000)]
Select all cutandpaste

19 years agoDon't exit if file not found and not headless
amwaterhouse [Fri, 7 Oct 2005 10:20:49 +0000 (10:20 +0000)]
Don't exit if file not found and not headless

19 years agoSequence start end added for the time being
amwaterhouse [Wed, 5 Oct 2005 12:34:32 +0000 (12:34 +0000)]
Sequence start end added for the time being

19 years agoRemove float width
amwaterhouse [Mon, 3 Oct 2005 16:14:54 +0000 (16:14 +0000)]
Remove float width

19 years agoRequest focus for new frames
amwaterhouse [Mon, 3 Oct 2005 11:08:22 +0000 (11:08 +0000)]
Request focus for new frames

19 years agoReturn if no searchString
amwaterhouse [Mon, 3 Oct 2005 11:07:55 +0000 (11:07 +0000)]
Return if no searchString

19 years agoKeylistener added to internalFrame
amwaterhouse [Mon, 3 Oct 2005 11:07:40 +0000 (11:07 +0000)]
Keylistener added to internalFrame

19 years agoRemove development code
amwaterhouse [Mon, 3 Oct 2005 10:30:04 +0000 (10:30 +0000)]
Remove development code

19 years agoRemove redundancy from eclipse
amwaterhouse [Mon, 3 Oct 2005 08:33:08 +0000 (08:33 +0000)]
Remove redundancy from eclipse

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