jalview.git
19 years agolots of tidying in doco.
jprocter [Thu, 16 Jun 2005 17:39:14 +0000 (17:39 +0000)]
lots of tidying in doco.

19 years agoMoved to new repository
amwaterhouse [Thu, 16 Jun 2005 15:56:39 +0000 (15:56 +0000)]
Moved to new repository

19 years agomoved to new repository
amwaterhouse [Thu, 16 Jun 2005 15:54:10 +0000 (15:54 +0000)]
moved to new repository

19 years agoInstallAnywhere config
amwaterhouse [Thu, 16 Jun 2005 15:40:10 +0000 (15:40 +0000)]
InstallAnywhere config

19 years agobetter clustalw reference
jprocter [Thu, 16 Jun 2005 14:50:15 +0000 (14:50 +0000)]
better clustalw reference

19 years agoexport moved to its own file.
jprocter [Thu, 16 Jun 2005 14:21:55 +0000 (14:21 +0000)]
export moved to its own file.

19 years agoexport alignment
jprocter [Thu, 16 Jun 2005 14:21:35 +0000 (14:21 +0000)]
export alignment
graphics

19 years agoferedoxin startup alignment with a tree.
jprocter [Thu, 16 Jun 2005 14:14:04 +0000 (14:14 +0000)]
feredoxin startup alignment with a tree.

19 years agomore menu doco.
jprocter [Thu, 16 Jun 2005 13:50:34 +0000 (13:50 +0000)]
more menu doco.

19 years agodont add sequence twice to new group
amwaterhouse [Thu, 16 Jun 2005 13:32:02 +0000 (13:32 +0000)]
dont add sequence twice to new group

19 years agoSort Groups modified
amwaterhouse [Thu, 16 Jun 2005 13:31:23 +0000 (13:31 +0000)]
Sort Groups modified

19 years agodont convert to uppercase
amwaterhouse [Thu, 16 Jun 2005 09:48:26 +0000 (09:48 +0000)]
dont convert to uppercase

19 years agotextarea replaces textfield - can cut and paste sequence from seqpanel
amwaterhouse [Thu, 16 Jun 2005 09:35:21 +0000 (09:35 +0000)]
textarea replaces textfield - can cut and paste sequence from seqpanel

19 years agoremove gaps applies to selected area
amwaterhouse [Thu, 16 Jun 2005 09:34:31 +0000 (09:34 +0000)]
remove gaps applies to selected area

19 years agouse .jalview.uniprot.xml
amwaterhouse [Wed, 15 Jun 2005 15:06:22 +0000 (15:06 +0000)]
use .jalview.uniprot.xml

19 years agoCheck colours not null
amwaterhouse [Wed, 15 Jun 2005 15:05:22 +0000 (15:05 +0000)]
Check colours not null

19 years agocheck colourscheme is not null
amwaterhouse [Wed, 15 Jun 2005 15:04:28 +0000 (15:04 +0000)]
check colourscheme is not null

19 years agopaintrefresher
amwaterhouse [Wed, 15 Jun 2005 15:03:19 +0000 (15:03 +0000)]
paintrefresher

19 years agoadd/remove updated
amwaterhouse [Wed, 15 Jun 2005 15:02:30 +0000 (15:02 +0000)]
add/remove updated

19 years agoColumn selection changed
amwaterhouse [Wed, 15 Jun 2005 15:01:37 +0000 (15:01 +0000)]
Column selection changed

19 years agoREmove commented out lines
amwaterhouse [Wed, 15 Jun 2005 14:59:27 +0000 (14:59 +0000)]
REmove commented out lines

19 years agoallow for fastpaint
amwaterhouse [Wed, 15 Jun 2005 14:59:03 +0000 (14:59 +0000)]
allow for fastpaint

19 years agoadd / remove editable columns
amwaterhouse [Wed, 15 Jun 2005 14:56:59 +0000 (14:56 +0000)]
add / remove editable columns

19 years agoTooltip changed
amwaterhouse [Wed, 15 Jun 2005 14:55:41 +0000 (14:55 +0000)]
Tooltip changed

19 years agofirst jalarchive entry.
jprocter [Wed, 15 Jun 2005 13:05:55 +0000 (13:05 +0000)]
first jalarchive entry.

19 years agochange name of uniprot file
amwaterhouse [Tue, 14 Jun 2005 16:37:38 +0000 (16:37 +0000)]
change name of uniprot file

19 years agoadd version
amwaterhouse [Tue, 14 Jun 2005 16:37:10 +0000 (16:37 +0000)]
add version

19 years agoremove system.out
amwaterhouse [Tue, 14 Jun 2005 16:36:43 +0000 (16:36 +0000)]
remove system.out

19 years agode-os-specificised some bits. Commented the file association entries
jprocter [Tue, 14 Jun 2005 16:31:47 +0000 (16:31 +0000)]
de-os-specificised some bits. Commented the file association entries
in jnlp for the moment.

19 years agoremoves jarsign.
jprocter [Tue, 14 Jun 2005 16:29:59 +0000 (16:29 +0000)]
removes jarsign.

19 years agohelp file bits.
jprocter [Tue, 14 Jun 2005 16:29:21 +0000 (16:29 +0000)]
help file bits.

19 years agopad-1 gaps fixed.
jprocter [Tue, 14 Jun 2005 15:57:56 +0000 (15:57 +0000)]
pad-1 gaps fixed.

19 years agoslight modification to srs query so it takes both uniprot accessions and names
jprocter [Tue, 14 Jun 2005 15:44:32 +0000 (15:44 +0000)]
slight modification to srs query so it takes both uniprot accessions and names

19 years agoArbitrary decision to keep friendly id name when reading in uniprot headered fastA...
jprocter [Tue, 14 Jun 2005 15:44:03 +0000 (15:44 +0000)]
Arbitrary decision to keep friendly id name when reading in uniprot headered fastA files.

19 years agoupdate conservation colours after edit
amwaterhouse [Tue, 14 Jun 2005 15:06:34 +0000 (15:06 +0000)]
update conservation colours after edit

19 years agoToolTip updated
amwaterhouse [Tue, 14 Jun 2005 15:06:03 +0000 (15:06 +0000)]
ToolTip updated

19 years agoadd value to conservation mouseover
amwaterhouse [Tue, 14 Jun 2005 15:04:47 +0000 (15:04 +0000)]
add value to conservation mouseover

19 years agoif seq is null, dont check pdb
amwaterhouse [Tue, 14 Jun 2005 15:03:55 +0000 (15:03 +0000)]
if seq is null, dont check pdb

19 years agomouse pressed moved to mouseclicked
amwaterhouse [Tue, 14 Jun 2005 15:03:02 +0000 (15:03 +0000)]
mouse pressed moved to mouseclicked

19 years agoDeselect sets annotationPanel activeres null
amwaterhouse [Tue, 14 Jun 2005 15:02:08 +0000 (15:02 +0000)]
Deselect sets annotationPanel activeres null

19 years agoreset if clustalX colouring
amwaterhouse [Tue, 14 Jun 2005 15:01:21 +0000 (15:01 +0000)]
reset if clustalX colouring

19 years agoDont delete nextSeq
amwaterhouse [Tue, 14 Jun 2005 15:00:20 +0000 (15:00 +0000)]
Dont delete nextSeq

19 years agoPaintRefresher must be sent alignment
amwaterhouse [Tue, 14 Jun 2005 11:33:41 +0000 (11:33 +0000)]
PaintRefresher must be sent alignment

19 years agosuper.paintComponent
amwaterhouse [Tue, 14 Jun 2005 11:33:09 +0000 (11:33 +0000)]
super.paintComponent

19 years agoSet background colour of applet RGB
amwaterhouse [Tue, 14 Jun 2005 11:32:45 +0000 (11:32 +0000)]
Set background colour of applet RGB

19 years agoprotected now public
amwaterhouse [Tue, 14 Jun 2005 10:44:55 +0000 (10:44 +0000)]
protected now public

19 years agoDouble click to launch file browser
amwaterhouse [Tue, 14 Jun 2005 10:44:14 +0000 (10:44 +0000)]
Double click to launch file browser

19 years agotooltips instant (hopefully)
amwaterhouse [Tue, 14 Jun 2005 10:43:46 +0000 (10:43 +0000)]
tooltips instant (hopefully)

19 years agoNo spaces allowed in sequence name
amwaterhouse [Tue, 14 Jun 2005 10:41:52 +0000 (10:41 +0000)]
No spaces allowed in sequence name

19 years agoLoad/Save trees
amwaterhouse [Tue, 14 Jun 2005 10:41:25 +0000 (10:41 +0000)]
Load/Save trees

19 years agoReturns TreePanel when opening Newick
amwaterhouse [Tue, 14 Jun 2005 10:41:00 +0000 (10:41 +0000)]
Returns TreePanel when opening Newick

19 years agoSaves trees
amwaterhouse [Tue, 14 Jun 2005 10:40:13 +0000 (10:40 +0000)]
Saves trees

19 years agonull pointer fix.
jprocter [Mon, 13 Jun 2005 14:23:17 +0000 (14:23 +0000)]
null pointer fix.

19 years agouses paintrefresher
amwaterhouse [Mon, 13 Jun 2005 12:04:30 +0000 (12:04 +0000)]
uses paintrefresher

19 years agoclustal probs
amwaterhouse [Mon, 13 Jun 2005 12:04:01 +0000 (12:04 +0000)]
clustal probs

19 years agoquit saves screen size
amwaterhouse [Mon, 13 Jun 2005 11:35:41 +0000 (11:35 +0000)]
quit saves screen size

19 years agoUpdates checkboxes on load
amwaterhouse [Mon, 13 Jun 2005 11:34:56 +0000 (11:34 +0000)]
Updates checkboxes on load

19 years agoPaintRefresh changed
amwaterhouse [Mon, 13 Jun 2005 11:34:15 +0000 (11:34 +0000)]
PaintRefresh changed

19 years agoprotected now public
amwaterhouse [Mon, 13 Jun 2005 11:31:48 +0000 (11:31 +0000)]
protected now public

19 years agoQuit actionPerformed
amwaterhouse [Mon, 13 Jun 2005 11:30:00 +0000 (11:30 +0000)]
Quit actionPerformed

19 years agoGet colourScheme with seqs and width
amwaterhouse [Mon, 13 Jun 2005 11:28:11 +0000 (11:28 +0000)]
Get colourScheme with seqs and width

19 years agoSeqFetcher modified
amwaterhouse [Fri, 10 Jun 2005 13:22:09 +0000 (13:22 +0000)]
SeqFetcher modified

19 years agoremove imports
amwaterhouse [Fri, 10 Jun 2005 13:21:30 +0000 (13:21 +0000)]
remove imports

19 years agoFastpaint is false initially
amwaterhouse [Fri, 10 Jun 2005 13:19:23 +0000 (13:19 +0000)]
Fastpaint is false initially

19 years agolatest
amwaterhouse [Fri, 10 Jun 2005 12:53:24 +0000 (12:53 +0000)]
latest

19 years agoadded logs.Castor.level
jprocter [Fri, 10 Jun 2005 09:43:25 +0000 (09:43 +0000)]
added logs.Castor.level

19 years agoadded castor logger configuration.
jprocter [Fri, 10 Jun 2005 09:42:32 +0000 (09:42 +0000)]
added castor logger configuration.

19 years agoRemove imports
amwaterhouse [Fri, 10 Jun 2005 09:26:50 +0000 (09:26 +0000)]
Remove imports

19 years agoset conservation/consensus in constructor
amwaterhouse [Fri, 10 Jun 2005 08:53:51 +0000 (08:53 +0000)]
set conservation/consensus in constructor

19 years agoremoved exception name from server error state (to not alarm the casual user).
jprocter [Fri, 10 Jun 2005 07:27:03 +0000 (07:27 +0000)]
removed exception name from server error state (to not alarm the casual user).

19 years agoremoved
amwaterhouse [Thu, 9 Jun 2005 16:29:54 +0000 (16:29 +0000)]
removed

19 years agodeleted
amwaterhouse [Thu, 9 Jun 2005 16:28:48 +0000 (16:28 +0000)]
deleted

19 years agomoved from lib
amwaterhouse [Thu, 9 Jun 2005 16:27:31 +0000 (16:27 +0000)]
moved from lib

19 years agofor obfuscating
amwaterhouse [Thu, 9 Jun 2005 16:27:10 +0000 (16:27 +0000)]
for obfuscating

19 years agoneeded for applet search
amwaterhouse [Thu, 9 Jun 2005 15:29:47 +0000 (15:29 +0000)]
needed for applet search

19 years agoBuild Applet added
amwaterhouse [Thu, 9 Jun 2005 15:24:21 +0000 (15:24 +0000)]
Build Applet added

19 years agoMonospaced
amwaterhouse [Thu, 9 Jun 2005 10:02:08 +0000 (10:02 +0000)]
Monospaced

19 years agoWarn if Textarea limit has been reached
amwaterhouse [Thu, 9 Jun 2005 09:58:53 +0000 (09:58 +0000)]
Warn if Textarea limit has been reached

19 years agoreplace space
amwaterhouse [Wed, 8 Jun 2005 17:06:55 +0000 (17:06 +0000)]
replace space

19 years agogroup recalc conserve
amwaterhouse [Wed, 8 Jun 2005 16:37:43 +0000 (16:37 +0000)]
group recalc conserve

19 years agorecalc group conserve
amwaterhouse [Wed, 8 Jun 2005 16:36:57 +0000 (16:36 +0000)]
recalc group conserve

19 years agoif missing forward slash
amwaterhouse [Wed, 8 Jun 2005 16:23:11 +0000 (16:23 +0000)]
if missing forward slash

19 years agoRecalc accelerated
amwaterhouse [Wed, 8 Jun 2005 16:22:17 +0000 (16:22 +0000)]
Recalc accelerated

19 years agostyle change.
jprocter [Wed, 8 Jun 2005 15:35:54 +0000 (15:35 +0000)]
style change.

19 years agoheading
jprocter [Wed, 8 Jun 2005 15:32:53 +0000 (15:32 +0000)]
heading

19 years agopunctuation (sorry ;-)
jprocter [Wed, 8 Jun 2005 15:28:10 +0000 (15:28 +0000)]
punctuation (sorry ;-)

19 years agogrammar.
jprocter [Wed, 8 Jun 2005 15:27:50 +0000 (15:27 +0000)]
grammar.

19 years agounterminated ul
jprocter [Wed, 8 Jun 2005 15:18:24 +0000 (15:18 +0000)]
unterminated ul

19 years agonicer help.
jprocter [Wed, 8 Jun 2005 14:21:25 +0000 (14:21 +0000)]
nicer help.

19 years agoSets sequence features
amwaterhouse [Wed, 8 Jun 2005 14:20:21 +0000 (14:20 +0000)]
Sets sequence features

19 years agospelling
amwaterhouse [Wed, 8 Jun 2005 14:10:02 +0000 (14:10 +0000)]
spelling

19 years agoSpelling
amwaterhouse [Wed, 8 Jun 2005 14:09:02 +0000 (14:09 +0000)]
Spelling

19 years agoFormatted source
amwaterhouse [Wed, 8 Jun 2005 13:41:35 +0000 (13:41 +0000)]
Formatted source

19 years agoGPL
amwaterhouse [Wed, 8 Jun 2005 13:22:22 +0000 (13:22 +0000)]
GPL

19 years agoGPL license added
amwaterhouse [Wed, 8 Jun 2005 13:14:54 +0000 (13:14 +0000)]
GPL license added

19 years ago*** empty log message ***
amwaterhouse [Wed, 8 Jun 2005 13:12:26 +0000 (13:12 +0000)]
*** empty log message ***

19 years agoAdd email to about
amwaterhouse [Wed, 8 Jun 2005 12:32:30 +0000 (12:32 +0000)]
Add email to about

19 years agomore truthful comment.
jprocter [Tue, 7 Jun 2005 17:06:07 +0000 (17:06 +0000)]
more truthful comment.

19 years agoquickie build instructions.
jprocter [Tue, 7 Jun 2005 13:39:15 +0000 (13:39 +0000)]
quickie  build instructions.

19 years agovery basic code convention. no licensing/stripping yet.
jprocter [Tue, 7 Jun 2005 13:20:11 +0000 (13:20 +0000)]
very basic code convention. no licensing/stripping yet.