jalview.git
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.

19 years agobetter code convention name
jprocter [Tue, 7 Jun 2005 13:18:18 +0000 (13:18 +0000)]
better code convention name

19 years agojalopy is used for sourcescrub target of build.xml (sourcescrub is not
jprocter [Tue, 7 Jun 2005 13:09:41 +0000 (13:09 +0000)]
jalopy is used for sourcescrub target of build.xml (sourcescrub is not
a standard target name;-)

19 years agoremoved signature for this jar
jprocter [Tue, 7 Jun 2005 13:04:30 +0000 (13:04 +0000)]
removed signature for this jar

19 years agoloads of changes. Jalopy source formatting, better WS client build (but still not...
jprocter [Tue, 7 Jun 2005 13:02:44 +0000 (13:02 +0000)]
loads of changes. Jalopy source formatting, better WS client build (but still not automatic) and jar building (still not optimised yet).

19 years agoadded a couple of debug statements for unix browser launching problems.
jprocter [Tue, 7 Jun 2005 13:01:39 +0000 (13:01 +0000)]
added a couple of debug statements for unix browser launching problems.

19 years agocloses if accepted
amwaterhouse [Mon, 6 Jun 2005 10:00:32 +0000 (10:00 +0000)]
closes if accepted

19 years agomade error for browser configuration on unix a bit easier to see.
jprocter [Sun, 5 Jun 2005 17:38:38 +0000 (17:38 +0000)]
made error for browser configuration on unix a bit easier to see.

19 years agofirefox now default for unixen.
jprocter [Sun, 5 Jun 2005 17:36:38 +0000 (17:36 +0000)]
firefox now default for unixen.

19 years agomore subtle rearrangements
jprocter [Sun, 5 Jun 2005 17:01:52 +0000 (17:01 +0000)]
more subtle rearrangements

19 years agoReinstated 'create tree from selected region only' with better indication that only...
jprocter [Fri, 3 Jun 2005 13:16:56 +0000 (13:16 +0000)]
Reinstated 'create tree from selected region only' with better indication that only part of an alignment was used to calculate the tree.

19 years agotidied the exceptions and ws server error behaviour
jprocter [Thu, 2 Jun 2005 15:27:20 +0000 (15:27 +0000)]
tidied the exceptions and ws server error behaviour

19 years agoMenus
amwaterhouse [Thu, 2 Jun 2005 14:56:31 +0000 (14:56 +0000)]
Menus

19 years agonew
amwaterhouse [Thu, 2 Jun 2005 12:28:08 +0000 (12:28 +0000)]
new

19 years ago*** empty log message ***
amwaterhouse [Thu, 2 Jun 2005 12:24:29 +0000 (12:24 +0000)]
*** empty log message ***

19 years agoWarn if URL not found
amwaterhouse [Thu, 2 Jun 2005 11:07:20 +0000 (11:07 +0000)]
Warn if URL not found

19 years agoCut and paste changed
amwaterhouse [Thu, 2 Jun 2005 11:06:56 +0000 (11:06 +0000)]
Cut and paste changed

19 years agoReverse order for windows, readin from url
amwaterhouse [Thu, 2 Jun 2005 11:06:21 +0000 (11:06 +0000)]
Reverse order for windows, readin from url

19 years agostartup file is jalview.org
amwaterhouse [Thu, 2 Jun 2005 11:05:08 +0000 (11:05 +0000)]
startup file is jalview.org

19 years agoName of xml file changed
amwaterhouse [Thu, 2 Jun 2005 11:04:04 +0000 (11:04 +0000)]
Name of xml file changed

19 years agoCheck startup file is not null
amwaterhouse [Thu, 2 Jun 2005 11:02:59 +0000 (11:02 +0000)]
Check startup file is not null

19 years agominor changes to make jalopy happy
jprocter [Thu, 2 Jun 2005 10:16:36 +0000 (10:16 +0000)]
minor changes to make jalopy happy

19 years agominor changes to try and make jalopy happy
jprocter [Thu, 2 Jun 2005 10:16:13 +0000 (10:16 +0000)]
minor changes to try and make jalopy happy

19 years agoMoved comment so it doesn't break jalopy (this is not good!)
jprocter [Tue, 31 May 2005 16:39:57 +0000 (16:39 +0000)]
Moved comment so it doesn't break jalopy (this is not good!)

19 years agoadded the sorting entry to calculations, and corrected the PID
jprocter [Mon, 30 May 2005 17:02:34 +0000 (17:02 +0000)]
added the sorting entry to calculations, and corrected the PID
ordering and the redundancy calculation help description.

19 years agoChanged sortByPID to use the gapped PID function.
jprocter [Mon, 30 May 2005 16:38:44 +0000 (16:38 +0000)]
Changed sortByPID to use the gapped PID function.

19 years agocomments
jprocter [Mon, 30 May 2005 16:33:29 +0000 (16:33 +0000)]
comments

19 years agoAdded clustalW 'realignment' (primitive)
jprocter [Mon, 30 May 2005 16:10:11 +0000 (16:10 +0000)]
Added clustalW 'realignment' (primitive)

19 years agoadded default ClustalWS or MuscleWS to remove gaps.
jprocter [Mon, 30 May 2005 15:47:36 +0000 (15:47 +0000)]
added default ClustalWS or MuscleWS to remove gaps.

19 years agopropagated use of jalview.util.GapChars for gap removal.
jprocter [Mon, 30 May 2005 15:46:56 +0000 (15:46 +0000)]
propagated use of jalview.util.GapChars for gap removal.

19 years agomore robust parsing for DBset/DBname|id1|id2 type ids
jprocter [Mon, 30 May 2005 14:58:53 +0000 (14:58 +0000)]
more robust parsing for DBset/DBname|id1|id2 type ids

19 years agomodified history for redundancy removal.
jprocter [Mon, 30 May 2005 11:04:29 +0000 (11:04 +0000)]
modified history for redundancy removal.

19 years agofixed stacktrace potential for pairwise alignment action.
jprocter [Mon, 30 May 2005 11:03:27 +0000 (11:03 +0000)]
fixed stacktrace potential for pairwise alignment action.

19 years agoModified output on stdout for similarity matrix.
jprocter [Mon, 30 May 2005 11:01:57 +0000 (11:01 +0000)]
Modified output on stdout for similarity matrix.

19 years agoimages moved
amwaterhouse [Fri, 27 May 2005 15:54:33 +0000 (15:54 +0000)]
images moved