jalview.git
19 years agoThe archetypal Multiple Sequence Alignment Web Service
jprocter [Thu, 19 May 2005 14:08:37 +0000 (14:08 +0000)]
The archetypal Multiple Sequence Alignment Web Service

19 years agoconservation removed
amwaterhouse [Thu, 12 May 2005 09:09:44 +0000 (09:09 +0000)]
conservation removed

19 years agoseparator added
amwaterhouse [Thu, 12 May 2005 09:09:19 +0000 (09:09 +0000)]
separator added

19 years agocorrections for find when edit takes place
amwaterhouse [Thu, 12 May 2005 09:08:34 +0000 (09:08 +0000)]
corrections for find when edit takes place

19 years agoJalviewApplet jbuilder project
amwaterhouse [Wed, 11 May 2005 10:44:04 +0000 (10:44 +0000)]
JalviewApplet jbuilder project

19 years agooutput newick to textbox
amwaterhouse [Wed, 11 May 2005 10:42:18 +0000 (10:42 +0000)]
output newick to textbox

19 years agoreads in treeFile from applet parameter
amwaterhouse [Wed, 11 May 2005 10:40:48 +0000 (10:40 +0000)]
reads in treeFile from applet parameter

19 years agopaintComponent. not paint
amwaterhouse [Mon, 9 May 2005 11:02:57 +0000 (11:02 +0000)]
paintComponent. not paint

19 years agocorrect conservation errors after edit
amwaterhouse [Mon, 9 May 2005 11:02:00 +0000 (11:02 +0000)]
correct conservation errors after edit

19 years agoif imgWidth <0
amwaterhouse [Mon, 9 May 2005 11:00:34 +0000 (11:00 +0000)]
if imgWidth <0

19 years agowrap align correction for last row
amwaterhouse [Fri, 6 May 2005 17:07:02 +0000 (17:07 +0000)]
wrap align correction for last row

19 years agoadd 1 to fastPaint, in case seqs of different length
amwaterhouse [Fri, 6 May 2005 12:35:41 +0000 (12:35 +0000)]
add 1 to fastPaint, in case seqs of different length

19 years agoif clustal + edit, make new clustal
amwaterhouse [Fri, 6 May 2005 12:34:47 +0000 (12:34 +0000)]
if clustal + edit, make new clustal

19 years agopdb end seq and startseq determined here
amwaterhouse [Thu, 5 May 2005 13:25:49 +0000 (13:25 +0000)]
pdb end seq and startseq determined here

19 years agocolour by sequence just about works
amwaterhouse [Thu, 5 May 2005 13:25:12 +0000 (13:25 +0000)]
colour by sequence just about works

19 years agoAccelerator on menu takes care of actionkey
amwaterhouse [Thu, 5 May 2005 13:24:28 +0000 (13:24 +0000)]
Accelerator on menu takes care of actionkey

19 years agoAdded cancel interface for JPred Client and fixed some messages.
jprocter [Thu, 5 May 2005 13:16:39 +0000 (13:16 +0000)]
Added cancel interface for JPred Client and fixed some messages.

19 years agoMoved tree leafname to alignment set matching into SequenceIdMatcher class for
jprocter [Thu, 5 May 2005 13:15:25 +0000 (13:15 +0000)]
Moved tree leafname to alignment set matching into SequenceIdMatcher class for
use in other contexts.

19 years ago<No Comment Entered>
jprocter [Thu, 5 May 2005 11:40:24 +0000 (11:40 +0000)]
<No Comment Entered>

19 years agosaveAs .....
amwaterhouse [Thu, 5 May 2005 11:21:59 +0000 (11:21 +0000)]
saveAs .....

19 years agosaveAsNewick
amwaterhouse [Thu, 5 May 2005 11:21:42 +0000 (11:21 +0000)]
saveAsNewick

19 years agomoved to jalview.io
amwaterhouse [Thu, 5 May 2005 10:36:19 +0000 (10:36 +0000)]
moved to jalview.io

19 years agonew place for sequencefeaturefetcher
amwaterhouse [Thu, 5 May 2005 10:35:44 +0000 (10:35 +0000)]
new place for sequencefeaturefetcher

19 years agosend rotCanvas sequence and viewport
amwaterhouse [Thu, 5 May 2005 10:35:00 +0000 (10:35 +0000)]
send rotCanvas sequence and viewport

19 years agopdbfile details not essential to sequence
amwaterhouse [Thu, 5 May 2005 10:34:02 +0000 (10:34 +0000)]
pdbfile details not essential to sequence

19 years agoaddelement replaces add
amwaterhouse [Thu, 5 May 2005 08:54:37 +0000 (08:54 +0000)]
addelement replaces add

19 years agoadded remark about right mouse in awt
amwaterhouse [Wed, 4 May 2005 16:00:13 +0000 (16:00 +0000)]
added remark about right mouse in awt

19 years agovalidate and repaint after changing panels
amwaterhouse [Wed, 4 May 2005 15:59:50 +0000 (15:59 +0000)]
validate and repaint after changing panels

19 years agomouse listeners added
amwaterhouse [Wed, 4 May 2005 15:59:27 +0000 (15:59 +0000)]
mouse listeners added

19 years agorenderer removed
amwaterhouse [Wed, 4 May 2005 15:22:42 +0000 (15:22 +0000)]
renderer removed

19 years agono need to send pid, seqnum
amwaterhouse [Wed, 4 May 2005 15:22:13 +0000 (15:22 +0000)]
no need to send pid, seqnum

19 years agoSequenceRenderer changes
amwaterhouse [Wed, 4 May 2005 15:21:38 +0000 (15:21 +0000)]
SequenceRenderer changes

19 years agono need to send vector pid or seqnum
amwaterhouse [Wed, 4 May 2005 15:20:50 +0000 (15:20 +0000)]
no need to send vector pid or seqnum

19 years agoNo need for this interface
amwaterhouse [Wed, 4 May 2005 15:20:12 +0000 (15:20 +0000)]
No need for this interface

19 years agoApplet files
amwaterhouse [Wed, 4 May 2005 15:10:21 +0000 (15:10 +0000)]
Applet files

19 years agoBetter treatment of error states and cancellability in wsclient.
jprocter [Tue, 3 May 2005 13:20:27 +0000 (13:20 +0000)]
Better treatment of error states and cancellability in wsclient.

19 years agoformatAdapter.formatSequences and maintain annotation after undo
amwaterhouse [Tue, 3 May 2005 12:49:40 +0000 (12:49 +0000)]
formatAdapter.formatSequences and maintain annotation after undo

19 years agoformatAdapter.formats
amwaterhouse [Tue, 3 May 2005 12:48:35 +0000 (12:48 +0000)]
formatAdapter.formats

19 years agoformatAdapter.readFile
amwaterhouse [Tue, 3 May 2005 12:48:08 +0000 (12:48 +0000)]
formatAdapter.readFile

19 years agochange Container to Component
amwaterhouse [Tue, 3 May 2005 12:47:18 +0000 (12:47 +0000)]
change Container to Component

19 years agoformatAdapter.formats, remove redundant code
amwaterhouse [Tue, 3 May 2005 12:46:13 +0000 (12:46 +0000)]
formatAdapter.formats, remove redundant code

19 years ago1.1 compatible, formatting changes
amwaterhouse [Tue, 3 May 2005 12:43:54 +0000 (12:43 +0000)]
1.1 compatible, formatting changes

19 years agoFormatAdapter readFile
amwaterhouse [Tue, 3 May 2005 12:42:25 +0000 (12:42 +0000)]
FormatAdapter readFile

19 years ago1.1 compatible
amwaterhouse [Tue, 3 May 2005 12:41:39 +0000 (12:41 +0000)]
1.1 compatible

19 years agofindKmers and fetchSequenceFeatures removed
amwaterhouse [Tue, 3 May 2005 12:39:06 +0000 (12:39 +0000)]
findKmers and fetchSequenceFeatures removed

19 years agoRemoved as obfuscation of classes wiill change class names
amwaterhouse [Tue, 3 May 2005 12:38:04 +0000 (12:38 +0000)]
Removed as obfuscation of classes wiill change class names

19 years agoselects default colour
amwaterhouse [Fri, 29 Apr 2005 15:27:31 +0000 (15:27 +0000)]
selects default colour

19 years agojust tidying up unused imports
amwaterhouse [Fri, 29 Apr 2005 15:26:51 +0000 (15:26 +0000)]
just tidying up unused imports

19 years agostopped duplicate jars appearing in jalview.jar
jprocter [Fri, 29 Apr 2005 14:50:01 +0000 (14:50 +0000)]
stopped duplicate jars appearing in jalview.jar
beginning of 'automatic ws client' generation.

19 years agoREad in defaultColour
amwaterhouse [Fri, 29 Apr 2005 11:05:11 +0000 (11:05 +0000)]
REad in defaultColour

19 years agopreferences held statically
amwaterhouse [Fri, 29 Apr 2005 10:42:48 +0000 (10:42 +0000)]
preferences held statically

19 years agopreferences moved to desktop
amwaterhouse [Fri, 29 Apr 2005 10:41:47 +0000 (10:41 +0000)]
preferences moved to desktop

19 years agoread in preferences at start up
amwaterhouse [Fri, 29 Apr 2005 10:40:43 +0000 (10:40 +0000)]
read in preferences at start up

19 years agoAdded MuscleWS back in
jprocter [Thu, 28 Apr 2005 16:15:18 +0000 (16:15 +0000)]
Added MuscleWS back in

19 years agoFirst try with MuscleWS and vamsas.simple.objects
jprocter [Thu, 28 Apr 2005 15:50:11 +0000 (15:50 +0000)]
First try with MuscleWS and vamsas.simple.objects

19 years agoFirst try with MuscleWS
jprocter [Thu, 28 Apr 2005 15:46:32 +0000 (15:46 +0000)]
First try with MuscleWS

19 years agono longer used
amwaterhouse [Thu, 28 Apr 2005 15:44:35 +0000 (15:44 +0000)]
no longer used

19 years agoLabel changes as AF recommended
amwaterhouse [Thu, 28 Apr 2005 15:42:34 +0000 (15:42 +0000)]
Label changes as AF recommended

19 years agomust set consensus in child colourscheme
amwaterhouse [Thu, 28 Apr 2005 15:41:58 +0000 (15:41 +0000)]
must set consensus in child colourscheme

19 years agoUpdated for use by preferences panel
amwaterhouse [Thu, 28 Apr 2005 15:41:34 +0000 (15:41 +0000)]
Updated for use by preferences panel

19 years agoGUI changes
amwaterhouse [Thu, 28 Apr 2005 15:35:30 +0000 (15:35 +0000)]
GUI changes

19 years agoPreferences panel added
amwaterhouse [Thu, 28 Apr 2005 15:33:56 +0000 (15:33 +0000)]
Preferences panel added

19 years agoViewport now looks at preferences when loading up
amwaterhouse [Thu, 28 Apr 2005 15:33:12 +0000 (15:33 +0000)]
Viewport now looks at preferences when loading up

19 years agoSet fullscreen if in preferences
amwaterhouse [Thu, 28 Apr 2005 15:32:28 +0000 (15:32 +0000)]
Set fullscreen if in preferences

19 years agocan search ids
amwaterhouse [Thu, 28 Apr 2005 15:31:43 +0000 (15:31 +0000)]
can search ids

19 years agoset as default added
amwaterhouse [Thu, 28 Apr 2005 15:31:28 +0000 (15:31 +0000)]
set as default added

19 years agosearch ids added
amwaterhouse [Thu, 28 Apr 2005 15:31:09 +0000 (15:31 +0000)]
search ids added

19 years agoMenu names changed
amwaterhouse [Thu, 28 Apr 2005 15:30:28 +0000 (15:30 +0000)]
Menu names changed

19 years agoJInternalFrame is within class. Method to load default added
amwaterhouse [Thu, 28 Apr 2005 15:29:54 +0000 (15:29 +0000)]
JInternalFrame is within class. Method to load default added

19 years agoPreferences panel added
amwaterhouse [Thu, 28 Apr 2005 15:28:28 +0000 (15:28 +0000)]
Preferences panel added

19 years agoset gap char modified
amwaterhouse [Thu, 28 Apr 2005 15:27:57 +0000 (15:27 +0000)]
set gap char modified

19 years agoadded MuscleWS and did a bit more standardisation of WS threads.
jprocter [Thu, 28 Apr 2005 14:28:43 +0000 (14:28 +0000)]
added MuscleWS and did a bit more standardisation of WS threads.

19 years agoif applet, load properties in void init
amwaterhouse [Mon, 25 Apr 2005 16:50:52 +0000 (16:50 +0000)]
if applet, load properties in void init

19 years ago+1 in fastpaint sends coloured text outofbounds
amwaterhouse [Mon, 25 Apr 2005 16:50:27 +0000 (16:50 +0000)]
+1 in fastpaint sends coloured text outofbounds

19 years agodont update overview every repaint
amwaterhouse [Mon, 25 Apr 2005 08:58:03 +0000 (08:58 +0000)]
dont update overview every repaint

19 years agoLoading alignment threaded
amwaterhouse [Mon, 25 Apr 2005 08:52:13 +0000 (08:52 +0000)]
Loading alignment threaded

19 years agoSyncronize drawPanel, as overviewpanel is threaded
amwaterhouse [Mon, 25 Apr 2005 08:51:33 +0000 (08:51 +0000)]
Syncronize drawPanel, as overviewpanel is threaded

19 years agoOverviewpanel allows for large alignments
amwaterhouse [Mon, 25 Apr 2005 08:50:50 +0000 (08:50 +0000)]
Overviewpanel allows for large alignments

19 years agoadd consslider to palette layer
amwaterhouse [Thu, 21 Apr 2005 17:24:58 +0000 (17:24 +0000)]
add consslider to palette layer

19 years agoAllow for clipped region when printing
amwaterhouse [Thu, 21 Apr 2005 17:23:30 +0000 (17:23 +0000)]
Allow for clipped region when printing

19 years agoTick 5 and 10 marks
amwaterhouse [Thu, 21 Apr 2005 17:23:03 +0000 (17:23 +0000)]
Tick 5 and 10 marks

19 years agoPrinting changes
amwaterhouse [Thu, 21 Apr 2005 17:22:27 +0000 (17:22 +0000)]
Printing changes

19 years agoupdate conSlider when colour changes
amwaterhouse [Thu, 21 Apr 2005 17:21:59 +0000 (17:21 +0000)]
update conSlider when colour changes

19 years agoAllow for -open arg
amwaterhouse [Thu, 21 Apr 2005 17:21:20 +0000 (17:21 +0000)]
Allow for -open arg

19 years agono need to keep setting selected, its on the palette layer
amwaterhouse [Tue, 19 Apr 2005 16:18:04 +0000 (16:18 +0000)]
no need to keep setting selected, its on the palette layer

19 years agoadd splash to palette layer
amwaterhouse [Tue, 19 Apr 2005 16:17:37 +0000 (16:17 +0000)]
add splash to palette layer

19 years agoPrinting of trees corrected. Antialiasing on
amwaterhouse [Tue, 19 Apr 2005 12:15:13 +0000 (12:15 +0000)]
Printing of trees corrected. Antialiasing on

19 years agopainting syncronized, spin increments in units, not loops of the thread
amwaterhouse [Mon, 18 Apr 2005 16:05:30 +0000 (16:05 +0000)]
painting syncronized, spin increments in units, not loops of the thread

19 years agowrap alignment box paints correctly
amwaterhouse [Mon, 18 Apr 2005 16:04:37 +0000 (16:04 +0000)]
wrap alignment box paints correctly

19 years agoblosum62 must have its on consensus
amwaterhouse [Mon, 18 Apr 2005 16:03:51 +0000 (16:03 +0000)]
blosum62 must have its on consensus

19 years agosetendres -1
amwaterhouse [Mon, 18 Apr 2005 16:03:24 +0000 (16:03 +0000)]
setendres -1

19 years agoposition of bioinformatics
amwaterhouse [Mon, 18 Apr 2005 16:02:56 +0000 (16:02 +0000)]
position of bioinformatics

19 years agoset PNG antialiasing on
amwaterhouse [Mon, 18 Apr 2005 16:02:27 +0000 (16:02 +0000)]
set PNG antialiasing on

19 years agoshow sliders when first selecting conservation,PID
amwaterhouse [Mon, 18 Apr 2005 16:01:42 +0000 (16:01 +0000)]
show sliders when first selecting conservation,PID

19 years agodont drag beyond end of alignment
amwaterhouse [Mon, 18 Apr 2005 08:08:05 +0000 (08:08 +0000)]
dont drag beyond end of alignment

19 years agoselected group draws last residue
amwaterhouse [Mon, 18 Apr 2005 08:07:27 +0000 (08:07 +0000)]
selected group draws last residue

19 years agorepaint removed
amwaterhouse [Mon, 18 Apr 2005 08:05:41 +0000 (08:05 +0000)]
repaint removed

19 years agofastPaint modified incase scroll is more than page size
amwaterhouse [Mon, 18 Apr 2005 08:04:44 +0000 (08:04 +0000)]
fastPaint modified incase scroll is more than page size

19 years agocalls fontChanged
amwaterhouse [Mon, 18 Apr 2005 08:03:56 +0000 (08:03 +0000)]
calls fontChanged

19 years agofontChanged method added, componentListener removed
amwaterhouse [Mon, 18 Apr 2005 08:03:41 +0000 (08:03 +0000)]
fontChanged method added, componentListener removed