jalview.git
19 years agousercolours added
amwaterhouse [Wed, 25 May 2005 16:24:27 +0000 (16:24 +0000)]
usercolours added

19 years agoadded jalview.browser property so a linux user can choose which browser they want...
jprocter [Wed, 25 May 2005 16:09:55 +0000 (16:09 +0000)]
added jalview.browser property so a linux user can choose which browser they want to open swissprot entries with.

19 years agodoh - compile before commit!
jprocter [Wed, 25 May 2005 13:59:57 +0000 (13:59 +0000)]
doh - compile before commit!

19 years agotidied up system.out messages and moved many to stderr.
jprocter [Wed, 25 May 2005 13:35:22 +0000 (13:35 +0000)]
tidied up system.out messages and moved many to stderr.

19 years agoImproved consistency between JPredWS and MsaWS
jprocter [Wed, 25 May 2005 13:00:33 +0000 (13:00 +0000)]
Improved consistency between JPredWS and MsaWS

19 years agobase class for web service clients.
jprocter [Wed, 25 May 2005 13:00:02 +0000 (13:00 +0000)]
base class for web service clients.

19 years agotitle parameter for single sequence prediction.
jprocter [Tue, 24 May 2005 17:18:35 +0000 (17:18 +0000)]
title parameter for single sequence prediction.

19 years agoAdded more firePropertyChange calls - mainly for sequence paste events.
jprocter [Tue, 24 May 2005 17:18:14 +0000 (17:18 +0000)]
Added more firePropertyChange calls - mainly for sequence paste events.

19 years agoextended the UpdatePlaceholders to check for any new associations.
jprocter [Tue, 24 May 2005 17:17:08 +0000 (17:17 +0000)]
extended the UpdatePlaceholders to check for any new associations.

19 years agoadded PropertyChangeListeners for alignviewport.alignment.sequences
jprocter [Tue, 24 May 2005 16:37:26 +0000 (16:37 +0000)]
added PropertyChangeListeners for alignviewport.alignment.sequences
vector. TreeViewer windows now properly reflect deletions to sequence
set.

19 years agoremove .
amwaterhouse [Tue, 24 May 2005 13:02:57 +0000 (13:02 +0000)]
remove .

19 years agoURL getresource adds %20 for spaces. Use user.dir instead
amwaterhouse [Tue, 24 May 2005 11:23:15 +0000 (11:23 +0000)]
URL getresource adds %20 for spaces. Use user.dir instead

19 years agofilefilter might not be JalviewFileFilter
amwaterhouse [Tue, 24 May 2005 09:35:14 +0000 (09:35 +0000)]
filefilter might not be JalviewFileFilter

19 years agoformatting.
jprocter [Tue, 24 May 2005 09:08:13 +0000 (09:08 +0000)]
formatting.

19 years agoequalsIgnoreCase
amwaterhouse [Tue, 24 May 2005 09:04:33 +0000 (09:04 +0000)]
equalsIgnoreCase

19 years agosetDefaultFileFormat
amwaterhouse [Tue, 24 May 2005 09:04:15 +0000 (09:04 +0000)]
setDefaultFileFormat

19 years agoreplace get with elementAt
amwaterhouse [Tue, 24 May 2005 09:03:29 +0000 (09:03 +0000)]
replace get with elementAt

19 years agosetgraphics black
amwaterhouse [Tue, 24 May 2005 09:02:44 +0000 (09:02 +0000)]
setgraphics black

19 years agoslight changes.
jprocter [Tue, 24 May 2005 08:55:01 +0000 (08:55 +0000)]
slight changes.

19 years agoadded sorting alignments documentation.
jprocter [Tue, 24 May 2005 08:51:43 +0000 (08:51 +0000)]
added sorting alignments documentation.

19 years agosetgraphics black
amwaterhouse [Tue, 24 May 2005 08:49:28 +0000 (08:49 +0000)]
setgraphics black

19 years agoseveral ordering bug fixes.
jprocter [Tue, 24 May 2005 08:42:45 +0000 (08:42 +0000)]
several ordering bug fixes.

19 years agoAdded PadGaps and made treeSortMenu dynamic (it gets added when there is a tree order...
jprocter [Mon, 23 May 2005 17:55:18 +0000 (17:55 +0000)]
Added PadGaps and made treeSortMenu dynamic (it gets added when there is a tree ordering added). Alignment orderings are now added to the main sort menu.

19 years agoadded some assertions and rangechecks for insert/deleteChar methods.
jprocter [Mon, 23 May 2005 17:49:04 +0000 (17:49 +0000)]
added some assertions and rangechecks for insert/deleteChar methods.

19 years agoadded getSequencesInOrder (part of refactor from AlignPanel menu action for cut'n...
jprocter [Mon, 23 May 2005 17:48:35 +0000 (17:48 +0000)]
added getSequencesInOrder (part of refactor from AlignPanel menu action for cut'n'paste).

19 years agoeditMenuPadGaps and sortByTree/sort items
jprocter [Mon, 23 May 2005 17:47:14 +0000 (17:47 +0000)]
editMenuPadGaps and sortByTree/sort items

19 years agofixed window title names for prediction on MSA or Sequence.
jprocter [Mon, 23 May 2005 17:45:51 +0000 (17:45 +0000)]
fixed window title names for prediction on MSA or Sequence.

19 years agocolour groups by text colour
amwaterhouse [Mon, 23 May 2005 16:31:26 +0000 (16:31 +0000)]
colour groups by text colour

19 years agomake sure fonts are not null
amwaterhouse [Mon, 23 May 2005 16:31:07 +0000 (16:31 +0000)]
make sure fonts are not null

19 years agoremove separator
amwaterhouse [Mon, 23 May 2005 16:30:46 +0000 (16:30 +0000)]
remove separator

19 years agonew savestate method
amwaterhouse [Mon, 23 May 2005 16:30:20 +0000 (16:30 +0000)]
new savestate method

19 years agoUgly but improved recovery of sequence names, starts/ends and other SequenceI propert...
jprocter [Mon, 23 May 2005 13:27:56 +0000 (13:27 +0000)]
Ugly but improved recovery of sequence names, starts/ends and other SequenceI properties for an alignment returned from a webservice.

19 years agobug fix for wierdness retrieving QUERY sequence index.
jprocter [Mon, 23 May 2005 13:26:49 +0000 (13:26 +0000)]
bug fix for wierdness retrieving QUERY sequence index.

19 years agoboxes, colour text, show text added to groups
amwaterhouse [Mon, 23 May 2005 11:23:55 +0000 (11:23 +0000)]
boxes, colour text, show text added to groups

19 years agohistoryitem added
amwaterhouse [Mon, 23 May 2005 09:27:33 +0000 (09:27 +0000)]
historyitem added

19 years agoinclude MsaWS ordering but not perfect (undo destroys ordering efficacy).
jprocter [Sun, 22 May 2005 18:18:38 +0000 (18:18 +0000)]
include MsaWS ordering but not perfect (undo destroys ordering efficacy).

19 years agomarginal improvements - still no automated client constructor.
jprocter [Sun, 22 May 2005 17:57:01 +0000 (17:57 +0000)]
marginal improvements - still no automated client constructor.

19 years agoAdded alignment ordering option to 'Sort by' and implemented generic
jprocter [Sun, 22 May 2005 17:56:13 +0000 (17:56 +0000)]
Added alignment ordering option to 'Sort by' and implemented generic
MsaWS client.

19 years agolater version of client-side WSDL2Java generated simple Alignment
jprocter [Sun, 22 May 2005 17:12:22 +0000 (17:12 +0000)]
later version of client-side WSDL2Java generated simple Alignment
container.

19 years agoSemiworking generic MSA client
jprocter [Fri, 20 May 2005 16:43:39 +0000 (16:43 +0000)]
Semiworking generic MSA client

19 years agoadded placeholder indicators and menu item
jprocter [Fri, 20 May 2005 15:18:11 +0000 (15:18 +0000)]
added placeholder indicators and menu item

19 years agoVarious sort methods added and bugs fixed (coping with associated trees and alignment...
jprocter [Fri, 20 May 2005 15:17:00 +0000 (15:17 +0000)]
Various sort methods added and bugs fixed (coping with associated trees and alignment orders from web services)

19 years agoDEFAULT_FILE_FORMAT added
amwaterhouse [Fri, 20 May 2005 14:57:29 +0000 (14:57 +0000)]
DEFAULT_FILE_FORMAT added

19 years agosequence place holder reveal menu item.
jprocter [Fri, 20 May 2005 14:54:29 +0000 (14:54 +0000)]
sequence place holder reveal menu item.

19 years agoadded tree node property for sequence placeholders.
jprocter [Fri, 20 May 2005 14:52:52 +0000 (14:52 +0000)]
added tree node property for sequence placeholders.

19 years agoif fullid shown, resize fonts
amwaterhouse [Fri, 20 May 2005 13:40:07 +0000 (13:40 +0000)]
if fullid shown, resize fonts

19 years agostartup file added
amwaterhouse [Fri, 20 May 2005 13:30:06 +0000 (13:30 +0000)]
startup file added

19 years agoa flauss changes
amwaterhouse [Fri, 20 May 2005 13:29:48 +0000 (13:29 +0000)]
a flauss changes

19 years agoscroller is now a panel
amwaterhouse [Fri, 20 May 2005 13:29:06 +0000 (13:29 +0000)]
scroller is now a panel

19 years agolook for startup file
amwaterhouse [Fri, 20 May 2005 13:28:20 +0000 (13:28 +0000)]
look for startup file

19 years agoscroller is now a panel, removes border
amwaterhouse [Fri, 20 May 2005 13:27:48 +0000 (13:27 +0000)]
scroller is now a panel, removes border

19 years agochange ActionListeners to ItemListeners
amwaterhouse [Fri, 20 May 2005 11:01:07 +0000 (11:01 +0000)]
change ActionListeners to ItemListeners

19 years agonot centered
amwaterhouse [Fri, 20 May 2005 10:48:32 +0000 (10:48 +0000)]
not centered

19 years agoremoved
amwaterhouse [Fri, 20 May 2005 10:47:51 +0000 (10:47 +0000)]
removed

19 years agoapostrophes
amwaterhouse [Fri, 20 May 2005 10:47:21 +0000 (10:47 +0000)]
apostrophes

19 years agocopy order maintained
amwaterhouse [Fri, 20 May 2005 09:27:38 +0000 (09:27 +0000)]
copy order maintained

19 years agoxml-apis from the same place as xercesImpl.jar
jprocter [Fri, 20 May 2005 09:18:05 +0000 (09:18 +0000)]
xml-apis from the same place as xercesImpl.jar
This was needed to make the axis.jar happy using my (jims)
Jbuilder2005 buid environment.

19 years agoThis is the xercesImpl.jar from xerces-2_6_2
jprocter [Fri, 20 May 2005 09:04:54 +0000 (09:04 +0000)]
This is the xercesImpl.jar from xerces-2_6_2

19 years agodeleted
amwaterhouse [Fri, 20 May 2005 09:01:33 +0000 (09:01 +0000)]
deleted

19 years agoUpdated
amwaterhouse [Fri, 20 May 2005 08:57:27 +0000 (08:57 +0000)]
Updated

19 years agoUpdated
amwaterhouse [Fri, 20 May 2005 08:56:40 +0000 (08:56 +0000)]
Updated

19 years agoUpdated
amwaterhouse [Fri, 20 May 2005 08:55:10 +0000 (08:55 +0000)]
Updated

19 years agoFixing the broken cvs.
jprocter [Fri, 20 May 2005 08:26:37 +0000 (08:26 +0000)]
Fixing the broken cvs.

19 years agoupdated
amwaterhouse [Fri, 20 May 2005 08:19:38 +0000 (08:19 +0000)]
updated

19 years agoxml schemas
amwaterhouse [Fri, 20 May 2005 08:16:59 +0000 (08:16 +0000)]
xml schemas

19 years agocastor lib
amwaterhouse [Fri, 20 May 2005 08:14:56 +0000 (08:14 +0000)]
castor lib

19 years agoFasta FASTA
amwaterhouse [Fri, 20 May 2005 07:55:26 +0000 (07:55 +0000)]
Fasta FASTA

19 years agoimage changes
amwaterhouse [Thu, 19 May 2005 18:01:47 +0000 (18:01 +0000)]
image changes

19 years agonew libraries for XML binding
amwaterhouse [Thu, 19 May 2005 18:01:01 +0000 (18:01 +0000)]
new libraries for XML binding

19 years agoreturns name if given colourscheme
amwaterhouse [Thu, 19 May 2005 18:00:03 +0000 (18:00 +0000)]
returns name if given colourscheme

19 years agoA Flauss reccommends
amwaterhouse [Thu, 19 May 2005 17:59:20 +0000 (17:59 +0000)]
A Flauss reccommends

19 years agoA Flauss recommends
amwaterhouse [Thu, 19 May 2005 17:59:01 +0000 (17:59 +0000)]
A Flauss recommends

19 years agoA flauss recommendations
amwaterhouse [Thu, 19 May 2005 17:58:27 +0000 (17:58 +0000)]
A flauss recommendations

19 years agofilechooser has multiple filters
amwaterhouse [Thu, 19 May 2005 17:57:57 +0000 (17:57 +0000)]
filechooser has multiple filters

19 years agoloading/saving changes
amwaterhouse [Thu, 19 May 2005 17:57:34 +0000 (17:57 +0000)]
loading/saving changes

19 years agochanges to jalviewfilechooser
amwaterhouse [Thu, 19 May 2005 17:56:57 +0000 (17:56 +0000)]
changes to jalviewfilechooser

19 years ago% identity is consensus
amwaterhouse [Thu, 19 May 2005 17:56:31 +0000 (17:56 +0000)]
% identity is consensus

19 years agono need for right mouse click
amwaterhouse [Thu, 19 May 2005 17:55:34 +0000 (17:55 +0000)]
no need for right mouse click

19 years agoLoad and Save State added
amwaterhouse [Thu, 19 May 2005 17:55:04 +0000 (17:55 +0000)]
Load and Save State added

19 years agodont show redundant menuitems
amwaterhouse [Thu, 19 May 2005 17:54:30 +0000 (17:54 +0000)]
dont show redundant menuitems

19 years agoload in gap symbol
amwaterhouse [Thu, 19 May 2005 17:54:11 +0000 (17:54 +0000)]
load in gap symbol

19 years agoblock edit bug fixed
amwaterhouse [Thu, 19 May 2005 17:53:46 +0000 (17:53 +0000)]
block edit bug fixed

19 years agomaintain original threshold value
amwaterhouse [Thu, 19 May 2005 17:53:14 +0000 (17:53 +0000)]
maintain original threshold value

19 years agochanges to JalviewFileChooser
amwaterhouse [Thu, 19 May 2005 17:52:55 +0000 (17:52 +0000)]
changes to JalviewFileChooser

19 years agonew class
amwaterhouse [Thu, 19 May 2005 17:51:18 +0000 (17:51 +0000)]
new class

19 years agocalculate max and min for graph
amwaterhouse [Thu, 19 May 2005 17:50:45 +0000 (17:50 +0000)]
calculate max and min for graph

19 years agorelease version
amwaterhouse [Thu, 19 May 2005 17:49:36 +0000 (17:49 +0000)]
release version

19 years agoCopied sequences title altered
amwaterhouse [Thu, 19 May 2005 17:49:08 +0000 (17:49 +0000)]
Copied sequences title altered

19 years agoremove redundant menuitems
amwaterhouse [Thu, 19 May 2005 17:48:21 +0000 (17:48 +0000)]
remove redundant menuitems

19 years agoremove actionevents
amwaterhouse [Thu, 19 May 2005 17:48:02 +0000 (17:48 +0000)]
remove actionevents

19 years agogroup editing bug fixed
amwaterhouse [Thu, 19 May 2005 17:47:37 +0000 (17:47 +0000)]
group editing bug fixed

19 years agotoString () method added
amwaterhouse [Thu, 19 May 2005 17:47:12 +0000 (17:47 +0000)]
toString ()   method added

19 years agoCreated by Castor
amwaterhouse [Thu, 19 May 2005 17:46:40 +0000 (17:46 +0000)]
Created by Castor

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