jalview.git
19 years agoAddred GapChar string for convenient regex construction
jprocter [Fri, 27 May 2005 09:32:00 +0000 (09:32 +0000)]
Addred GapChar string for convenient regex construction

19 years agoResponse to bug mantis?id=8187 - some quick hacks to read and write david's MSF file...
jprocter [Fri, 27 May 2005 09:31:14 +0000 (09:31 +0000)]
Response to bug mantis?id=8187 - some quick hacks to read and write david's MSF file with '~' as a gap character.

19 years agoRemove desc for conserve graph
amwaterhouse [Fri, 27 May 2005 09:30:53 +0000 (09:30 +0000)]
Remove desc for conserve graph

19 years agoOld MSF Format writer now renamed.
jprocter [Fri, 27 May 2005 09:29:27 +0000 (09:29 +0000)]
Old MSF Format writer now renamed.

19 years agofixed use of PID rather than 'Comparison' Alignment percentage id
jprocter [Thu, 26 May 2005 17:21:48 +0000 (17:21 +0000)]
fixed use of PID rather than 'Comparison' Alignment percentage id
calculation.

19 years agofairly pointless catch exception error information added. (attempt to
jprocter [Thu, 26 May 2005 17:21:01 +0000 (17:21 +0000)]
fairly pointless catch exception error information added. (attempt to
catch case when a parse() call breaks in an unexpected fashion...)

19 years agofixed redundancy Undo and allowed it to work on UNALIGNED SEQUENCES
jprocter [Thu, 26 May 2005 17:19:40 +0000 (17:19 +0000)]
fixed redundancy Undo and allowed it to work on UNALIGNED SEQUENCES
(ho ho)

19 years agobug fix in jpred client. TreeViewer display state and gui consistency
jprocter [Thu, 26 May 2005 10:21:52 +0000 (10:21 +0000)]
bug fix in jpred client. TreeViewer display state and gui consistency
improved (treecanvas/Treepanel state exchange functions).

19 years agopartially updated help. Added separate treeviewing item in the root
jprocter [Thu, 26 May 2005 10:20:12 +0000 (10:20 +0000)]
partially updated help. Added separate treeviewing item in the root
menu.

19 years agocheck for null residues
amwaterhouse [Thu, 26 May 2005 09:54:29 +0000 (09:54 +0000)]
check for null residues

19 years agoDOnt add Conservation graph to every residue
amwaterhouse [Thu, 26 May 2005 09:54:05 +0000 (09:54 +0000)]
DOnt add Conservation graph to every residue

19 years agotoString modified
amwaterhouse [Thu, 26 May 2005 09:51:43 +0000 (09:51 +0000)]
toString modified

19 years agoreset colours added
amwaterhouse [Wed, 25 May 2005 17:46:17 +0000 (17:46 +0000)]
reset colours added

19 years agomore clustalx bugs fixed
amwaterhouse [Wed, 25 May 2005 17:45:55 +0000 (17:45 +0000)]
more clustalx bugs fixed

19 years agogetHexString added
amwaterhouse [Wed, 25 May 2005 16:44:43 +0000 (16:44 +0000)]
getHexString added

19 years agoall can threshold
amwaterhouse [Wed, 25 May 2005 16:44:11 +0000 (16:44 +0000)]
all can threshold

19 years agooutput to textbox
amwaterhouse [Wed, 25 May 2005 16:43:47 +0000 (16:43 +0000)]
output to textbox

19 years agolayout changes
amwaterhouse [Wed, 25 May 2005 16:43:29 +0000 (16:43 +0000)]
layout changes

19 years agocapitals
amwaterhouse [Wed, 25 May 2005 16:43:10 +0000 (16:43 +0000)]
capitals

19 years agoformat changes
amwaterhouse [Wed, 25 May 2005 16:42:41 +0000 (16:42 +0000)]
format changes

19 years agoremove scrollpane
amwaterhouse [Wed, 25 May 2005 16:42:15 +0000 (16:42 +0000)]
remove scrollpane

19 years agoCapitalise
amwaterhouse [Wed, 25 May 2005 16:41:46 +0000 (16:41 +0000)]
Capitalise

19 years agoc&p changed
amwaterhouse [Wed, 25 May 2005 16:41:15 +0000 (16:41 +0000)]
c&p changed

19 years agouse getHexString in util
amwaterhouse [Wed, 25 May 2005 16:40:38 +0000 (16:40 +0000)]
use getHexString in util

19 years agousercolours changed
amwaterhouse [Wed, 25 May 2005 16:40:13 +0000 (16:40 +0000)]
usercolours changed

19 years agooutput text to textbox
amwaterhouse [Wed, 25 May 2005 16:39:57 +0000 (16:39 +0000)]
output text to textbox

19 years agoall colours can threshold
amwaterhouse [Wed, 25 May 2005 16:39:37 +0000 (16:39 +0000)]
all colours can threshold

19 years agoselectiongroup could be null
amwaterhouse [Wed, 25 May 2005 16:36:57 +0000 (16:36 +0000)]
selectiongroup could be null

19 years agosaves usercolours
amwaterhouse [Wed, 25 May 2005 16:36:40 +0000 (16:36 +0000)]
saves usercolours

19 years agoformatforoutput never used
amwaterhouse [Wed, 25 May 2005 16:35:44 +0000 (16:35 +0000)]
formatforoutput never used

19 years agooutput values to textbox
amwaterhouse [Wed, 25 May 2005 16:35:16 +0000 (16:35 +0000)]
output values to textbox

19 years agotoString method added
amwaterhouse [Wed, 25 May 2005 16:34:04 +0000 (16:34 +0000)]
toString method added

19 years agoXML schema changes
amwaterhouse [Wed, 25 May 2005 16:33:25 +0000 (16:33 +0000)]
XML schema changes

19 years agousercolourscheme changed
amwaterhouse [Wed, 25 May 2005 16:32:31 +0000 (16:32 +0000)]
usercolourscheme changed

19 years agoformatting changes
amwaterhouse [Wed, 25 May 2005 16:32:04 +0000 (16:32 +0000)]
formatting changes

19 years agoall colours can threshold
amwaterhouse [Wed, 25 May 2005 16:30:38 +0000 (16:30 +0000)]
all colours can threshold

19 years agousercolours changed
amwaterhouse [Wed, 25 May 2005 16:26:38 +0000 (16:26 +0000)]
usercolours changed

19 years agoremove comment
amwaterhouse [Wed, 25 May 2005 16:26:13 +0000 (16:26 +0000)]
remove comment

19 years agocan output details to textbox
amwaterhouse [Wed, 25 May 2005 16:25:16 +0000 (16:25 +0000)]
can output details to textbox

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