jalview.git
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

19 years agofixed brain interruption bug.
jprocter [Fri, 27 May 2005 15:46:14 +0000 (15:46 +0000)]
fixed brain interruption bug.

19 years agoignores blank lines read in and write out
amwaterhouse [Fri, 27 May 2005 15:40:31 +0000 (15:40 +0000)]
ignores blank lines read in and write out

19 years agoright ordering for RedundancyPanel constructor
jprocter [Fri, 27 May 2005 15:09:33 +0000 (15:09 +0000)]
right ordering for RedundancyPanel constructor

19 years agoadded proper state check for failedJob flag.
jprocter [Fri, 27 May 2005 15:07:27 +0000 (15:07 +0000)]
added proper state check for failedJob flag.

19 years agoAdded jobFail state
jprocter [Fri, 27 May 2005 15:03:26 +0000 (15:03 +0000)]
Added jobFail state

19 years agobetter recognition of MSF files.
jprocter [Fri, 27 May 2005 15:02:18 +0000 (15:02 +0000)]
better recognition of MSF files.

19 years agoAdded menus
amwaterhouse [Fri, 27 May 2005 14:43:56 +0000 (14:43 +0000)]
Added menus

19 years agoedits
amwaterhouse [Fri, 27 May 2005 14:33:10 +0000 (14:33 +0000)]
edits

19 years agoimage moved
amwaterhouse [Fri, 27 May 2005 14:31:17 +0000 (14:31 +0000)]
image moved

19 years agopref
amwaterhouse [Fri, 27 May 2005 14:30:33 +0000 (14:30 +0000)]
pref

19 years agomenus
amwaterhouse [Fri, 27 May 2005 14:28:34 +0000 (14:28 +0000)]
menus

19 years agoImage moved
amwaterhouse [Fri, 27 May 2005 14:24:31 +0000 (14:24 +0000)]
Image moved

19 years agoidentity changed
amwaterhouse [Fri, 27 May 2005 14:17:23 +0000 (14:17 +0000)]
identity changed

19 years agoCut and paste menus added
amwaterhouse [Fri, 27 May 2005 14:16:38 +0000 (14:16 +0000)]
Cut and paste menus added

19 years agoCut and paste changes
amwaterhouse [Fri, 27 May 2005 14:14:54 +0000 (14:14 +0000)]
Cut and paste changes

19 years agoC&P changes
amwaterhouse [Fri, 27 May 2005 14:13:49 +0000 (14:13 +0000)]
C&P changes

19 years agoCheck if colos are null
amwaterhouse [Fri, 27 May 2005 14:12:36 +0000 (14:12 +0000)]
Check if colos are null

19 years agoCut and paste changes
amwaterhouse [Fri, 27 May 2005 14:06:36 +0000 (14:06 +0000)]
Cut and paste changes

19 years agoAdd cut and paste menus
amwaterhouse [Fri, 27 May 2005 14:05:45 +0000 (14:05 +0000)]
Add cut and paste menus

19 years agoCutAndPaste changed
amwaterhouse [Fri, 27 May 2005 14:05:07 +0000 (14:05 +0000)]
CutAndPaste changed

19 years agoAdded nicer header formatting for MSFfile output.
jprocter [Fri, 27 May 2005 11:47:10 +0000 (11:47 +0000)]
Added nicer header formatting for MSFfile output.

19 years agorecovered changes from v 1.84
jprocter [Fri, 27 May 2005 09:55:12 +0000 (09:55 +0000)]
recovered changes from v 1.84

19 years agoCheck if usrCol is null
amwaterhouse [Fri, 27 May 2005 09:33:12 +0000 (09:33 +0000)]
Check if usrCol is null

19 years agoNew cut and paste
amwaterhouse [Fri, 27 May 2005 09:32:30 +0000 (09:32 +0000)]
New cut and paste

19 years agoJpredfile now uses the PileUpfile io class.
jprocter [Fri, 27 May 2005 09:32:28 +0000 (09:32 +0000)]
Jpredfile now uses the PileUpfile io class.

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