jalview.git
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

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