amwaterhouse [Tue, 10 Oct 2006 10:44:03 +0000 (10:44 +0000)]
1.1 compatible
amwaterhouse [Tue, 10 Oct 2006 10:43:52 +0000 (10:43 +0000)]
Use AAFrequency final keys
amwaterhouse [Tue, 10 Oct 2006 10:29:03 +0000 (10:29 +0000)]
SetTooltip empty
amwaterhouse [Tue, 10 Oct 2006 10:28:31 +0000 (10:28 +0000)]
Optimized
amwaterhouse [Tue, 10 Oct 2006 10:28:05 +0000 (10:28 +0000)]
aaIndex replaces aaHash
amwaterhouse [Tue, 10 Oct 2006 10:27:36 +0000 (10:27 +0000)]
static final strings for consensus keys
amwaterhouse [Tue, 10 Oct 2006 10:26:58 +0000 (10:26 +0000)]
Consensus and conservation updated in threads
jprocter [Mon, 9 Oct 2006 17:15:57 +0000 (17:15 +0000)]
fixed log4j complaints for vamsas logging (again)
jprocter [Mon, 9 Oct 2006 17:13:05 +0000 (17:13 +0000)]
fixed log4j complaints for vamsas logging.
jprocter [Mon, 9 Oct 2006 17:02:33 +0000 (17:02 +0000)]
excluded log4j properties.
jprocter [Mon, 9 Oct 2006 16:45:45 +0000 (16:45 +0000)]
java 1.4 compliant classes.
jprocter [Mon, 9 Oct 2006 16:13:13 +0000 (16:13 +0000)]
imported Vamsas bindings and alpha vamsas client code from VamJalview cvs branch. Compilation requires vamsas-client.jar but Jalview can be distributed without the vamsas-client.jar.
jprocter [Mon, 9 Oct 2006 16:10:39 +0000 (16:10 +0000)]
set firstColumn property for an alignmentView object.
jprocter [Mon, 9 Oct 2006 16:07:31 +0000 (16:07 +0000)]
fixed getCompactAlignment method to return proper cigarArray and added 'firstColumn' parameter to AlignmentView object.
jprocter [Fri, 6 Oct 2006 16:54:03 +0000 (16:54 +0000)]
Added filter so that input to a JPred job is *solely* the visible residues, and the profile and prediction are correctly mapped back to the original seuence.
jprocter [Fri, 6 Oct 2006 16:16:04 +0000 (16:16 +0000)]
javadoc
jprocter [Fri, 6 Oct 2006 16:15:29 +0000 (16:15 +0000)]
new getVisibleContigs method mirrors the getVisibleContigs method in AlignmentView
amwaterhouse [Fri, 6 Oct 2006 13:52:06 +0000 (13:52 +0000)]
AAFrequency optimized
amwaterhouse [Fri, 6 Oct 2006 13:50:44 +0000 (13:50 +0000)]
Set consensus as hashtble[]
amwaterhouse [Thu, 5 Oct 2006 16:24:09 +0000 (16:24 +0000)]
Multiple Views
amwaterhouse [Thu, 5 Oct 2006 16:22:31 +0000 (16:22 +0000)]
BatchSize now 10
amwaterhouse [Thu, 5 Oct 2006 16:22:07 +0000 (16:22 +0000)]
OutOfMemoryError test
amwaterhouse [Thu, 5 Oct 2006 16:21:43 +0000 (16:21 +0000)]
TabbedPanes for views
amwaterhouse [Thu, 5 Oct 2006 16:20:39 +0000 (16:20 +0000)]
lower case available
amwaterhouse [Thu, 5 Oct 2006 16:18:50 +0000 (16:18 +0000)]
AlignFrame must take width and height
amwaterhouse [Thu, 5 Oct 2006 16:18:19 +0000 (16:18 +0000)]
Sequenceset may be empty, multiple views
amwaterhouse [Thu, 5 Oct 2006 16:17:35 +0000 (16:17 +0000)]
DEFAULT_WIDTH
amwaterhouse [Thu, 5 Oct 2006 16:16:40 +0000 (16:16 +0000)]
Viewname, sequencesetid, gatheredViews
amwaterhouse [Thu, 5 Oct 2006 16:16:17 +0000 (16:16 +0000)]
Sequences are optionalcvs diff vamsas.xsd
amwaterhouse [Tue, 3 Oct 2006 09:27:35 +0000 (09:27 +0000)]
Check annotation is editable
amwaterhouse [Tue, 3 Oct 2006 09:25:24 +0000 (09:25 +0000)]
Send DAS requests in batches of 20
amwaterhouse [Tue, 3 Oct 2006 09:24:56 +0000 (09:24 +0000)]
DB seqs may be lower or upper case
amwaterhouse [Tue, 3 Oct 2006 09:21:12 +0000 (09:21 +0000)]
BoldFont upperCase
amwaterhouse [Tue, 3 Oct 2006 09:20:53 +0000 (09:20 +0000)]
Remove empty() from feature ToolTip
amwaterhouse [Tue, 3 Oct 2006 09:19:11 +0000 (09:19 +0000)]
Check selection scroll beyond aligmnment height
amwaterhouse [Tue, 3 Oct 2006 09:18:22 +0000 (09:18 +0000)]
Check on vscrollMax values
amwaterhouse [Tue, 3 Oct 2006 09:17:40 +0000 (09:17 +0000)]
upperCaseBold
amwaterhouse [Tue, 3 Oct 2006 09:16:50 +0000 (09:16 +0000)]
TurnColour bug on popupmenu applet
jprocter [Wed, 27 Sep 2006 14:35:43 +0000 (14:35 +0000)]
fixed tree building exception when one residue or a single column of residues is selected.
amwaterhouse [Mon, 18 Sep 2006 14:14:29 +0000 (14:14 +0000)]
Draw hidden column marker correctly
amwaterhouse [Mon, 18 Sep 2006 13:25:27 +0000 (13:25 +0000)]
click node to select sequences
amwaterhouse [Fri, 15 Sep 2006 14:42:33 +0000 (14:42 +0000)]
Simplified schema
amwaterhouse [Fri, 15 Sep 2006 14:38:45 +0000 (14:38 +0000)]
Simplified layout
amwaterhouse [Tue, 12 Sep 2006 16:37:46 +0000 (16:37 +0000)]
hideSequence hide all before recalc consensus
amwaterhouse [Tue, 12 Sep 2006 10:01:52 +0000 (10:01 +0000)]
Copy consensus
amwaterhouse [Tue, 12 Sep 2006 09:32:17 +0000 (09:32 +0000)]
2.1.1 bug fix
amwaterhouse [Tue, 12 Sep 2006 09:31:04 +0000 (09:31 +0000)]
2.1.1 bug fix
amwaterhouse [Tue, 12 Sep 2006 09:24:00 +0000 (09:24 +0000)]
Add copy consensus sequence
amwaterhouse [Tue, 12 Sep 2006 09:20:18 +0000 (09:20 +0000)]
Allow alt for group editing
amwaterhouse [Tue, 12 Sep 2006 09:19:45 +0000 (09:19 +0000)]
For now ignore middle mouse font resize on Mac applet
amwaterhouse [Tue, 12 Sep 2006 09:19:18 +0000 (09:19 +0000)]
Allow alt button for Mac applet group editing
amwaterhouse [Mon, 11 Sep 2006 16:24:41 +0000 (16:24 +0000)]
Comment out lower case colouring for bug fix release
amwaterhouse [Mon, 11 Sep 2006 15:43:31 +0000 (15:43 +0000)]
Remove system.outs
amwaterhouse [Mon, 11 Sep 2006 15:42:43 +0000 (15:42 +0000)]
get idWidth should use italic font when getting size
amwaterhouse [Mon, 11 Sep 2006 15:28:53 +0000 (15:28 +0000)]
Error message if file not found moved for headless state
amwaterhouse [Mon, 11 Sep 2006 15:27:34 +0000 (15:27 +0000)]
visWidth allows borders to be drawn around offscreen images when making images
amwaterhouse [Mon, 11 Sep 2006 14:44:48 +0000 (14:44 +0000)]
Remove system.out
amwaterhouse [Mon, 11 Sep 2006 11:30:23 +0000 (11:30 +0000)]
getVisibleIdWidth() for making images
jprocter [Thu, 7 Sep 2006 11:39:36 +0000 (11:39 +0000)]
added copy consensus sequence to consensus annotation popup menu
jprocter [Tue, 5 Sep 2006 13:36:07 +0000 (13:36 +0000)]
getVisibleContigs() returns start and end positions of visible regions of an alignmentView.
jprocter [Tue, 5 Sep 2006 13:03:19 +0000 (13:03 +0000)]
javadoc on contigs
amwaterhouse [Fri, 1 Sep 2006 12:30:07 +0000 (12:30 +0000)]
Dont look for middle mouse on the Mac
amwaterhouse [Fri, 1 Sep 2006 12:25:34 +0000 (12:25 +0000)]
MAC moved to viewport
amwaterhouse [Fri, 1 Sep 2006 11:23:03 +0000 (11:23 +0000)]
feature settings
amwaterhouse [Fri, 1 Sep 2006 11:22:33 +0000 (11:22 +0000)]
Feature Settings
amwaterhouse [Wed, 30 Aug 2006 16:10:07 +0000 (16:10 +0000)]
GraphHeight might be zero
amwaterhouse [Wed, 30 Aug 2006 16:09:47 +0000 (16:09 +0000)]
jnet file is 1 to 1 mapping
amwaterhouse [Wed, 30 Aug 2006 16:09:25 +0000 (16:09 +0000)]
Remove unnecessary separotor
amwaterhouse [Wed, 30 Aug 2006 16:08:58 +0000 (16:08 +0000)]
Gap added to aa3Hash
amwaterhouse [Wed, 30 Aug 2006 16:08:36 +0000 (16:08 +0000)]
User colours are case sensitive
amwaterhouse [Tue, 29 Aug 2006 15:31:04 +0000 (15:31 +0000)]
Can shrink graph to zero
amwaterhouse [Tue, 29 Aug 2006 15:24:40 +0000 (15:24 +0000)]
No stacktrace
amwaterhouse [Tue, 29 Aug 2006 15:24:22 +0000 (15:24 +0000)]
createMapping alreadyMapped
amwaterhouse [Tue, 29 Aug 2006 15:22:59 +0000 (15:22 +0000)]
Additional repaint
amwaterhouse [Tue, 29 Aug 2006 15:22:15 +0000 (15:22 +0000)]
jnetfile can be loaded onto alignment
amwaterhouse [Tue, 29 Aug 2006 15:21:39 +0000 (15:21 +0000)]
SequenceMapping updated
amwaterhouse [Tue, 29 Aug 2006 15:15:25 +0000 (15:15 +0000)]
Jnet files sent to servlet as annotations
amwaterhouse [Thu, 24 Aug 2006 13:03:23 +0000 (13:03 +0000)]
unbalanced head tag
amwaterhouse [Wed, 23 Aug 2006 08:03:04 +0000 (08:03 +0000)]
volume 20
amwaterhouse [Tue, 22 Aug 2006 16:54:40 +0000 (16:54 +0000)]
2.1 updates
amwaterhouse [Tue, 22 Aug 2006 16:25:21 +0000 (16:25 +0000)]
add link.gif
amwaterhouse [Tue, 22 Aug 2006 15:31:31 +0000 (15:31 +0000)]
2.1 update
amwaterhouse [Tue, 22 Aug 2006 14:29:10 +0000 (14:29 +0000)]
To uppercase only visible
jprocter [Tue, 22 Aug 2006 13:47:47 +0000 (13:47 +0000)]
documentation - adding new Input data menu entries.
jprocter [Tue, 22 Aug 2006 13:25:47 +0000 (13:25 +0000)]
added note on column-separability
jprocter [Tue, 22 Aug 2006 13:13:23 +0000 (13:13 +0000)]
documentation
jprocter [Tue, 22 Aug 2006 13:01:50 +0000 (13:01 +0000)]
getSequenceStrings() bug fixed.
amwaterhouse [Tue, 22 Aug 2006 10:39:03 +0000 (10:39 +0000)]
Remove group when hiding cols from scalePanel
amwaterhouse [Tue, 22 Aug 2006 09:11:05 +0000 (09:11 +0000)]
2006
amwaterhouse [Tue, 22 Aug 2006 09:10:48 +0000 (09:10 +0000)]
Put transparency back
amwaterhouse [Tue, 22 Aug 2006 09:10:28 +0000 (09:10 +0000)]
make 1.1 compatible
jprocter [Tue, 22 Aug 2006 08:34:04 +0000 (08:34 +0000)]
hidden region recovery in JPred and new hidden region pruning function
jprocter [Tue, 22 Aug 2006 08:32:40 +0000 (08:32 +0000)]
off by one bug in hiden column unmarshalling
amwaterhouse [Mon, 21 Aug 2006 15:36:21 +0000 (15:36 +0000)]
header updated
amwaterhouse [Mon, 21 Aug 2006 15:29:26 +0000 (15:29 +0000)]
header updated
amwaterhouse [Mon, 21 Aug 2006 14:48:49 +0000 (14:48 +0000)]
validate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:39:50 +0000 (14:39 +0000)]
validate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:39:36 +0000 (14:39 +0000)]
Add uniprot DBref
amwaterhouse [Mon, 21 Aug 2006 14:14:07 +0000 (14:14 +0000)]
Remove system.out
amwaterhouse [Mon, 21 Aug 2006 14:13:49 +0000 (14:13 +0000)]
1.1 compatible
git://source.jalview.org / jalview.git / log