jprocter [Fri, 13 Jul 2007 14:54:55 +0000 (14:54 +0000)]
bugfix and comments
jprocter [Fri, 13 Jul 2007 14:54:00 +0000 (14:54 +0000)]
moved to castor-1.1-cycle - a specially patched version of castor relating to jira bugs : jira.codehaus.org/browse/CASTOR-2027 http://jira.codehaus.org/browse/CASTOR-2012 http://jira.codehaus.org/browse/CASTOR-2011
jprocter [Mon, 18 Jun 2007 14:08:57 +0000 (14:08 +0000)]
ensure lines are drawn from first alignment column.
jprocter [Mon, 18 Jun 2007 13:25:26 +0000 (13:25 +0000)]
1.1 methods
jprocter [Sun, 17 Jun 2007 13:11:18 +0000 (13:11 +0000)]
vamsas-client-1.2 schema (mappings and Treenodes) and begun refactoring object binding code
jprocter [Sun, 17 Jun 2007 13:08:15 +0000 (13:08 +0000)]
vamsas mouseOvers
jprocter [Sun, 17 Jun 2007 13:06:23 +0000 (13:06 +0000)]
enable mouseover between DNA coding regions and translated peptide location
jprocter [Sun, 17 Jun 2007 13:04:30 +0000 (13:04 +0000)]
enable mouseover between DNA coding regions and translated peptide location and broadcast to vamsas session.
jprocter [Sun, 17 Jun 2007 13:02:19 +0000 (13:02 +0000)]
fix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings for each translated sequence
jprocter [Sun, 17 Jun 2007 13:01:14 +0000 (13:01 +0000)]
recovery of identical dataset sequence object on undo (rather than creation of a new ds sequence with re-inserted residues)
jprocter [Sun, 17 Jun 2007 12:59:15 +0000 (12:59 +0000)]
AlignedCodonFrame holds mapping information between individual cDNA regions on dna and translated peptide sequences
jprocter [Sun, 17 Jun 2007 12:55:50 +0000 (12:55 +0000)]
fix modeller generated PDB file reading bug (missing HEADER line with PDB code)
jprocter [Sun, 17 Jun 2007 12:54:05 +0000 (12:54 +0000)]
JnetFIle is a readable format
jprocter [Sun, 17 Jun 2007 12:52:25 +0000 (12:52 +0000)]
score only annotation IO
jprocter [Sun, 17 Jun 2007 12:51:27 +0000 (12:51 +0000)]
mouseOver highlighting and broadcasting efficiency
jprocter [Sun, 17 Jun 2007 12:47:44 +0000 (12:47 +0000)]
thread safety during repaint
jprocter [Sun, 17 Jun 2007 12:46:32 +0000 (12:46 +0000)]
null pointer exception fix
jprocter [Sun, 17 Jun 2007 12:45:25 +0000 (12:45 +0000)]
searchresult highlighting on common dataset or specific sequenceI residue range
jprocter [Sun, 17 Jun 2007 12:43:25 +0000 (12:43 +0000)]
correct construction of new dataset sequence when residues are deleted
jprocter [Sun, 17 Jun 2007 12:41:36 +0000 (12:41 +0000)]
javadoc
jprocter [Mon, 4 Jun 2007 09:54:31 +0000 (09:54 +0000)]
fix for 'RF' annotation tags and ensured parser is robust to new/unknown two letter annotation tag codes.
jprocter [Mon, 28 May 2007 11:15:40 +0000 (11:15 +0000)]
prototype DBRef and Feature Type semantics (for annotating coding regions and distinguishing between DNA and peptide sequence databases)
jprocter [Mon, 28 May 2007 11:14:05 +0000 (11:14 +0000)]
moved castor-mapping.xsd to schemas
jprocter [Mon, 28 May 2007 11:12:19 +0000 (11:12 +0000)]
jalview source development documentation
jprocter [Mon, 28 May 2007 10:02:06 +0000 (10:02 +0000)]
fix compact annotation array routine
jprocter [Mon, 28 May 2007 09:57:21 +0000 (09:57 +0000)]
castor mapping file schema (for mappings in resources dir) - this is put in for development documentation purposes.
jprocter [Mon, 28 May 2007 09:54:09 +0000 (09:54 +0000)]
mapping file change for castor-1.1 upgrade
jprocter [Mon, 28 May 2007 09:53:19 +0000 (09:53 +0000)]
castor mapping unmarshalling logging
jprocter [Mon, 28 May 2007 09:51:11 +0000 (09:51 +0000)]
loglevel property constants and castor validation logger config
jprocter [Thu, 24 May 2007 15:20:45 +0000 (15:20 +0000)]
castor-1.1 classes (descriptors moved to subpackage)
jprocter [Thu, 24 May 2007 15:19:17 +0000 (15:19 +0000)]
castor-1.1 compatible classes from ant task
jprocter [Thu, 24 May 2007 15:16:11 +0000 (15:16 +0000)]
jalview 2.0 XML schema versions for backwards compatibility in future castor upgrades
jprocter [Thu, 24 May 2007 09:08:54 +0000 (09:08 +0000)]
New file for /homes/www-jalview
jprocter [Tue, 22 May 2007 21:17:26 +0000 (21:17 +0000)]
fixed jalview 2.3 bug where gapped aligned codons were always translated as inserted residues rather than aligned with eachother
jprocter [Tue, 22 May 2007 16:35:04 +0000 (16:35 +0000)]
1.4 version of vamsas-client
jprocter [Tue, 22 May 2007 15:54:32 +0000 (15:54 +0000)]
refactored document objects and bugfix on jvdataset-vamsasdataset binding
amwaterhouse [Tue, 22 May 2007 14:25:38 +0000 (14:25 +0000)]
DONT SET PICKING LABEL
jprocter [Mon, 21 May 2007 13:55:35 +0000 (13:55 +0000)]
vamsas svn 14.55 May 21
jprocter [Fri, 18 May 2007 15:45:58 +0000 (15:45 +0000)]
fixed getObject(VorbaId) lookup in vamsas-client
amwaterhouse [Fri, 18 May 2007 13:59:44 +0000 (13:59 +0000)]
2.3
jprocter [Fri, 18 May 2007 11:03:18 +0000 (11:03 +0000)]
update to and from document (and remove deprecated classes)
jprocter [Fri, 18 May 2007 10:43:32 +0000 (10:43 +0000)]
removed uneccessary vamsasLoad commented out.
jprocter [Thu, 17 May 2007 18:03:10 +0000 (18:03 +0000)]
refining - still debugging.
jprocter [Thu, 17 May 2007 17:09:00 +0000 (17:09 +0000)]
updated source generator properties for castor-1.1
jprocter [Thu, 17 May 2007 17:07:40 +0000 (17:07 +0000)]
use of proper vamsas client API by Jalview
jprocter [Thu, 17 May 2007 17:06:31 +0000 (17:06 +0000)]
modified castor-1.1 library and refactored uk.ac.vamsas
amwaterhouse [Wed, 16 May 2007 09:16:42 +0000 (09:16 +0000)]
visible
amwaterhouse [Tue, 15 May 2007 15:35:07 +0000 (15:35 +0000)]
SequenceListener highlights SearchResults, not just a single sequence
amwaterhouse [Mon, 14 May 2007 14:56:09 +0000 (14:56 +0000)]
Invert mouse drag controls
jprocter [Thu, 10 May 2007 13:59:37 +0000 (13:59 +0000)]
apparent bug in JpredFile parser where annotation was not being removed from alignment profile when reading in a concise file as an alignment.
amwaterhouse [Thu, 10 May 2007 09:00:26 +0000 (09:00 +0000)]
Airbrush out Uniprot
jprocter [Thu, 10 May 2007 08:42:35 +0000 (08:42 +0000)]
ensure that only annotation referenced in given alignment is duplicated on returned sequence selection set
jprocter [Thu, 10 May 2007 08:41:07 +0000 (08:41 +0000)]
documentation
jprocter [Thu, 10 May 2007 08:40:31 +0000 (08:40 +0000)]
bugfix on copy only referenced annotation in copy constructor
jprocter [Thu, 10 May 2007 08:39:40 +0000 (08:39 +0000)]
fixed array index out of bounds when not removing alignment annotation
amwaterhouse [Thu, 10 May 2007 08:10:03 +0000 (08:10 +0000)]
visibility setting
amwaterhouse [Thu, 10 May 2007 08:08:47 +0000 (08:08 +0000)]
Keep record of last tooltip
amwaterhouse [Thu, 10 May 2007 07:14:18 +0000 (07:14 +0000)]
Visible state of annotation
amwaterhouse [Thu, 10 May 2007 07:13:53 +0000 (07:13 +0000)]
Add show all hidden menu
amwaterhouse [Thu, 10 May 2007 07:13:03 +0000 (07:13 +0000)]
Dont duplicate annotations in multiple views
amwaterhouse [Thu, 10 May 2007 07:12:06 +0000 (07:12 +0000)]
save visible state of annotation
jprocter [Wed, 9 May 2007 15:51:59 +0000 (15:51 +0000)]
main method for running from command line and better binary file/archive detection
jprocter [Wed, 9 May 2007 13:48:37 +0000 (13:48 +0000)]
reword jmol state storage
jprocter [Wed, 9 May 2007 13:20:16 +0000 (13:20 +0000)]
image size
amwaterhouse [Wed, 9 May 2007 13:12:47 +0000 (13:12 +0000)]
minor formatting of tooltip
jprocter [Wed, 9 May 2007 13:08:33 +0000 (13:08 +0000)]
new binary image
amwaterhouse [Wed, 9 May 2007 12:59:02 +0000 (12:59 +0000)]
9th may
jprocter [Tue, 8 May 2007 17:19:06 +0000 (17:19 +0000)]
removed cdna coding region 'new feature'
jprocter [Tue, 8 May 2007 17:18:42 +0000 (17:18 +0000)]
embl mapping and das feature retrieval
jprocter [Tue, 8 May 2007 17:18:23 +0000 (17:18 +0000)]
optimise order
jprocter [Tue, 8 May 2007 17:18:09 +0000 (17:18 +0000)]
multiple view pdb view association
jprocter [Tue, 8 May 2007 16:53:56 +0000 (16:53 +0000)]
formatting and wording
jprocter [Tue, 8 May 2007 16:52:49 +0000 (16:52 +0000)]
grammar, clarity and typos
jprocter [Tue, 8 May 2007 16:52:05 +0000 (16:52 +0000)]
typo
jprocter [Tue, 8 May 2007 16:51:47 +0000 (16:51 +0000)]
formatting
jprocter [Tue, 8 May 2007 16:51:26 +0000 (16:51 +0000)]
page setup entry
jprocter [Tue, 8 May 2007 16:51:14 +0000 (16:51 +0000)]
dialog box menu item naming
jprocter [Tue, 8 May 2007 16:50:52 +0000 (16:50 +0000)]
correct menu entry names and typos
jprocter [Tue, 8 May 2007 16:50:28 +0000 (16:50 +0000)]
PID distance measure and finishing sentence.
jprocter [Tue, 8 May 2007 16:49:47 +0000 (16:49 +0000)]
sort by score
jprocter [Tue, 8 May 2007 14:01:12 +0000 (14:01 +0000)]
rightalign and italic ids docs
jprocter [Tue, 8 May 2007 13:48:40 +0000 (13:48 +0000)]
added jmol documentation
amwaterhouse [Tue, 8 May 2007 13:47:57 +0000 (13:47 +0000)]
check for null annotations
amwaterhouse [Tue, 8 May 2007 13:47:43 +0000 (13:47 +0000)]
set picking label
amwaterhouse [Tue, 8 May 2007 11:01:06 +0000 (11:01 +0000)]
state jmol 11.0.2
amwaterhouse [Tue, 8 May 2007 10:58:50 +0000 (10:58 +0000)]
More issues resolved
amwaterhouse [Tue, 8 May 2007 10:58:23 +0000 (10:58 +0000)]
instant update when seq colour is pressed
amwaterhouse [Tue, 8 May 2007 10:44:13 +0000 (10:44 +0000)]
must specify .CA
amwaterhouse [Tue, 8 May 2007 10:09:27 +0000 (10:09 +0000)]
remove system.out
amwaterhouse [Tue, 8 May 2007 10:08:11 +0000 (10:08 +0000)]
small sphere for alpha carbon
amwaterhouse [Tue, 8 May 2007 08:18:08 +0000 (08:18 +0000)]
addElement
amwaterhouse [Tue, 8 May 2007 07:56:43 +0000 (07:56 +0000)]
mirror image recitified
amwaterhouse [Mon, 7 May 2007 15:21:39 +0000 (15:21 +0000)]
2.3 updates
amwaterhouse [Mon, 7 May 2007 15:16:54 +0000 (15:16 +0000)]
2.3 updates
amwaterhouse [Mon, 7 May 2007 14:12:13 +0000 (14:12 +0000)]
Can compile and obfuscate applet with Jmol
amwaterhouse [Mon, 7 May 2007 13:59:56 +0000 (13:59 +0000)]
Image size must allow for scale height
amwaterhouse [Mon, 7 May 2007 13:59:27 +0000 (13:59 +0000)]
dif is never used
amwaterhouse [Mon, 7 May 2007 13:59:10 +0000 (13:59 +0000)]
Allow for large font sizes
amwaterhouse [Mon, 7 May 2007 13:58:55 +0000 (13:58 +0000)]
dont use gold highlights
amwaterhouse [Mon, 7 May 2007 13:58:46 +0000 (13:58 +0000)]
Max width for tooltip
git://source.jalview.org / jalview.git / log