jalview.git
17 years agomapping file change for castor-1.1 upgrade
jprocter [Mon, 28 May 2007 09:54:09 +0000 (09:54 +0000)]
mapping file change for castor-1.1 upgrade

17 years agocastor mapping unmarshalling logging
jprocter [Mon, 28 May 2007 09:53:19 +0000 (09:53 +0000)]
castor mapping unmarshalling logging

17 years agologlevel property constants and castor validation logger config
jprocter [Mon, 28 May 2007 09:51:11 +0000 (09:51 +0000)]
loglevel property constants and castor validation logger config

17 years agocastor-1.1 classes (descriptors moved to subpackage)
jprocter [Thu, 24 May 2007 15:20:45 +0000 (15:20 +0000)]
castor-1.1 classes (descriptors moved to subpackage)

17 years agocastor-1.1 compatible classes from ant task
jprocter [Thu, 24 May 2007 15:19:17 +0000 (15:19 +0000)]
castor-1.1 compatible classes from ant task

17 years agojalview 2.0 XML schema versions for backwards compatibility in future castor upgrades
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

17 years agoNew file for /homes/www-jalview
jprocter [Thu, 24 May 2007 09:08:54 +0000 (09:08 +0000)]
New file for /homes/www-jalview

17 years agofixed jalview 2.3 bug where gapped aligned codons were always translated as inserted...
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

17 years ago1.4 version of vamsas-client
jprocter [Tue, 22 May 2007 16:35:04 +0000 (16:35 +0000)]
1.4 version of vamsas-client

17 years agorefactored document objects and bugfix on jvdataset-vamsasdataset binding
jprocter [Tue, 22 May 2007 15:54:32 +0000 (15:54 +0000)]
refactored document objects and bugfix on jvdataset-vamsasdataset binding

17 years agoDONT SET PICKING LABEL
amwaterhouse [Tue, 22 May 2007 14:25:38 +0000 (14:25 +0000)]
DONT SET PICKING LABEL

17 years agovamsas svn 14.55 May 21
jprocter [Mon, 21 May 2007 13:55:35 +0000 (13:55 +0000)]
vamsas svn 14.55 May 21

17 years agofixed getObject(VorbaId) lookup in vamsas-client
jprocter [Fri, 18 May 2007 15:45:58 +0000 (15:45 +0000)]
fixed getObject(VorbaId) lookup in vamsas-client

17 years ago2.3
amwaterhouse [Fri, 18 May 2007 13:59:44 +0000 (13:59 +0000)]
2.3

17 years agoupdate to and from document (and remove deprecated classes)
jprocter [Fri, 18 May 2007 11:03:18 +0000 (11:03 +0000)]
update to and from document (and remove deprecated classes)

17 years agoremoved uneccessary vamsasLoad commented out.
jprocter [Fri, 18 May 2007 10:43:32 +0000 (10:43 +0000)]
removed uneccessary vamsasLoad commented out.

17 years agorefining - still debugging.
jprocter [Thu, 17 May 2007 18:03:10 +0000 (18:03 +0000)]
refining - still debugging.

17 years agoupdated source generator properties for castor-1.1
jprocter [Thu, 17 May 2007 17:09:00 +0000 (17:09 +0000)]
updated source generator properties for castor-1.1

17 years agouse of proper vamsas client API by Jalview
jprocter [Thu, 17 May 2007 17:07:40 +0000 (17:07 +0000)]
use of proper vamsas client API by Jalview

17 years agomodified castor-1.1 library and refactored uk.ac.vamsas
jprocter [Thu, 17 May 2007 17:06:31 +0000 (17:06 +0000)]
modified castor-1.1 library and refactored uk.ac.vamsas

17 years agovisible
amwaterhouse [Wed, 16 May 2007 09:16:42 +0000 (09:16 +0000)]
visible

17 years agoSequenceListener highlights SearchResults, not just a single sequence
amwaterhouse [Tue, 15 May 2007 15:35:07 +0000 (15:35 +0000)]
SequenceListener highlights SearchResults, not just a single sequence

17 years agoInvert mouse drag controls
amwaterhouse [Mon, 14 May 2007 14:56:09 +0000 (14:56 +0000)]
Invert mouse drag controls

17 years agoapparent bug in JpredFile parser where annotation was not being removed from alignmen...
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.

17 years agoAirbrush out Uniprot Release_2_3 Release_2_3_buildfix
amwaterhouse [Thu, 10 May 2007 09:00:26 +0000 (09:00 +0000)]
Airbrush out Uniprot

17 years agoensure that only annotation referenced in given alignment is duplicated on returned...
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

17 years agodocumentation
jprocter [Thu, 10 May 2007 08:41:07 +0000 (08:41 +0000)]
documentation

17 years agobugfix on copy only referenced annotation in copy constructor
jprocter [Thu, 10 May 2007 08:40:31 +0000 (08:40 +0000)]
bugfix on copy only referenced annotation in copy constructor

17 years agofixed array index out of bounds when not removing alignment annotation
jprocter [Thu, 10 May 2007 08:39:40 +0000 (08:39 +0000)]
fixed array index out of bounds when not removing alignment annotation

17 years agovisibility setting
amwaterhouse [Thu, 10 May 2007 08:10:03 +0000 (08:10 +0000)]
visibility setting

17 years agoKeep record of last tooltip
amwaterhouse [Thu, 10 May 2007 08:08:47 +0000 (08:08 +0000)]
Keep record of last tooltip

17 years agoVisible state of annotation
amwaterhouse [Thu, 10 May 2007 07:14:18 +0000 (07:14 +0000)]
Visible state of annotation

17 years agoAdd show all hidden menu
amwaterhouse [Thu, 10 May 2007 07:13:53 +0000 (07:13 +0000)]
Add show all hidden menu

17 years agoDont duplicate annotations in multiple views
amwaterhouse [Thu, 10 May 2007 07:13:03 +0000 (07:13 +0000)]
Dont duplicate annotations in multiple views

17 years agosave visible state of annotation
amwaterhouse [Thu, 10 May 2007 07:12:06 +0000 (07:12 +0000)]
save visible state of annotation

17 years agomain method for running from command line and better binary file/archive detection
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

17 years agoreword jmol state storage
jprocter [Wed, 9 May 2007 13:48:37 +0000 (13:48 +0000)]
reword jmol state storage

17 years agoimage size
jprocter [Wed, 9 May 2007 13:20:16 +0000 (13:20 +0000)]
image size

17 years agominor formatting of tooltip
amwaterhouse [Wed, 9 May 2007 13:12:47 +0000 (13:12 +0000)]
minor formatting of tooltip

17 years agonew binary image
jprocter [Wed, 9 May 2007 13:08:33 +0000 (13:08 +0000)]
new binary image

17 years ago9th may
amwaterhouse [Wed, 9 May 2007 12:59:02 +0000 (12:59 +0000)]
9th may

17 years agoremoved cdna coding region 'new feature'
jprocter [Tue, 8 May 2007 17:19:06 +0000 (17:19 +0000)]
removed cdna coding region 'new feature'

17 years agoembl mapping and das feature retrieval
jprocter [Tue, 8 May 2007 17:18:42 +0000 (17:18 +0000)]
embl mapping and das feature retrieval

17 years agooptimise order
jprocter [Tue, 8 May 2007 17:18:23 +0000 (17:18 +0000)]
optimise order

17 years agomultiple view pdb view association
jprocter [Tue, 8 May 2007 17:18:09 +0000 (17:18 +0000)]
multiple view pdb view association

17 years agoformatting and wording
jprocter [Tue, 8 May 2007 16:53:56 +0000 (16:53 +0000)]
formatting and wording

17 years agogrammar, clarity and typos
jprocter [Tue, 8 May 2007 16:52:49 +0000 (16:52 +0000)]
grammar, clarity and typos

17 years agotypo
jprocter [Tue, 8 May 2007 16:52:05 +0000 (16:52 +0000)]
typo

17 years agoformatting
jprocter [Tue, 8 May 2007 16:51:47 +0000 (16:51 +0000)]
formatting

17 years agopage setup entry
jprocter [Tue, 8 May 2007 16:51:26 +0000 (16:51 +0000)]
page setup entry

17 years agodialog box menu item naming
jprocter [Tue, 8 May 2007 16:51:14 +0000 (16:51 +0000)]
dialog box menu item naming

17 years agocorrect menu entry names and typos
jprocter [Tue, 8 May 2007 16:50:52 +0000 (16:50 +0000)]
correct menu entry names and typos

17 years agoPID distance measure and finishing sentence.
jprocter [Tue, 8 May 2007 16:50:28 +0000 (16:50 +0000)]
PID distance measure and finishing sentence.

17 years agosort by score
jprocter [Tue, 8 May 2007 16:49:47 +0000 (16:49 +0000)]
sort by score

17 years agorightalign and italic ids docs
jprocter [Tue, 8 May 2007 14:01:12 +0000 (14:01 +0000)]
rightalign and italic ids docs

17 years agoadded jmol documentation
jprocter [Tue, 8 May 2007 13:48:40 +0000 (13:48 +0000)]
added jmol documentation

17 years agocheck for null annotations
amwaterhouse [Tue, 8 May 2007 13:47:57 +0000 (13:47 +0000)]
check for null annotations

17 years agoset picking label
amwaterhouse [Tue, 8 May 2007 13:47:43 +0000 (13:47 +0000)]
set picking label

17 years agostate jmol 11.0.2
amwaterhouse [Tue, 8 May 2007 11:01:06 +0000 (11:01 +0000)]
state jmol 11.0.2

17 years agoMore issues resolved
amwaterhouse [Tue, 8 May 2007 10:58:50 +0000 (10:58 +0000)]
More issues resolved

17 years agoinstant update when seq colour is pressed
amwaterhouse [Tue, 8 May 2007 10:58:23 +0000 (10:58 +0000)]
instant update when seq colour is pressed

17 years agomust specify .CA
amwaterhouse [Tue, 8 May 2007 10:44:13 +0000 (10:44 +0000)]
must specify .CA

17 years agoremove system.out
amwaterhouse [Tue, 8 May 2007 10:09:27 +0000 (10:09 +0000)]
remove system.out

17 years agosmall sphere for alpha carbon
amwaterhouse [Tue, 8 May 2007 10:08:11 +0000 (10:08 +0000)]
small sphere for alpha carbon

17 years agoaddElement
amwaterhouse [Tue, 8 May 2007 08:18:08 +0000 (08:18 +0000)]
addElement

17 years agomirror image recitified
amwaterhouse [Tue, 8 May 2007 07:56:43 +0000 (07:56 +0000)]
mirror image recitified

17 years ago2.3 updates
amwaterhouse [Mon, 7 May 2007 15:21:39 +0000 (15:21 +0000)]
2.3 updates

17 years ago2.3 updates
amwaterhouse [Mon, 7 May 2007 15:16:54 +0000 (15:16 +0000)]
2.3 updates

17 years agoCan compile and obfuscate applet with Jmol
amwaterhouse [Mon, 7 May 2007 14:12:13 +0000 (14:12 +0000)]
Can compile and obfuscate applet with Jmol

17 years agoImage size must allow for scale height
amwaterhouse [Mon, 7 May 2007 13:59:56 +0000 (13:59 +0000)]
Image size must allow for scale height

17 years agodif is never used
amwaterhouse [Mon, 7 May 2007 13:59:27 +0000 (13:59 +0000)]
dif is never used

17 years agoAllow for large font sizes
amwaterhouse [Mon, 7 May 2007 13:59:10 +0000 (13:59 +0000)]
Allow for large font sizes

17 years agodont use gold highlights
amwaterhouse [Mon, 7 May 2007 13:58:55 +0000 (13:58 +0000)]
dont use gold highlights

17 years agoMax width for tooltip
amwaterhouse [Mon, 7 May 2007 13:58:46 +0000 (13:58 +0000)]
Max width for tooltip

17 years agostill trying to prevent null painting
amwaterhouse [Mon, 7 May 2007 13:58:31 +0000 (13:58 +0000)]
still trying to prevent null painting

17 years agoUse id hash to add pdb mappings back to alignment
amwaterhouse [Mon, 7 May 2007 13:58:17 +0000 (13:58 +0000)]
Use id hash to add pdb mappings back to alignment

17 years agotIndex prevented deletion of last annotation
amwaterhouse [Mon, 7 May 2007 13:57:40 +0000 (13:57 +0000)]
tIndex prevented deletion of last annotation

17 years agoDont use gold colouring for highlight
amwaterhouse [Mon, 7 May 2007 13:57:03 +0000 (13:57 +0000)]
Dont use gold colouring for highlight

17 years agoUse PDB id for grouping mappings
amwaterhouse [Mon, 7 May 2007 13:56:30 +0000 (13:56 +0000)]
Use PDB id for grouping mappings

17 years agoPDBViewer available if necessary
amwaterhouse [Mon, 7 May 2007 13:55:58 +0000 (13:55 +0000)]
PDBViewer available if necessary

17 years agoCheck bounds of loaded comp
amwaterhouse [Fri, 4 May 2007 13:56:18 +0000 (13:56 +0000)]
Check bounds of loaded comp

17 years agoremove system.out
amwaterhouse [Fri, 4 May 2007 13:55:59 +0000 (13:55 +0000)]
remove system.out

17 years agoadded
amwaterhouse [Fri, 4 May 2007 13:34:04 +0000 (13:34 +0000)]
added

17 years agoAdd dbrefs before zero length features
amwaterhouse [Fri, 4 May 2007 13:33:50 +0000 (13:33 +0000)]
Add dbrefs before zero length features

17 years agolastCommand check
amwaterhouse [Fri, 4 May 2007 13:33:15 +0000 (13:33 +0000)]
lastCommand check

17 years agoRename AppJMol to AppJmol - also AppJmol works with independant sequence sets
amwaterhouse [Fri, 4 May 2007 13:32:23 +0000 (13:32 +0000)]
Rename AppJMol to AppJmol - also AppJmol works with independant sequence sets

17 years agoRenamed to AppJmol
amwaterhouse [Fri, 4 May 2007 13:30:58 +0000 (13:30 +0000)]
Renamed to AppJmol

17 years agoNew example file for version 2.3
amwaterhouse [Fri, 4 May 2007 10:48:38 +0000 (10:48 +0000)]
New example file for version 2.3

17 years agoNew example file for version 2.3
amwaterhouse [Fri, 4 May 2007 10:48:24 +0000 (10:48 +0000)]
New example file for version 2.3

17 years agoSplash screen is not added using normal method, prevents null paint bug
amwaterhouse [Fri, 4 May 2007 10:32:03 +0000 (10:32 +0000)]
Splash screen is not added using normal method, prevents null paint bug

17 years agoAnnotations do not extend when full alignment is adjusted
amwaterhouse [Fri, 4 May 2007 10:31:18 +0000 (10:31 +0000)]
Annotations do not extend when full alignment is adjusted

17 years agopdb id toUpperCase
amwaterhouse [Thu, 3 May 2007 14:41:17 +0000 (14:41 +0000)]
pdb id toUpperCase

17 years agooptimize repaints
amwaterhouse [Thu, 3 May 2007 14:40:57 +0000 (14:40 +0000)]
optimize repaints

17 years agoremove system.out
amwaterhouse [Thu, 3 May 2007 14:40:36 +0000 (14:40 +0000)]
remove system.out

17 years agofeature locations are retrieved by associated accession string and public debug repor...
jprocter [Wed, 2 May 2007 15:20:18 +0000 (15:20 +0000)]
feature locations are retrieved by associated accession string and public debug report request in case embl parsing fails

17 years agofeature locations are retrieved by associated accession string
jprocter [Wed, 2 May 2007 15:19:23 +0000 (15:19 +0000)]
feature locations are retrieved by associated accession string

17 years agopublic debug report log message to gather any cases where Das coordinate frame mappin...
jprocter [Wed, 2 May 2007 14:30:02 +0000 (14:30 +0000)]
public debug report log message to gather any cases where Das coordinate frame mapping fails

17 years agofixed getIntervals bug to ensure it returns range from start of token at fromPosition...
jprocter [Wed, 2 May 2007 14:28:40 +0000 (14:28 +0000)]
fixed getIntervals bug to ensure it returns range from start of token at fromPosition to end of token in toPosition in the direction from fromPosition to toPosition

17 years agodocumentation and proxy call to util.MapList.getToWord(mpos)
jprocter [Wed, 2 May 2007 14:27:25 +0000 (14:27 +0000)]
documentation and proxy call to util.MapList.getToWord(mpos)

17 years agoextractScores menu item disabled for release
jprocter [Wed, 2 May 2007 13:46:56 +0000 (13:46 +0000)]
extractScores menu item disabled for release