jalview.git
17 years agoenable mouseover between DNA coding regions and translated peptide location and broad...
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.

17 years agofix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings...
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

17 years agorecovery of identical dataset sequence object on undo (rather than creation of a...
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)

17 years agoAlignedCodonFrame holds mapping information between individual cDNA regions on dna...
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

17 years agofix modeller generated PDB file reading bug (missing HEADER line with PDB code)
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)

17 years agoJnetFIle is a readable format
jprocter [Sun, 17 Jun 2007 12:54:05 +0000 (12:54 +0000)]
JnetFIle is a readable format

17 years agoscore only annotation IO
jprocter [Sun, 17 Jun 2007 12:52:25 +0000 (12:52 +0000)]
score only annotation IO

17 years agomouseOver highlighting and broadcasting efficiency
jprocter [Sun, 17 Jun 2007 12:51:27 +0000 (12:51 +0000)]
mouseOver highlighting and broadcasting efficiency

17 years agothread safety during repaint
jprocter [Sun, 17 Jun 2007 12:47:44 +0000 (12:47 +0000)]
thread safety during repaint

17 years agonull pointer exception fix
jprocter [Sun, 17 Jun 2007 12:46:32 +0000 (12:46 +0000)]
null pointer exception fix

17 years agosearchresult highlighting on common dataset or specific sequenceI residue range
jprocter [Sun, 17 Jun 2007 12:45:25 +0000 (12:45 +0000)]
searchresult highlighting on common dataset or specific sequenceI residue range

17 years agocorrect construction of new dataset sequence when residues are deleted
jprocter [Sun, 17 Jun 2007 12:43:25 +0000 (12:43 +0000)]
correct construction of new dataset sequence when residues are deleted

17 years agojavadoc
jprocter [Sun, 17 Jun 2007 12:41:36 +0000 (12:41 +0000)]
javadoc

17 years agofix for 'RF' annotation tags and ensured parser is robust to new/unknown two letter...
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.

17 years agoprototype DBRef and Feature Type semantics (for annotating coding regions and disting...
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)

17 years agomoved castor-mapping.xsd to schemas
jprocter [Mon, 28 May 2007 11:14:05 +0000 (11:14 +0000)]
moved castor-mapping.xsd to schemas

17 years agojalview source development documentation
jprocter [Mon, 28 May 2007 11:12:19 +0000 (11:12 +0000)]
jalview source development documentation

17 years agofix compact annotation array routine
jprocter [Mon, 28 May 2007 10:02:06 +0000 (10:02 +0000)]
fix compact annotation array routine

17 years agocastor mapping file schema (for mappings in resources dir) - this is put in for devel...
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.

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