jalview.git
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

17 years agoonly return non-empty subsequences when getting selection as new sequences
jprocter [Wed, 2 May 2007 13:41:22 +0000 (13:41 +0000)]
only return non-empty subsequences when getting selection as new sequences

17 years agoAllow expansion of textarea for many sequence input
amwaterhouse [Wed, 2 May 2007 13:03:14 +0000 (13:03 +0000)]
Allow expansion of textarea for many sequence input

17 years agoAMSA input set padgaps true
amwaterhouse [Wed, 2 May 2007 13:02:47 +0000 (13:02 +0000)]
AMSA input set padgaps true

17 years agoconvert space to gapchar
amwaterhouse [Wed, 2 May 2007 13:02:21 +0000 (13:02 +0000)]
convert space to gapchar

17 years agoundo stackempty error fix, refactored do and undo() method to take array of alignment...
jprocter [Wed, 2 May 2007 12:25:44 +0000 (12:25 +0000)]
undo stackempty error fix, refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation, convenience method for getting alignment object array for all views

17 years agorefactored do and undo() method to take array of alignments for operations that resul...
jprocter [Wed, 2 May 2007 12:24:41 +0000 (12:24 +0000)]
refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation

17 years agocopy only the sequence associated alignment annotation displayed in the current view
jprocter [Wed, 2 May 2007 12:23:17 +0000 (12:23 +0000)]
copy only the sequence associated alignment annotation displayed in the current view

17 years agosubsequence bound checks and constructor for selectively duplicating sequence associa...
jprocter [Wed, 2 May 2007 12:21:26 +0000 (12:21 +0000)]
subsequence bound checks and constructor for selectively duplicating sequence associated alignment annotation in copy constructor

17 years agoreturn flag indicating if annotations were actually deleted from alignment
jprocter [Wed, 2 May 2007 12:20:10 +0000 (12:20 +0000)]
return flag indicating if annotations were actually deleted from alignment

17 years agochecks for negative start column in restrict
jprocter [Wed, 2 May 2007 12:19:55 +0000 (12:19 +0000)]
checks for negative start column in restrict

17 years agoPadgaps is false by default
amwaterhouse [Wed, 2 May 2007 10:47:29 +0000 (10:47 +0000)]
Padgaps is false by default

17 years agosetVisible flag sent to EditNameDialog
amwaterhouse [Tue, 1 May 2007 16:34:53 +0000 (16:34 +0000)]
setVisible flag sent to EditNameDialog

17 years agoPad gaps method
amwaterhouse [Tue, 1 May 2007 16:33:57 +0000 (16:33 +0000)]
Pad gaps method

17 years agoMake sure annots are alignment width
amwaterhouse [Tue, 1 May 2007 16:33:27 +0000 (16:33 +0000)]
Make sure annots are alignment width

17 years agouse jalviewLite to addFrame
amwaterhouse [Tue, 1 May 2007 14:18:56 +0000 (14:18 +0000)]
use jalviewLite to addFrame

17 years agoremove system.out
amwaterhouse [Tue, 1 May 2007 14:18:36 +0000 (14:18 +0000)]
remove system.out

17 years agoset chains available
amwaterhouse [Tue, 1 May 2007 13:58:22 +0000 (13:58 +0000)]
set chains available

17 years agoMultiple views/hidden region/undo out of index bug
amwaterhouse [Tue, 1 May 2007 13:40:02 +0000 (13:40 +0000)]
Multiple views/hidden region/undo out of index bug

17 years agoCan specify PDB chain to map sequence to - only used by applet so far
amwaterhouse [Tue, 1 May 2007 12:25:38 +0000 (12:25 +0000)]
Can specify PDB chain to map sequence to - only used by applet so far

17 years agojavadoc
jprocter [Tue, 1 May 2007 11:47:32 +0000 (11:47 +0000)]
javadoc

17 years agoremoveAlignmentAnnotation only removes annotation objects referenced by the alignment...
jprocter [Tue, 1 May 2007 11:46:38 +0000 (11:46 +0000)]
removeAlignmentAnnotation only removes annotation objects referenced by the alignmentI and will do nothing otherwise.

17 years agosort-by-score works of sequence-annotation, not alignment annotation vector
jprocter [Tue, 1 May 2007 10:42:59 +0000 (10:42 +0000)]
sort-by-score works of sequence-annotation, not alignment annotation vector

17 years agoSave seqset properties
amwaterhouse [Tue, 1 May 2007 10:04:43 +0000 (10:04 +0000)]
Save seqset properties

17 years agoSeqset properties saved
amwaterhouse [Tue, 1 May 2007 10:03:45 +0000 (10:03 +0000)]
Seqset properties saved

17 years ago2.3 what's new
jprocter [Tue, 1 May 2007 09:51:03 +0000 (09:51 +0000)]
2.3 what's new

17 years agopreliminary EMBL and mapping documentation
jprocter [Tue, 1 May 2007 09:50:49 +0000 (09:50 +0000)]
preliminary EMBL and mapping documentation