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
amwaterhouse [Mon, 7 May 2007 13:58:31 +0000 (13:58 +0000)]
still trying to prevent null painting
amwaterhouse [Mon, 7 May 2007 13:58:17 +0000 (13:58 +0000)]
Use id hash to add pdb mappings back to alignment
amwaterhouse [Mon, 7 May 2007 13:57:40 +0000 (13:57 +0000)]
tIndex prevented deletion of last annotation
amwaterhouse [Mon, 7 May 2007 13:57:03 +0000 (13:57 +0000)]
Dont use gold colouring for highlight
amwaterhouse [Mon, 7 May 2007 13:56:30 +0000 (13:56 +0000)]
Use PDB id for grouping mappings
amwaterhouse [Mon, 7 May 2007 13:55:58 +0000 (13:55 +0000)]
PDBViewer available if necessary
amwaterhouse [Fri, 4 May 2007 13:56:18 +0000 (13:56 +0000)]
Check bounds of loaded comp
amwaterhouse [Fri, 4 May 2007 13:55:59 +0000 (13:55 +0000)]
remove system.out
amwaterhouse [Fri, 4 May 2007 13:34:04 +0000 (13:34 +0000)]
added
amwaterhouse [Fri, 4 May 2007 13:33:50 +0000 (13:33 +0000)]
Add dbrefs before zero length features
amwaterhouse [Fri, 4 May 2007 13:33:15 +0000 (13:33 +0000)]
lastCommand check
amwaterhouse [Fri, 4 May 2007 13:32:23 +0000 (13:32 +0000)]
Rename AppJMol to AppJmol - also AppJmol works with independant sequence sets
amwaterhouse [Fri, 4 May 2007 13:30:58 +0000 (13:30 +0000)]
Renamed to AppJmol
amwaterhouse [Fri, 4 May 2007 10:48:38 +0000 (10:48 +0000)]
New 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
amwaterhouse [Fri, 4 May 2007 10:32:03 +0000 (10:32 +0000)]
Splash screen is not added using normal method, prevents null paint bug
amwaterhouse [Fri, 4 May 2007 10:31:18 +0000 (10:31 +0000)]
Annotations do not extend when full alignment is adjusted
amwaterhouse [Thu, 3 May 2007 14:41:17 +0000 (14:41 +0000)]
pdb id toUpperCase
amwaterhouse [Thu, 3 May 2007 14:40:57 +0000 (14:40 +0000)]
optimize repaints
amwaterhouse [Thu, 3 May 2007 14:40:36 +0000 (14:40 +0000)]
remove system.out
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
jprocter [Wed, 2 May 2007 15:19:23 +0000 (15:19 +0000)]
feature locations are retrieved by associated accession string
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
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
jprocter [Wed, 2 May 2007 14:27:25 +0000 (14:27 +0000)]
documentation and proxy call to util.MapList.getToWord(mpos)
jprocter [Wed, 2 May 2007 13:46:56 +0000 (13:46 +0000)]
extractScores menu item disabled for release
jprocter [Wed, 2 May 2007 13:41:22 +0000 (13:41 +0000)]
only return non-empty subsequences when getting selection as new sequences
amwaterhouse [Wed, 2 May 2007 13:03:14 +0000 (13:03 +0000)]
Allow expansion of textarea for many sequence input
amwaterhouse [Wed, 2 May 2007 13:02:47 +0000 (13:02 +0000)]
AMSA input set padgaps true
amwaterhouse [Wed, 2 May 2007 13:02:21 +0000 (13:02 +0000)]
convert space to gapchar
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
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
jprocter [Wed, 2 May 2007 12:23:17 +0000 (12:23 +0000)]
copy only the sequence associated alignment annotation displayed in the current view
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
jprocter [Wed, 2 May 2007 12:20:10 +0000 (12:20 +0000)]
return flag indicating if annotations were actually deleted from alignment
jprocter [Wed, 2 May 2007 12:19:55 +0000 (12:19 +0000)]
checks for negative start column in restrict
amwaterhouse [Wed, 2 May 2007 10:47:29 +0000 (10:47 +0000)]
Padgaps is false by default
amwaterhouse [Tue, 1 May 2007 16:34:53 +0000 (16:34 +0000)]
setVisible flag sent to EditNameDialog
amwaterhouse [Tue, 1 May 2007 16:33:57 +0000 (16:33 +0000)]
Pad gaps method
amwaterhouse [Tue, 1 May 2007 16:33:27 +0000 (16:33 +0000)]
Make sure annots are alignment width
amwaterhouse [Tue, 1 May 2007 14:18:56 +0000 (14:18 +0000)]
use jalviewLite to addFrame
amwaterhouse [Tue, 1 May 2007 14:18:36 +0000 (14:18 +0000)]
remove system.out
amwaterhouse [Tue, 1 May 2007 13:58:22 +0000 (13:58 +0000)]
set chains available
amwaterhouse [Tue, 1 May 2007 13:40:02 +0000 (13:40 +0000)]
Multiple views/hidden region/undo out of index bug
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
jprocter [Tue, 1 May 2007 11:47:32 +0000 (11:47 +0000)]
javadoc
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.
jprocter [Tue, 1 May 2007 10:42:59 +0000 (10:42 +0000)]
sort-by-score works of sequence-annotation, not alignment annotation vector
amwaterhouse [Tue, 1 May 2007 10:04:43 +0000 (10:04 +0000)]
Save seqset properties
amwaterhouse [Tue, 1 May 2007 10:03:45 +0000 (10:03 +0000)]
Seqset properties saved
jprocter [Tue, 1 May 2007 09:51:03 +0000 (09:51 +0000)]
2.3 what's new
jprocter [Tue, 1 May 2007 09:50:49 +0000 (09:50 +0000)]
preliminary EMBL and mapping documentation
jprocter [Mon, 30 Apr 2007 15:36:20 +0000 (15:36 +0000)]
'no sources selected' calls method on feature settings dialog to prompt user.
fixed never-ending das feature retrieval bug.
jprocter [Mon, 30 Apr 2007 15:35:17 +0000 (15:35 +0000)]
fixed deadlock
amwaterhouse [Mon, 30 Apr 2007 15:02:27 +0000 (15:02 +0000)]
setVisible replaces show
amwaterhouse [Mon, 30 Apr 2007 15:00:45 +0000 (15:00 +0000)]
Version 11.0.2
amwaterhouse [Mon, 30 Apr 2007 14:59:57 +0000 (14:59 +0000)]
REmoved
jprocter [Mon, 30 Apr 2007 13:50:33 +0000 (13:50 +0000)]
rebuild sort by scores menu when new annotation is available
jprocter [Mon, 30 Apr 2007 13:48:36 +0000 (13:48 +0000)]
pad should leave null annotations array null
jprocter [Mon, 30 Apr 2007 13:24:07 +0000 (13:24 +0000)]
convenient creation of 'score only' annotation.
jprocter [Mon, 30 Apr 2007 13:23:14 +0000 (13:23 +0000)]
parse alignment properties and add annotation rows for general alignment position annotation.
jprocter [Mon, 30 Apr 2007 13:22:25 +0000 (13:22 +0000)]
alignment properties and embedded newick strings can be retrieved from parsed files
jprocter [Mon, 30 Apr 2007 13:14:17 +0000 (13:14 +0000)]
dssp 7-state to three state lookup
jprocter [Mon, 30 Apr 2007 09:44:38 +0000 (09:44 +0000)]
javadoc
amwaterhouse [Fri, 27 Apr 2007 16:21:01 +0000 (16:21 +0000)]
remove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:20:41 +0000 (16:20 +0000)]
REmove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:20:22 +0000 (16:20 +0000)]
Repaint after feature added
amwaterhouse [Fri, 27 Apr 2007 16:19:57 +0000 (16:19 +0000)]
Prevent err when editing and overview drawing
amwaterhouse [Fri, 27 Apr 2007 16:19:25 +0000 (16:19 +0000)]
FeatureRenderer mixups fixed
amwaterhouse [Fri, 27 Apr 2007 15:36:36 +0000 (15:36 +0000)]
Remove system.out AppletPDBViewer.java
amwaterhouse [Fri, 27 Apr 2007 15:32:46 +0000 (15:32 +0000)]
Check pdbid size >0
amwaterhouse [Fri, 27 Apr 2007 15:32:12 +0000 (15:32 +0000)]
Trouble with featureRenderers fixed
amwaterhouse [Fri, 27 Apr 2007 14:53:33 +0000 (14:53 +0000)]
Move repaint in thread
amwaterhouse [Fri, 27 Apr 2007 14:47:00 +0000 (14:47 +0000)]
Put alignmentProperties in scrollpane
amwaterhouse [Fri, 27 Apr 2007 14:45:31 +0000 (14:45 +0000)]
Check feature group is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:45:04 +0000 (14:45 +0000)]
remove System.out
amwaterhouse [Fri, 27 Apr 2007 14:44:30 +0000 (14:44 +0000)]
Add param to Jmol path
amwaterhouse [Fri, 27 Apr 2007 14:44:10 +0000 (14:44 +0000)]
padGaps moved
amwaterhouse [Fri, 27 Apr 2007 14:43:36 +0000 (14:43 +0000)]
Make sure mainContainer and owner are not null
amwaterhouse [Fri, 27 Apr 2007 14:43:20 +0000 (14:43 +0000)]
Must check that featureGroup is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:42:59 +0000 (14:42 +0000)]
amendFeatures