amwaterhouse [Fri, 7 Jul 2006 13:34:14 +0000 (13:34 +0000)]
Redundant Remove Redundancy Removed
amwaterhouse [Fri, 7 Jul 2006 13:30:38 +0000 (13:30 +0000)]
Sequence numbering maintained
amwaterhouse [Fri, 7 Jul 2006 13:09:38 +0000 (13:09 +0000)]
Changeable background colour
amwaterhouse [Fri, 7 Jul 2006 13:08:58 +0000 (13:08 +0000)]
Make sure bond has a colour
amwaterhouse [Fri, 7 Jul 2006 13:08:40 +0000 (13:08 +0000)]
Make sure atom has a colour
amwaterhouse [Fri, 7 Jul 2006 13:07:32 +0000 (13:07 +0000)]
Highlight sequences before seleting
amwaterhouse [Fri, 7 Jul 2006 13:07:04 +0000 (13:07 +0000)]
Corrected for hidden rows
amwaterhouse [Fri, 7 Jul 2006 13:06:29 +0000 (13:06 +0000)]
Row might have height of zero
amwaterhouse [Fri, 7 Jul 2006 13:05:54 +0000 (13:05 +0000)]
check control down if c pressed in cursor mode
amwaterhouse [Fri, 7 Jul 2006 13:05:15 +0000 (13:05 +0000)]
changeColour is public
amwaterhouse [Fri, 7 Jul 2006 13:04:21 +0000 (13:04 +0000)]
Coms might be null
amwaterhouse [Fri, 7 Jul 2006 13:03:39 +0000 (13:03 +0000)]
New panel layouts
amwaterhouse [Fri, 7 Jul 2006 13:03:13 +0000 (13:03 +0000)]
Offsets
amwaterhouse [Fri, 7 Jul 2006 13:02:53 +0000 (13:02 +0000)]
Optimised PID method
amwaterhouse [Fri, 7 Jul 2006 13:02:20 +0000 (13:02 +0000)]
Make 1.1 compatible
amwaterhouse [Fri, 7 Jul 2006 13:02:02 +0000 (13:02 +0000)]
Move position of stopLoading for 1.5 people
amwaterhouse [Fri, 7 Jul 2006 13:01:34 +0000 (13:01 +0000)]
make 1.1 compatible
amwaterhouse [Fri, 7 Jul 2006 13:01:17 +0000 (13:01 +0000)]
Dont write graph type twice
amwaterhouse [Fri, 7 Jul 2006 13:00:45 +0000 (13:00 +0000)]
Checks on drawing characters and if sequence ref has been deleted
amwaterhouse [Fri, 7 Jul 2006 13:00:01 +0000 (13:00 +0000)]
Colour argument added, to mirror applet view
amwaterhouse [Fri, 7 Jul 2006 12:58:26 +0000 (12:58 +0000)]
Prepare for launchFullApplication
amwaterhouse [Fri, 7 Jul 2006 12:56:57 +0000 (12:56 +0000)]
Highlight sequences to be deleted before deleting, and apply button exists
amwaterhouse [Fri, 7 Jul 2006 12:56:13 +0000 (12:56 +0000)]
Check row.annotations is not null
amwaterhouse [Fri, 7 Jul 2006 12:55:51 +0000 (12:55 +0000)]
SelectionGroup is initially null
amwaterhouse [Fri, 7 Jul 2006 12:55:08 +0000 (12:55 +0000)]
Replaced by AnnotationFile
amwaterhouse [Fri, 23 Jun 2006 16:25:17 +0000 (16:25 +0000)]
Uniprot may have several accession ids
amwaterhouse [Fri, 23 Jun 2006 15:33:56 +0000 (15:33 +0000)]
Parse HTML links from jalview features file
amwaterhouse [Fri, 23 Jun 2006 13:47:22 +0000 (13:47 +0000)]
DBRefFetcher replaces SequenceFeatureFetcher
amwaterhouse [Fri, 23 Jun 2006 13:46:52 +0000 (13:46 +0000)]
Check if featuresDisplayed is null
amwaterhouse [Fri, 23 Jun 2006 13:46:10 +0000 (13:46 +0000)]
Case wrapped jar file, wrapped preference true dealt with
amwaterhouse [Fri, 23 Jun 2006 13:45:41 +0000 (13:45 +0000)]
No need for repaint
amwaterhouse [Fri, 23 Jun 2006 13:45:06 +0000 (13:45 +0000)]
Uses FeaturesFile parser, GFF and Jalview
amwaterhouse [Fri, 23 Jun 2006 13:44:18 +0000 (13:44 +0000)]
++ --
amwaterhouse [Thu, 22 Jun 2006 08:54:10 +0000 (08:54 +0000)]
Check featureLinks is not null
amwaterhouse [Thu, 22 Jun 2006 08:53:17 +0000 (08:53 +0000)]
ParseFeaturesFile takes protocol as arg
amwaterhouse [Thu, 22 Jun 2006 08:52:25 +0000 (08:52 +0000)]
Takes AlignFrame as arg, to update progressbar
amwaterhouse [Thu, 22 Jun 2006 08:51:03 +0000 (08:51 +0000)]
AlignFrame is now the FeatureListener
amwaterhouse [Thu, 22 Jun 2006 08:50:35 +0000 (08:50 +0000)]
Fetch DBRefs
amwaterhouse [Thu, 22 Jun 2006 08:50:07 +0000 (08:50 +0000)]
Ye olde SequenceFeatureFetcher
amwaterhouse [Thu, 22 Jun 2006 08:49:34 +0000 (08:49 +0000)]
Renamed to DBRefFetcher
amwaterhouse [Thu, 22 Jun 2006 08:48:48 +0000 (08:48 +0000)]
Not used in Jalview
amwaterhouse [Thu, 15 Jun 2006 15:37:18 +0000 (15:37 +0000)]
Use spice-3d das1 source list for nowjalview/gui/DasSourceBrowser.java
amwaterhouse [Thu, 15 Jun 2006 14:19:06 +0000 (14:19 +0000)]
Fixed to trial registry at the moment
amwaterhouse [Thu, 15 Jun 2006 14:06:37 +0000 (14:06 +0000)]
new files
amwaterhouse [Thu, 15 Jun 2006 14:06:00 +0000 (14:06 +0000)]
Not using AxisDasRegistry
amwaterhouse [Thu, 15 Jun 2006 14:04:44 +0000 (14:04 +0000)]
Not needed
amwaterhouse [Thu, 15 Jun 2006 14:02:03 +0000 (14:02 +0000)]
check helperUrl is not null
amwaterhouse [Thu, 15 Jun 2006 13:03:02 +0000 (13:03 +0000)]
Das client files
amwaterhouse [Thu, 15 Jun 2006 12:57:49 +0000 (12:57 +0000)]
Correction - use start and end
amwaterhouse [Thu, 15 Jun 2006 12:56:35 +0000 (12:56 +0000)]
Dont add start and end for the moment
amwaterhouse [Thu, 15 Jun 2006 12:56:08 +0000 (12:56 +0000)]
Wrap alignment moved to alignFrame
amwaterhouse [Thu, 15 Jun 2006 12:55:45 +0000 (12:55 +0000)]
Non positional features shown as mouse over
amwaterhouse [Thu, 15 Jun 2006 12:55:25 +0000 (12:55 +0000)]
fr.findAllFeatures on init
amwaterhouse [Thu, 15 Jun 2006 12:54:39 +0000 (12:54 +0000)]
Correct citation
amwaterhouse [Thu, 15 Jun 2006 12:54:19 +0000 (12:54 +0000)]
Unnecessary import
amwaterhouse [Thu, 15 Jun 2006 12:53:37 +0000 (12:53 +0000)]
FeatureRenderer synchronized featuresAdded method
amwaterhouse [Thu, 15 Jun 2006 12:51:52 +0000 (12:51 +0000)]
Maintain status and position only for uniprot parsing
amwaterhouse [Wed, 14 Jun 2006 10:19:54 +0000 (10:19 +0000)]
Fileloading progressbar
amwaterhouse [Wed, 14 Jun 2006 10:17:45 +0000 (10:17 +0000)]
Status is now in otherData of feature
amwaterhouse [Wed, 14 Jun 2006 10:16:23 +0000 (10:16 +0000)]
Sequence checks for duplicate features
amwaterhouse [Wed, 14 Jun 2006 10:15:39 +0000 (10:15 +0000)]
parseAppletParam
amwaterhouse [Wed, 14 Jun 2006 10:14:31 +0000 (10:14 +0000)]
parseAppletParameter
amwaterhouse [Fri, 9 Jun 2006 16:37:51 +0000 (16:37 +0000)]
Retrieve multiple EMBL ids
amwaterhouse [Fri, 9 Jun 2006 16:22:32 +0000 (16:22 +0000)]
Size adjustments for MacOSX
amwaterhouse [Fri, 9 Jun 2006 16:22:09 +0000 (16:22 +0000)]
Remove unnecessary lines
amwaterhouse [Fri, 9 Jun 2006 16:21:48 +0000 (16:21 +0000)]
createColourFromName if not specified
amwaterhouse [Fri, 9 Jun 2006 16:21:15 +0000 (16:21 +0000)]
Export annotations as Jalview format
amwaterhouse [Fri, 9 Jun 2006 16:20:57 +0000 (16:20 +0000)]
Feature and annotation parsing moved to io
amwaterhouse [Fri, 9 Jun 2006 16:20:13 +0000 (16:20 +0000)]
otherDetails
amwaterhouse [Fri, 9 Jun 2006 16:19:48 +0000 (16:19 +0000)]
Remove getsfarray
amwaterhouse [Fri, 9 Jun 2006 16:19:23 +0000 (16:19 +0000)]
getSequencesArray
amwaterhouse [Fri, 9 Jun 2006 16:18:14 +0000 (16:18 +0000)]
setAcceptAllFileFilter fixes bug on MacOSX
amwaterhouse [Fri, 9 Jun 2006 16:17:41 +0000 (16:17 +0000)]
Export features / annotations
amwaterhouse [Fri, 9 Jun 2006 16:17:01 +0000 (16:17 +0000)]
Save text to file
amwaterhouse [Fri, 9 Jun 2006 16:16:40 +0000 (16:16 +0000)]
createColourFromName
amwaterhouse [Fri, 9 Jun 2006 16:16:14 +0000 (16:16 +0000)]
Function not used
amwaterhouse [Fri, 9 Jun 2006 16:15:41 +0000 (16:15 +0000)]
readAnnotationFile
amwaterhouse [Fri, 9 Jun 2006 16:15:23 +0000 (16:15 +0000)]
parseFeaturesFile
amwaterhouse [Fri, 9 Jun 2006 16:14:17 +0000 (16:14 +0000)]
Annotation/feature exporter
jprocter [Thu, 8 Jun 2006 18:17:35 +0000 (18:17 +0000)]
Introduced DbRefEntry to DasSourceCoordinateSystem check to only call sources for sequences with a particular DBRefEntry id (PDB or Uniprot currently)
jprocter [Thu, 8 Jun 2006 18:16:15 +0000 (18:16 +0000)]
DBRefEntry.source enum type
jprocter [Thu, 8 Jun 2006 15:16:47 +0000 (15:16 +0000)]
bugfixed and podded.
jprocter [Thu, 8 Jun 2006 13:56:37 +0000 (13:56 +0000)]
simplest conversion of gff to jalview annotation format files.
amwaterhouse [Wed, 7 Jun 2006 14:48:18 +0000 (14:48 +0000)]
New link image
amwaterhouse [Wed, 7 Jun 2006 14:47:55 +0000 (14:47 +0000)]
Wrap alignment added to preferences
amwaterhouse [Wed, 7 Jun 2006 13:35:15 +0000 (13:35 +0000)]
Checks in case DasSource is null
amwaterhouse [Wed, 7 Jun 2006 13:03:41 +0000 (13:03 +0000)]
Smaller file size
amwaterhouse [Wed, 7 Jun 2006 13:03:20 +0000 (13:03 +0000)]
New link image
amwaterhouse [Wed, 7 Jun 2006 13:01:38 +0000 (13:01 +0000)]
DAS client libraries
amwaterhouse [Wed, 7 Jun 2006 12:59:48 +0000 (12:59 +0000)]
Remove unnecessary ints
amwaterhouse [Wed, 7 Jun 2006 12:59:26 +0000 (12:59 +0000)]
DAS sources added
amwaterhouse [Wed, 7 Jun 2006 12:59:07 +0000 (12:59 +0000)]
PopupMenu displays URL links
amwaterhouse [Wed, 7 Jun 2006 12:58:21 +0000 (12:58 +0000)]
ignore begin==0 and end==0 for the moment
amwaterhouse [Wed, 7 Jun 2006 12:57:38 +0000 (12:57 +0000)]
Create random colour only if Colour is not specified
amwaterhouse [Wed, 7 Jun 2006 12:57:01 +0000 (12:57 +0000)]
Implements FeatureListener
amwaterhouse [Wed, 7 Jun 2006 12:56:42 +0000 (12:56 +0000)]
new DasSequenceFetcher
amwaterhouse [Wed, 7 Jun 2006 12:56:06 +0000 (12:56 +0000)]
DAS Settings tab added
amwaterhouse [Wed, 7 Jun 2006 12:55:42 +0000 (12:55 +0000)]
Use a label with html instead of textarea
amwaterhouse [Wed, 7 Jun 2006 12:54:50 +0000 (12:54 +0000)]
Remove position, add score and links
amwaterhouse [Wed, 7 Jun 2006 12:53:25 +0000 (12:53 +0000)]
Parameter to show feature settings