jalview.git
18 years agoWrap alignment moved to alignFrame
amwaterhouse [Thu, 15 Jun 2006 12:56:08 +0000 (12:56 +0000)]
Wrap alignment moved to alignFrame

18 years agoNon positional features shown as mouse over
amwaterhouse [Thu, 15 Jun 2006 12:55:45 +0000 (12:55 +0000)]
Non positional features shown as mouse over

18 years agofr.findAllFeatures on init
amwaterhouse [Thu, 15 Jun 2006 12:55:25 +0000 (12:55 +0000)]
fr.findAllFeatures on init

18 years agoCorrect citation
amwaterhouse [Thu, 15 Jun 2006 12:54:39 +0000 (12:54 +0000)]
Correct citation

18 years agoUnnecessary import
amwaterhouse [Thu, 15 Jun 2006 12:54:19 +0000 (12:54 +0000)]
Unnecessary import

18 years agoFeatureRenderer synchronized featuresAdded method
amwaterhouse [Thu, 15 Jun 2006 12:53:37 +0000 (12:53 +0000)]
FeatureRenderer synchronized featuresAdded method

18 years agoMaintain status and position only for uniprot parsing
amwaterhouse [Thu, 15 Jun 2006 12:51:52 +0000 (12:51 +0000)]
Maintain status and position only for uniprot parsing

18 years agoFileloading progressbar
amwaterhouse [Wed, 14 Jun 2006 10:19:54 +0000 (10:19 +0000)]
Fileloading progressbar

18 years agoStatus is now in otherData of feature
amwaterhouse [Wed, 14 Jun 2006 10:17:45 +0000 (10:17 +0000)]
Status is now in otherData of feature

18 years agoSequence checks for duplicate features
amwaterhouse [Wed, 14 Jun 2006 10:16:23 +0000 (10:16 +0000)]
Sequence checks for duplicate features

18 years agoparseAppletParam
amwaterhouse [Wed, 14 Jun 2006 10:15:39 +0000 (10:15 +0000)]
parseAppletParam

18 years agoparseAppletParameter
amwaterhouse [Wed, 14 Jun 2006 10:14:31 +0000 (10:14 +0000)]
parseAppletParameter

18 years agoRetrieve multiple EMBL ids
amwaterhouse [Fri, 9 Jun 2006 16:37:51 +0000 (16:37 +0000)]
Retrieve multiple EMBL ids

18 years agoSize adjustments for MacOSX
amwaterhouse [Fri, 9 Jun 2006 16:22:32 +0000 (16:22 +0000)]
Size adjustments for MacOSX

18 years agoRemove unnecessary lines
amwaterhouse [Fri, 9 Jun 2006 16:22:09 +0000 (16:22 +0000)]
Remove unnecessary lines

18 years agocreateColourFromName if not specified
amwaterhouse [Fri, 9 Jun 2006 16:21:48 +0000 (16:21 +0000)]
createColourFromName if not specified

18 years agoExport annotations as Jalview format
amwaterhouse [Fri, 9 Jun 2006 16:21:15 +0000 (16:21 +0000)]
Export annotations as Jalview format

18 years agoFeature and annotation parsing moved to io
amwaterhouse [Fri, 9 Jun 2006 16:20:57 +0000 (16:20 +0000)]
Feature and annotation parsing moved to io

18 years agootherDetails
amwaterhouse [Fri, 9 Jun 2006 16:20:13 +0000 (16:20 +0000)]
otherDetails

18 years agoRemove getsfarray
amwaterhouse [Fri, 9 Jun 2006 16:19:48 +0000 (16:19 +0000)]
Remove getsfarray

18 years agogetSequencesArray
amwaterhouse [Fri, 9 Jun 2006 16:19:23 +0000 (16:19 +0000)]
getSequencesArray

18 years agosetAcceptAllFileFilter fixes bug on MacOSX
amwaterhouse [Fri, 9 Jun 2006 16:18:14 +0000 (16:18 +0000)]
setAcceptAllFileFilter fixes bug on MacOSX

18 years agoExport features / annotations
amwaterhouse [Fri, 9 Jun 2006 16:17:41 +0000 (16:17 +0000)]
Export features / annotations

18 years agoSave text to file
amwaterhouse [Fri, 9 Jun 2006 16:17:01 +0000 (16:17 +0000)]
Save text to file

18 years agocreateColourFromName
amwaterhouse [Fri, 9 Jun 2006 16:16:40 +0000 (16:16 +0000)]
createColourFromName

18 years agoFunction not used
amwaterhouse [Fri, 9 Jun 2006 16:16:14 +0000 (16:16 +0000)]
Function not used

18 years agoreadAnnotationFile
amwaterhouse [Fri, 9 Jun 2006 16:15:41 +0000 (16:15 +0000)]
readAnnotationFile

18 years agoparseFeaturesFile
amwaterhouse [Fri, 9 Jun 2006 16:15:23 +0000 (16:15 +0000)]
parseFeaturesFile

18 years agoAnnotation/feature exporter
amwaterhouse [Fri, 9 Jun 2006 16:14:17 +0000 (16:14 +0000)]
Annotation/feature exporter

18 years agoIntroduced DbRefEntry to DasSourceCoordinateSystem check to only call sources for...
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)

18 years agoDBRefEntry.source enum type
jprocter [Thu, 8 Jun 2006 18:16:15 +0000 (18:16 +0000)]
DBRefEntry.source enum type

18 years agobugfixed and podded.
jprocter [Thu, 8 Jun 2006 15:16:47 +0000 (15:16 +0000)]
bugfixed and podded.

18 years agosimplest conversion of gff to jalview annotation format files.
jprocter [Thu, 8 Jun 2006 13:56:37 +0000 (13:56 +0000)]
simplest conversion of gff to jalview annotation format files.

18 years agoNew link image
amwaterhouse [Wed, 7 Jun 2006 14:48:18 +0000 (14:48 +0000)]
New link image

18 years agoWrap alignment added to preferences
amwaterhouse [Wed, 7 Jun 2006 14:47:55 +0000 (14:47 +0000)]
Wrap alignment added to preferences

18 years agoChecks in case DasSource is null
amwaterhouse [Wed, 7 Jun 2006 13:35:15 +0000 (13:35 +0000)]
Checks in case DasSource is null

18 years agoSmaller file size
amwaterhouse [Wed, 7 Jun 2006 13:03:41 +0000 (13:03 +0000)]
Smaller file size

18 years agoNew link image
amwaterhouse [Wed, 7 Jun 2006 13:03:20 +0000 (13:03 +0000)]
New link image

18 years agoDAS client libraries
amwaterhouse [Wed, 7 Jun 2006 13:01:38 +0000 (13:01 +0000)]
DAS client libraries

18 years agoRemove unnecessary ints
amwaterhouse [Wed, 7 Jun 2006 12:59:48 +0000 (12:59 +0000)]
Remove unnecessary ints

18 years agoDAS sources added
amwaterhouse [Wed, 7 Jun 2006 12:59:26 +0000 (12:59 +0000)]
DAS sources added

18 years agoPopupMenu displays URL links
amwaterhouse [Wed, 7 Jun 2006 12:59:07 +0000 (12:59 +0000)]
PopupMenu displays URL links

18 years agoignore begin==0 and end==0 for the moment
amwaterhouse [Wed, 7 Jun 2006 12:58:21 +0000 (12:58 +0000)]
ignore begin==0 and end==0 for the moment

18 years agoCreate random colour only if Colour is not specified
amwaterhouse [Wed, 7 Jun 2006 12:57:38 +0000 (12:57 +0000)]
Create random colour only if Colour is not specified

18 years agoImplements FeatureListener
amwaterhouse [Wed, 7 Jun 2006 12:57:01 +0000 (12:57 +0000)]
Implements FeatureListener

18 years agonew DasSequenceFetcher
amwaterhouse [Wed, 7 Jun 2006 12:56:42 +0000 (12:56 +0000)]
new DasSequenceFetcher

18 years agoDAS Settings tab added
amwaterhouse [Wed, 7 Jun 2006 12:56:06 +0000 (12:56 +0000)]
DAS Settings tab added

18 years agoUse a label with html instead of textarea
amwaterhouse [Wed, 7 Jun 2006 12:55:42 +0000 (12:55 +0000)]
Use a label with html instead of textarea

18 years agoRemove position, add score and links
amwaterhouse [Wed, 7 Jun 2006 12:54:50 +0000 (12:54 +0000)]
Remove position, add score and links

18 years agoParameter to show feature settings
amwaterhouse [Wed, 7 Jun 2006 12:53:25 +0000 (12:53 +0000)]
Parameter to show feature settings

18 years agoTooltips for features, links for features added
amwaterhouse [Wed, 7 Jun 2006 12:52:43 +0000 (12:52 +0000)]
Tooltips for features, links for features added

18 years agoNEW FILES
amwaterhouse [Wed, 7 Jun 2006 12:51:47 +0000 (12:51 +0000)]
NEW FILES

18 years agobroken link typo. (SEVENtwentyfour alert)
jprocter [Wed, 7 Jun 2006 10:20:18 +0000 (10:20 +0000)]
broken link typo. (SEVENtwentyfour alert)

18 years agoadded future method comment
jprocter [Thu, 18 May 2006 09:22:26 +0000 (09:22 +0000)]
added future method comment

18 years agoadded the jnetfile parameter to specify a JNet concise file to be
jprocter [Wed, 17 May 2006 16:54:44 +0000 (16:54 +0000)]
added the jnetfile parameter to specify a JNet concise file to be
parsed to add jnet predictions to the first sequence in the alignment

18 years agoadded unofficial support for concise output parsing from the JNet server to extract...
jprocter [Wed, 17 May 2006 16:52:58 +0000 (16:52 +0000)]
added unofficial support for concise output parsing from the JNet server to extract the sequence profile.

18 years agorefactored code for creating JNet annotations
jprocter [Wed, 17 May 2006 16:51:29 +0000 (16:51 +0000)]
refactored code for creating JNet annotations

18 years agoRefactored code for creating annotation objects from a jnetfile object.
jprocter [Wed, 17 May 2006 16:48:49 +0000 (16:48 +0000)]
Refactored code for creating annotation objects from a jnetfile object.

18 years agoRestrict annotation panel to 50% window on load
amwaterhouse [Wed, 17 May 2006 16:24:32 +0000 (16:24 +0000)]
Restrict annotation panel to 50% window on load

18 years agographColour, graphGroup, more relaxed annotation requirements
amwaterhouse [Tue, 16 May 2006 13:06:01 +0000 (13:06 +0000)]
graphColour, graphGroup, more relaxed annotation requirements

18 years agoSave annotation colours, hideConsevation etc, graphGroups
amwaterhouse [Tue, 16 May 2006 13:04:56 +0000 (13:04 +0000)]
Save annotation colours, hideConsevation etc, graphGroups

18 years agoSwitch off dashedline after drawing groups
amwaterhouse [Tue, 16 May 2006 12:01:13 +0000 (12:01 +0000)]
Switch off dashedline after drawing groups

18 years agoRemove unwanted line
amwaterhouse [Tue, 16 May 2006 11:09:02 +0000 (11:09 +0000)]
Remove unwanted line

18 years agoAllow for scroller position
amwaterhouse [Tue, 16 May 2006 11:08:34 +0000 (11:08 +0000)]
Allow for scroller position

18 years agoRemove system.out
amwaterhouse [Tue, 16 May 2006 10:24:02 +0000 (10:24 +0000)]
Remove system.out

18 years agoRearrange annotations
amwaterhouse [Tue, 16 May 2006 10:23:48 +0000 (10:23 +0000)]
Rearrange annotations

18 years agoadded popup warning when proxy settings must be configured.
jprocter [Tue, 16 May 2006 09:32:56 +0000 (09:32 +0000)]
added popup warning when proxy settings must be configured.

18 years agoMonospaced font not allowed if charWidth stretched
amwaterhouse [Mon, 15 May 2006 14:52:51 +0000 (14:52 +0000)]
Monospaced font not allowed if charWidth stretched

18 years agoBrackets around orgin calculation
amwaterhouse [Mon, 15 May 2006 14:52:26 +0000 (14:52 +0000)]
Brackets around orgin calculation

18 years agoAll or nothing drawing display char
amwaterhouse [Mon, 15 May 2006 14:09:34 +0000 (14:09 +0000)]
All or nothing drawing display char

18 years agoEPS font width is a double, check this for monospacedFont
amwaterhouse [Mon, 15 May 2006 13:28:35 +0000 (13:28 +0000)]
EPS font width is a double, check this for monospacedFont

18 years agoIf headless, get the width of Jalview wrapped window correct
amwaterhouse [Mon, 15 May 2006 13:28:07 +0000 (13:28 +0000)]
If headless, get the width of Jalview wrapped window correct

18 years agorearranged discoverer to dynamically update on demand
jprocter [Fri, 12 May 2006 16:00:21 +0000 (16:00 +0000)]
rearranged discoverer to dynamically update on demand

18 years agoreturns to zero degrees when stopped
amwaterhouse [Fri, 12 May 2006 10:55:27 +0000 (10:55 +0000)]
returns to zero degrees when stopped

18 years agopass viewport to fileloader, as we need to firepropertychange once sequences are...
amwaterhouse [Fri, 12 May 2006 08:47:16 +0000 (08:47 +0000)]
pass viewport to fileloader, as we need to firepropertychange once sequences are added

18 years agoSlight mod url chooser for Mac users
amwaterhouse [Thu, 11 May 2006 15:07:21 +0000 (15:07 +0000)]
Slight mod url chooser for Mac users

18 years agoRemove commented line
amwaterhouse [Thu, 11 May 2006 14:54:59 +0000 (14:54 +0000)]
Remove commented line

18 years agoSlightly smaller recent panel
amwaterhouse [Thu, 11 May 2006 14:54:42 +0000 (14:54 +0000)]
Slightly smaller recent panel

18 years agoMaintain numbering if remove left is undone
amwaterhouse [Thu, 11 May 2006 14:06:16 +0000 (14:06 +0000)]
Maintain numbering if remove left is undone

18 years agoTypo
amwaterhouse [Thu, 11 May 2006 13:54:27 +0000 (13:54 +0000)]
Typo

18 years agoInvert selection
amwaterhouse [Thu, 11 May 2006 13:54:10 +0000 (13:54 +0000)]
Invert selection

18 years agoRecently loaded files, urls, append sequences to Alignment
amwaterhouse [Thu, 11 May 2006 13:53:49 +0000 (13:53 +0000)]
Recently loaded files, urls, append sequences to Alignment

18 years agosequenceRef added to annotation
amwaterhouse [Wed, 10 May 2006 14:06:51 +0000 (14:06 +0000)]
sequenceRef added to annotation

18 years agoCorrection for sequences with start not equal to 1
amwaterhouse [Wed, 10 May 2006 13:30:10 +0000 (13:30 +0000)]
Correction for sequences with start not equal to 1

18 years agoCopy and paste of annotations with seqrefs
amwaterhouse [Wed, 10 May 2006 12:59:19 +0000 (12:59 +0000)]
Copy and paste of annotations with seqrefs

18 years agoimplements ClipboardOwner
amwaterhouse [Wed, 10 May 2006 12:58:44 +0000 (12:58 +0000)]
implements ClipboardOwner

18 years agosaves and loads annotations with seqrefs
amwaterhouse [Wed, 10 May 2006 12:57:56 +0000 (12:57 +0000)]
saves and loads annotations with seqrefs

18 years agoDraw an offscreen Image
amwaterhouse [Wed, 10 May 2006 12:57:39 +0000 (12:57 +0000)]
Draw an offscreen Image

18 years agoAnnotations must createSequenceMapping if seqRef not null
amwaterhouse [Wed, 10 May 2006 12:57:21 +0000 (12:57 +0000)]
Annotations must createSequenceMapping if seqRef not null

18 years agoCreate sequence mapping for annotations
amwaterhouse [Wed, 10 May 2006 12:56:30 +0000 (12:56 +0000)]
Create sequence mapping for annotations

18 years agoaddAnnotation with seqRef
amwaterhouse [Wed, 10 May 2006 12:56:02 +0000 (12:56 +0000)]
addAnnotation with seqRef

18 years agoChanges case to end of alignment
amwaterhouse [Wed, 10 May 2006 12:55:17 +0000 (12:55 +0000)]
Changes case to end of alignment

18 years agoremove import
amwaterhouse [Wed, 10 May 2006 12:54:52 +0000 (12:54 +0000)]
remove import

18 years agoSave seqref with annotations
amwaterhouse [Wed, 10 May 2006 12:52:11 +0000 (12:52 +0000)]
Save seqref with annotations

18 years agospelling err
amwaterhouse [Tue, 2 May 2006 16:44:32 +0000 (16:44 +0000)]
spelling err

18 years ago2.08.1
amwaterhouse [Tue, 2 May 2006 12:24:48 +0000 (12:24 +0000)]
2.08.1

18 years agoMake nullFrame only once
amwaterhouse [Tue, 2 May 2006 12:23:48 +0000 (12:23 +0000)]
Make nullFrame only once

18 years agoRemove unnecessary panel, also nullFrame created only once
amwaterhouse [Tue, 2 May 2006 12:23:28 +0000 (12:23 +0000)]
Remove unnecessary panel, also nullFrame created only once

18 years agoMiddle mouse to compress alignment
amwaterhouse [Tue, 2 May 2006 12:23:01 +0000 (12:23 +0000)]
Middle mouse to compress alignment

18 years agoCheck that fontsize > 0
amwaterhouse [Tue, 2 May 2006 12:22:20 +0000 (12:22 +0000)]
Check that fontsize > 0