jalview.git
18 years agoCan read from zip file
amwaterhouse [Wed, 8 Mar 2006 16:58:16 +0000 (16:58 +0000)]
Can read from zip file

18 years agoBlank space is white
amwaterhouse [Wed, 8 Mar 2006 16:55:43 +0000 (16:55 +0000)]
Blank space is white

18 years agoReveal All added
amwaterhouse [Wed, 8 Mar 2006 16:55:30 +0000 (16:55 +0000)]
Reveal All added

18 years ago<= fastPaints hidden columns
amwaterhouse [Wed, 8 Mar 2006 16:54:51 +0000 (16:54 +0000)]
<= fastPaints hidden columns

18 years agoCheck for visibleGroup==null
amwaterhouse [Wed, 8 Mar 2006 16:54:28 +0000 (16:54 +0000)]
Check for visibleGroup==null

18 years agoIdentfyFile should not be static
amwaterhouse [Wed, 8 Mar 2006 16:53:36 +0000 (16:53 +0000)]
IdentfyFile should not be static

18 years agoRevealAllHiddenColumns
amwaterhouse [Wed, 8 Mar 2006 16:53:18 +0000 (16:53 +0000)]
RevealAllHiddenColumns

18 years agoAllow for hidden columns
amwaterhouse [Wed, 8 Mar 2006 16:52:59 +0000 (16:52 +0000)]
Allow for hidden columns

18 years agoAble to read resources from Zip file
amwaterhouse [Wed, 8 Mar 2006 16:51:44 +0000 (16:51 +0000)]
Able to read resources from Zip file

18 years agoBlank space is white
amwaterhouse [Wed, 8 Mar 2006 16:50:34 +0000 (16:50 +0000)]
Blank space is white

18 years agoPASTE is constant in AppletFormatAdapter
amwaterhouse [Wed, 8 Mar 2006 16:49:09 +0000 (16:49 +0000)]
PASTE is constant in AppletFormatAdapter

18 years agoPack resources in Zip file
amwaterhouse [Wed, 8 Mar 2006 16:48:32 +0000 (16:48 +0000)]
Pack resources in Zip file

18 years agofixed after refactoring of SequenceFeature[] seq.getSequenceFeatures
jprocter [Wed, 1 Mar 2006 16:23:15 +0000 (16:23 +0000)]
fixed after refactoring of SequenceFeature[] seq.getSequenceFeatures

18 years agopropagate SearchResult object use to MCView's highlighted residue renderer.
jprocter [Wed, 1 Mar 2006 14:03:52 +0000 (14:03 +0000)]
propagate SearchResult object use to MCView's highlighted residue renderer.

18 years agoP1 changed to N1
amwaterhouse [Fri, 24 Feb 2006 11:48:23 +0000 (11:48 +0000)]
P1 changed to N1

18 years agoAdd Annotation to specific sequence
amwaterhouse [Fri, 24 Feb 2006 11:47:51 +0000 (11:47 +0000)]
Add Annotation to specific sequence

18 years agoCannot delete residues
amwaterhouse [Fri, 24 Feb 2006 11:47:03 +0000 (11:47 +0000)]
Cannot delete residues

18 years agoFeatures now array
amwaterhouse [Fri, 24 Feb 2006 11:46:41 +0000 (11:46 +0000)]
Features now array

18 years agoKeeps original threshold value
amwaterhouse [Fri, 24 Feb 2006 11:45:36 +0000 (11:45 +0000)]
Keeps original threshold value

18 years agosetShowSequenceFeatures
amwaterhouse [Fri, 24 Feb 2006 11:44:59 +0000 (11:44 +0000)]
setShowSequenceFeatures

18 years agoFirst attempt at hidden regions
amwaterhouse [Fri, 24 Feb 2006 11:44:36 +0000 (11:44 +0000)]
First attempt at hidden regions

18 years agoLess args, faster rendering
amwaterhouse [Fri, 24 Feb 2006 11:44:20 +0000 (11:44 +0000)]
Less args, faster rendering

18 years agoFeatures now an array
amwaterhouse [Fri, 24 Feb 2006 11:44:02 +0000 (11:44 +0000)]
Features now an array

18 years agoFirst attempt to install hidden regions
amwaterhouse [Fri, 24 Feb 2006 11:43:25 +0000 (11:43 +0000)]
First attempt to install hidden regions

18 years agoUse add seq feature instead of replacing existing features
amwaterhouse [Fri, 24 Feb 2006 11:42:57 +0000 (11:42 +0000)]
Use add seq feature instead of replacing existing features

18 years agoFeatures added
amwaterhouse [Fri, 24 Feb 2006 11:41:38 +0000 (11:41 +0000)]
Features added

18 years agoFeatures now array for speed of rendering
amwaterhouse [Fri, 24 Feb 2006 11:41:26 +0000 (11:41 +0000)]
Features now array for speed of rendering

18 years agoUse add feature instead of replacing existing values
amwaterhouse [Fri, 24 Feb 2006 11:40:45 +0000 (11:40 +0000)]
Use add feature instead of replacing existing values

18 years agoFeatures now array
amwaterhouse [Fri, 24 Feb 2006 11:40:07 +0000 (11:40 +0000)]
Features now array

18 years agoUse annotation colour for graph
amwaterhouse [Fri, 24 Feb 2006 11:39:40 +0000 (11:39 +0000)]
Use annotation colour for graph

18 years agoMake variable public for speed of rendering
amwaterhouse [Fri, 24 Feb 2006 11:39:09 +0000 (11:39 +0000)]
Make variable public for speed of rendering

18 years agoFeatures are now an array, not vector
amwaterhouse [Fri, 24 Feb 2006 11:38:44 +0000 (11:38 +0000)]
Features are now an array, not vector

18 years agoTypo
amwaterhouse [Fri, 24 Feb 2006 11:38:21 +0000 (11:38 +0000)]
Typo

18 years agoRecord of featuresDisplayed
amwaterhouse [Fri, 24 Feb 2006 11:37:54 +0000 (11:37 +0000)]
Record of featuresDisplayed

18 years agoInform user of groups error parsing
amwaterhouse [Fri, 24 Feb 2006 11:37:35 +0000 (11:37 +0000)]
Inform user of groups error parsing

18 years agoDrawpanel needs fewer args
amwaterhouse [Fri, 24 Feb 2006 11:37:13 +0000 (11:37 +0000)]
Drawpanel needs fewer args

18 years agoFeature text mouse over modified
amwaterhouse [Fri, 24 Feb 2006 11:36:51 +0000 (11:36 +0000)]
Feature text mouse over modified

18 years agoIf overview, residues are gray
amwaterhouse [Fri, 24 Feb 2006 11:35:52 +0000 (11:35 +0000)]
If overview, residues are gray

18 years agoFeatures are an array, rendering is faster
amwaterhouse [Fri, 24 Feb 2006 11:35:27 +0000 (11:35 +0000)]
Features are an array, rendering is faster

18 years agotranslate cDNA adjusted
amwaterhouse [Thu, 16 Feb 2006 17:30:04 +0000 (17:30 +0000)]
translate cDNA adjusted

18 years agoDont colour gaps
amwaterhouse [Thu, 16 Feb 2006 16:51:36 +0000 (16:51 +0000)]
Dont colour gaps

18 years agoRead startgroup and endgroup in features file
amwaterhouse [Thu, 16 Feb 2006 15:51:07 +0000 (15:51 +0000)]
Read startgroup and endgroup in features file

18 years agoIncorporated threshold slider
amwaterhouse [Thu, 16 Feb 2006 15:50:44 +0000 (15:50 +0000)]
Incorporated threshold slider

18 years agoSliderPanel removed
amwaterhouse [Thu, 16 Feb 2006 15:50:01 +0000 (15:50 +0000)]
SliderPanel removed

18 years agoFeatureGroups added
amwaterhouse [Thu, 16 Feb 2006 15:49:43 +0000 (15:49 +0000)]
FeatureGroups added

18 years agoShowSeqFeatures selected
amwaterhouse [Thu, 16 Feb 2006 15:49:21 +0000 (15:49 +0000)]
ShowSeqFeatures selected

18 years agoSave featureGroup
amwaterhouse [Thu, 16 Feb 2006 15:48:05 +0000 (15:48 +0000)]
Save featureGroup

18 years agoUse featureGroups from featureRenderer
amwaterhouse [Thu, 16 Feb 2006 15:47:47 +0000 (15:47 +0000)]
Use featureGroups from featureRenderer

18 years agoNo longer used for annotation gradient
amwaterhouse [Thu, 16 Feb 2006 15:47:21 +0000 (15:47 +0000)]
No longer used for annotation gradient

18 years agoFetch Sequence Features menu added
amwaterhouse [Thu, 16 Feb 2006 15:45:36 +0000 (15:45 +0000)]
Fetch Sequence Features menu added

18 years agoUse original colour scheme as base for annotation colouring
amwaterhouse [Thu, 16 Feb 2006 15:45:06 +0000 (15:45 +0000)]
Use original colour scheme as base for annotation colouring

18 years agoAllows saving of sequence description
amwaterhouse [Thu, 16 Feb 2006 15:44:31 +0000 (15:44 +0000)]
Allows saving of sequence description

18 years agoTypo
amwaterhouse [Thu, 16 Feb 2006 15:44:04 +0000 (15:44 +0000)]
Typo

18 years agoDont use FeatureFetcher if nucleotide
amwaterhouse [Wed, 15 Feb 2006 15:25:52 +0000 (15:25 +0000)]
Dont use FeatureFetcher if nucleotide

18 years agoThreshold single element
amwaterhouse [Wed, 15 Feb 2006 15:25:27 +0000 (15:25 +0000)]
Threshold single element

18 years agoAdd new Feature
amwaterhouse [Wed, 15 Feb 2006 15:25:09 +0000 (15:25 +0000)]
Add new Feature

18 years agoSet as feature, not new group
amwaterhouse [Wed, 15 Feb 2006 15:24:50 +0000 (15:24 +0000)]
Set as feature, not new group

18 years agoSaves and loads sequence description
amwaterhouse [Wed, 15 Feb 2006 15:24:24 +0000 (15:24 +0000)]
Saves and loads sequence description

18 years agoKeeps up to date with featureRenderer
amwaterhouse [Wed, 15 Feb 2006 15:24:07 +0000 (15:24 +0000)]
Keeps up to date with featureRenderer

18 years agoThreshold is single element
amwaterhouse [Wed, 15 Feb 2006 15:23:49 +0000 (15:23 +0000)]
Threshold is single element

18 years agoif shift down bug fixed
amwaterhouse [Wed, 15 Feb 2006 15:23:26 +0000 (15:23 +0000)]
if shift down bug fixed

18 years agoNo more supergroup, set Sequence name / Description
amwaterhouse [Wed, 15 Feb 2006 15:23:03 +0000 (15:23 +0000)]
No more supergroup, set Sequence name / Description

18 years agoNew FEature replaces new group
amwaterhouse [Wed, 15 Feb 2006 15:22:07 +0000 (15:22 +0000)]
New FEature replaces new group

18 years agoThreshold is a single element
amwaterhouse [Wed, 15 Feb 2006 15:21:45 +0000 (15:21 +0000)]
Threshold is a single element

18 years agoSetThreshold replaces addGraphLine
amwaterhouse [Wed, 15 Feb 2006 15:21:21 +0000 (15:21 +0000)]
SetThreshold replaces addGraphLine

18 years agoFeatureGroups added
amwaterhouse [Wed, 15 Feb 2006 15:20:51 +0000 (15:20 +0000)]
FeatureGroups added

18 years agoRemoved SuperGroup
amwaterhouse [Wed, 15 Feb 2006 15:20:26 +0000 (15:20 +0000)]
Removed SuperGroup

18 years agoSave sequence description in VAMSAS sequence
amwaterhouse [Wed, 15 Feb 2006 15:19:49 +0000 (15:19 +0000)]
Save sequence description in VAMSAS sequence

18 years agoCheck description and status are not null in mouse over
amwaterhouse [Wed, 15 Feb 2006 15:19:22 +0000 (15:19 +0000)]
Check description and status are not null in mouse over

18 years agoKeeps up to date with features
amwaterhouse [Wed, 15 Feb 2006 15:18:57 +0000 (15:18 +0000)]
Keeps up to date with features

18 years agoFeature replaces new superGroup
amwaterhouse [Wed, 15 Feb 2006 15:18:41 +0000 (15:18 +0000)]
Feature replaces new superGroup

18 years agoFeature Groups added
amwaterhouse [Wed, 15 Feb 2006 15:18:21 +0000 (15:18 +0000)]
Feature Groups added

18 years agoGraphline is a single line
amwaterhouse [Wed, 15 Feb 2006 15:17:55 +0000 (15:17 +0000)]
Graphline is a single line

18 years agoFeatures file has startgroup, endgroup
amwaterhouse [Wed, 15 Feb 2006 15:17:29 +0000 (15:17 +0000)]
Features file has startgroup, endgroup

18 years agoNo longer used
amwaterhouse [Wed, 15 Feb 2006 15:16:16 +0000 (15:16 +0000)]
No longer used

18 years agoMissing brace
amwaterhouse [Mon, 13 Feb 2006 15:30:45 +0000 (15:30 +0000)]
Missing brace

18 years agoParsing features file - dont adjust for alignment position
amwaterhouse [Mon, 13 Feb 2006 15:26:40 +0000 (15:26 +0000)]
Parsing features file - dont adjust for alignment position

18 years agoUpdate overview if features updated
amwaterhouse [Fri, 10 Feb 2006 16:05:27 +0000 (16:05 +0000)]
Update overview if features updated

18 years agoOverview displays features
amwaterhouse [Fri, 10 Feb 2006 16:03:03 +0000 (16:03 +0000)]
Overview displays features

18 years agoRemoved file
amwaterhouse [Thu, 9 Feb 2006 16:49:25 +0000 (16:49 +0000)]
Removed file

18 years agoFeature Settings added to Applet
amwaterhouse [Thu, 9 Feb 2006 16:48:57 +0000 (16:48 +0000)]
Feature Settings added to Applet

18 years agoIf conservation is zero, colour is white
amwaterhouse [Thu, 9 Feb 2006 14:43:28 +0000 (14:43 +0000)]
If conservation is zero, colour is white

18 years agoDrop target must initialise sequences
amwaterhouse [Thu, 9 Feb 2006 14:42:54 +0000 (14:42 +0000)]
Drop target must initialise sequences

18 years agoNew implementation for holding search results
amwaterhouse [Thu, 9 Feb 2006 14:42:18 +0000 (14:42 +0000)]
New implementation for holding search results

18 years agoparseResult takes the title as string. usually null
amwaterhouse [Wed, 8 Feb 2006 15:27:00 +0000 (15:27 +0000)]
parseResult takes the title as string. usually null

18 years agoMake URL input window bigger
amwaterhouse [Wed, 8 Feb 2006 15:26:11 +0000 (15:26 +0000)]
Make URL input window bigger

18 years agoFormatAdapter throws exception
amwaterhouse [Wed, 8 Feb 2006 15:25:50 +0000 (15:25 +0000)]
FormatAdapter throws exception

18 years agoCheck endRes
amwaterhouse [Wed, 8 Feb 2006 15:25:19 +0000 (15:25 +0000)]
Check endRes

18 years agoCopy dataset annotations for paste(this)
amwaterhouse [Wed, 8 Feb 2006 15:23:31 +0000 (15:23 +0000)]
Copy dataset annotations for paste(this)

18 years agoColour above or below threshold
amwaterhouse [Wed, 8 Feb 2006 15:22:23 +0000 (15:22 +0000)]
Colour above or below threshold

18 years agoReport invalid chars
amwaterhouse [Wed, 8 Feb 2006 15:21:42 +0000 (15:21 +0000)]
Report invalid chars

18 years agoAdded graphtype
amwaterhouse [Fri, 3 Feb 2006 17:52:15 +0000 (17:52 +0000)]
Added graphtype

18 years agoGraphtype added
amwaterhouse [Fri, 3 Feb 2006 17:50:14 +0000 (17:50 +0000)]
Graphtype added

18 years agoConservation colouring does what it should always have done
amwaterhouse [Fri, 3 Feb 2006 17:48:22 +0000 (17:48 +0000)]
Conservation colouring does what it should always have done

18 years agoMake java 1.1 compatible
amwaterhouse [Fri, 3 Feb 2006 17:47:55 +0000 (17:47 +0000)]
Make java 1.1 compatible

18 years agoSlight adjustments
amwaterhouse [Fri, 3 Feb 2006 17:47:32 +0000 (17:47 +0000)]
Slight adjustments

18 years agoFetch sequence(s)
amwaterhouse [Fri, 3 Feb 2006 17:47:05 +0000 (17:47 +0000)]
Fetch sequence(s)

18 years agoJava 1.1 compatible
amwaterhouse [Fri, 3 Feb 2006 17:46:25 +0000 (17:46 +0000)]
Java 1.1 compatible

18 years agoMany changes
amwaterhouse [Fri, 3 Feb 2006 17:46:11 +0000 (17:46 +0000)]
Many changes

18 years agoSave and load graph type
amwaterhouse [Fri, 3 Feb 2006 17:45:32 +0000 (17:45 +0000)]
Save and load graph type