jalview.git
17 years agotooltips
amwaterhouse [Thu, 1 Feb 2007 12:49:24 +0000 (12:49 +0000)]
tooltips

17 years agoset description for groups
amwaterhouse [Thu, 1 Feb 2007 12:40:06 +0000 (12:40 +0000)]
set description for groups

17 years agoDoesnt move with mouse, friendlier for mac users
amwaterhouse [Thu, 1 Feb 2007 12:37:08 +0000 (12:37 +0000)]
Doesnt move with mouse, friendlier for mac users

17 years agoDont repaint tooltip
amwaterhouse [Thu, 1 Feb 2007 12:36:46 +0000 (12:36 +0000)]
Dont repaint tooltip

17 years agoOne class for edit name/description
amwaterhouse [Thu, 1 Feb 2007 12:36:22 +0000 (12:36 +0000)]
One class for edit name/description

17 years agoslightly larger window edit name/desc
amwaterhouse [Wed, 31 Jan 2007 16:39:00 +0000 (16:39 +0000)]
slightly larger window edit name/desc

17 years agoedit annotation name/description
amwaterhouse [Wed, 31 Jan 2007 16:38:44 +0000 (16:38 +0000)]
edit annotation name/description

17 years agoCan edit annotation name/description
amwaterhouse [Wed, 31 Jan 2007 16:23:19 +0000 (16:23 +0000)]
Can edit annotation name/description

17 years agoConsensus, conservation, quality labels may have changed
amwaterhouse [Wed, 31 Jan 2007 16:22:34 +0000 (16:22 +0000)]
Consensus, conservation, quality labels may have changed

17 years agoaligned not used
amwaterhouse [Wed, 31 Jan 2007 15:33:00 +0000 (15:33 +0000)]
aligned not used

17 years agoDont export annotations if not visible
amwaterhouse [Wed, 31 Jan 2007 15:29:13 +0000 (15:29 +0000)]
Dont export annotations if not visible

17 years agoUnique name for new group and treegroup
amwaterhouse [Wed, 31 Jan 2007 15:28:47 +0000 (15:28 +0000)]
Unique name for new group and treegroup

17 years agoAdjust features when cutting and pasting
amwaterhouse [Wed, 31 Jan 2007 14:47:57 +0000 (14:47 +0000)]
Adjust features when cutting and pasting

17 years agomake new dataset seq if residues deleted
amwaterhouse [Wed, 31 Jan 2007 14:47:35 +0000 (14:47 +0000)]
make new dataset seq if residues deleted

17 years agocopy feature: check for null values
amwaterhouse [Wed, 31 Jan 2007 14:46:57 +0000 (14:46 +0000)]
copy feature: check for null values

17 years agoaligned not used
amwaterhouse [Wed, 31 Jan 2007 14:44:28 +0000 (14:44 +0000)]
aligned not used

17 years agoCheck valid residues in ss
amwaterhouse [Tue, 30 Jan 2007 18:23:35 +0000 (18:23 +0000)]
Check valid residues in ss

17 years agoCheck seqs in group exist in this alignment
amwaterhouse [Tue, 30 Jan 2007 15:35:26 +0000 (15:35 +0000)]
Check seqs in group exist in this alignment

17 years agoAny character non aa or nucleotide is a space
amwaterhouse [Tue, 30 Jan 2007 15:35:01 +0000 (15:35 +0000)]
Any character non aa or nucleotide is a space

17 years agomoved painting routine
amwaterhouse [Tue, 30 Jan 2007 15:11:09 +0000 (15:11 +0000)]
moved painting routine

17 years agoconsensusColouring never used
amwaterhouse [Tue, 30 Jan 2007 13:40:16 +0000 (13:40 +0000)]
consensusColouring never used

17 years agoDraw helices correctly
amwaterhouse [Tue, 30 Jan 2007 13:39:53 +0000 (13:39 +0000)]
Draw helices correctly

17 years agoUse util toHexString
amwaterhouse [Tue, 30 Jan 2007 12:53:04 +0000 (12:53 +0000)]
Use util toHexString

17 years agoOutput groups in annotation file
amwaterhouse [Tue, 30 Jan 2007 12:52:50 +0000 (12:52 +0000)]
Output groups in annotation file

17 years agoDont clear graphics g before drawing the image
amwaterhouse [Mon, 29 Jan 2007 17:42:02 +0000 (17:42 +0000)]
Dont clear graphics g before drawing the image

17 years agoImage for labels, stops flickering
amwaterhouse [Mon, 29 Jan 2007 17:41:31 +0000 (17:41 +0000)]
Image for labels, stops flickering

17 years agoNew view copies annotations across
amwaterhouse [Mon, 29 Jan 2007 17:41:12 +0000 (17:41 +0000)]
New view copies annotations across

17 years agoTooltips for group names, descriptions
amwaterhouse [Mon, 29 Jan 2007 17:40:50 +0000 (17:40 +0000)]
Tooltips for group names, descriptions

17 years agoDescription added
amwaterhouse [Mon, 29 Jan 2007 17:40:30 +0000 (17:40 +0000)]
Description added

17 years agoSequenceGroup parsing added to annotation file
amwaterhouse [Mon, 29 Jan 2007 17:39:59 +0000 (17:39 +0000)]
SequenceGroup parsing added to annotation file

17 years agoID_ITALICS option in preferences
amwaterhouse [Mon, 29 Jan 2007 11:33:02 +0000 (11:33 +0000)]
ID_ITALICS option in preferences

17 years agoscaleAbove, left and right set when tab selection changes
amwaterhouse [Mon, 29 Jan 2007 11:31:52 +0000 (11:31 +0000)]
scaleAbove, left and right set when tab selection changes

17 years agoMarios annotation bug fixed
amwaterhouse [Mon, 29 Jan 2007 11:31:23 +0000 (11:31 +0000)]
Marios annotation bug fixed

17 years agoAnnotationId is hashcode of object
amwaterhouse [Fri, 26 Jan 2007 17:31:51 +0000 (17:31 +0000)]
AnnotationId is hashcode of object

17 years agoOnly set the sequence oncecvs diff datamodel/Alignment.java
amwaterhouse [Fri, 26 Jan 2007 17:30:49 +0000 (17:30 +0000)]
Only set the sequence oncecvs diff datamodel/Alignment.java

17 years agoAdjusts annotations for sequence edits
amwaterhouse [Fri, 26 Jan 2007 17:30:23 +0000 (17:30 +0000)]
Adjusts annotations for sequence edits

17 years agoIf its null, set tip empty
amwaterhouse [Fri, 26 Jan 2007 17:30:07 +0000 (17:30 +0000)]
If its null, set tip empty

17 years agopreliminary documentation for DNA->protein codon features and EMBL coding region...
jprocter [Fri, 26 Jan 2007 10:24:08 +0000 (10:24 +0000)]
preliminary documentation for DNA->protein codon features and EMBL coding region parsing

17 years agoadded doc for PDBResNum features
jprocter [Fri, 26 Jan 2007 10:23:23 +0000 (10:23 +0000)]
added doc for PDBResNum features

17 years agoCommand takes alignment, not gapChar
amwaterhouse [Thu, 25 Jan 2007 18:47:18 +0000 (18:47 +0000)]
Command takes alignment, not gapChar

17 years agoAnnotations move when full alignment edited
amwaterhouse [Thu, 25 Jan 2007 18:46:31 +0000 (18:46 +0000)]
Annotations move when full alignment edited

17 years agoAnnotation adjustment moved to EditCommand
amwaterhouse [Thu, 25 Jan 2007 18:45:46 +0000 (18:45 +0000)]
Annotation adjustment moved to EditCommand

17 years agoRemove unneccessary lines
amwaterhouse [Thu, 25 Jan 2007 18:45:14 +0000 (18:45 +0000)]
Remove unneccessary lines

17 years agoAlignmentAnnotations require id
amwaterhouse [Thu, 25 Jan 2007 18:44:47 +0000 (18:44 +0000)]
AlignmentAnnotations require id

17 years agoAllow for hidden columns
amwaterhouse [Thu, 25 Jan 2007 16:03:20 +0000 (16:03 +0000)]
Allow for hidden columns

17 years agoOnly output visible annotations
amwaterhouse [Thu, 25 Jan 2007 16:02:36 +0000 (16:02 +0000)]
Only output visible annotations

17 years agoload/get Annotation
amwaterhouse [Thu, 25 Jan 2007 16:02:21 +0000 (16:02 +0000)]
load/get Annotation

17 years agoRemove unnecessary line
amwaterhouse [Thu, 25 Jan 2007 16:01:59 +0000 (16:01 +0000)]
Remove unnecessary line

17 years agoOutput annotations
amwaterhouse [Thu, 25 Jan 2007 16:00:41 +0000 (16:00 +0000)]
Output annotations

17 years ago1.1 enabled
amwaterhouse [Thu, 25 Jan 2007 16:00:21 +0000 (16:00 +0000)]
1.1 enabled

17 years agoreinstating class implementation.
jprocter [Thu, 25 Jan 2007 15:38:27 +0000 (15:38 +0000)]
reinstating class implementation.

17 years agochecks for irreflexive mapping in main tester
jprocter [Thu, 25 Jan 2007 15:36:51 +0000 (15:36 +0000)]
checks for irreflexive mapping in main tester

17 years agoConservation etc have autoCalculated flag set true
amwaterhouse [Wed, 24 Jan 2007 17:30:49 +0000 (17:30 +0000)]
Conservation etc have autoCalculated flag set true

17 years agoAdjustAnnotations needs position, number and insert
amwaterhouse [Wed, 24 Jan 2007 17:30:12 +0000 (17:30 +0000)]
AdjustAnnotations needs position, number and insert

17 years agoThis constructor is never called
amwaterhouse [Wed, 24 Jan 2007 17:29:38 +0000 (17:29 +0000)]
This constructor is never called

17 years agoFeatures output for javascript
amwaterhouse [Wed, 24 Jan 2007 17:29:20 +0000 (17:29 +0000)]
Features output for javascript

17 years agooutput now takes alignment, not just sequences
amwaterhouse [Wed, 24 Jan 2007 17:28:58 +0000 (17:28 +0000)]
output now takes alignment, not just sequences

17 years agoExtension to fastaFile for myhits
amwaterhouse [Wed, 24 Jan 2007 17:27:44 +0000 (17:27 +0000)]
Extension to fastaFile for myhits

17 years agorefactored to use jalview.analysis.Finder for searching alignment.
jprocter [Wed, 24 Jan 2007 17:15:23 +0000 (17:15 +0000)]
refactored to use jalview.analysis.Finder for searching alignment.

17 years agokkv change
jprocter [Wed, 24 Jan 2007 17:09:40 +0000 (17:09 +0000)]
kkv change

17 years agoMap arbitrary series of non-overlapping integer intervals on one range to another...
jprocter [Wed, 24 Jan 2007 17:08:58 +0000 (17:08 +0000)]
Map arbitrary series of non-overlapping integer intervals on one range to another on another range - with an integer ratio for each range

17 years agoPage setup added
amwaterhouse [Wed, 24 Jan 2007 10:48:38 +0000 (10:48 +0000)]
Page setup added

17 years agoboolean for internal copies
amwaterhouse [Tue, 23 Jan 2007 17:24:13 +0000 (17:24 +0000)]
boolean for internal copies

17 years agoHidden representatives moved from sequence to viewport
amwaterhouse [Tue, 23 Jan 2007 17:05:19 +0000 (17:05 +0000)]
Hidden representatives moved from sequence to viewport

17 years agorefactoring (added seqIndex/resIndex state for incremental search)
jprocter [Tue, 23 Jan 2007 08:06:06 +0000 (08:06 +0000)]
refactoring (added seqIndex/resIndex state for incremental search)

17 years agorefactored search algorithm from gui classes
jprocter [Tue, 23 Jan 2007 07:49:32 +0000 (07:49 +0000)]
refactored search algorithm from gui classes

17 years agotransfer resnum features now returns features (could be passed to feature renderer)
jprocter [Tue, 23 Jan 2007 06:40:43 +0000 (06:40 +0000)]
transfer resnum features now returns features (could be passed to feature renderer)

17 years agoreoganization of PDB sequence fetching for sequence annotation generated by PDBFile
jprocter [Fri, 19 Jan 2007 16:04:05 +0000 (16:04 +0000)]
reoganization of PDB sequence fetching for sequence annotation generated by PDBFile

17 years agoPDBChain maintains reference to dataset of sequences created by PDBfile reader.
jprocter [Fri, 19 Jan 2007 16:01:33 +0000 (16:01 +0000)]
PDBChain maintains reference to dataset of sequences created by PDBfile reader.

17 years agodatasetSequence derive method and some checks
jprocter [Fri, 19 Jan 2007 15:57:42 +0000 (15:57 +0000)]
datasetSequence derive method and some checks

17 years agoexport features/annotations not for import
amwaterhouse [Fri, 19 Jan 2007 15:55:10 +0000 (15:55 +0000)]
export features/annotations not for import

17 years agoApplet can output and load annotations, features
amwaterhouse [Fri, 19 Jan 2007 15:53:13 +0000 (15:53 +0000)]
Applet can output and load annotations, features

17 years agoNeeed to know protocol for annotation loading
amwaterhouse [Fri, 19 Jan 2007 15:52:21 +0000 (15:52 +0000)]
Neeed to know protocol for annotation loading

17 years agoNeed to know protocol to load anntotations
amwaterhouse [Fri, 19 Jan 2007 15:51:12 +0000 (15:51 +0000)]
Need to know protocol to load anntotations

17 years agojavadoc
jprocter [Fri, 19 Jan 2007 11:22:35 +0000 (11:22 +0000)]
javadoc

17 years agoadded sequence feature copy constructor.
jprocter [Fri, 19 Jan 2007 11:19:58 +0000 (11:19 +0000)]
added sequence feature copy constructor.

17 years agotransfer and update of sequenceFeatures for associated alignment sequence
jprocter [Thu, 18 Jan 2007 18:29:57 +0000 (18:29 +0000)]
transfer and update of sequenceFeatures for associated alignment sequence
fixed mapping bug for sequences that do not start at 1.

17 years agorandom ';'
jprocter [Thu, 18 Jan 2007 18:22:22 +0000 (18:22 +0000)]
random ';'

17 years agotransfer and update of sequenceFeatures for associated alignment sequence
jprocter [Thu, 18 Jan 2007 18:21:42 +0000 (18:21 +0000)]
transfer and update of sequenceFeatures for associated alignment sequence

17 years agofixed last-residue bug and added sequence feature creation and transfer for resNum...
jprocter [Thu, 18 Jan 2007 18:19:04 +0000 (18:19 +0000)]
fixed last-residue bug and added sequence feature creation and transfer for resNum+insCode annotation for each sequence residue

17 years agoadded resNum+insCode string field for truly unambiguous PDB atom entry referencing...
jprocter [Thu, 18 Jan 2007 18:17:36 +0000 (18:17 +0000)]
added resNum+insCode string field for truly unambiguous PDB atom entry referencing/display

17 years agoAdd the last sequence before annotations
amwaterhouse [Thu, 18 Jan 2007 17:22:38 +0000 (17:22 +0000)]
Add the last sequence before annotations

17 years agoTake scrollOffset into account
amwaterhouse [Thu, 18 Jan 2007 17:11:31 +0000 (17:11 +0000)]
Take scrollOffset into account

17 years agoTool tip for annotation description
amwaterhouse [Thu, 18 Jan 2007 17:11:10 +0000 (17:11 +0000)]
Tool tip for annotation description

17 years agoSet description on copy
amwaterhouse [Thu, 18 Jan 2007 16:47:01 +0000 (16:47 +0000)]
Set description on copy

17 years agoSet tooltip
amwaterhouse [Thu, 18 Jan 2007 16:46:34 +0000 (16:46 +0000)]
Set tooltip

17 years ago1.1 enabled
amwaterhouse [Thu, 18 Jan 2007 16:46:10 +0000 (16:46 +0000)]
1.1 enabled

17 years agoput vamsas bit back in
amwaterhouse [Thu, 18 Jan 2007 16:45:56 +0000 (16:45 +0000)]
put vamsas bit back in

17 years agoFile Parsing returns Alignments, not Sequence[]
amwaterhouse [Thu, 18 Jan 2007 16:21:03 +0000 (16:21 +0000)]
File Parsing returns Alignments, not Sequence[]

17 years agoIs secondary structure label modified
amwaterhouse [Thu, 18 Jan 2007 16:16:34 +0000 (16:16 +0000)]
Is secondary structure label modified

17 years agoDisplay description
amwaterhouse [Thu, 18 Jan 2007 16:15:39 +0000 (16:15 +0000)]
Display description

17 years agoDescriptions can be added to annotations
amwaterhouse [Thu, 18 Jan 2007 16:15:22 +0000 (16:15 +0000)]
Descriptions can be added to annotations

17 years agoEdit name/description added to applet
amwaterhouse [Wed, 17 Jan 2007 17:01:57 +0000 (17:01 +0000)]
Edit name/description added to applet

17 years agoFit to Window bug fixed
amwaterhouse [Wed, 17 Jan 2007 15:32:10 +0000 (15:32 +0000)]
Fit to Window bug fixed

17 years agomade atom attributes public (rather than put in get/set pairs)
jprocter [Wed, 17 Jan 2007 14:28:17 +0000 (14:28 +0000)]
made atom attributes public (rather than put in get/set pairs)

17 years agoDont set the font of alignFrameMenubarcvs update appletgui/AlignFrame.java
amwaterhouse [Wed, 17 Jan 2007 14:22:30 +0000 (14:22 +0000)]
Dont set the font of alignFrameMenubarcvs update appletgui/AlignFrame.java

17 years agoSend new sequences when firing alignment changed
amwaterhouse [Thu, 4 Jan 2007 16:18:59 +0000 (16:18 +0000)]
Send new sequences when firing alignment changed

17 years agoReads in anything following seq id as a description
amwaterhouse [Thu, 4 Jan 2007 16:13:10 +0000 (16:13 +0000)]
Reads in anything following seq id as a description

17 years agoHEADER and ATOM must be position 0
amwaterhouse [Thu, 4 Jan 2007 16:12:29 +0000 (16:12 +0000)]
HEADER and ATOM must be position 0

17 years agotype change
jprocter [Thu, 21 Dec 2006 14:11:18 +0000 (14:11 +0000)]
type change