jalview.git
17 years agosort-by-score works of sequence-annotation, not alignment annotation vector
jprocter [Tue, 1 May 2007 10:42:59 +0000 (10:42 +0000)]
sort-by-score works of sequence-annotation, not alignment annotation vector

17 years agoSave seqset properties
amwaterhouse [Tue, 1 May 2007 10:04:43 +0000 (10:04 +0000)]
Save seqset properties

17 years agoSeqset properties saved
amwaterhouse [Tue, 1 May 2007 10:03:45 +0000 (10:03 +0000)]
Seqset properties saved

17 years ago2.3 what's new
jprocter [Tue, 1 May 2007 09:51:03 +0000 (09:51 +0000)]
2.3 what's new

17 years agopreliminary EMBL and mapping documentation
jprocter [Tue, 1 May 2007 09:50:49 +0000 (09:50 +0000)]
preliminary EMBL and mapping documentation

17 years ago'no sources selected' calls method on feature settings dialog to prompt user.
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.

17 years agofixed deadlock
jprocter [Mon, 30 Apr 2007 15:35:17 +0000 (15:35 +0000)]
fixed deadlock

17 years agosetVisible replaces show
amwaterhouse [Mon, 30 Apr 2007 15:02:27 +0000 (15:02 +0000)]
setVisible replaces show

17 years agoVersion 11.0.2
amwaterhouse [Mon, 30 Apr 2007 15:00:45 +0000 (15:00 +0000)]
Version 11.0.2

17 years agoREmoved
amwaterhouse [Mon, 30 Apr 2007 14:59:57 +0000 (14:59 +0000)]
REmoved

17 years agorebuild sort by scores menu when new annotation is available
jprocter [Mon, 30 Apr 2007 13:50:33 +0000 (13:50 +0000)]
rebuild sort by scores menu when new annotation is available

17 years agopad should leave null annotations array null
jprocter [Mon, 30 Apr 2007 13:48:36 +0000 (13:48 +0000)]
pad should leave null annotations array null

17 years agoconvenient creation of 'score only' annotation.
jprocter [Mon, 30 Apr 2007 13:24:07 +0000 (13:24 +0000)]
convenient creation of 'score only' annotation.

17 years agoparse alignment properties and add annotation rows for general alignment position...
jprocter [Mon, 30 Apr 2007 13:23:14 +0000 (13:23 +0000)]
parse alignment properties and add annotation rows for general alignment position annotation.

17 years agoalignment properties and embedded newick strings can be retrieved from parsed files
jprocter [Mon, 30 Apr 2007 13:22:25 +0000 (13:22 +0000)]
alignment properties and embedded newick strings can be retrieved from parsed files

17 years agodssp 7-state to three state lookup
jprocter [Mon, 30 Apr 2007 13:14:17 +0000 (13:14 +0000)]
dssp 7-state to three state lookup

17 years agojavadoc
jprocter [Mon, 30 Apr 2007 09:44:38 +0000 (09:44 +0000)]
javadoc

17 years agoremove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:21:01 +0000 (16:21 +0000)]
remove excessive painting

17 years agoREmove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:20:41 +0000 (16:20 +0000)]
REmove excessive painting

17 years agoRepaint after feature added
amwaterhouse [Fri, 27 Apr 2007 16:20:22 +0000 (16:20 +0000)]
Repaint after feature added

17 years agoPrevent err when editing and overview drawing
amwaterhouse [Fri, 27 Apr 2007 16:19:57 +0000 (16:19 +0000)]
Prevent err when editing and overview drawing

17 years agoFeatureRenderer mixups fixed
amwaterhouse [Fri, 27 Apr 2007 16:19:25 +0000 (16:19 +0000)]
FeatureRenderer mixups fixed

17 years agoRemove system.out AppletPDBViewer.java
amwaterhouse [Fri, 27 Apr 2007 15:36:36 +0000 (15:36 +0000)]
Remove system.out AppletPDBViewer.java

17 years agoCheck pdbid size >0
amwaterhouse [Fri, 27 Apr 2007 15:32:46 +0000 (15:32 +0000)]
Check pdbid size >0

17 years agoTrouble with featureRenderers fixed
amwaterhouse [Fri, 27 Apr 2007 15:32:12 +0000 (15:32 +0000)]
Trouble with featureRenderers fixed

17 years agoMove repaint in thread
amwaterhouse [Fri, 27 Apr 2007 14:53:33 +0000 (14:53 +0000)]
Move repaint in thread

17 years agoPut alignmentProperties in scrollpane
amwaterhouse [Fri, 27 Apr 2007 14:47:00 +0000 (14:47 +0000)]
Put alignmentProperties in scrollpane

17 years agoCheck feature group is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:45:31 +0000 (14:45 +0000)]
Check feature group is visible for mouse over features

17 years agoremove System.out
amwaterhouse [Fri, 27 Apr 2007 14:45:04 +0000 (14:45 +0000)]
remove System.out

17 years agoAdd param to Jmol path
amwaterhouse [Fri, 27 Apr 2007 14:44:30 +0000 (14:44 +0000)]
Add param to Jmol path

17 years agopadGaps moved
amwaterhouse [Fri, 27 Apr 2007 14:44:10 +0000 (14:44 +0000)]
padGaps moved

17 years agoMake sure mainContainer and owner are not null
amwaterhouse [Fri, 27 Apr 2007 14:43:36 +0000 (14:43 +0000)]
Make sure mainContainer and owner are not null

17 years agoMust check that featureGroup is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:43:20 +0000 (14:43 +0000)]
Must check that featureGroup is visible for mouse over features

17 years agoamendFeatures
amwaterhouse [Fri, 27 Apr 2007 14:42:59 +0000 (14:42 +0000)]
amendFeatures

17 years agopaintAlignment(true)
amwaterhouse [Fri, 27 Apr 2007 14:42:45 +0000 (14:42 +0000)]
paintAlignment(true)

17 years agoPlace new feature on top of existing features
amwaterhouse [Fri, 27 Apr 2007 14:42:27 +0000 (14:42 +0000)]
Place new feature on top of existing features

17 years agoMake sure sequence is in mouse over alignment
amwaterhouse [Fri, 27 Apr 2007 14:41:54 +0000 (14:41 +0000)]
Make sure sequence is in mouse over alignment

17 years agoAmend Features
amwaterhouse [Fri, 27 Apr 2007 14:41:30 +0000 (14:41 +0000)]
Amend Features

17 years agoColourByStructure not ready yet
amwaterhouse [Fri, 27 Apr 2007 14:40:59 +0000 (14:40 +0000)]
ColourByStructure not ready yet

17 years agonewlines in alignment properties converted to <br>
jprocter [Fri, 27 Apr 2007 12:24:40 +0000 (12:24 +0000)]
newlines in alignment properties converted to <br>

17 years agoblc header lines inserted as 'comment' alignment property
jprocter [Fri, 27 Apr 2007 12:24:09 +0000 (12:24 +0000)]
blc header lines inserted as 'comment' alignment property

17 years agoparsers can generate alignment properties
jprocter [Fri, 27 Apr 2007 12:23:33 +0000 (12:23 +0000)]
parsers can generate alignment properties

17 years agogetProperties returns nullk for no properties
jprocter [Fri, 27 Apr 2007 10:47:21 +0000 (10:47 +0000)]
getProperties returns nullk for no properties

17 years agodocumentation and getProperties method
jprocter [Fri, 27 Apr 2007 10:46:49 +0000 (10:46 +0000)]
documentation and getProperties method

17 years agoaligned boxes
amwaterhouse [Fri, 27 Apr 2007 10:00:27 +0000 (10:00 +0000)]
aligned boxes

17 years agoThresholdIsMin available in applet
amwaterhouse [Fri, 27 Apr 2007 09:54:58 +0000 (09:54 +0000)]
ThresholdIsMin available in applet

17 years agoSet black if colour null
amwaterhouse [Fri, 27 Apr 2007 09:54:41 +0000 (09:54 +0000)]
Set black if colour null

17 years agoAlignment properties available
amwaterhouse [Fri, 27 Apr 2007 09:54:13 +0000 (09:54 +0000)]
Alignment properties available

17 years agohide the initial window after selection made
amwaterhouse [Fri, 27 Apr 2007 09:53:47 +0000 (09:53 +0000)]
hide the initial window after selection made

17 years agoone colour flag in annotation export
amwaterhouse [Fri, 27 Apr 2007 09:53:27 +0000 (09:53 +0000)]
one colour flag in annotation export

17 years agobugfix for deleted annotation undo
jprocter [Fri, 27 Apr 2007 08:51:13 +0000 (08:51 +0000)]
bugfix for deleted annotation undo

17 years agoAnnotation gradient will use direct colours if no graph exists
amwaterhouse [Fri, 27 Apr 2007 08:50:06 +0000 (08:50 +0000)]
Annotation gradient will use direct colours if no graph exists

17 years agoAllow threshold to be min/max
amwaterhouse [Fri, 27 Apr 2007 08:21:09 +0000 (08:21 +0000)]
Allow threshold to be min/max

17 years agohide annotation colouring options
amwaterhouse [Fri, 27 Apr 2007 08:20:45 +0000 (08:20 +0000)]
hide annotation colouring options

17 years agoDont colour labels
amwaterhouse [Fri, 27 Apr 2007 08:20:03 +0000 (08:20 +0000)]
Dont colour labels

17 years agoadded/tested sort by scores menu and added basic extractScores function.
jprocter [Thu, 26 Apr 2007 17:16:07 +0000 (17:16 +0000)]
added/tested sort by scores menu and added basic extractScores function.

17 years agouse hasScore method to test presence of score in annotation.
jprocter [Thu, 26 Apr 2007 17:15:13 +0000 (17:15 +0000)]
use hasScore method to test presence of score in annotation.

17 years agoadded 'sort by sequence associated annotation score'
jprocter [Thu, 26 Apr 2007 17:13:47 +0000 (17:13 +0000)]
added 'sort by sequence associated annotation score'

17 years agobug fixed basic score extraction by regex on description method
jprocter [Thu, 26 Apr 2007 17:13:12 +0000 (17:13 +0000)]
bug fixed basic score extraction by regex on description method

17 years agoget annotation by label string
jprocter [Thu, 26 Apr 2007 17:12:27 +0000 (17:12 +0000)]
get annotation by label string

17 years agofix '\0' bug from score-only positional annotation
jprocter [Thu, 26 Apr 2007 17:11:56 +0000 (17:11 +0000)]
fix '\0' bug from score-only positional annotation

17 years agoscore is a double, fix bugs for score only annotation not being associated with sequences
jprocter [Thu, 26 Apr 2007 17:11:27 +0000 (17:11 +0000)]
score is a double, fix bugs for score only annotation not being associated with sequences

17 years agodouble sort functions
jprocter [Thu, 26 Apr 2007 17:10:20 +0000 (17:10 +0000)]
double sort functions

17 years agototal annotation score is a double for maximum precision.
jprocter [Thu, 26 Apr 2007 17:10:05 +0000 (17:10 +0000)]
total annotation score is a double for maximum precision.

17 years agocheck for null ss character
amwaterhouse [Thu, 26 Apr 2007 15:14:51 +0000 (15:14 +0000)]
check for null ss character

17 years agocolourText = false
amwaterhouse [Thu, 26 Apr 2007 15:14:31 +0000 (15:14 +0000)]
colourText = false

17 years agoscore and visible copy construction
jprocter [Thu, 26 Apr 2007 15:02:37 +0000 (15:02 +0000)]
score and visible copy construction

17 years agoEdit seqs
amwaterhouse [Thu, 26 Apr 2007 11:51:26 +0000 (11:51 +0000)]
Edit seqs

17 years agoquick fix for verbose fortranesque comments in preamble of AMPS BLC files (lines...
jprocter [Thu, 26 Apr 2007 11:24:42 +0000 (11:24 +0000)]
quick fix for verbose fortranesque comments in preamble of AMPS BLC files (lines were being recognised as JPred concise files)

17 years agofixed bug in prefix extraction for application
jprocter [Thu, 26 Apr 2007 11:23:18 +0000 (11:23 +0000)]
fixed bug in prefix extraction for application

17 years agobasic methods for adding scores extracted from description
jprocter [Thu, 26 Apr 2007 10:36:42 +0000 (10:36 +0000)]
basic methods for adding scores extracted from description

17 years agofix for null annotations
jprocter [Thu, 26 Apr 2007 10:35:43 +0000 (10:35 +0000)]
fix for null annotations

17 years agogroovy support without compile-time dependency.
jprocter [Thu, 26 Apr 2007 10:35:19 +0000 (10:35 +0000)]
groovy support without compile-time dependency.

17 years agoremove should be removeElement
amwaterhouse [Thu, 26 Apr 2007 09:26:53 +0000 (09:26 +0000)]
remove should be removeElement

17 years agoAlignment Properties required for annotation file
amwaterhouse [Thu, 26 Apr 2007 09:26:34 +0000 (09:26 +0000)]
Alignment Properties required for annotation file

17 years agomoving word methods to MapList and begin bug-fix for single-residue codon span featur...
jprocter [Wed, 25 Apr 2007 16:46:11 +0000 (16:46 +0000)]
moving word methods to MapList and begin bug-fix for single-residue codon span feature location (see TODOs)

17 years agogetContentPane().add alignmentProperties popup.
jprocter [Wed, 25 Apr 2007 15:41:25 +0000 (15:41 +0000)]
getContentPane().add alignmentProperties popup.

17 years agoproperties + colours
amwaterhouse [Wed, 25 Apr 2007 14:16:21 +0000 (14:16 +0000)]
properties + colours

17 years agoShow scores
amwaterhouse [Wed, 25 Apr 2007 14:07:29 +0000 (14:07 +0000)]
Show scores

17 years agoExport annotations with properties
amwaterhouse [Wed, 25 Apr 2007 14:07:10 +0000 (14:07 +0000)]
Export annotations with properties

17 years agoView Properties
amwaterhouse [Wed, 25 Apr 2007 14:06:31 +0000 (14:06 +0000)]
View Properties

17 years agofix recent file type bug
amwaterhouse [Wed, 25 Apr 2007 14:06:11 +0000 (14:06 +0000)]
fix recent file type bug

17 years agoalignmentProperties added
amwaterhouse [Wed, 25 Apr 2007 14:05:45 +0000 (14:05 +0000)]
alignmentProperties added

17 years agoFunctions for parsing free text properties on sequences, alignments and annotations.
jprocter [Wed, 25 Apr 2007 11:52:32 +0000 (11:52 +0000)]
Functions for parsing free text properties on sequences, alignments and annotations.

17 years agotransfer of residue numbering as alignment annotation
jprocter [Wed, 25 Apr 2007 11:50:51 +0000 (11:50 +0000)]
transfer of residue numbering as alignment annotation

17 years agoAlignmentAnnotation: added annotation score attribute and allowed for annotation...
jprocter [Wed, 25 Apr 2007 11:47:48 +0000 (11:47 +0000)]
AlignmentAnnotation: added annotation score attribute and allowed for annotation[] array to be null

17 years agobugfix for sequence features mapped to multiple contigs on local sequence frame
jprocter [Tue, 24 Apr 2007 14:34:08 +0000 (14:34 +0000)]
bugfix for sequence features mapped to multiple contigs on local sequence frame

17 years agoupdated mapping for EMBL_Services_V1.1.xsd and tested with basic CDS feature detection.
jprocter [Tue, 24 Apr 2007 14:33:28 +0000 (14:33 +0000)]
updated mapping for EMBL_Services_V1.1.xsd and tested with basic CDS feature detection.

17 years agofunctions that operate on references to sequences in alignment rather than copies.
jprocter [Mon, 23 Apr 2007 15:13:00 +0000 (15:13 +0000)]
functions that operate on references to sequences in alignment rather than copies.

17 years agodistinct methods for getting references to selected sequences or getting new seuqence...
jprocter [Mon, 23 Apr 2007 15:11:55 +0000 (15:11 +0000)]
distinct methods for getting references to selected sequences or getting new seuqence objects corresponding to selection.

17 years agogetColour method added
amwaterhouse [Mon, 23 Apr 2007 12:47:53 +0000 (12:47 +0000)]
getColour method added

17 years agoCheck for null displayCharacters
amwaterhouse [Mon, 23 Apr 2007 12:46:14 +0000 (12:46 +0000)]
Check for null displayCharacters

17 years agoDbref fetcher takes sequences, not alignment
amwaterhouse [Mon, 23 Apr 2007 12:30:25 +0000 (12:30 +0000)]
Dbref fetcher takes sequences, not alignment

17 years agogetColour added to structures
amwaterhouse [Mon, 23 Apr 2007 11:50:12 +0000 (11:50 +0000)]
getColour added to structures

17 years agoTest out new arrangement
amwaterhouse [Mon, 23 Apr 2007 11:49:36 +0000 (11:49 +0000)]
Test out new arrangement

17 years agoGet colour from structure added
amwaterhouse [Mon, 23 Apr 2007 11:48:54 +0000 (11:48 +0000)]
Get colour from structure added

17 years agocheck dispalyChar is not null
amwaterhouse [Mon, 23 Apr 2007 11:47:47 +0000 (11:47 +0000)]
check dispalyChar is not null

17 years agoCheck displayChar is not null
amwaterhouse [Mon, 23 Apr 2007 11:47:10 +0000 (11:47 +0000)]
Check displayChar is not null

17 years agoColour is null
amwaterhouse [Mon, 23 Apr 2007 11:46:26 +0000 (11:46 +0000)]
Colour is null

17 years agoremove seqref annotations
amwaterhouse [Mon, 23 Apr 2007 11:46:06 +0000 (11:46 +0000)]
remove seqref annotations