jalview.git
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

17 years agoremove alignmentAnnotation added
amwaterhouse [Mon, 23 Apr 2007 11:45:34 +0000 (11:45 +0000)]
remove alignmentAnnotation added

17 years agoOnly fetch refs for seelcted sequences
amwaterhouse [Mon, 23 Apr 2007 11:44:46 +0000 (11:44 +0000)]
Only fetch refs for seelcted sequences

17 years agofix null annotation values
jprocter [Fri, 20 Apr 2007 15:34:06 +0000 (15:34 +0000)]
fix null annotation values

17 years agoglobal dbref fetch option in web services menu.
jprocter [Fri, 20 Apr 2007 15:30:33 +0000 (15:30 +0000)]
global dbref fetch option in web services menu.

17 years agovalue only annotation
jprocter [Fri, 20 Apr 2007 14:14:31 +0000 (14:14 +0000)]
value only annotation

17 years agoadds annotation for display (with flag to set alignmentAnnotation as hidden initially)
jprocter [Fri, 20 Apr 2007 14:06:19 +0000 (14:06 +0000)]
adds annotation for display (with flag to set alignmentAnnotation as hidden initially)

17 years agoannotation and seqs vectors are protected members for use by file parsers for adding...
jprocter [Fri, 20 Apr 2007 14:05:50 +0000 (14:05 +0000)]
annotation and seqs vectors are protected members for use by file parsers for adding data for import.

17 years agotfactor annotation description includes full sequenceID
jprocter [Thu, 19 Apr 2007 16:25:22 +0000 (16:25 +0000)]
tfactor annotation description includes full sequenceID

17 years agotfactor and occupancy extracted from PDB file, and tfactor added as sequence associat...
jprocter [Thu, 19 Apr 2007 16:17:39 +0000 (16:17 +0000)]
tfactor and occupancy extracted from PDB file, and tfactor added as sequence associated alignment annotation.

17 years agobugfix
jprocter [Thu, 19 Apr 2007 16:16:23 +0000 (16:16 +0000)]
bugfix

17 years agofixed column selection cut/paste and self paste.
jprocter [Thu, 19 Apr 2007 15:23:18 +0000 (15:23 +0000)]
fixed column selection cut/paste and self paste.

17 years agosequence associated alignment annotation copy for column range selection
jprocter [Thu, 19 Apr 2007 15:22:40 +0000 (15:22 +0000)]
sequence associated alignment annotation copy for column range selection

17 years agoensure edit command gapChar is updated and used for padding when no alignmentI refere...
jprocter [Thu, 19 Apr 2007 15:21:16 +0000 (15:21 +0000)]
ensure edit command gapChar is updated and used for padding when no alignmentI reference is available

17 years agopadGaps flag in copy constructor
jprocter [Thu, 19 Apr 2007 15:00:52 +0000 (15:00 +0000)]
padGaps flag in copy constructor

17 years agojavadoc note on padding AlignmentAnnotation to alignment width
jprocter [Thu, 19 Apr 2007 14:55:39 +0000 (14:55 +0000)]
javadoc note on padding AlignmentAnnotation to alignment width

17 years agocopying sequenceMapping, restrict(alstart/end) and pad(alwidth) method.
jprocter [Thu, 19 Apr 2007 14:54:43 +0000 (14:54 +0000)]
copying sequenceMapping, restrict(alstart/end) and pad(alwidth) method.

17 years agoREPLACE added to edit command
amwaterhouse [Thu, 19 Apr 2007 14:42:24 +0000 (14:42 +0000)]
REPLACE added to edit command

17 years agoOnly setDropTarget if Desktop is not null
amwaterhouse [Thu, 19 Apr 2007 09:56:55 +0000 (09:56 +0000)]
Only setDropTarget if Desktop is not null

17 years agoValidate range for all annotations
amwaterhouse [Wed, 18 Apr 2007 16:11:28 +0000 (16:11 +0000)]
Validate range for all annotations

17 years agoRedundant code commented out
amwaterhouse [Wed, 18 Apr 2007 16:10:53 +0000 (16:10 +0000)]
Redundant code commented out

17 years agohastext = false
amwaterhouse [Wed, 18 Apr 2007 13:42:37 +0000 (13:42 +0000)]
hastext = false

17 years agodont set seqref null if index incorrect
amwaterhouse [Wed, 18 Apr 2007 13:35:07 +0000 (13:35 +0000)]
dont set seqref null if index incorrect

17 years agofeatureGroups not null
amwaterhouse [Wed, 18 Apr 2007 13:29:46 +0000 (13:29 +0000)]
featureGroups not null

17 years agoPad gaps when annotation editing
amwaterhouse [Wed, 18 Apr 2007 12:32:39 +0000 (12:32 +0000)]
Pad gaps when annotation editing

17 years agoquality has text false
amwaterhouse [Wed, 18 Apr 2007 12:06:17 +0000 (12:06 +0000)]
quality has text false

17 years agoQuality does not have text
amwaterhouse [Wed, 18 Apr 2007 12:04:28 +0000 (12:04 +0000)]
Quality does not have text

17 years agoAlignment of labels and text
amwaterhouse [Wed, 18 Apr 2007 12:03:49 +0000 (12:03 +0000)]
Alignment of labels and text

17 years agochecks for scrollbar height
amwaterhouse [Wed, 18 Apr 2007 12:03:28 +0000 (12:03 +0000)]
checks for scrollbar height

17 years agoDisable memory checker for now
amwaterhouse [Wed, 18 Apr 2007 12:02:16 +0000 (12:02 +0000)]
Disable memory checker for now

17 years agoadjustForAlignment on new seq ref
amwaterhouse [Wed, 18 Apr 2007 12:01:56 +0000 (12:01 +0000)]
adjustForAlignment on new seq ref

17 years agoCheck values not null in copy constructor
amwaterhouse [Wed, 18 Apr 2007 12:01:33 +0000 (12:01 +0000)]
Check values not null in copy constructor

17 years agomade compileApplet and obfuscate depend on the presence of a java 1.1 jdk to ensure...
jprocter [Wed, 18 Apr 2007 10:55:22 +0000 (10:55 +0000)]
made compileApplet and obfuscate depend on the presence of a java 1.1 jdk to ensure that applet jar is properly 1.1 compliant.

17 years agojava 1.1 compliance
jprocter [Wed, 18 Apr 2007 10:51:30 +0000 (10:51 +0000)]
java 1.1 compliance

17 years agobugfix for jalviewApplet run from command line.
jprocter [Tue, 17 Apr 2007 17:05:41 +0000 (17:05 +0000)]
bugfix for jalviewApplet run from command line.

17 years agobugfix.
jprocter [Tue, 17 Apr 2007 16:55:47 +0000 (16:55 +0000)]
bugfix.

17 years agojmol lib dependency for proguard and castorbinding target.
jprocter [Tue, 17 Apr 2007 16:39:45 +0000 (16:39 +0000)]
jmol lib dependency for proguard and castorbinding target.

17 years agouse of suffix string (filename.blc#suffixstring) to read a specified iteration from...
jprocter [Tue, 17 Apr 2007 15:58:47 +0000 (15:58 +0000)]
use of suffix string (filename.blc#suffixstring) to read a specified iteration from blc file.

17 years agorefactored to allow seeks on a FileParse datasource so IdentifyFile can be applied...
jprocter [Tue, 17 Apr 2007 15:57:41 +0000 (15:57 +0000)]
refactored to allow seeks on a FileParse datasource so IdentifyFile can be applied to an inputstream.

17 years agojavadoc
jprocter [Tue, 17 Apr 2007 15:55:04 +0000 (15:55 +0000)]
javadoc

17 years agoascii type
jprocter [Tue, 17 Apr 2007 11:32:26 +0000 (11:32 +0000)]
ascii type

17 years agopaste adds or creates full copies of objects in clipboard, and properly copies sequen...
jprocter [Tue, 17 Apr 2007 11:31:15 +0000 (11:31 +0000)]
paste adds or creates full copies of objects in clipboard, and properly copies sequence associated alignment annotation.

17 years agopdb files are global to all alignments with new mapping mechanism.
jprocter [Tue, 17 Apr 2007 11:29:11 +0000 (11:29 +0000)]
pdb files are global to all alignments with new mapping mechanism.

17 years agopaste/cut now adds or removes associated AlignmentAnnotation.
jprocter [Tue, 17 Apr 2007 11:05:40 +0000 (11:05 +0000)]
paste/cut now adds or removes associated AlignmentAnnotation.

17 years agocopy constructors and AlignmentAnnotation sequenceRef mechanisms for pasting sequence...
jprocter [Tue, 17 Apr 2007 11:03:38 +0000 (11:03 +0000)]
copy constructors and AlignmentAnnotation sequenceRef mechanisms for pasting sequences and annotation.

17 years agocopy constructor and ascii type change.
jprocter [Tue, 17 Apr 2007 11:02:43 +0000 (11:02 +0000)]
copy constructor and ascii type change.

17 years agoproper copy constructor (not clone)
jprocter [Tue, 17 Apr 2007 11:01:57 +0000 (11:01 +0000)]
proper copy constructor (not clone)

17 years agoApplet remembers PDBEntries, can launch multiple structures from popupmenu
amwaterhouse [Tue, 17 Apr 2007 10:42:39 +0000 (10:42 +0000)]
Applet remembers PDBEntries, can launch multiple structures from popupmenu

17 years agoAdd system.out for Mcview / Jmol detection
amwaterhouse [Tue, 17 Apr 2007 09:37:10 +0000 (09:37 +0000)]
Add system.out for Mcview / Jmol detection

17 years agoRemove system.out
amwaterhouse [Tue, 17 Apr 2007 09:35:45 +0000 (09:35 +0000)]
Remove system.out

17 years agodrawSequence must be synchronized
amwaterhouse [Mon, 16 Apr 2007 11:24:16 +0000 (11:24 +0000)]
drawSequence must be synchronized

17 years agoToo many calls to paintAlignment
amwaterhouse [Mon, 16 Apr 2007 11:23:25 +0000 (11:23 +0000)]
Too many calls to paintAlignment

17 years agoFeatureRenderer takes alignmentPanel
amwaterhouse [Fri, 13 Apr 2007 15:52:18 +0000 (15:52 +0000)]
FeatureRenderer takes alignmentPanel

17 years agoCheck alignment has same sequence
amwaterhouse [Fri, 13 Apr 2007 15:51:20 +0000 (15:51 +0000)]
Check alignment has same sequence

17 years agobasic support for multi-exon CDS features
jprocter [Thu, 12 Apr 2007 14:46:07 +0000 (14:46 +0000)]
basic support for multi-exon CDS features

17 years agoNumber pad keys can be used in cursor mode
amwaterhouse [Thu, 12 Apr 2007 14:00:59 +0000 (14:00 +0000)]
Number pad keys can be used in cursor mode

17 years agoSetTargetColour before dialog.show
amwaterhouse [Wed, 11 Apr 2007 14:30:49 +0000 (14:30 +0000)]
SetTargetColour before dialog.show

17 years agoModified to compile applet with Jmol jar present
amwaterhouse [Wed, 11 Apr 2007 14:29:44 +0000 (14:29 +0000)]
Modified to compile applet with Jmol jar present

17 years agofixed for display of 'null' group features
jprocter [Wed, 11 Apr 2007 14:16:55 +0000 (14:16 +0000)]
fixed for display of 'null' group features

17 years agofixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard...
jprocter [Wed, 11 Apr 2007 13:57:45 +0000 (13:57 +0000)]
fixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard aa and na codes are preserved in aligned sequences.

17 years agoCan add features with no group
amwaterhouse [Wed, 11 Apr 2007 13:02:43 +0000 (13:02 +0000)]
Can add features with no group

17 years agoAdjustment for hidden columns
amwaterhouse [Wed, 11 Apr 2007 13:01:44 +0000 (13:01 +0000)]
Adjustment for hidden columns

17 years agoUse same mouse events as scalePanel
amwaterhouse [Wed, 11 Apr 2007 13:01:18 +0000 (13:01 +0000)]
Use same mouse events as scalePanel

17 years agoAmend features/annotations in applet
amwaterhouse [Wed, 11 Apr 2007 13:00:48 +0000 (13:00 +0000)]
Amend features/annotations in applet

17 years agoUsed several places
amwaterhouse [Wed, 11 Apr 2007 13:00:28 +0000 (13:00 +0000)]
Used several places

17 years agoIf hiddenColumns are null, then column is viisble
amwaterhouse [Wed, 11 Apr 2007 13:00:09 +0000 (13:00 +0000)]
If hiddenColumns are null, then column is viisble

17 years agofeatureAdded not in applet
amwaterhouse [Wed, 11 Apr 2007 12:59:27 +0000 (12:59 +0000)]
featureAdded not in applet

17 years agoPaste menu item dispalyed on right click. Memory settings visible in this version
amwaterhouse [Thu, 5 Apr 2007 11:22:35 +0000 (11:22 +0000)]
Paste menu item dispalyed on right click. Memory settings visible in this version