jalview.git
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

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