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popup for non-fatal tree parsing error
[jalview.git]
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src
/
jalview
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io
/
2007-08-22
jprocter
introduce beginning of bug fix for parsing atv style...
tree
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commitdiff
2007-08-22
jprocter
added facility for sending non-fatal warnings back...
tree
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commitdiff
2007-08-06
jprocter
comment concerning null exceptions generated when annot...
tree
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commitdiff
2007-08-01
jprocter
javadoc
tree
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commitdiff
2007-07-25
jprocter
todo comment
tree
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commitdiff
2007-07-25
jprocter
better vamsas tree io (for when there are no nodemappings)
tree
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commitdiff
2007-07-25
jprocter
bugfix for vamsas demo
tree
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commitdiff
2007-07-25
jprocter
IO rearrangement for AMSAFile output
tree
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commitdiff
2007-07-13
jprocter
preliminary IO classes - read javadoc for purpose
tree
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commitdiff
2007-07-13
jprocter
new DBRef management and generalised source and entry...
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commitdiff
2007-07-13
jprocter
updated to iscb demo vamsas-client version
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commitdiff
2007-07-13
jprocter
refactored form of vamsas document interaction code
tree
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commitdiff
2007-06-18
jprocter
1.1 methods
tree
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commitdiff
2007-06-17
jprocter
vamsas-client-1.2 schema (mappings and Treenodes) and...
tree
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commitdiff
2007-06-17
jprocter
JnetFIle is a readable format
tree
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commitdiff
2007-06-17
jprocter
score only annotation IO
tree
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commitdiff
2007-06-04
jprocter
fix for 'RF' annotation tags and ensured parser is...
tree
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commitdiff
2007-05-22
jprocter
refactored document objects and bugfix on jvdataset...
tree
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commitdiff
2007-05-18
jprocter
fixed getObject(VorbaId) lookup in vamsas-client
tree
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commitdiff
2007-05-18
jprocter
update to and from document (and remove deprecated...
tree
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commitdiff
2007-05-17
jprocter
use of proper vamsas client API by Jalview
tree
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commitdiff
2007-05-17
jprocter
modified castor-1.1 library and refactored uk.ac.vamsas
tree
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commitdiff
2007-05-10
jprocter
apparent bug in JpredFile parser where annotation was...
tree
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commitdiff
2007-05-09
jprocter
main method for running from command line and better...
tree
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commitdiff
2007-05-08
amwaterhouse
addElement
tree
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commitdiff
2007-05-02
jprocter
public debug report log message to gather any cases...
tree
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commitdiff
2007-05-02
amwaterhouse
AMSA input set padgaps true
tree
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commitdiff
2007-05-01
amwaterhouse
Make sure annots are alignment width
tree
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commitdiff
2007-04-30
jprocter
'no sources selected' calls method on feature settings...
tree
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commitdiff
2007-04-30
jprocter
parse alignment properties and add annotation rows...
tree
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commitdiff
2007-04-30
jprocter
alignment properties and embedded newick strings can...
tree
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commitdiff
2007-04-27
jprocter
blc header lines inserted as 'comment' alignment property
tree
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commitdiff
2007-04-27
jprocter
parsers can generate alignment properties
tree
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commitdiff
2007-04-27
amwaterhouse
one colour flag in annotation export
tree
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commitdiff
2007-04-26
jprocter
use hasScore method to test presence of score in annota...
tree
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commitdiff
2007-04-26
jprocter
quick fix for verbose fortranesque comments in preamble...
tree
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commitdiff
2007-04-26
jprocter
fixed bug in prefix extraction for application
tree
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commitdiff
2007-04-25
amwaterhouse
properties + colours
tree
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commitdiff
2007-04-25
amwaterhouse
fix recent file type bug
tree
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commitdiff
2007-04-25
jprocter
AlignmentAnnotation: added annotation score attribute...
tree
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commitdiff
2007-04-23
amwaterhouse
Check displayChar is not null
tree
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commitdiff
2007-04-23
amwaterhouse
Only fetch refs for seelcted sequences
tree
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commitdiff
2007-04-20
jprocter
annotation and seqs vectors are protected members for...
tree
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commitdiff
2007-04-18
amwaterhouse
dont set seqref null if index incorrect
tree
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commitdiff
2007-04-18
amwaterhouse
adjustForAlignment on new seq ref
tree
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commitdiff
2007-04-18
jprocter
java 1.1 compliance
tree
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commitdiff
2007-04-17
jprocter
bugfix.
tree
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commitdiff
2007-04-17
jprocter
use of suffix string (filename.blc#suffixstring) to...
tree
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commitdiff
2007-04-17
jprocter
refactored to allow seeks on a FileParse datasource...
tree
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commitdiff
2007-04-17
jprocter
javadoc
tree
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commitdiff
2007-04-13
amwaterhouse
FeatureRenderer takes alignmentPanel
tree
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commitdiff
2007-04-05
amwaterhouse
Pasted file doesnt have title and not reloadable
tree
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commitdiff
2007-04-05
amwaterhouse
call getAllframes on desktop instance
tree
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commitdiff
2007-04-04
amwaterhouse
flag for dasCoordSysFound added
tree
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commitdiff
2007-03-19
jprocter
DAS features mapped to local reference frame
tree
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commitdiff
2007-03-19
jprocter
disambiguate jalview.datamodel.Mapping from castor...
tree
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commitdiff
2007-02-27
amwaterhouse
Use paintAlignment
tree
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commitdiff
2007-02-27
amwaterhouse
remove p+3 < query.length
tree
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commitdiff
2007-02-07
amwaterhouse
Formatting
tree
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commitdiff
2007-02-05
amwaterhouse
applet can define groups as parameters
tree
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commitdiff
2007-02-02
amwaterhouse
Dont add group if seqs not found
tree
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commitdiff
2007-01-30
amwaterhouse
Any character non aa or nucleotide is a space
tree
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commitdiff
2007-01-30
amwaterhouse
Use util toHexString
tree
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commitdiff
2007-01-30
amwaterhouse
Output groups in annotation file
tree
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commitdiff
2007-01-29
amwaterhouse
SequenceGroup parsing added to annotation file
tree
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commitdiff
2007-01-25
amwaterhouse
Remove unneccessary lines
tree
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commitdiff
2007-01-25
amwaterhouse
Only output visible annotations
tree
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commitdiff
2007-01-25
jprocter
reinstating class implementation.
tree
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commitdiff
2007-01-24
amwaterhouse
output now takes alignment, not just sequences
tree
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commitdiff
2007-01-24
amwaterhouse
Extension to fastaFile for myhits
tree
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commitdiff
2007-01-19
amwaterhouse
Need to know protocol to load anntotations
tree
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commitdiff
2007-01-18
amwaterhouse
Add the last sequence before annotations
tree
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commitdiff
2007-01-18
amwaterhouse
1.1 enabled
tree
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commitdiff
2007-01-18
amwaterhouse
File Parsing returns Alignments, not Sequence[]
tree
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commitdiff
2007-01-18
amwaterhouse
Descriptions can be added to annotations
tree
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commitdiff
2007-01-04
amwaterhouse
Reads in anything following seq id as a description
tree
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commitdiff
2007-01-04
amwaterhouse
HEADER and ATOM must be position 0
tree
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commitdiff
2006-12-21
jprocter
description from vamsas sequence and file type change
tree
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commitdiff
2006-12-21
amwaterhouse
remove unnecessary import
tree
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commitdiff
2006-12-19
amwaterhouse
description may be null
tree
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commitdiff
2006-12-14
amwaterhouse
set sequence_ref alignment
tree
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commitdiff
2006-12-14
amwaterhouse
Are the labels all secondary Strutures? are the display...
tree
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commitdiff
2006-12-11
jprocter
fixed introduced bug (doh)
tree
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commitdiff
2006-12-11
jprocter
clarified help documentation for annotation file format...
tree
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commitdiff
2006-12-05
amwaterhouse
Sequence is char []
tree
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commitdiff
2006-11-30
amwaterhouse
DasRegistry moved again
tree
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commitdiff
2006-11-28
jprocter
EBI web service interface update (and SequenceFetcher...
tree
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commitdiff
2006-11-21
amwaterhouse
Memory check on loading file
tree
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commitdiff
2006-11-21
amwaterhouse
Set fsettings in constuctor
tree
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commitdiff
2006-11-20
amwaterhouse
Cancel added
tree
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commitdiff
2006-11-14
amwaterhouse
Single seq Blc file detection
tree
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commitdiff
2006-11-13
amwaterhouse
Use j not i
tree
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commitdiff
2006-11-13
amwaterhouse
Fasta files with * read not identified as BLC
tree
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commitdiff
2006-11-13
amwaterhouse
Querystring made from line tokenized seq name, seq...
tree
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commitdiff
2006-11-09
amwaterhouse
alignFrame.setFileName
tree
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commitdiff
2006-11-06
amwaterhouse
Remember fileName in alignFrame
tree
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commitdiff
2006-11-02
amwaterhouse
dasregistry is now dasregistry.org
tree
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commitdiff
2006-10-30
amwaterhouse
Append html
tree
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commitdiff
2006-10-24
amwaterhouse
Only send one call per sequence at the moment
tree
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commitdiff
2006-10-18
amwaterhouse
Wait for response from server before next sequence
tree
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commitdiff
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