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undo stackempty error fix, refactored do and undo() method to take array of alignment...
2007-05-02
jprocter
undo stackempty error fix, refactored do and undo(...
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2007-05-02
jprocter
refactored do and undo() method to take array of alignments...
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2007-05-02
jprocter
copy only the sequence associated alignment annotation...
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2007-05-02
jprocter
subsequence bound checks and constructor for selectively...
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2007-05-02
jprocter
return flag indicating if annotations were actually...
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2007-05-02
jprocter
checks for negative start column in restrict
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2007-05-01
jprocter
javadoc
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2007-05-01
jprocter
removeAlignmentAnnotation only removes annotation objects...
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2007-05-01
jprocter
sort-by-score works of sequence-annotation, not alignment...
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2007-05-01
jprocter
2.3 what's new
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2007-05-01
jprocter
preliminary EMBL and mapping documentation
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2007-04-30
jprocter
'no sources selected' calls method on feature settings...
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2007-04-30
jprocter
fixed deadlock
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2007-04-30
jprocter
rebuild sort by scores menu when new annotation is...
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2007-04-30
jprocter
pad should leave null annotations array null
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2007-04-30
jprocter
convenient creation of 'score only' annotation.
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2007-04-30
jprocter
parse alignment properties and add annotation rows...
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2007-04-30
jprocter
alignment properties and embedded newick strings can...
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2007-04-30
jprocter
dssp 7-state to three state lookup
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2007-04-30
jprocter
javadoc
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2007-04-27
jprocter
newlines in alignment properties converted to <br>
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2007-04-27
jprocter
blc header lines inserted as 'comment' alignment property
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2007-04-27
jprocter
parsers can generate alignment properties
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2007-04-27
jprocter
getProperties returns nullk for no properties
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2007-04-27
jprocter
documentation and getProperties method
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2007-04-27
jprocter
bugfix for deleted annotation undo
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2007-04-26
jprocter
added/tested sort by scores menu and added basic extractScor...
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2007-04-26
jprocter
use hasScore method to test presence of score in annotation.
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2007-04-26
jprocter
added 'sort by sequence associated annotation score'
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2007-04-26
jprocter
bug fixed basic score extraction by regex on description...
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2007-04-26
jprocter
get annotation by label string
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2007-04-26
jprocter
fix '\0' bug from score-only positional annotation
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2007-04-26
jprocter
score is a double, fix bugs for score only annotation...
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2007-04-26
jprocter
double sort functions
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2007-04-26
jprocter
total annotation score is a double for maximum precision.
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2007-04-26
jprocter
score and visible copy construction
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2007-04-26
jprocter
quick fix for verbose fortranesque comments in preamble...
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2007-04-26
jprocter
fixed bug in prefix extraction for application
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2007-04-26
jprocter
basic methods for adding scores extracted from description
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2007-04-26
jprocter
fix for null annotations
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2007-04-26
jprocter
groovy support without compile-time dependency.
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2007-04-25
jprocter
moving word methods to MapList and begin bug-fix for...
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2007-04-25
jprocter
getContentPane().add alignmentProperties popup.
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2007-04-25
jprocter
Functions for parsing free text properties on sequences...
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2007-04-25
jprocter
transfer of residue numbering as alignment annotation
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2007-04-25
jprocter
AlignmentAnnotation: added annotation score attribute...
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2007-04-24
jprocter
bugfix for sequence features mapped to multiple contigs...
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2007-04-24
jprocter
updated mapping for EMBL_Services_V1.1.xsd and tested...
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2007-04-23
jprocter
functions that operate on references to sequences in...
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2007-04-23
jprocter
distinct methods for getting references to selected...
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2007-04-20
jprocter
fix null annotation values
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2007-04-20
jprocter
global dbref fetch option in web services menu.
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2007-04-20
jprocter
value only annotation
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2007-04-20
jprocter
adds annotation for display (with flag to set alignmentAnnot...
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2007-04-20
jprocter
annotation and seqs vectors are protected members for...
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2007-04-19
jprocter
tfactor annotation description includes full sequenceID
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2007-04-19
jprocter
tfactor and occupancy extracted from PDB file, and...
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2007-04-19
jprocter
bugfix
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2007-04-19
jprocter
fixed column selection cut/paste and self paste.
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2007-04-19
jprocter
sequence associated alignment annotation copy for column...
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2007-04-19
jprocter
ensure edit command gapChar is updated and used for...
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2007-04-19
jprocter
padGaps flag in copy constructor
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2007-04-19
jprocter
javadoc note on padding AlignmentAnnotation to alignment...
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2007-04-19
jprocter
copying sequenceMapping, restrict(alstart/end) and...
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2007-04-18
jprocter
made compileApplet and obfuscate depend on the presence...
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2007-04-18
jprocter
java 1.1 compliance
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2007-04-17
jprocter
bugfix for jalviewApplet run from command line.
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2007-04-17
jprocter
bugfix.
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2007-04-17
jprocter
jmol lib dependency for proguard and castorbinding...
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2007-04-17
jprocter
use of suffix string (filename.blc#suffixstring) to...
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2007-04-17
jprocter
refactored to allow seeks on a FileParse datasource...
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2007-04-17
jprocter
javadoc
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2007-04-17
jprocter
ascii type
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2007-04-17
jprocter
paste adds or creates full copies of objects in clipboard...
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2007-04-17
jprocter
pdb files are global to all alignments with new mapping...
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2007-04-17
jprocter
paste/cut now adds or removes associated AlignmentAnnotation.
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2007-04-17
jprocter
copy constructors and AlignmentAnnotation sequenceRef...
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2007-04-17
jprocter
copy constructor and ascii type change.
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2007-04-17
jprocter
proper copy constructor (not clone)
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2007-04-12
jprocter
basic support for multi-exon CDS features
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2007-04-11
jprocter
fixed for display of 'null' group features
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2007-04-11
jprocter
fixed base lookup bug in dna pairwise alignment and...
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2007-04-02
jprocter
doco change.
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2007-04-02
jprocter
update settings for new groups (always displayed) and...
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2007-04-02
jprocter
bugfix + create/amend whilst feature panel open (still...
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2007-04-02
jprocter
typo fix.
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2007-04-02
jprocter
featuresAdded method introduced for consistency with...
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2007-04-02
jprocter
fr==null check.
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2007-04-02
jprocter
feature group state and type order preference storage...
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2007-04-02
jprocter
featuresAdded call for transferred PDB features
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2007-04-02
jprocter
featuresAdded() method, state change support between...
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2007-04-02
jprocter
added feature type order preference attribute and visible...
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2007-03-26
jprocter
fix single sequence features added rendering bug.
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2007-03-26
jprocter
PDB residue numberings transfered and alignment view...
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2007-03-26
jprocter
grammar.
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2007-03-23
jprocter
generalised feature attribute parsing slightly (no...
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2007-03-23
jprocter
bugfix for 1.1 conversion.
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2007-03-23
jprocter
reenable canceldas after a cancel and subsequence fetch
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2007-03-23
jprocter
lastSeq==null to force refresh of sequencefeature array...
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2007-03-23
jprocter
removed Iterator usage.
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