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Use Jalview2XML to copy AlignmentPanel
2006-10-24
jprocter
fixes bug reported by Christopher Tan (help@jalview...
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2006-10-15
jprocter
fixed array out of bounds exception in copy constructor
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2006-10-11
jprocter
fixes exception (array index out of bounds - due to...
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2006-10-10
jprocter
refined id matching to pick the closest match (by length...
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2006-10-10
jprocter
debug message bugfix on duplicate tree leaf names.
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2006-10-10
jprocter
bugfix for dodgy trees which contain the same leafname...
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2006-10-09
jprocter
fixed log4j complaints for vamsas logging (again)
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2006-10-09
jprocter
fixed log4j complaints for vamsas logging.
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2006-10-09
jprocter
excluded log4j properties.
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2006-10-09
jprocter
java 1.4 compliant classes.
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2006-10-09
jprocter
imported Vamsas bindings and alpha vamsas client code...
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2006-10-09
jprocter
set firstColumn property for an alignmentView object.
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2006-10-09
jprocter
fixed getCompactAlignment method to return proper cigarArray...
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2006-10-06
jprocter
Added filter so that input to a JPred job is *solely...
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2006-10-06
jprocter
javadoc
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2006-10-06
jprocter
new getVisibleContigs method mirrors the getVisibleContigs...
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2006-09-27
jprocter
fixed tree building exception when one residue or a...
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2006-09-07
jprocter
added copy consensus sequence to consensus annotation...
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2006-09-05
jprocter
getVisibleContigs() returns start and end positions...
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2006-09-05
jprocter
javadoc on contigs
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2006-08-22
jprocter
documentation - adding new Input data menu entries.
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2006-08-22
jprocter
added note on column-separability
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2006-08-22
jprocter
documentation
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2006-08-22
jprocter
getSequenceStrings() bug fixed.
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2006-08-22
jprocter
hidden region recovery in JPred and new hidden region...
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2006-08-22
jprocter
off by one bug in hiden column unmarshalling
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2006-08-21
jprocter
Refactored Jnet and added hidden columns support.
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2006-08-21
jprocter
fixed undo-redo bug, hidden columns are moved with...
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2006-08-21
jprocter
removeGaps method can record changes in alignment columns...
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2006-08-21
jprocter
fix for truncation of sequence associated annotation...
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2006-08-21
jprocter
added shiftList to record changes in alignment column...
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2006-08-21
jprocter
remove gaps method from AlignFrame.remove_gaps_actionPerformed
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2006-08-21
jprocter
inverse ShiftList and SequenceI.gapMap->ShiftList methods.
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2006-08-21
jprocter
avoid null pointer exceptions
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2006-08-20
jprocter
javadoc
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2006-08-17
jprocter
moved visible sub-alignment extraction and update from...
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2006-08-17
jprocter
javadoc
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2006-08-15
jprocter
make annotation label font size follow alignment font...
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2006-08-15
jprocter
first stage of adapting JNet client to hidden regions...
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2006-08-15
jprocter
fixed alignment ordering name.
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2006-08-15
jprocter
ensure that close widget is available for jobs that...
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2006-08-14
jprocter
refactored to create generic polling thread and subjobs
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2006-08-14
jprocter
function to indicate job has finished but no results...
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2006-08-14
jprocter
multiple subjobs can be cancelled and gui only allows...
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2006-08-14
jprocter
fixed off by one bug in end sequence from getSubSequence...
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2006-08-14
jprocter
end<start for empty sequences in Sequence[] from SeqCigar[]
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2006-08-14
jprocter
fixing residue clip bug in MsaWSThread and adding minimum...
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2006-08-13
jprocter
fixed end-residue bug and subjob panel names bug
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2006-08-11
jprocter
multiple web service jobs from visible blocks of an...
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2006-08-09
jprocter
new SequenceI method for making a sub sequence from...
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2006-08-09
jprocter
alignment from seqCigars will correctly mark deleted...
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2006-08-09
jprocter
refactored hidden regions methods and made an AlignmentView...
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2006-08-09
jprocter
fixed multiple shifts bug.
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2006-08-08
jprocter
removed extraneous classes.
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2006-08-08
jprocter
locally modified biojava-dasobert package is now org...
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2006-08-07
jprocter
added commented out seqStrings comment.
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2006-08-04
jprocter
recover original data for tree and pca as alignment...
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2006-07-26
jprocter
accidental commit of a build
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2006-07-26
jprocter
Ignore list created
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2006-07-26
jprocter
Cigars for representing alignment view as used for...
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2006-07-26
jprocter
CigarBase class and derivatives.
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2006-07-26
jprocter
Implemented CIGAR representation of an Alignment view...
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2006-07-26
jprocter
Compact Idiosyncratic Gapped Alignment Representation...
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2006-07-24
jprocter
partly finished pods.
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2006-07-21
jprocter
Item added to ignoreList
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2006-07-21
jprocter
Item added to ignoreList
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2006-07-21
jprocter
Ignore list created
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2006-07-20
jprocter
annotation label font size change in applet.
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2006-07-18
jprocter
use of GapChars
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2006-06-08
jprocter
Introduced DbRefEntry to DasSourceCoordinateSystem...
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2006-06-08
jprocter
DBRefEntry.source enum type
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2006-06-08
jprocter
bugfixed and podded.
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2006-06-08
jprocter
simplest conversion of gff to jalview annotation format...
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2006-06-07
jprocter
broken link typo. (SEVENtwentyfour alert)
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2006-05-18
jprocter
added future method comment
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2006-05-17
jprocter
added the jnetfile parameter to specify a JNet concise...
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2006-05-17
jprocter
added unofficial support for concise output parsing...
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2006-05-17
jprocter
refactored code for creating JNet annotations
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2006-05-17
jprocter
Refactored code for creating annotation objects from...
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2006-05-16
jprocter
added popup warning when proxy settings must be configured.
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2006-05-12
jprocter
rearranged discoverer to dynamically update on demand
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2006-04-10
jprocter
load features/annotations typo.
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2006-04-10
jprocter
added note about cursor mode disabling the popup menu.
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2006-04-10
jprocter
typo and explanation for ignore gaps in consensus
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2006-04-10
jprocter
reworded pad gaps
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2006-04-10
jprocter
reworded pad gaps.
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2006-04-10
jprocter
put modellerpir in correct place!
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2006-04-10
jprocter
updated menus and rearranged seqfeatures (again)
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2006-04-10
jprocter
fix links to complex html (that don't display) by quoting...
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2006-04-10
jprocter
moved Modeller/PIR description to its own home.
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2006-04-10
jprocter
moved modellerpir to io
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2006-04-10
jprocter
describing the Modeller/PIR output.
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2006-04-10
jprocter
Fixed table border and updated restrictions
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2006-04-10
jprocter
added bit about modeller/pir
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2006-04-10
jprocter
added annotationColouring to whats new and updated...
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2006-04-10
jprocter
extended preamble and added new heading for user defined...
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2006-04-10
jprocter
doco
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2006-04-10
jprocter
doco changes.
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2006-04-10
jprocter
added 2.08 application version dialog box.
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2006-04-10
jprocter
feature settings dialog box for jalview 2.08 application
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