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Add pdb ref
2005-06-16
jprocter
moved clustal to clustalw
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2005-06-16
jprocter
lots of tidying in doco.
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2005-06-16
jprocter
better clustalw reference
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2005-06-16
jprocter
export moved to its own file.
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2005-06-16
jprocter
export alignment
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2005-06-16
jprocter
feredoxin startup alignment with a tree.
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2005-06-16
jprocter
more menu doco.
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2005-06-15
jprocter
first jalarchive entry.
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2005-06-14
jprocter
de-os-specificised some bits. Commented the file association...
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2005-06-14
jprocter
removes jarsign.
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2005-06-14
jprocter
help file bits.
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2005-06-14
jprocter
pad-1 gaps fixed.
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2005-06-14
jprocter
slight modification to srs query so it takes both uniprot...
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2005-06-14
jprocter
Arbitrary decision to keep friendly id name when reading...
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2005-06-13
jprocter
null pointer fix.
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2005-06-10
jprocter
added logs.Castor.level
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2005-06-10
jprocter
added castor logger configuration.
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2005-06-10
jprocter
removed exception name from server error state (to...
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2005-06-08
jprocter
style change.
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2005-06-08
jprocter
heading
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2005-06-08
jprocter
punctuation (sorry ;-)
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2005-06-08
jprocter
grammar.
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2005-06-08
jprocter
unterminated ul
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2005-06-08
jprocter
nicer help.
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2005-06-07
jprocter
more truthful comment.
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2005-06-07
jprocter
quickie build instructions.
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2005-06-07
jprocter
very basic code convention. no licensing/stripping...
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2005-06-07
jprocter
better code convention name
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2005-06-07
jprocter
jalopy is used for sourcescrub target of build.xml...
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2005-06-07
jprocter
removed signature for this jar
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2005-06-07
jprocter
loads of changes. Jalopy source formatting, better...
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2005-06-07
jprocter
added a couple of debug statements for unix browser...
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2005-06-05
jprocter
made error for browser configuration on unix a bit...
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2005-06-05
jprocter
firefox now default for unixen.
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2005-06-05
jprocter
more subtle rearrangements
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2005-06-03
jprocter
Reinstated 'create tree from selected region only'...
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2005-06-02
jprocter
tidied the exceptions and ws server error behaviour
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2005-06-02
jprocter
minor changes to make jalopy happy
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2005-06-02
jprocter
minor changes to try and make jalopy happy
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2005-05-31
jprocter
Moved comment so it doesn't break jalopy (this is not...
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2005-05-30
jprocter
added the sorting entry to calculations, and corrected...
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2005-05-30
jprocter
Changed sortByPID to use the gapped PID function.
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2005-05-30
jprocter
comments
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2005-05-30
jprocter
Added clustalW 'realignment' (primitive)
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2005-05-30
jprocter
added default ClustalWS or MuscleWS to remove gaps.
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2005-05-30
jprocter
propagated use of jalview.util.GapChars for gap removal.
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2005-05-30
jprocter
more robust parsing for DBset/DBname|id1|id2 type ids
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2005-05-30
jprocter
modified history for redundancy removal.
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2005-05-30
jprocter
fixed stacktrace potential for pairwise alignment action.
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2005-05-30
jprocter
Modified output on stdout for similarity matrix.
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2005-05-27
jprocter
fixed brain interruption bug.
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2005-05-27
jprocter
right ordering for RedundancyPanel constructor
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2005-05-27
jprocter
added proper state check for failedJob flag.
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2005-05-27
jprocter
Added jobFail state
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2005-05-27
jprocter
better recognition of MSF files.
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2005-05-27
jprocter
Added nicer header formatting for MSFfile output.
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2005-05-27
jprocter
recovered changes from v 1.84
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2005-05-27
jprocter
Jpredfile now uses the PileUpfile io class.
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2005-05-27
jprocter
Addred GapChar string for convenient regex construction
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2005-05-27
jprocter
Response to bug mantis?id=8187 - some quick hacks to...
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2005-05-27
jprocter
Old MSF Format writer now renamed.
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2005-05-26
jprocter
fixed use of PID rather than 'Comparison' Alignment...
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2005-05-26
jprocter
fairly pointless catch exception error information...
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2005-05-26
jprocter
fixed redundancy Undo and allowed it to work on UNALIGNED...
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2005-05-26
jprocter
bug fix in jpred client. TreeViewer display state and...
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2005-05-26
jprocter
partially updated help. Added separate treeviewing...
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2005-05-25
jprocter
added jalview.browser property so a linux user can...
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2005-05-25
jprocter
doh - compile before commit!
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2005-05-25
jprocter
tidied up system.out messages and moved many to stderr.
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2005-05-25
jprocter
Improved consistency between JPredWS and MsaWS
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2005-05-25
jprocter
base class for web service clients.
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2005-05-24
jprocter
title parameter for single sequence prediction.
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2005-05-24
jprocter
Added more firePropertyChange calls - mainly for sequence...
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2005-05-24
jprocter
extended the UpdatePlaceholders to check for any new...
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2005-05-24
jprocter
added PropertyChangeListeners for alignviewport.alignment...
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2005-05-24
jprocter
formatting.
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2005-05-24
jprocter
slight changes.
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2005-05-24
jprocter
added sorting alignments documentation.
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2005-05-24
jprocter
several ordering bug fixes.
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2005-05-23
jprocter
Added PadGaps and made treeSortMenu dynamic (it gets...
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2005-05-23
jprocter
added some assertions and rangechecks for insert/deleteChar...
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2005-05-23
jprocter
added getSequencesInOrder (part of refactor from AlignPanel...
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2005-05-23
jprocter
editMenuPadGaps and sortByTree/sort items
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2005-05-23
jprocter
fixed window title names for prediction on MSA or Sequence.
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2005-05-23
jprocter
Ugly but improved recovery of sequence names, starts...
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2005-05-23
jprocter
bug fix for wierdness retrieving QUERY sequence index.
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2005-05-22
jprocter
include MsaWS ordering but not perfect (undo destroys...
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2005-05-22
jprocter
marginal improvements - still no automated client constructor.
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2005-05-22
jprocter
Added alignment ordering option to 'Sort by' and implemented...
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2005-05-22
jprocter
later version of client-side WSDL2Java generated simple...
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2005-05-20
jprocter
Semiworking generic MSA client
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2005-05-20
jprocter
added placeholder indicators and menu item
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2005-05-20
jprocter
Various sort methods added and bugs fixed (coping with...
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2005-05-20
jprocter
sequence place holder reveal menu item.
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2005-05-20
jprocter
added tree node property for sequence placeholders.
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2005-05-20
jprocter
xml-apis from the same place as xercesImpl.jar
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2005-05-20
jprocter
This is the xercesImpl.jar from xerces-2_6_2
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2005-05-20
jprocter
Fixing the broken cvs.
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2005-05-19
jprocter
The archetypal Multiple Sequence Alignment Web Service
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2005-05-05
jprocter
Added cancel interface for JPred Client and fixed some...
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