added CSV export of annotation rows to application.
151 lines of code changed in:
appdata bugfix in vamsas client library
0 lines of code changed in:
*really* make sure database references are stored and recovered for all sequences
23 lines of code changed in:
ensure codon mappings and database references are merged back onto alignment
112 lines of code changed in:
sequenceMappings go on boh datasets involved in a mapping (if a mapping spans two datasets)
1 lines of code changed in:
refactored and ensured alCodonMappings are propagated to new alignments
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store dataset references, sequence dataset ids, and reconstruct dataset alignment shared by several alignments. Store and recover alignCodonMaps and dna/protein sequence relations.
764 lines of code changed in:
improved vamsas treenode node binding support
233 lines of code changed in:
moved dataset sequence creation onto sequence method
2 lines of code changed in:
create dataset sequence method
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removed autogenerated todo
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updated source generation for castor-1.1-cycle patched
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added aligned codon frames, and dataset reference ids for sequenceSet and sequences to project xml
166 lines of code changed in:
applet and application menu entry differences and consensus only differences
12 lines of code changed in:
dataset alignments have a reference count which must be zero before they are finalized.
23 lines of code changed in:
remove null pointer exception when embl file is not retrieved and comment about selecting for peptide or na sequences
0 lines of code changed in:
todo comments
4 lines of code changed in:
proper vamsas style binding of alignment sequence objects to newick node labels. modified binding of vamsas alignment to the SequenceSet id from the alignment viewport.
128 lines of code changed in:
slightly faster validation patch (logging message concatenation and IdentityHashset patch to 1.1-cycle source)
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bugfixed and removed some inefficiencies in marshalling
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popup for non-fatal tree parsing error
12 lines of code changed in:
quick fix for exceptions due to invalid embl refs
7 lines of code changed in:
fix serious repetitive exceptions if user closes colour dialog box without selecting colour
5 lines of code changed in:
catch occasional -ve imgWidth exception
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added failsafe fix for cases where null sequence names are passed to constructor
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introduce beginning of bug fix for parsing atv style newick tree files where the NHX comment appears between the node info (label bootstrap:distance[nhx&...]). Comments now raise a non-fatal warning message about incorrect tree parsing.
56 lines of code changed in:
added facility for sending non-fatal warnings back to caller.
15 lines of code changed in:
fixed typo in new 2_3 startup file default value
559 lines of code changed in:
give treeviewer description its own contents entry and link it in better.
27 lines of code changed in:
generalise name of prediction method
13 lines of code changed in:
ensure default source dist is relative to basedir of build
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allow source dist archive to be an absolute filename
1 lines of code changed in:
added source-dist task
28 lines of code changed in:
histidine should be midblue (noticed by Peter Knight via jalview-help)
40 lines of code changed in:
comment concerning null exceptions generated when annotations read from a file are rendered in the applet
0 lines of code changed in:
null pointer exception blocked redraw of annotation added to alignment via applet's annotations parameter
1 lines of code changed in:
javadoc and bugfix for 'save' when jalview is default format
12 lines of code changed in:
updated vamsas library (version for iscb demo)
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ignore contents of this directory
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added the '-tree' parameter to open a tree from the command line
41 lines of code changed in:
javadoc
3 lines of code changed in:
ensure current dataset reference is passed to the crossReference search method
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added tree as an applet to application servlet parameter
8 lines of code changed in:
null pointer exception bug fix
0 lines of code changed in: