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[jalview.git] / src / jalview / analysis /
2006-12-06 jproctergeneral pairwise substitution score models for pairwise...
2006-12-05 amwaterhousesequence is char []
2006-11-28 amwaterhouseoff by one group consensus calculation
2006-11-21 jprocterfix unselectable tree leaf nodes when node mapping...
2006-11-15 amwaterhouseCheck if groupWidth is greater than sequence width
2006-11-09 amwaterhouse1.1 compatible
2006-11-07 amwaterhousewarning note added to consequence
2006-11-07 amwaterhousehidden seqs and setOrder bug fixed
2006-11-06 amwaterhouseIf start is not zero, we need to put -- at the start
2006-10-26 amwaterhouseError message changed
2006-10-26 amwaterhouseSequences may be hidden, not in this aligment
2006-10-24 amwaterhousesetOrder is public
2006-10-24 jprocterfixes bug reported by Christopher Tan (help@jalview...
2006-10-12 amwaterhouseComment out debug to compile applet
2006-10-11 jprocterfixes exception (array index out of bounds - due to...
2006-10-10 jprocterrefined id matching to pick the closest match (by lengt...
2006-10-10 jprocterdebug message bugfix on duplicate tree leaf names.
2006-10-10 jprocterbugfix for dodgy trees which contain the same leafname...
2006-10-10 amwaterhouseMaxResidue must be at least 2
2006-10-10 amwaterhouseOptimized
2006-10-10 amwaterhouseaaIndex replaces aaHash
2006-10-10 amwaterhousestatic final strings for consensus keys
2006-10-09 jprocterimported Vamsas bindings and alpha vamsas client code...
2006-10-06 amwaterhouseAAFrequency optimized
2006-08-21 amwaterhouseheader updated
2006-08-04 jprocterrecover original data for tree and pca as alignment...
2006-07-27 amwaterhouseSends gapChar to seqData
2006-07-26 jprocterIgnore list created
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view...
2006-07-21 amwaterhousethis.seqs = seqs
2006-07-21 amwaterhouseLoad tree from file constructor fixed
2006-07-19 amwaterhouseOriginal tree data output in PFAM format
2006-07-19 amwaterhouseCheck for all gapped seqs
2006-07-18 amwaterhouseWorks on strings, not seqs
2006-07-18 amwaterhouseTakes string[] instead of seq[]
2006-07-12 amwaterhousesequences are private in SequenceGroup
2006-07-07 amwaterhouseSequence numbering maintained
2006-04-10 amwaterhousedont need to set - to -
2006-04-07 amwaterhouseSet all gaps to - symbol
2006-03-01 jprocterfixed after refactoring of SequenceFeature[] seq.getSeq...
2006-02-24 amwaterhouseFeatures now array
2005-12-15 amwaterhousePrevents confusing extra line being output in Java...
2005-12-08 jprocterexception checks for (de)uniquify
2005-12-08 amwaterhouseAfter merge
2005-12-06 amwaterhousehasDistances added
2005-12-06 amwaterhouseafter merge
2005-11-18 jprocterFixed bug dragonfly.compbio.dundee.ac.uk/mantis/view...
2005-10-03 amwaterhouseRemove redundancy from eclipse
2005-09-30 amwaterhouseRestore file before eclipse changes
2005-09-30 amwaterhouseRemove redundancy in Eclipse
2005-09-23 amwaterhouseCapture output as details
2005-09-08 amwaterhouseREmove unnecessary imports
2005-08-23 amwaterhouseFinalize calculate method
2005-08-22 jprocterfixed uniquify seq[]
2005-08-22 jproctercomment on WORD_SEP values
2005-08-18 amwaterhouseCharacter methods don't exist in java 1.1
2005-08-18 jproctervarious case sensitivity bugs fixed in residue comparis...
2005-08-17 jprocterFixed basic name to sequence ID matching (bug dragonfly...
2005-08-15 amwaterhouseDeclare variables outside loops
2005-08-15 amwaterhouseCalculate gap and nogap ratio here
2005-08-12 jprocterfixed leafMapping bug for Id's like SequenceX (where...
2005-06-30 amwaterhouseFormatting changes
2005-06-30 amwaterhouseNot used in Jalview
2005-06-16 amwaterhouseSort Groups modified
2005-06-10 amwaterhouseRemove imports
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-06-03 jprocterReinstated 'create tree from selected region only'...
2005-06-02 jprocterminor changes to try and make jalopy happy
2005-05-30 jprocterChanged sortByPID to use the gapped PID function.
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-24 jprocterextended the UpdatePlaceholders to check for any new...
2005-05-24 jprocteradded PropertyChangeListeners for alignviewport.alignme...
2005-05-24 jprocterseveral ordering bug fixes.
2005-05-23 jprocterUgly but improved recovery of sequence names, starts...
2005-05-22 jprocterAdded alignment ordering option to 'Sort by' and implem...
2005-05-20 jprocterVarious sort methods added and bugs fixed (coping with...
2005-05-20 jprocteradded tree node property for sequence placeholders.
2005-05-19 amwaterhousetoString () method added
2005-05-05 jprocterMoved tree leafname to alignment set matching into...
2005-05-05 amwaterhousemoved to jalview.io
2005-05-03 amwaterhouse1.1 compatible
2005-05-03 amwaterhousefindKmers and fetchSequenceFeatures removed
2005-04-16 amwaterhouseAlignPanel RefreshPanels put into paintComponent
2005-04-13 jprocterGap characters are now properly detected in the conserv...
2005-04-11 jprocteradded the alignment quality calculation from the old...
2005-04-08 jprocterremember: do not check in quick bug fixes that you...
2005-04-08 jprocterAlignment quality with funky coloured histograms.
2005-04-07 amwaterhousecheckfor gap characters
2005-03-23 amwaterhousedrawableSequence removed
2005-03-18 jprocterNew constructors for turning NewickFile objects into...
2005-03-09 amwaterhousedont perform blast search at present
2005-03-08 jprocterfixed so that alignment percentage ID is used for dista...
2005-02-11 amwaterhousemust add all features even if start and end res are...
2005-02-11 amwaterhousebug fixed if featureEnd is beyond end of sequence
2005-02-08 amwaterhouseLooks for missing ids using BlastClient
2005-02-07 amwaterhouseProperties bug fixed
2005-02-07 amwaterhouseNow displays sequence features
2005-02-07 amwaterhouseNew class for fetching sequence features
2005-02-04 amwaterhouseSequenceFeature display added
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