FileParse object can be re-used to read different files concatenated together
[jalview.git] / src / jalview / analysis /
2008-01-29 jprocterreinstated proper case insensitive searching for both...
2007-12-21 jprocterfurther bugfix and annotation transfer for dna/protein...
2007-12-21 jprocterjavadoc and bugfix
2007-11-16 jproctertodo for sortbyPID operating on current selection rathe...
2007-11-16 jprocterrefactor abstract sequence fetching and DBSource machin...
2007-11-12 jproctercrossrefs have properly updated pdbId lists
2007-09-07 jprocterformatting and ensure that dataset is actually searched...
2007-08-01 jprocternull pointer exception bug fix
2007-07-25 jprocterfix crossRef retrieval so either protein OR nucleotide
2007-07-13 jprocterbugfixes, partially working code for translation using...
2007-07-13 jproctercomments for future viz/detection of internal sequence...
2007-07-13 jproctermethods for traversing database reference space
2007-06-17 jprocterfix aligned DNA codon translation bug(s) and generate...
2007-06-17 jprocterjavadoc
2007-05-22 jprocterfixed jalview 2.3 bug where gapped aligned codons were...
2007-04-26 jprocteradded 'sort by sequence associated annotation score'
2007-04-26 jprocterbug fixed basic score extraction by regex on descriptio...
2007-04-26 jprocterbasic methods for adding scores extracted from description
2007-04-25 jprocterFunctions for parsing free text properties on sequences...
2007-04-25 jprocterAlignmentAnnotation: added annotation score attribute...
2007-04-11 jprocterfixed base lookup bug in dna pairwise alignment and...
2007-03-19 jproctertranslate aligned cDNA to aligned peptide
2007-02-07 amwaterhouseFormatting
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space
2007-01-25 amwaterhouse1.1 enabled
2007-01-23 amwaterhouseHidden representatives moved from sequence to viewport
2007-01-23 jprocterrefactoring (added seqIndex/resIndex state for incremen...
2007-01-23 jprocterrefactored search algorithm from gui classes
2006-12-14 amwaterhouseone less cast
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.
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