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sequence db fetcher and db reference validation/annotation transfer
[jalview.git] / src / jalview / analysis /
2007-11-16 jproctertodo for sortbyPID operating on current selection rathe... tree | commitdiff
2007-11-16 jprocterrefactor abstract sequence fetching and DBSource machin... tree | commitdiff
2007-11-12 jproctercrossrefs have properly updated pdbId lists tree | commitdiff
2007-09-07 jprocterformatting and ensure that dataset is actually searched... tree | commitdiff
2007-08-01 jprocternull pointer exception bug fix tree | commitdiff
2007-07-25 jprocterfix crossRef retrieval so either protein OR nucleotide tree | commitdiff
2007-07-13 jprocterbugfixes, partially working code for translation using... tree | commitdiff
2007-07-13 jproctercomments for future viz/detection of internal sequence... tree | commitdiff
2007-07-13 jproctermethods for traversing database reference space tree | commitdiff
2007-06-17 jprocterfix aligned DNA codon translation bug(s) and generate... tree | commitdiff
2007-06-17 jprocterjavadoc tree | commitdiff
2007-05-22 jprocterfixed jalview 2.3 bug where gapped aligned codons were... tree | commitdiff
2007-04-26 jprocteradded 'sort by sequence associated annotation score' tree | commitdiff
2007-04-26 jprocterbug fixed basic score extraction by regex on descriptio... tree | commitdiff
2007-04-26 jprocterbasic methods for adding scores extracted from description tree | commitdiff
2007-04-25 jprocterFunctions for parsing free text properties on sequences... tree | commitdiff
2007-04-25 jprocterAlignmentAnnotation: added annotation score attribute... tree | commitdiff
2007-04-11 jprocterfixed base lookup bug in dna pairwise alignment and... tree | commitdiff
2007-03-19 jproctertranslate aligned cDNA to aligned peptide tree | commitdiff
2007-02-07 amwaterhouseFormatting tree | commitdiff
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space tree | commitdiff
2007-01-25 amwaterhouse1.1 enabled tree | commitdiff
2007-01-23 amwaterhouseHidden representatives moved from sequence to viewport tree | commitdiff
2007-01-23 jprocterrefactoring (added seqIndex/resIndex state for incremen... tree | commitdiff
2007-01-23 jprocterrefactored search algorithm from gui classes tree | commitdiff
2006-12-14 amwaterhouseone less cast tree | commitdiff
2006-12-06 jproctergeneral pairwise substitution score models for pairwise... tree | commitdiff
2006-12-05 amwaterhousesequence is char [] tree | commitdiff
2006-11-28 amwaterhouseoff by one group consensus calculation tree | commitdiff
2006-11-21 jprocterfix unselectable tree leaf nodes when node mapping... tree | commitdiff
2006-11-15 amwaterhouseCheck if groupWidth is greater than sequence width tree | commitdiff
2006-11-09 amwaterhouse1.1 compatible tree | commitdiff
2006-11-07 amwaterhousewarning note added to consequence tree | commitdiff
2006-11-07 amwaterhousehidden seqs and setOrder bug fixed tree | commitdiff
2006-11-06 amwaterhouseIf start is not zero, we need to put -- at the start tree | commitdiff
2006-10-26 amwaterhouseError message changed tree | commitdiff
2006-10-26 amwaterhouseSequences may be hidden, not in this aligment tree | commitdiff
2006-10-24 amwaterhousesetOrder is public tree | commitdiff
2006-10-24 jprocterfixes bug reported by Christopher Tan (help@jalview... tree | commitdiff
2006-10-12 amwaterhouseComment out debug to compile applet tree | commitdiff
2006-10-11 jprocterfixes exception (array index out of bounds - due to... tree | commitdiff
2006-10-10 jprocterrefined id matching to pick the closest match (by lengt... tree | commitdiff
2006-10-10 jprocterdebug message bugfix on duplicate tree leaf names. tree | commitdiff
2006-10-10 jprocterbugfix for dodgy trees which contain the same leafname... tree | commitdiff
2006-10-10 amwaterhouseMaxResidue must be at least 2 tree | commitdiff
2006-10-10 amwaterhouseOptimized tree | commitdiff
2006-10-10 amwaterhouseaaIndex replaces aaHash tree | commitdiff
2006-10-10 amwaterhousestatic final strings for consensus keys tree | commitdiff
2006-10-09 jprocterimported Vamsas bindings and alpha vamsas client code... tree | commitdiff
2006-10-06 amwaterhouseAAFrequency optimized tree | commitdiff
2006-08-21 amwaterhouseheader updated tree | commitdiff
2006-08-04 jprocterrecover original data for tree and pca as alignment... tree | commitdiff
2006-07-27 amwaterhouseSends gapChar to seqData tree | commitdiff
2006-07-26 jprocterIgnore list created tree | commitdiff
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view... tree | commitdiff
2006-07-21 amwaterhousethis.seqs = seqs tree | commitdiff
2006-07-21 amwaterhouseLoad tree from file constructor fixed tree | commitdiff
2006-07-19 amwaterhouseOriginal tree data output in PFAM format tree | commitdiff
2006-07-19 amwaterhouseCheck for all gapped seqs tree | commitdiff
2006-07-18 amwaterhouseWorks on strings, not seqs tree | commitdiff
2006-07-18 amwaterhouseTakes string[] instead of seq[] tree | commitdiff
2006-07-12 amwaterhousesequences are private in SequenceGroup tree | commitdiff
2006-07-07 amwaterhouseSequence numbering maintained tree | commitdiff
2006-04-10 amwaterhousedont need to set - to - tree | commitdiff
2006-04-07 amwaterhouseSet all gaps to - symbol tree | commitdiff
2006-03-01 jprocterfixed after refactoring of SequenceFeature[] seq.getSeq... tree | commitdiff
2006-02-24 amwaterhouseFeatures now array tree | commitdiff
2005-12-15 amwaterhousePrevents confusing extra line being output in Java... tree | commitdiff
2005-12-08 jprocterexception checks for (de)uniquify tree | commitdiff
2005-12-08 amwaterhouseAfter merge tree | commitdiff
2005-12-06 amwaterhousehasDistances added tree | commitdiff
2005-12-06 amwaterhouseafter merge tree | commitdiff
2005-11-18 jprocterFixed bug dragonfly.compbio.dundee.ac.uk/mantis/view... tree | commitdiff
2005-10-03 amwaterhouseRemove redundancy from eclipse tree | commitdiff
2005-09-30 amwaterhouseRestore file before eclipse changes tree | commitdiff
2005-09-30 amwaterhouseRemove redundancy in Eclipse tree | commitdiff
2005-09-23 amwaterhouseCapture output as details tree | commitdiff
2005-09-08 amwaterhouseREmove unnecessary imports tree | commitdiff
2005-08-23 amwaterhouseFinalize calculate method tree | commitdiff
2005-08-22 jprocterfixed uniquify seq[] tree | commitdiff
2005-08-22 jproctercomment on WORD_SEP values tree | commitdiff
2005-08-18 amwaterhouseCharacter methods don't exist in java 1.1 tree | commitdiff
2005-08-18 jproctervarious case sensitivity bugs fixed in residue comparis... tree | commitdiff
2005-08-17 jprocterFixed basic name to sequence ID matching (bug dragonfly... tree | commitdiff
2005-08-15 amwaterhouseDeclare variables outside loops tree | commitdiff
2005-08-15 amwaterhouseCalculate gap and nogap ratio here tree | commitdiff
2005-08-12 jprocterfixed leafMapping bug for Id's like SequenceX (where... tree | commitdiff
2005-06-30 amwaterhouseFormatting changes tree | commitdiff
2005-06-30 amwaterhouseNot used in Jalview tree | commitdiff
2005-06-16 amwaterhouseSort Groups modified tree | commitdiff
2005-06-10 amwaterhouseRemove imports tree | commitdiff
2005-06-08 amwaterhouseFormatted source tree | commitdiff
2005-06-08 amwaterhouseGPL license added tree | commitdiff
2005-06-03 jprocterReinstated 'create tree from selected region only'... tree | commitdiff
2005-06-02 jprocterminor changes to try and make jalopy happy tree | commitdiff
2005-05-30 jprocterChanged sortByPID to use the gapped PID function. tree | commitdiff
2005-05-25 jproctertidied up system.out messages and moved many to stderr. tree | commitdiff
2005-05-24 jprocterextended the UpdatePlaceholders to check for any new... tree | commitdiff
2005-05-24 jprocteradded PropertyChangeListeners for alignviewport.alignme... tree | commitdiff
2005-05-24 jprocterseveral ordering bug fixes. tree | commitdiff
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