FileParse object can be re-used to read different files concatenated together
[jalview.git] / src / jalview / datamodel /
2007-03-19 jprocterinitial support for EMBL file parsing.
2007-03-19 jprocterequals operation used for canonicalisation of DBRefList...
2007-03-19 jproctermapping implemented by MapList added to DBRefEntry.
2007-03-19 jprocterjavadoc typo
2007-03-19 jproctercopy constructor
2007-02-07 amwaterhouseFormatting
2007-01-31 amwaterhouseUnique name for new group and treegroup
2007-01-31 amwaterhousemake new dataset seq if residues deleted
2007-01-31 amwaterhousecopy feature: check for null values
2007-01-30 amwaterhouseCheck valid residues in ss
2007-01-29 amwaterhouseDescription added
2007-01-26 amwaterhouseAnnotationId is hashcode of object
2007-01-26 amwaterhouseOnly set the sequence oncecvs diff datamodel/Alignment...
2007-01-25 amwaterhouseAnnotation adjustment moved to EditCommand
2007-01-24 amwaterhouseAdjustAnnotations needs position, number and insert
2007-01-23 amwaterhouseHidden representatives moved from sequence to viewport
2007-01-19 jprocterdatasetSequence derive method and some checks
2007-01-19 jprocterjavadoc
2007-01-19 jprocteradded sequence feature copy constructor.
2007-01-18 amwaterhouseSet description on copy
2007-01-18 amwaterhouseIs secondary structure label modified
2006-12-21 amwaterhousecheck on sequence length
2006-12-21 amwaterhousegetSequenceAsString
2006-12-21 amwaterhousegetSequenceAsString
2006-12-21 amwaterhouseremove unnecessary import
2006-12-21 jproctertype change
2006-12-14 amwaterhouseWatch out for - symbol lin jnet files
2006-12-14 amwaterhouseAre the labels all secondary Strutures? are the display...
2006-12-07 amwaterhousedont add char[] ref to a string
2006-12-06 jproctergeneral pairwise substitution score models for pairwise...
2006-12-05 amwaterhouseSequence is char []
2006-11-24 amwaterhouseFix load 1 col hidden bug
2006-11-23 amwaterhouseDont make groups of hidden sequences
2006-11-20 amwaterhousewarning message changed
2006-11-20 amwaterhouseMust copy old dbrefs
2006-11-13 amwaterhouseDont readd identical DBRef
2006-11-13 amwaterhouseSequence colour moved to viewport
2006-11-13 amwaterhouseText colour for group
2006-11-08 amwaterhouseSet description
2006-11-08 amwaterhousecurrentSeq and set description in dataset
2006-11-06 amwaterhouseOnly calculate consenus from start to end
2006-11-03 amwaterhouseConsensus may already have been removed
2006-10-30 amwaterhousedeleteSequenceFeature
2006-10-27 amwaterhouseIf sequence is null, dont add it
2006-10-27 amwaterhouseNew padgaps works out number of gaps to insert, delete
2006-10-26 amwaterhouseNo need to reduce length if inserting more gaps at...
2006-10-26 amwaterhouseCheck if hiddenSequence has been deleted
2006-10-25 amwaterhouseWe can delete sequence 0
2006-10-25 amwaterhouseCheck hiddenSequence before placing in tmp
2006-10-25 amwaterhouseAdjusts hiddenColumns correctly
2006-10-24 amwaterhousechangeCase, removeGaps moved to commands package
2006-10-24 amwaterhousemaxIdLength redundant, deleteCols, trimLeft, removeGaps...
2006-10-24 amwaterhouseIts historycvs remove jalview/datamodel/HistoryItem...
2006-10-15 jprocterfixed array out of bounds exception in copy constructor
2006-10-12 amwaterhouseConvenient function findEndRes
2006-10-12 amwaterhouseOverview may request index beyond alignment height
2006-10-12 amwaterhouseHiddenSequences now array, not hashtable
2006-10-10 amwaterhouseRemove growing hashtable
2006-10-10 amwaterhouse1.1 compatible
2006-10-10 amwaterhouseaaIndex replaces aaHash
2006-10-09 jprocterfixed getCompactAlignment method to return proper cigar...
2006-10-06 jprocterjavadoc
2006-10-06 jprocternew getVisibleContigs method mirrors the getVisibleCont...
2006-10-06 amwaterhouseAAFrequency optimized
2006-09-07 jprocteradded copy consensus sequence to consensus annotation...
2006-09-05 jproctergetVisibleContigs() returns start and end positions...
2006-09-05 jprocterjavadoc on contigs
2006-08-29 amwaterhouseSequenceMapping updated
2006-08-22 jproctergetSequenceStrings() bug fixed.
2006-08-22 amwaterhousemake 1.1 compatible
2006-08-22 jprocterhidden region recovery in JPred and new hidden region...
2006-08-21 amwaterhouseheader updated
2006-08-21 amwaterhouse1.1 compatible
2006-08-21 jprocterremoveGaps method can record changes in alignment colum...
2006-08-21 jprocterfix for truncation of sequence associated annotation...
2006-08-21 jprocteradded shiftList to record changes in alignment column...
2006-08-21 jprocterremove gaps method from AlignFrame.remove_gaps_actionPe...
2006-08-20 jprocterjavadoc
2006-08-18 amwaterhousedont remove all representative seqs on delete groups
2006-08-18 amwaterhouseremove all representative seqs on delete groups
2006-08-17 jproctermoved visible sub-alignment extraction and update from...
2006-08-17 jprocterjavadoc
2006-08-15 amwaterhouseSelect revealed seqs
2006-08-15 amwaterhouseMove features to dataset
2006-08-14 amwaterhousefindSequenceMatch returns multiple sequences
2006-08-14 jprocterfixed off by one bug in end sequence from getSubSequenc...
2006-08-14 jprocterend<start for empty sequences in Sequence[] from SeqCigar[]
2006-08-14 amwaterhouseelementAt instead of get for 1.1 compatibility
2006-08-14 jprocterfixing residue clip bug in MsaWSThread and adding minim...
2006-08-13 jprocterfixed end-residue bug and subjob panel names bug
2006-08-11 jproctermultiple web service jobs from visible blocks of an...
2006-08-10 amwaterhouse1.1 compatible
2006-08-09 jprocternew SequenceI method for making a sub sequence from...
2006-08-09 jprocteralignment from seqCigars will correctly mark deleted...
2006-08-09 jprocterrefactored hidden regions methods and made an Alignment...
2006-08-09 amwaterhouseSave links and scores and keyValues for features
2006-08-08 amwaterhouseOut by 1 error on show columns
2006-08-07 amwaterhouse1.1 compatible
2006-08-07 amwaterhousecatch out of memory error for consensus when loading...
2006-08-04 jprocterrecover original data for tree and pca as alignment...
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