JnetFIle is a readable format
[jalview.git] / src / jalview / datamodel /
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...
2006-07-28 amwaterhouseOut by one error on reveal columns
2006-07-28 amwaterhouse1.1 compatible
2006-07-26 jprocterIgnore list created
2006-07-26 jprocterCigars for representing alignment view as used for...
2006-07-26 jprocterCigarBase class and derivatives.
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view...
2006-07-26 amwaterhouseseqs[j] replaces current
2006-07-26 amwaterhouseCalculate overlap hidden regions
2006-07-26 amwaterhouseRemove left, right, empty cols work on hidden reps
2006-07-25 amwaterhouseColumnSelection moved to datamodel
2006-07-25 amwaterhouse1.1 compatible
2006-07-25 amwaterhouseMust be 1.1 compliant
2006-07-25 amwaterhouseCan have local file
2006-07-25 amwaterhouseIf seq has a dataset, dont clear it
2006-07-21 amwaterhousegetFullAlignment
2006-07-21 amwaterhouseRemove note
2006-07-21 amwaterhouseDBRef is an array, not vector
2006-07-19 amwaterhousedatasetSeq bug
2006-07-18 amwaterhousegetSelectionAsNewSequence added
2006-07-18 amwaterhouseTakes a string, not sequence
2006-07-18 jprocteruse of GapChars
2006-07-13 amwaterhouseSequence is private
2006-07-12 amwaterhousesequences are private in SequenceGroup
2006-07-07 amwaterhouseRedundant Remove Redundancy Removed
2006-07-07 amwaterhouseChecks on drawing characters and if sequence ref has...
2006-06-15 amwaterhouseMaintain status and position only for uniprot parsing
2006-06-14 amwaterhouseStatus is now in otherData of feature
2006-06-09 amwaterhouseotherDetails
2006-06-09 amwaterhouseRemove getsfarray
2006-06-09 amwaterhousegetSequencesArray
2006-06-08 jprocterDBRefEntry.source enum type
2006-06-07 amwaterhouseRemove position, add score and links
2006-05-15 amwaterhouseAll or nothing drawing display char
2006-05-11 amwaterhouseMaintain numbering if remove left is undone
2006-05-11 amwaterhouseRecently loaded files, urls, append sequences to Alignment
2006-05-10 amwaterhouseCorrection for sequences with start not equal to 1
2006-05-10 amwaterhouseCreate sequence mapping for annotations
2006-05-10 amwaterhouseaddAnnotation with seqRef
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