javadoc
[jalview.git] / src / jalview / datamodel / Alignment.java
2007-05-10 jprocterfixed array index out of bounds when not removing align...
2007-05-07 amwaterhousetIndex prevented deletion of last annotation
2007-05-02 jprocterreturn flag indicating if annotations were actually...
2007-05-01 jprocterremoveAlignmentAnnotation only removes annotation objec...
2007-04-27 jprocterdocumentation and getProperties method
2007-04-25 amwaterhousealignmentProperties added
2007-04-23 amwaterhouseremove seqref annotations
2007-04-17 jproctercopy constructors and AlignmentAnnotation sequenceRef...
2007-04-02 amwaterhouseDestroy alignment moved to finalize
2007-04-02 amwaterhouseDestroy aligment method added
2007-02-07 amwaterhouseFormatting
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
2006-12-21 amwaterhouseremove unnecessary import
2006-12-05 amwaterhouseSequence is char []
2006-11-23 amwaterhouseDont make groups of hidden sequences
2006-11-13 amwaterhouseSequence colour moved to viewport
2006-11-08 amwaterhousecurrentSeq and set description in dataset
2006-11-03 amwaterhouseConsensus may already have been removed
2006-10-27 amwaterhouseNew padgaps works out number of gaps to insert, delete
2006-10-25 amwaterhouseWe can delete sequence 0
2006-10-24 amwaterhousemaxIdLength redundant, deleteCols, trimLeft, removeGaps...
2006-10-12 amwaterhouseHiddenSequences now array, not hashtable
2006-10-09 jprocterfixed getCompactAlignment method to return proper cigar...
2006-10-06 amwaterhouseAAFrequency optimized
2006-08-21 amwaterhouseheader updated
2006-08-21 jprocterremoveGaps method can record changes in alignment colum...
2006-08-18 amwaterhousedont remove all representative seqs on delete groups
2006-08-18 amwaterhouseremove all representative seqs on delete groups
2006-08-15 amwaterhouseMove features to dataset
2006-08-14 amwaterhousefindSequenceMatch returns multiple sequences
2006-08-09 jprocteralignment from seqCigars will correctly mark deleted...
2006-08-04 jprocterrecover original data for tree and pca as alignment...
2006-07-28 amwaterhouse1.1 compatible
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view...
2006-07-26 amwaterhouseseqs[j] replaces current
2006-07-26 amwaterhouseRemove left, right, empty cols work on hidden reps
2006-07-25 amwaterhouseIf seq has a dataset, dont clear it
2006-07-21 amwaterhouseRemove note
2006-07-13 amwaterhouseSequence is private
2006-07-12 amwaterhousesequences are private in SequenceGroup
2006-07-07 amwaterhouseRedundant Remove Redundancy Removed
2006-06-09 amwaterhousegetSequencesArray
2006-05-11 amwaterhouseRecently loaded files, urls, append sequences to Alignment
2006-05-10 amwaterhouseaddAnnotation with seqRef
2006-04-04 amwaterhousePad gaps removes excess gaps
2006-03-16 amwaterhousegetHiddenSequences
2006-02-15 amwaterhouseRemoved SuperGroup
2006-02-03 amwaterhouseAdd annotation with sequence ref updated
2006-01-30 amwaterhouseAddAnnotation with start index
2006-01-11 jprocterrefactored Alignframe padGaps code to Alignment and...
2005-12-22 amwaterhouseWatch for trim left/right null widths
2005-12-06 amwaterhouseafter merge
2005-09-22 amwaterhouseisNucleotide
2005-07-06 amwaterhouseRemove group if sequences are null
2005-06-30 amwaterhouseFormatting changes
2005-06-08 amwaterhousereplace space
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-05-26 jprocterfixed use of PID rather than 'Comparison' Alignment...
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-12 amwaterhouseconservation removed
2005-05-03 amwaterhouse1.1 compatible
2005-04-28 amwaterhouseset gap char modified
2005-04-01 amwaterhouseAlignment Annotation added
2005-02-18 amwaterhousefeaturesAdded = false
2005-02-11 amwaterhousedont add new seqs to group
2005-02-10 amwaterhousedont add new sequences to null groups!
2005-02-10 amwaterhouseisAligned method added
2005-01-24 amwaterhouseAllow removal of colour when deleting groups
2005-01-21 amwaterhouseSuperGroups added
2005-01-13 amwaterhouseFindAllGroups added
2004-12-17 amwaterhouseUse the isGap method in utils
2004-12-16 amwaterhouseRemove redundancy implemented
2004-12-14 amwaterhouseHastable is not used anywhere
2004-12-14 amwaterhouseIf groups doesnt contain group, addition is allowed
2004-12-03 amwaterhousedefault gap char is -. Getting ready for group select...
2004-12-01 amwaterhouseSet gap chararcter replaces all existing gap chars
2004-11-16 amwaterhouseSequenceGroup may have name
2004-11-02 amwaterhouseJalview Imported Sources start