remove p+3 < query.length
[jalview.git] / src / jalview / datamodel /
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
2006-05-10 amwaterhouseChanges case to end of alignment
2006-05-02 amwaterhouseToggle case added to popup menu
2006-04-28 amwaterhouseMake sure end is less than sequence width
2006-04-28 amwaterhousechangeCase
2006-04-10 amwaterhouseFixed protein desc bug
2006-04-04 amwaterhousePad gaps removes excess gaps
2006-03-24 amwaterhouseAdd check if sequence already exists
2006-03-24 amwaterhouseFeaturesGroup added to constructor
2006-03-16 amwaterhouseGethidden sequences
2006-03-16 amwaterhouseHiddenSequence methods
2006-03-16 amwaterhousegetHiddenSequences
2006-03-16 amwaterhouseKeeps a record of hidden sequences
2006-02-24 amwaterhouseMake variable public for speed of rendering
2006-02-24 amwaterhouseFeatures are now an array, not vector
2006-02-24 amwaterhouseTypo
2006-02-15 amwaterhouseFeatureGroups added
2006-02-15 amwaterhouseRemoved SuperGroup
2006-02-15 amwaterhouseNo longer used
2006-02-09 amwaterhouseNew implementation for holding search results
2006-02-03 amwaterhousehas ref to annotation
2006-02-03 amwaterhouseAdd annotation with sequence ref updated
2006-01-30 amwaterhouseAddAnnotation with start index
2006-01-30 amwaterhouseNew files
2006-01-11 jprocterrefactored Alignframe padGaps code to Alignment and...
2005-12-22 amwaterhousegraph now has type, not a boolean
2005-12-22 amwaterhouseWatch for trim left/right null widths
2005-12-22 amwaterhouseREGEX CANNOT BE STATIC
2005-12-07 amwaterhouseLicense added to new files
2005-12-06 amwaterhouseafter merge
2005-09-30 amwaterhouseRemove redundancy in Eclipse
2005-09-22 amwaterhouseisNucleotide
2005-08-22 amwaterhouseConservation colour scheme is no more
2005-07-29 amwaterhouseif endRes <1, calc the endRes
2005-07-06 amwaterhouseRemove group if sequences are null
2005-06-30 amwaterhouseFormatting changes
2005-06-16 amwaterhouseSort Groups modified
2005-06-14 amwaterhouseremove system.out
2005-06-14 amwaterhousereset if clustalX colouring
2005-06-10 amwaterhouseremove imports
2005-06-10 amwaterhouseset conservation/consensus in constructor
2005-06-08 amwaterhousereplace space
2005-06-08 amwaterhouseRecalc accelerated
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-05-26 jprocterfixed use of PID rather than 'Comparison' Alignment...
2005-05-26 amwaterhousetoString modified
2005-05-25 amwaterhousetoString method added
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-24 amwaterhousereplace get with elementAt
2005-05-23 jprocteradded some assertions and rangechecks for insert/delete...
2005-05-23 jprocteradded getSequencesInOrder (part of refactor from AlignP...
2005-05-23 amwaterhousehistoryitem added
2005-05-22 jprocterAdded alignment ordering option to 'Sort by' and implem...
2005-05-20 jprocteradded tree node property for sequence placeholders.
2005-05-19 amwaterhousecalculate max and min for graph
2005-05-12 amwaterhouseconservation removed
2005-05-05 amwaterhousepdbfile details not essential to sequence
2005-05-03 amwaterhouse1.1 compatible
2005-04-28 amwaterhouseset gap char modified
2005-04-15 amwaterhouseconservation & consensus recalc if group changed
2005-04-08 jprocterAlignment quality with funky coloured histograms.
2005-04-06 jprocterNew method for helping to quickly map different aligned...
2005-04-01 amwaterhouseAlignment Annotation added
2005-03-23 amwaterhouseadjustForRemoveLeft / Right added
2005-03-21 amwaterhousegroup has outline colour
2005-03-18 jprocterTree io modifications, including support for polytomous...
2005-03-09 amwaterhouseallows deletion of chars
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