JAL-2788 possible adjustments to sequence accesses
[jalview.git] / src / jalview / datamodel / AlignmentI.java
2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced...
2017-09-04 Jim ProcterJAL-2675 source license
2017-06-07 kiramtJAL-2591 More refactoring (incomplete)
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding...
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of...
2017-02-15 Jim ProcterJAL-2374 javadoc - qualify that sequence argument to...
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt...
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth()
2016-07-04 gmungocJAL-2110 unused method removed
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-10-07 gmungocJAL-1264 wip
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm...
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-07-03 jprocterJAL-961 allow calcId to be specified independently...
2012-06-13 jprocterjavatidy
2012-06-12 jprocterJAL-1115 refactor reordering code operating directly...
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from...
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta...
2012-05-23 jprocterJAL-961 - annotatable datamodel objects can be queried...
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065...
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_...
2011-09-27 jprocterapply version 2.7 copyright
2011-08-11 janengelhardtJAL-885; hasRNAStructure method was introduced to Align...
2011-04-21 jprocterallow an alignment annotation row to be removed and...
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-06-03 jprocterjavadoc re JAL-554
2010-04-30 jprocterjalview 2.5 release banner
2010-04-29 jprocterisAligned assertion (bug 0008144)
2009-07-24 jprocterinsert annotation at specific position
2009-06-08 jprocterapply gpl development license
2008-12-19 jprocterleft and right justify method
2008-12-05 jproctersupport for multiple accession retrieval from a databas...
2008-11-12 jprocterjavadoc and new method to get alignment sequence index...
2008-09-04 jproctermerge from 2_4_Release branch
2008-07-18 jprocterallow findSeq to begin *after* a given sequence in...
2007-11-30 jproctercase invariant matching of seqeunce feature to sequence...
2007-06-17 jprocterAlignedCodonFrame holds mapping information between...
2007-05-02 jprocterreturn flag indicating if annotations were actually...
2007-05-01 jprocterjavadoc
2007-05-01 jprocterremoveAlignmentAnnotation only removes annotation objec...
2007-04-27 jproctergetProperties returns nullk for no properties
2007-04-27 jprocterdocumentation and getProperties method
2007-04-25 amwaterhousealignmentProperties added
2007-04-19 jprocterjavadoc note on padding AlignmentAnnotation to alignmen...
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
2007-01-25 amwaterhouseAnnotation adjustment moved to EditCommand
2007-01-24 amwaterhouseAdjustAnnotations needs position, number and insert
2006-12-21 amwaterhouseremove unnecessary import
2006-10-24 amwaterhousemaxIdLength redundant, deleteCols, trimLeft, removeGaps...
2006-10-12 amwaterhouseHiddenSequences now array, not hashtable
2006-10-06 amwaterhouseAAFrequency optimized
2006-08-21 amwaterhouseheader updated
2006-08-21 jprocterremoveGaps method can record changes in alignment colum...
2006-08-14 amwaterhousefindSequenceMatch returns multiple sequences
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view...
2006-07-26 amwaterhouseRemove left, right, empty cols work on hidden reps
2006-07-12 amwaterhousesequences are private in SequenceGroup
2006-07-07 amwaterhouseRedundant Remove Redundancy Removed
2006-06-09 amwaterhousegetSequencesArray
2006-05-10 amwaterhouseaddAnnotation with seqRef
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...
2005-12-06 amwaterhouseafter merge
2005-09-22 amwaterhouseisNucleotide
2005-06-30 amwaterhouseFormatting changes
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
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