JAL-1632 add score model params to PCAModel and PCA constructors
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
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...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi...
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
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-07 Jim ProcterJAL-1912 formatting
2015-10-07 Jim ProcterJAL-1912 javadoc for adjustForAlignment stating current...
2015-10-07 Jim ProcterJAL-1912 efficiency: look up sequenceMapping once per...
2015-10-05 tcofoegbuJAL-1912 added null check for SequenceMapping variable...
2015-10-01 tcofoegbuJAL-1912 Double.NaN breaks JSON serialization - added...
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
2015-06-18 gmungocJAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo...
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo...
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null...
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports)
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null...
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports)
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-24 Jim ProcterJAL-1595 annotation score is total number of rna helices
2014-11-21 Jim ProcterJAL-1489 change initial value to distinguish non-rna...
2014-11-20 Jim ProcterJAL-1569 rna pair code in secondary structure character...
2014-11-20 Jim ProcterJAL-674 JAL-1569 mark RNA helix number in the value...
2014-11-03 Jim ProcterJAL-1578 formatting and imports
2014-11-03 Jim ProcterJAL-1551 formatting
2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor...
2014-11-03 Jim Procterjavadoc
2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional informat...
2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method
2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation posit...
2014-10-21 Jim ProcterJAL-1551 source formatting
2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error...
2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequenc...
2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test...
2014-07-18 j.procter@dundee... JAL-1520 switch between Protein and non-canonical RNA...
2014-06-06 Jim ProcterJAL-1520 fix unicode translation errors.
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
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2012-12-07 jprocterrevised renderer and annotation model to support differ...
2012-12-07 jprocterconvenience function to get the RNA model for an annota...
2012-12-07 jprocteruse new secstructure process algorithm
2012-11-15 jprocterMerge branch 'develop' into menard
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-09-03 jprocterJAL-1153 ensure _linecolour is copied in copy constructor
2012-08-31 jprocterMerge branch 'develop' into menard
2012-08-29 jprocterJAL-1153 new runtime property set to first non-null...
2012-08-14 Anne Menardlast version stay many bugs ..
2012-07-10 Anne Menardv2
2012-05-22 jprocterupdate the copy constructor
2011-11-03 jprocter(JAL-811) new 'annotation type' field for marking annot...
2011-10-28 jprocterJAL-580 ensure WUSS annotation string is up to date...
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
2011-08-18 jprocterfix for JAL-701 - ensure '<' appears in tooltip in...
2011-07-25 janengelhardtFurther structure accessing feature
2011-07-25 janengelhardt'Update to Covariaton color scheme' merge; JAL-580
2011-07-25 janengelhardtStart merging of Laurens Code
2011-01-05 jproctergraphThreshold not being copied by constructor
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2010-04-28 jproctergroup/annotation association housekeeping
2010-04-23 jprocterjavadoc
2010-04-16 jprocterpatch for bug #36198 - more to follow on Monday.
2010-03-22 jproctertodo and sensible default setting of min/max for histog...
2010-03-11 jprocterindividual label format settings for each annotation...
2009-08-21 jproctertodo
2009-07-24 jprocteroptional sequencegroup ref for annotation row
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-20 jproctertooltip displays formatted annotation row description...
2008-05-01 jprocterfix for unicode char labels causing arrayOutOfBoundsExc...
2008-02-22 jprocterpossible fix for stockhom ss-annotation re-creation...
2007-11-30 jprocternull pointer bugfix
2007-10-02 jprocterconvenience constructor for duplicating an annotation...
2007-05-28 jprocterfix compact annotation array routine
2007-05-02 jprocterchecks for negative start column in restrict
2007-05-02 amwaterhousePadgaps is false by default
2007-05-01 amwaterhousePad gaps method
2007-04-30 jprocterpad should leave null annotations array null
2007-04-30 jprocterconvenient creation of 'score only' annotation.
2007-04-27 amwaterhousepadGaps moved
2007-04-26 jprocterscore is a double, fix bugs for score only annotation...
2007-04-26 jprocterscore and visible copy construction
2007-04-26 jprocterfix for null annotations
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