JAL-3949 fixed failing commandlinetests due to more output and line count limit
[jalview.git] / src / jalview / datamodel /
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview
2018-11-19 Jim ProcterJAL-3156 JAL-3127 code tidy
2018-11-19 Jim ProcterJAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen...
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH...
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit...
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth()
2018-08-27 Ben SoaresJAL-3061 / JAL-3053
2018-08-16 gmungocMerge branch 'bug/JAL-3082selectRegex' into Jalview...
2018-08-16 gmungocJAL-3082 handle regex error, exclusive threshold, unit...
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene...
2018-08-02 Ben SoaresJAL-3053
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS...
2018-07-26 gmungocMerge remote-tracking branch 'origin/bug/JAL-3072scroll...
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale...
2018-07-20 gmungocJAL-3048 revised AlignExportSettings dialog with respon...
2018-07-11 Jim ProcterJAL-3048 refactored export settings to bean+dialog... Jalview-BH/JAL-3048_exportSettingsrefactor
2018-07-06 gmungocJAL-3032 use Math.min/max not Float.min/max
2018-07-02 hansonrJAL-3026 GD#75 Stockholm file load fails
2018-06-22 gmungocJAL-3032 avoid assignments on the same line as synchronized
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot...
2018-06-02 Jim ProcterJAL-3017 parse multiple variant elements for uniprot...
2018-05-31 gmungocJAL-2808 don't capture or report min-max for mixed...
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue...
2018-05-10 Jim ProcterMerge branch 'bug/JAL-2920_uniprotvariantfeature' into...
2018-05-10 Jim ProcterJAL-2920 simplified logic and added corner cases for...
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject
2018-05-07 Jim ProcterJAL-2906 apply GPLv3 license source
2018-05-04 gmungocJAL-1767 refactorings to enable faithful restore of...
2018-04-27 gmungocJAL-1767 refactoring and tidying of RotatableCanvas...
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional...
2018-04-23 gmungocJAL-2954 more efficient SearchResults.markColumns
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
2018-03-13 gmungocJAL-2839 addResult ignores duplicates
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-26 Jim ProcterJAL-2920 parse variation and original elements of the...
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_...
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI...
2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests...
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses
2018-02-01 kiramtJAL-2759 use right iterator for getVisibleColsIterator
2018-01-31 kiramtJAL-2759 Rationalise VisibleColsIterator and HiddenCols...
2018-01-31 kiramtJAL-2759 Generalised HiddenColsIterator naming
2018-01-31 kiramtJAL-2759 minor refactor to hiding bitsets
2018-01-30 kiramtJAL-2759 Add missing hiddenColumns empty check
2018-01-30 kiramtJAL-2759 updateForDeletedRegion no longer needed
2018-01-30 kiramtJAL-2759 Rationalising hidden cols cursor, and sorting...
2018-01-30 kiramtJAL-2759 comment
2018-01-30 kiramtJAL-2759 Additional tests and tweaks to numColumns...
2018-01-30 kiramtJAL-2759 Keep numColumns up to date
2018-01-29 kiramtJAL-2759 Combine findRegionForColumn code in HiddenColu...
2018-01-29 kiramtJAL-2759 numColumns reset
2018-01-29 kiramtJAL-2759 remove redundant hiddenColumns.clear()
2018-01-29 kiramtJAL-2759 Tidy
2018-01-29 kiramtJAL-2759 make a new cursor instead of resetting, update...
2018-01-29 kiramtJAL-2759 Fix unintended type change
2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced...
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence...
2018-01-22 kiramtJAL-2759 Various minor HiddenColumns updates after...
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after...
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns
2018-01-19 kiramtJAL-2759 Update to getVisibleStartAndEndIndex after...
2018-01-18 kiramtJAL-2759 change subtractVisibleColumns and removal...
2018-01-18 kiramtJAL-2759 Updated test
2018-01-18 kiramtJAL-2759 unit tests (incomplete)
2018-01-17 gmungocMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2018-01-16 kjvdheideJAL-2750 startRes now directly assigned
2018-01-16 kiramtJAL-2759 setup hideBitSet over range for hideInsertions
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC...
2018-01-16 kiramtJAL-2759 Replaced StringBuffer with StringBuilder;...
2018-01-15 kiramtJAL-2759 More compact iterator usage; after review
2018-01-15 kiramtJAL-2759 First pass instantiate hiddenColumns collectio...
2018-01-15 kiramtJAL-2759 getVisContigsIterator returns VisibleContigsIt...
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after...
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review
2018-01-15 kiramtJAL-2759 Simplified HiddenColumns constructor after...
2018-01-15 kiramtJAL-2759 Changed VisibleColsCollection constructor...
2018-01-15 kiramtJAL-2759 Minor doc and naming changes
2018-01-15 kiramtJAL-2759 Updated absoluteToVisibleColumn doc (prev...
2018-01-15 kiramtJAL-2759 Rename findColumnPosition and adjustForHiddenC...
2018-01-15 kiramtJAL-2759 Renamed BoundedHiddenColsIterator to HiddenCol...
2018-01-15 kiramtJAL-2759 Comments and renaming for has(Many)HiddenColum...
2018-01-15 kiramtJAL-2759 Tidy up javadoc and naming in HiddenColumnsCur...
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