Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / test / jalview / datamodel / SequenceTest.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio...
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact...
2022-11-14 Ben SoaresJAL-4019 Put original test back
2022-11-13 Ben SoaresJAL-4019 Added tests for new Nucleotide sequence detection
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format...
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching...
2021-09-16 Jim ProcterJAL-3794 new test for recognition of protein or DNA...
2021-09-03 Jim ProcterJAL-3863 promote non-canonical version of dbref to...
2021-09-03 Jim ProcterJAL-3863 passing test to verify a uniprot accession...
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-06-10 gmungocJAL-3296 ensure sequence cursor reset when sequence... bug/JAL-3296changeStartInvalidateCursor
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL...
2019-03-01 gmungocJAL-3140 reduced coupling to intervalstore.jar feature/intervalStoreJ
2019-02-04 hansonrTest suite try/catch reverted
2019-01-29 hansonrtest package fix for List<DBRefEntry> DBrefs (untested)
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library
2018-05-11 gmungocJAL-2986 additional asserts for SequenceCursor updates
2018-05-11 gmungocJAL-2986 failing test added
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence...
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759
2017-11-13 gmungocMerge branch 'bug/JAL-2829deleteCharsWithGaps' into
2017-11-10 gmungocJAL-2829 fixes and unit tests bug/JAL-2829deleteCharsWithGaps
2017-11-10 gmungocJAL-2829 unit tests for failing cases
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-11-06 Jim ProcterMerge branch 'bug/JAL-2541cutRelocateFeatures' into...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2682parseId' into develop
2017-10-11 gmungocJAL-2772 check array bounds for sequence access bug/JAL-2772pdbArrayBounds
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-21 kiramtJAL-2674 unit test for gapBitSet
2017-09-14 gmungocJAL-2541 length check in deleteChars (redoing lost...
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation
2017-08-23 gmungocJAL-2481 a smidgin more test coverage of findFeatures
2017-08-23 gmungocJAL-2682 non-regex sequence id parsing, and tests added
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact...
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of...
2017-06-21 gmungocJAL-2480 tidy generic initialisations, SequenceFeatures...
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left...
2017-06-08 gmungocJAL-2526 cache first/last residue column positions...
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2291 fixed broken asserts for SequenceI.getInsertio...
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient...
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without...
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with...
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position...
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-24 gmungocJAL-2505 make SequenceFeature type, begin, end, feature...
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature...
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);...
2017-05-09 gmungocJAL-2480 include sequenceFeatureStore in createDatasetS...
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature
2016-11-24 tcofoegbuJAL-2326 added setup method for JvOptionPane in all... features/JAL-2326_JOptionPane-refactoring
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 format tests
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad...
2016-09-28 Jim ProcterJAL-2210 JAL-2235 fix deriveSequence test for tightened...
2016-09-28 Jim ProcterJAL-2235 implicit test to check that exception is raise...
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs
2016-09-04 Jim ProcterJAL-1803 JAL-2106 patch tests for tighter PDB Primary...
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection
2016-07-04 gmungocJAL-2110 added another test case (should fail but doesn't)
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version...
2016-05-17 tcofoegbuJAL-1270 Fixed anntatedPDBFileInputTest and updated...
2016-04-05 Jim ProcterJAL-2046 RFC about cyclic dataset sequence references...
2016-04-05 Jim ProcterJAL-2046 revise test for ambiguous case
2016-04-05 Jim ProcterJAL-2046 ambiguous test for addSequenceFeature when...
2016-04-05 Jim ProcterJAL-2046 RFC on addSequenceFeature behaviour after...
2016-04-05 Jim ProcterJAL-2046 test behaviour of copy constructor in differen...
2016-04-04 Jim ProcterJAL-2046 basic test to make sure any derived sequence...
2016-04-01 gmungocJAL-2046 fix for broken test for deriveSequence
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-04 gmungocJAL-1705 additional tests, validation regexp tweaks...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2015-11-30 gmungocJAL-1270 constructor tests added, compiler warnings...
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 licencing for new files in test and utils
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