Merge branch 'spotless_2' into JAL-1551_2_11_3_spotlett
[jalview.git] / src / jalview / util / MappingUtils.java
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache...
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_...
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen...
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting...
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS...
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into...
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature...
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature...
2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping... bug/JAL-3806_mappingCoversCDS_reprise
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature...
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
2020-07-21 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-27 kiramtJAL-2674 Removing most calls to getHiddenColumnsCopy
2017-09-22 gmungocJAL-2738 extract utility method to MappingUtils
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea...
2017-06-08 kiramtJAL-2591 More HiddenColumns refactoring. Tests passing.
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop
2017-04-24 kiramtJAL-2388 Finished split of hidden columns and selected...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
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...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-09-06 gmungocJAL-2147 additional test coverage for findMappingsForSe...
2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scopi...
2016-04-01 gmungocJAL-1705 generalised getLength() to handle [start1...
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support...
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-19 gmungocJAL-1705 helper method for mapping excluding stop codon
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-11 gmungocJAL-1989 map hidden column ranges
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from...
2015-12-03 gmungocJAL-653 handle reverse strand mappings also
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 src
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-05-05 gmungocJAL-1725 first version of Jetty server / chimera select...
2015-04-23 gmungocJAL-845 only 'follow' sort command in coding complement...
2015-04-08 gmungocJAL-1691 applet SplitFrame scrolling; pull up of 5...
2015-04-07 gmungocJAL-1691 linked scrollling in split frame (Desktop)
2015-04-01 gmungocJAL-845 fixed start/end range of a mapped SequenceGroup
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch