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Merge branch 'develop' into feature/JAL-4159_pasimap
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positions...
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2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to...
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2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature...
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2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
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2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
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2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature...
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2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
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2021-09-30 gmungocJAL-3371 more fine-grained slider; set Param slider...
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2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators
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2021-09-17 gmungocJAL-1260 unit test for FileFormats updated for GenBank/ENA
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2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for...
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2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser
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2021-09-16 gmungocJAL-3779 apply properties to all groups with given...
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2021-09-16 gmungocJAL-3761 more consistent parameter naming
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2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication
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2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused...
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2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable...
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2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateInFrom2/To2
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2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit
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2021-09-15 gmungocJAL-3761 unit test for MapList.countPos()
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2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed
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2021-09-15 gmungocJAL-3761 failing tests for locateInFrom/To with overlapping...
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2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
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2021-09-15 gmungocJAL-3788 synchronize concurrent findColour() and alignmentCh...
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2021-09-15 gmungocJAL-3818 process Jmol callbacks in AWT thread
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2021-09-02 gmungocJAL-1842 unit test updated for EnsemblGene feature...
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2021-09-02 gmungocJAL-1842 adjust code to match changed semantics of...
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2021-09-02 gmungocJAL-3509 JAL-1842 minor tidying of code
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2021-09-02 gmungocJAL-1842 remove redundant call to FeatureRenderer.featuresAd...
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2021-09-02 gmungocJAL-3509 better placement of call to notifyFeaturesChanged()
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2021-09-02 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetching...
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2021-02-18 gmungocJAL-3822 pass panel height and width to wrapped geometry...
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2021-02-18 gmungocJAL-2422 remove temporary patch (requires ChimeraX...
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2021-02-11 gmungocJAL-3818 process Jmol callbacks in AWT thread
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2021-02-05 gmungocJAL-2422 updated unit test for ChimeraX command change
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2021-02-04 gmungocJAL-2422 a fix and a fudge for two failing ChimeraX...
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2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping...
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2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop...
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2021-01-21 gmungocJAL-3038 corrected code that reads editable JComboBox...
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2020-12-19 gmungocJAL-1713 restore project with no Overview, regardless...
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2020-12-17 gmungocJAL-1713 close and replace auto-opened Overview with...
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2020-12-13 gmungocJAL-1713 unit test for save/restore Overview in project
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2020-12-13 gmungocJAL-1713 renamed method to OverviewPanel.get/setFrameBounds()
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2020-12-12 gmungocJAL-1713 JAL-3119 JAL-3785 refactored get/set Overview...
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2020-12-11 gmungocJAL-3785 set full title on automatically opened Overview...
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2020-12-11 gmungocJAL-3612 use _last_ drawn colour per feature type in...
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2020-12-11 gmungocJAL-1713 fix typo; overview in project with open overview...
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2020-12-10 gmungocJAL-3784 null the right overview reference when it...
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2020-12-10 gmungocJAL-1713 read/set OverviewPanel geometry on parent...
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2020-12-10 gmungocJAL-1713 save Overview title in project, don't save...
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2020-12-10 gmungocJAL-3119 include view name (if any) in Overview title
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2020-12-10 gmungocJAL-1713 save/restore Overview in project (todo: restore...
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2020-12-10 gmungocJAL-1713 refactorings to allow save/restore Overview...
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2020-12-10 gmungocJAL-1713 schema and JAXB changes to save Overview in...
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2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all...
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2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to...
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2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature...
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2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
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2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests
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2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
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2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMappedRegion
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2020-10-22 gmungocJAL-3700 JAL-3763 create datasets for test sequences
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2020-10-22 gmungocJAL-3763 failsafe check for null
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2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual...
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2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS...
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2020-10-22 gmungocJAL-3700 additions and corrections to unit tests
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2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests
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2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
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2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMappedRegion
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2020-10-15 gmungocJAL-3763 unused method removed
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2020-10-08 gmungocJAL-3700 JAL-3763 create datasets for test sequences
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2020-10-08 gmungocJAL-3763 failsafe check for null
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2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual...
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2020-10-08 gmungocJAL-3763 always make a new dataset sequence for CDS...
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2020-09-17 gmungocJAL-3700 additions and corrections to unit tests
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2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
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2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
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2020-09-10 gmungocJAL-3518 removed unneeded override in ChimeraCommands
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2020-09-10 gmungocJAL-2422 comments updated re ALTLOC handling
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2020-09-03 gmungocJAL-3648 resize annotation panel after dragging to...
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2020-09-03 gmungocJAL-3648 resize annotation panel after dragging to...
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2020-08-31 gmungocJAL-3018 Ensembl reviewed REST version updated to 13.0
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2020-08-31 gmungocJAL-1191 use Cache.log for logging
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2020-08-31 gmungocJAL-1191 reduce logging level for warnings
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2020-08-24 gmungocJAL-3018 updated reviewed REST version to 12.0
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2020-08-18 gmungocJAL-2656 Java 8 compatible test for gzipped, refactored...
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2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly
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2020-08-13 gmungocJAL-3597 slight tidying of code and Javadoc, passmark...
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2020-08-13 gmungocJAL-3597 additional references nulled, bug in test...
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2020-08-11 gmungocJAL-3371 more fine-grained slider; set Param slider...
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2020-08-10 gmungocJAL-3490 match count independent of contiguous matches...
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2020-08-05 gmungocJAL-3692 unit test updated for ?gzip download endpoint URL
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2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped...
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2020-08-05 gmungocJAL-3692 unit test updated for ?gzip download endpoint URL
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2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped...
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2020-08-05 gmungocJAL-3700 fix for propagation of sort commands
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2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching...
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2020-08-03 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description
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2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test...
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2020-08-03 gmungocJAL-3692 parse DE for description, and other refactoring...
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