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close filehandles straight after parse, without setting an error
[jalview.git] / src /
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... tree | commitdiff
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... tree | commitdiff
2021-12-14 Ben SoaresJAL-3933 Updated log4j jars with log4j-2.16.0 and compa... tree | commitdiff
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_1_4 tree | commitdiff
2021-06-09 Jim Procterfixes JAL-3840 tree | commitdiff
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows tree | commitdiff
2021-04-19 Ben SoaresJAL-3833 cap the scaling used by HiDPISetting for incor... tree | commitdiff
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc... tree | commitdiff
2021-02-26 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence' into... bug/JAL-3806_mappingCoversSequence tree | commitdiff
2021-02-24 Jim ProcterMerge branch 'bug/JAL-3818_jmolDeadlock' into releases... tree | commitdiff
2021-02-11 gmungocJAL-3818 process Jmol callbacks in AWT thread bug/JAL-3818_jmolDeadlock tree | commitdiff
2021-02-10 Ben SoaresJAL-3521 Change grouped Jalview windows on linux taskba... tree | commitdiff
2021-02-05 Jim ProcterJAL-3814 don’t automatically launch the news browser... tree | commitdiff
2021-02-05 Jim ProcterJAL-3813 NOIDENTIFIERSSERVICE preference disables jalvi... tree | commitdiff
2021-02-05 Jim ProcterJAL-3812 new argument ‘-nohtmltemplates’ and user prefe... tree | commitdiff
2021-02-05 Jim ProcterJAL-3811 document SHOW_JWS2_SERVICES user preference... tree | commitdiff
2021-02-05 Jim ProcterJAL-3814 NONEWS property tree | commitdiff
2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping... bug/JAL-3806_mappingCoversCDS_reprise tree | commitdiff
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop... tree | commitdiff
2020-10-29 Jim Procter JAL-3759 exclude hidden columns when processing... tree | commitdiff
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... tree | commitdiff
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3 tree | commitdiff
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon... tree | commitdiff
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2020-10-28 Jim ProcterMerge branch 'bug/JAL-3760_protsTreatedAsNucleotides... tree | commitdiff
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via... tree | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests tree | commitdiff
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... tree | commitdiff
2020-10-22 gmungocJAL-3763 failsafe check for null tree | commitdiff
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual... tree | commitdiff
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... tree | commitdiff
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests tree | commitdiff
2020-10-20 Jim Procterfix for JAL-3765 tree | commitdiff
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... tree | commitdiff
2020-09-24 Jim ProcterJAL-3757 JAL-3689 use AppletFormat.checkProtocol to... tree | commitdiff
2020-09-23 Ben SoaresJAL-3757 JAL-3689 Fixed checks for URLs by adding check... tree | commitdiff
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2 tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 fix compilation error tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally... tree | commitdiff
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct... tree | commitdiff
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2020-09-17 Jim ProcterJAL-3750 parse protocol before checking if argument... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 recover complement alignment from complement... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true... tree | commitdiff
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP... tree | commitdiff
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands tree | commitdiff
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement... tree | commitdiff
2020-09-03 gmungocJAL-3648 resize annotation panel after dragging to... tree | commitdiff
2020-09-02 Ben SoaresJAL-3280 Test for remote release build_properties file... tree | commitdiff
2020-09-01 Ben SoaresJAL-3280 fixes after CR-JAL-241. Now only checking... tree | commitdiff
2020-08-31 Ben SoaresJAL-3280 Pass appbase and appdir from getdown to jalvew... tree | commitdiff
2020-08-31 Jim ProcterJAL-3732 - sequences can be moved up/down in cursor... tree | commitdiff
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch tree | commitdiff
2020-08-25 Jim ProcterJAL-3671 hardwire log4j.root logger to INFO to supress... tree | commitdiff
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615... tree | commitdiff
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3691_No_score_models_available... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3561_JAL-3660_fileformatexport_... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3597_for_Release_2_11_1_Branch... tree | commitdiff
2020-08-14 Ben SoaresJAL-3676 More explicit tooltip about resetting log... tree | commitdiff
2020-08-13 gmungocJAL-3597 additional references nulled, bug in test... tree | commitdiff
2020-08-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... tree | commitdiff
2020-08-12 Ben SoaresJAL-3608 Changes from code review CR-JAL-236 tree | commitdiff
2020-08-11 Jim ProcterJAL-3673 make sure font metrics are updated if dealing... tree | commitdiff
2020-08-11 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
2020-08-11 gmungocJAL-3371 more fine-grained slider; set Param slider... tree | commitdiff
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 tree | commitdiff
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard... tree | commitdiff
2020-08-10 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-08-10 Jim ProcterJAL-3628 JAL-3708 call Cache.initLogger() before using... tree | commitdiff
2020-08-05 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL... tree | commitdiff
2020-08-04 Ben SoaresJAL-3477 Added -help text for jvmmempc and jvmmemmax... tree | commitdiff
2020-08-03 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description tree | commitdiff
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 parse DE for description, and other refactoring... tree | commitdiff
2020-08-03 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-07-29 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
2020-07-29 Jim ProcterJAL-3371 JAL-2983 don't modify 'extent' of slider ... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their... tree | commitdiff
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-07-27 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
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