JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[jalview.git] / src / jalview / io /
2019-01-28 Ben SoaresJAL-3141 improvement on BackupFilenameParts filename...
2019-01-25 Ben SoaresJAL-3141. This adds quite a lot of code to allow an...
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide...
2019-01-24 Ben SoaresJAL-3141 New layout and wording of Backups Preferences...
2019-01-24 Ben SoaresJAL-3141 Reformatted code in eclipse
2019-01-23 Ben SoaresJAL-3141 Added Presets options in the Backups Preferenc...
2019-01-22 Ben SoaresJAL-3141 Fixed what happens when suffix template has...
2019-01-20 Ben SoaresJAL-3141 removing diagnostic output
2019-01-20 Ben SoaresJAL-3141 Changed suffix position to after the extension...
2019-01-18 Jim ProcterMerge branch 'feature/JAL-3063jaxbNoCastor' into featur...
2019-01-14 Ben SoaresJAL-3141 Made more constants
2019-01-09 Ben SoaresJAL-3141 removed redundant method to tests
2019-01-09 Ben SoaresJAL-3141 forgot to add this file after extracting the...
2019-01-09 Ben SoaresJAL-3141 Made one more suggested change from code review
2019-01-08 Ben SoaresJAL-3141 Made some more suggested changes from code...
2019-01-08 Ben SoaresJAL-3141 Made some suggested changes from code review
2018-12-19 gmungocJAL-3178 include non-positional features in their group... bug/JAL-2791exportFilteredFeature
2018-12-13 Ben SoaresJAL-3130 Attempting to fix 8 tests that pass on a Mac...
2018-12-10 gmungocJAL-1421 added type to List and Vector feature/JAL-3169cancelOverwrite
2018-12-10 gmungocJAL-3169 leave file browser open on Cancel in overwrite...
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
2018-12-03 gmungocJAL-3063 Castor removed from codebase
2018-11-02 Ben SoaresJAL-3141 Tests now available and working, bringing...
2018-10-31 Ben SoaresJAL-3141 Preferences 'Backups' tab now working. Doesn...
2018-10-25 Ben SoaresJAL-3141 Ostensibly all backups working for alignment...
2018-10-24 Ben SoaresJAL-3141 Code checkout. Not compiling.
2018-10-24 Ben SoaresJAL-3141 Code checkout. Not compiling.
2018-10-23 Ben SoaresBackupFilter and other unfinished business
2018-10-22 Ben SoaresJAL-3141 Taken the backing up code out of FileChooser...
2018-10-22 Ben SoaresJAL-3141 Taken the backing up code out of FileChooser...
2018-10-22 Ben SoaresJAL-3141 Tidying
2018-10-19 Ben SoaresJAL-3141 Backup files being created with default suffix...
2018-10-09 Jim ProcterJAL-3127 TODO - resolve reference to Viewport for group...
2018-10-04 gmungocJAL-3132 set status message when over sequence id or...
2018-09-27 gmungocJAL-2791 refactored Export Features to apply all visibi...
2018-09-19 gmungocJAL-3063 use JAXB for 'Save as Project' and load projec...
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch
2018-09-09 Jim ProcterJAL-3106 normalise extension before checking if it...
2018-09-07 Jim ProcterJAL-2988 if selected file is null (On Java 10/OSX ...
2018-09-07 Jim ProcterJAL-2988 workaround: overload getSelectedFile() because...
2018-09-07 Jim ProcterJAL-3106 use .jvp as default
2018-09-03 Jim ProcterMerge branch 'patch/VAqua_saveload_update_JAL-2988...
2018-08-22 Jim ProcterJAL-2988 workaround for jalview save as dialogs - clear...
2018-08-03 Ben SoaresJAL-3061
2018-08-02 Ben SoaresJAL-3053
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS...
2018-06-26 Jim ProcterJAL-3042 don't allow user to change default history...
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-24 gmungocJAL-2997 additional tests
2018-05-23 gmungocJAL-2997 handle tab-delimited trailing column number...
2018-05-07 Jim ProcterJAL-2321 ensure default is ‘parseImmediately=true’
2018-05-07 Jim ProcterJAL-2321 isParseImmediately() allows the parse() method...
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC...
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after...
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review
2018-01-10 gmungocJAL-1793 update spike branch to latest
2017-12-08 gmungocJAL-2843 read/write feature filters from/to Jalview...
2017-12-05 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-12-04 gmungocJAL-2808 JAL-2850 update spike build to latest
2017-12-04 gmungocMerge branch 'spikes/mungo' into features/JAL-1793VCF
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere...
2017-12-04 gmungocJAL-2845 locate reverse strand insertion as complement...
2017-12-04 gmungocJAL-2835 small refactor to only extract transcript...
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term...
2017-12-01 gmungocJAL-2835 refactored to extract specific consequence...
2017-12-01 gmungocJAL-2835 additional sub-terms of sequence_variant added
2017-11-30 gmungocJAL-2850 improved use of htsjdk api to read contig...
2017-11-30 Jim ProcterJAL-2849 fix
2017-11-27 gmungocJAL-2850 VCFLoader refactored to load VCF to contig...
2017-11-23 gmungocJAL-2808 update spike to latest (filter range, Present...
2017-11-23 gmungocJAL-2808 removed field filters; sort CSQ data by key
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-15 gmungocJAL-2835 take all CSQ fields; catch invalid field match...
2017-11-15 gmungocJAL-2835 support filter/colour by nested attribute...
2017-11-15 gmungocJAL-2835 add filters for VCF/VEP 'fields of interest'
2017-11-13 gmungocJAL-2738 stubs for filtering VEP and VCF fields of...
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 Jim ProcterMerge branch 'imp/JAL-2810_ftsIDtab' into develop
2017-11-13 gmungocJAL-2176 removed unused Sequence.index
2017-11-07 gmungocJAL-2069 update spike branch with latest
2017-11-06 gmungocJAL-2820 include attribute value used for feature colou...
2017-10-27 Jim ProcterJAL-2804 kludge method to test if last key event handle...
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-27 gmungocJAL-2792 capture feature metadata and render in Feature...
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop
2017-10-26 gmungocJAL-2792 html table for Feature Details report
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome...
2017-10-24 gmungocJAL-2743 slightly fancier species/assembly matching...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd...
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-20 gmungocJAL-2755 update caller for method rename!
2017-10-19 gmungocJAL-2755 put chromosomal dbref first in report
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
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