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JAL-3628 improvement for visual selection of console text - fg color change if required
[jalview.git] / src / jalview / io /
2020-07-06 Ben SoaresJAL-3628 Fix for slightly incorrect boolean usage to... tree | commitdiff
2020-07-06 Ben SoaresJAL-3628 Even more Cache.log.debug statements tree | commitdiff
2020-07-04 Ben SoaresJAL-3628 More Cache.log.debug statements tree | commitdiff
2020-06-30 Ben SoaresJAL-3676 Added Log Level ComboBox and Copy to Clipboard... tree | commitdiff
2020-06-24 Ben SoaresJAL-3667 Fixed single backupfile error deleting the... tree | commitdiff
2020-06-15 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-06-08 Ben SoaresJAL-3628 Changed all file1.renameTo(file2) calls to... tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-04-21 Jim ProcterMerge branch 'bug/JAL-3567virtualFeatureCoordinates... tree | commitdiff
2020-04-17 gmungocJAL-3567 unit tests for linked feature tooltips tree | commitdiff
2020-04-16 gmungocJAL-3567 report mapped location for virtual features... tree | commitdiff
2020-04-14 Jim ProcterMerge branch 'bug/JAL-3529_uniprotidsinstockholm' into... tree | commitdiff
2020-03-30 Jim ProcterJAL-3407 JAL-3130 back out java 9+ syntax that breaks... tree | commitdiff
2020-03-06 gmungocMerge branch 'feature/JAL-3468featureDescriptionEllipsi... tree | commitdiff
2020-03-04 Ben SoaresJAL-3468 small tidy tree | commitdiff
2020-03-04 Ben SoaresJAL-3468 improvement to feature description truncation... tree | commitdiff
2020-03-04 Ben SoaresJAL-3468 Obsessively fixed self-closing <br/> tags tree | commitdiff
2020-03-03 soaresJAL-3468 Adapted methods to report how many features... tree | commitdiff
2020-02-18 Jim ProcterJAL-3529 attempt to guess database for a sequence’s... tree | commitdiff
2020-02-14 Jim ProcterJAL-3532 TODO comment tree | commitdiff
2020-02-14 Jim ProcterJAL-3529 preferentially output source dbrefs or princip... tree | commitdiff
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into... tree | commitdiff
2020-01-24 gmungocJAL=3121 more data format validation/tests, help text... feature/JAL-3121gffAttributeMap tree | commitdiff
2020-01-23 gmungocJAL-3121 'attributes map' in GFF3 without special ... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-10-31 gmungocJAL-3468 truncate feature description to 40 chars in... tree | commitdiff
2019-08-22 gmungocJAL-3121 slightly cleaner parsing of, and unit test... tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into tree | commitdiff
2019-07-26 gmungocJAL-1793 only decode specific special characters in... tree | commitdiff
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation tree | commitdiff
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields tree | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data tree | commitdiff
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests tree | commitdiff
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute... tree | commitdiff
2019-06-18 gmungocJAL-3187 javadoc tree | commitdiff
2019-06-18 gmungocJAL-3304 option to export linked features also for... tree | commitdiff
2019-06-18 gmungocJAL-3304 option to export linked features in Jalview... tree | commitdiff
2019-06-13 gmungocJAL-3143 recognise lnc_RNA as transcript tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-05-29 gmungocJAL-2738 error logging if no ##reference found tree | commitdiff
2019-05-29 gmungocJAL-2738 accept .csi, default to GRCh37:homo_sapiens... tree | commitdiff
2019-05-27 Ben SoaresJAL-3141 Added HashMap types for Java 1.8 compatibility tree | commitdiff
2019-05-25 Ben SoaresJAL-3141 One more error log fix tree | commitdiff
2019-05-25 Ben SoaresJAL-3141 Added tooltips on Schemes dropdown and Customi... tree | commitdiff
2019-05-24 Ben SoaresJAL-3141 Fixes recommended from gmc's test tree | commitdiff
2019-05-24 Ben SoaresJAL-3141 Reworked a lot of BackupFiles to allow the... tree | commitdiff
2019-04-29 gmungocJAL-2738 JAL-2743 update unit test to match new VCF... tree | commitdiff
2019-04-26 gmungocJAL-2738 JAL-2743 properties to map VCF header to speci... tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-19 Ben SoaresJAL-3130 Merge of JAL-3130_Java_11_investigations-Ben... tree | commitdiff
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'bug/JAL-2791exportFilteredFeature' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'feature/JAL-3093wrappedModeTooltips'... tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3169cancelOverwrite' into... tree | commitdiff
2019-02-28 gmungocMerge remote-tracking branch 'origin/feature/JAL-3141_b... tree | commitdiff
2019-02-28 Jim ProcterMerge branch 'feature/JAL-3141_backupfiles_for211'... merge/develop_feature/JAL-3141_backupfiles_for211 tree | commitdiff
2019-02-22 gmungocJAL-2738 don't set AF as feature score tree | commitdiff
2019-02-22 Ben SoaresJAL-3141 improved message for asking whether to delete... tree | commitdiff
2019-02-21 Ben SoaresJAL-3141 Sensible refactoring for confirming deleting... tree | commitdiff
2019-02-17 Ben SoaresJAL-3141 User warning when deleting old backup files... tree | commitdiff
2019-02-15 Ben SoaresJAL-3141 re-order deletion of old files and check lastM... tree | commitdiff
2019-02-14 Ben SoaresJAL-3141 Added warning/confirmation when suffixReverse... tree | commitdiff
2019-02-01 Ben SoaresJAL-3141 Slight efficiency gain in detecting backupfile... tree | commitdiff
2019-01-30 Ben SoaresJAL-3141 Enabled the 'Include backpup files' checkbox... tree | commitdiff
2019-01-29 Ben SoaresJAL-3141 Found a good fix for updating the FileChooser... tree | commitdiff
2019-01-29 Ben SoaresJAL-3141 Found a (not ideal) fix for updating the FileC... tree | commitdiff
2019-01-28 Ben SoaresJAL-3141 improvement on BackupFilenameParts filename... tree | commitdiff
2019-01-25 Ben SoaresJAL-3141. This adds quite a lot of code to allow an... tree | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... tree | commitdiff
2019-01-24 Ben SoaresJAL-3141 New layout and wording of Backups Preferences... tree | commitdiff
2019-01-24 Ben SoaresJAL-3141 Reformatted code in eclipse tree | commitdiff
2019-01-23 Ben SoaresJAL-3141 Added Presets options in the Backups Preferenc... tree | commitdiff
2019-01-22 Ben SoaresJAL-3141 Fixed what happens when suffix template has... tree | commitdiff
2019-01-20 Ben SoaresJAL-3141 removing diagnostic output tree | commitdiff
2019-01-20 Ben SoaresJAL-3141 Changed suffix position to after the extension... tree | commitdiff
2019-01-18 Jim ProcterMerge branch 'feature/JAL-3063jaxbNoCastor' into featur... tree | commitdiff
2019-01-14 Ben SoaresJAL-3141 Made more constants tree | commitdiff
2019-01-09 Ben SoaresJAL-3141 removed redundant method to tests tree | commitdiff
2019-01-09 Ben SoaresJAL-3141 forgot to add this file after extracting the... tree | commitdiff
2019-01-09 Ben SoaresJAL-3141 Made one more suggested change from code review tree | commitdiff
2019-01-08 Ben SoaresJAL-3141 Made some more suggested changes from code... tree | commitdiff
2019-01-08 Ben SoaresJAL-3141 Made some suggested changes from code review tree | commitdiff
2018-12-19 gmungocJAL-3178 include non-positional features in their group... bug/JAL-2791exportFilteredFeature tree | commitdiff
2018-12-13 Ben SoaresJAL-3130 Attempting to fix 8 tests that pass on a Mac... tree | commitdiff
2018-12-10 gmungocJAL-1421 added type to List and Vector feature/JAL-3169cancelOverwrite tree | commitdiff
2018-12-10 gmungocJAL-3169 leave file browser open on Cancel in overwrite... tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-12-03 gmungocJAL-3063 Castor removed from codebase tree | commitdiff
2018-11-02 Ben SoaresJAL-3141 Tests now available and working, bringing... tree | commitdiff
2018-10-31 Ben SoaresJAL-3141 Preferences 'Backups' tab now working. Doesn... tree | commitdiff
2018-10-25 Ben SoaresJAL-3141 Ostensibly all backups working for alignment... tree | commitdiff
2018-10-24 Ben SoaresJAL-3141 Code checkout. Not compiling. tree | commitdiff
2018-10-24 Ben SoaresJAL-3141 Code checkout. Not compiling. tree | commitdiff
2018-10-23 Ben SoaresBackupFilter and other unfinished business tree | commitdiff
2018-10-22 Ben SoaresJAL-3141 Taken the backing up code out of FileChooser... tree | commitdiff
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