JAL-3933 remove obsolete Castor logging configuration
[jalview.git] / src / jalview / io / FeaturesFile.java
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard...
2020-04-16 gmungocJAL-3567 report mapped location for virtual features...
2020-01-23 gmungocJAL-3121 'attributes map' in GFF3 without special ...
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued...
2019-06-18 gmungocJAL-3187 javadoc
2019-06-18 gmungocJAL-3304 option to export linked features also for...
2019-06-18 gmungocJAL-3304 option to export linked features in Jalview...
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2018-12-19 gmungocJAL-3178 include non-positional features in their group... bug/JAL-2791exportFilteredFeature
2018-09-27 gmungocJAL-2791 refactored Export Features to apply all visibi...
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-24 gmungocJAL-2997 additional tests
2018-01-10 gmungocJAL-1793 update spike branch to latest
2017-12-08 gmungocJAL-2843 read/write feature filters from/to Jalview...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-25 gmungocJAL-2490 test coverage of empty and null feature group...
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548...
2017-05-23 gmungocJAL-2490 tidy code and tests for feature export in...
2017-05-23 gmungocJAL-2490 improved lookup of features for Export Feature...
2017-05-22 gmungocJAL-2505 use setter not direct access to sf.description
2017-05-19 gmungocJAL-2490 refactored test for 'hasFeatures'
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum,
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-24 gmungocFileFormatI further tweaks, clean compile
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
2016-07-18 gmungocfileFormat enum wip changes
2016-07-11 gmungocfile format enum wip changes
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-05-09 gmungocJAL-2018 export graduated feature colours correctly
2016-02-25 gmungocJAL-2015 parse/write Jalview feature format pushed...
2016-02-24 gmungocJAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence...
2016-01-21 gmungocJAL-1705 include dummy sequences in returned alignment
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes
2015-11-30 gmungocJAL-652 further refactoring / tests
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-11-10 Jim ProcterJAL-653 added missing pragma string to processing filter
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-07 Jim ProcterJAL-1894 source formatting
2015-10-05 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-24 gmungocJAL-1904 parse feature file colours on to alignment...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs!
2015-06-23 Jim ProcterMerge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892...
2015-06-22 Jim ProcterJAL-1780 JAL-653 Format/AppletFormat import and export...
2015-06-11 Jim ProcterJAL-653 tidy comments
2015-06-07 Jim ProcterJAL-653 basic GFF3 alignment import wrapper class
2015-06-06 Jim ProcterJAL-653 make sure dummy sequences created during GFF...
2015-06-06 Jim ProcterJAL-653 first stab at parsing GFF3 pragmas to support...
2015-06-06 Jim ProcterJAL-653 gff version number field
2015-06-05 Jim ProcterJAL-653 set the warningMessage for the file source...
2015-06-05 Jim ProcterJAL-653 GFF attributes parsing mechanism, with first...
2015-06-05 Jim ProcterJAL-653 trim initial tab in sequence feature ATTRIBUTES
2015-06-05 Jim ProcterJAL-653 allow dummy sequences to be created if a sequen...
2015-06-05 Jim ProcterJAL-1551 formatting
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-08-08 j.procter@dundee... JAL-1482 feature renderer and manipulation code refacto...
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced...
2012-12-07 jprocterformatting and error report cleanup
2012-12-07 jprocterproxy commit for Anne Menard <menard.annec@gmail.com...
2012-12-04 jprocterJAL-1140 - IO classes should only raise generic IOExcep...
2012-11-15 jproctersource formatting
2012-11-15 jprocterMerge branch 'develop' into menard
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-08-14 Anne Menardlast version stay many bugs ..
2012-07-16 Anne MenardMerge branch 'develop' of https://source.jalview.org...
2012-07-10 Anne Menardv2
2012-07-05 Anne MenardAdd support RNAML format
2012-07-01 jprocterJAL-1117 alleviate lock starvation
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-08-19 jprocterJAL-908 JAL-701 refactored HTML escape/unescape code...
2011-01-21 jprocterrelaxed ID matching parameter JAL-753
2011-01-05 jprocterJAL-727
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-09-15 jprocteradded colour by label to feature type colourspec and...
2010-04-30 jprocterjalview 2.5 release banner
2010-04-22 jprocternon-positional feature export in gff and features file...
2010-03-26 jproctertodo for graduated feature colours
2009-11-06 jprocteronly append score if it is not NaN
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