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[jalview.git] / src / jalview / io / FeaturesFile.java

2020-08-10	Jim Procter	JAL-3691 toUpperCase(Locale.ROOT) for all standard...	blob \| commitdiff
2020-04-16	gmungoc	JAL-3567 report mapped location for virtual features...	blob \| commitdiff \| diff to current
2020-01-23	gmungoc	JAL-3121 'attributes map' in GFF3 without special ...	blob \| commitdiff \| diff to current
2019-08-22	gmungoc	JAL-3121 round trip GFF attributes including map-valued...	blob \| commitdiff \| diff to current
2019-06-18	gmungoc	JAL-3187 javadoc	blob \| commitdiff \| diff to current
2019-06-18	gmungoc	JAL-3304 option to export linked features also for...	blob \| commitdiff \| diff to current
2019-06-18	gmungoc	JAL-3304 option to export linked features in Jalview...	blob \| commitdiff \| diff to current
2019-03-20	Ben Soares	JAL-3130 Lots of deprecation fixes. See utils/deprecat...	blob \| commitdiff \| diff to current
2018-12-19	gmungoc	JAL-3178 include non-positional features in their group... bug/JAL-2791exportFilteredFeature	blob \| commitdiff \| diff to current
2018-09-27	gmungoc	JAL-2791 refactored Export Features to apply all visibi...	blob \| commitdiff \| diff to current
2018-05-28	gmungoc	Merge remote-tracking branch 'origin/releases/Release_2...	blob \| commitdiff \| diff to current
2018-05-24	gmungoc	JAL-2997 additional tests	blob \| commitdiff \| diff to current
2018-01-10	gmungoc	JAL-1793 update spike branch to latest	blob \| commitdiff \| diff to current
2017-12-08	gmungoc	JAL-2843 read/write feature filters from/to Jalview...	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2490 test coverage of empty and null feature group...	blob \| commitdiff \| diff to current
2017-05-23	gmungoc	JAL-2490 find features for export as GFF, JAL-2548...	blob \| commitdiff \| diff to current
2017-05-23	gmungoc	JAL-2490 tidy code and tests for feature export in...	blob \| commitdiff \| diff to current
2017-05-23	gmungoc	JAL-2490 improved lookup of features for Export Feature...	blob \| commitdiff \| diff to current
2017-05-22	gmungoc	JAL-2505 use setter not direct access to sf.description	blob \| commitdiff \| diff to current
2017-05-19	gmungoc	JAL-2490 refactored test for 'hasFeatures'	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-2360 refactoring for JalviewColourScheme enum,	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-24	gmungoc	FileFormatI further tweaks, clean compile	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-07-18	gmungoc	fileFormat enum wip changes	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-05-10	gmungoc	Merge branch 'develop' into features/JAL-1956_featureStyles	blob \| commitdiff \| diff to current
2016-05-09	gmungoc	JAL-2018 export graduated feature colours correctly	blob \| commitdiff \| diff to current
2016-02-25	gmungoc	JAL-2015 parse/write Jalview feature format pushed...	blob \| commitdiff \| diff to current
2016-02-24	gmungoc	JAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles	blob \| commitdiff \| diff to current
2016-01-26	gmungoc	JAL-1705 derive transcript sequences from gene sequence...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 include dummy sequences in returned alignment	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 GFF new/refactored helper classes	blob \| commitdiff \| diff to current
2015-11-30	gmungoc	JAL-652 further refactoring / tests	blob \| commitdiff \| diff to current
2015-11-21	gmungoc	JAL-653 JAL-1968 FeaturesFile now handles Jalview or...	blob \| commitdiff \| diff to current
2015-11-10	Jim Procter	JAL-653 added missing pragma string to processing filter	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-15	Jim Procter	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1894 source formatting	blob \| commitdiff \| diff to current
2015-10-05	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-09-24	gmungoc	JAL-1904 parse feature file colours on to alignment...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	JAL-1819 use Float.isNaN() to check for NaNs!	blob \| commitdiff \| diff to current
2015-06-23	Jim Procter	Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-11	Jim Procter	JAL-653 tidy comments	blob \| commitdiff \| diff to current
2015-06-07	Jim Procter	JAL-653 basic GFF3 alignment import wrapper class	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 make sure dummy sequences created during GFF...	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 first stab at parsing GFF3 pragmas to support...	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 gff version number field	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 set the warningMessage for the file source...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 GFF attributes parsing mechanism, with first...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 trim initial tab in sequence feature ATTRIBUTES	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 allow dummy sequences to be created if a sequen...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1482 feature renderer and manipulation code refacto...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-02-13	jprocter	fix merge conflicts for finess on JAL-1140 (introduced...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	formatting and error report cleanup	blob \| commitdiff \| diff to current
2012-12-07	jprocter	proxy commit for Anne Menard <menard.annec@gmail.com...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1140 - IO classes should only raise generic IOExcep...	blob \| commitdiff \| diff to current
2012-11-15	jprocter	source formatting	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-14	Anne Menard	last version stay many bugs ..	blob \| commitdiff \| diff to current
2012-07-16	Anne Menard	Merge branch 'develop' of https://source.jalview.org...	blob \| commitdiff \| diff to current
2012-07-10	Anne Menard	v2	blob \| commitdiff \| diff to current
2012-07-05	Anne Menard	Add support RNAML format	blob \| commitdiff \| diff to current
2012-07-01	jprocter	JAL-1117 alleviate lock starvation	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-08-19	jprocter	JAL-908 JAL-701 refactored HTML escape/unescape code...	blob \| commitdiff \| diff to current
2011-01-21	jprocter	relaxed ID matching parameter JAL-753	blob \| commitdiff \| diff to current
2011-01-05	jprocter	JAL-727	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-09-15	jprocter	added colour by label to feature type colourspec and...	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-22	jprocter	non-positional feature export in gff and features file...	blob \| commitdiff \| diff to current
2010-03-26	jprocter	todo for graduated feature colours	blob \| commitdiff \| diff to current
2009-11-06	jprocter	only append score if it is not NaN	blob \| commitdiff \| diff to current
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