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

2024-05-21	Ben Soares	JAL-1054 Change the rest of the url.openConnection...	blob \| commitdiff
2024-05-14	Ben Soares	JAL-1054 Also recognise UnknownHostException as a file...	blob \| commitdiff \| diff to current
2024-05-14	Ben Soares	JAL-4414 Add a FileNotFoundException when identifying...	blob \| commitdiff \| diff to current
2024-05-13	Ben Soares	JAL-1054 Add wrappers for URL.openConnection(), URL...	blob \| commitdiff \| diff to current
2023-08-10	Ben Soares	JAL-629 Change all stdout and stderr output to use...	blob \| commitdiff \| diff to current
2023-05-22	James Procter	JAL-1551 spotless	blob \| commitdiff \| diff to current
2023-05-19	James Procter	JAL-1551 spotlessApply	blob \| commitdiff \| diff to current
2023-05-19	James Procter	JAL-1551 spotlessApply	blob \| commitdiff \| diff to current
2022-10-06	Jim Procter	Patch for JAL-4074 - any content ending in ‘gzip’ recog...	blob \| commitdiff \| diff to current
2022-02-11	Jim Procter	JAL-3949 - refactor logging from jalview.bin.Cache...	blob \| commitdiff \| diff to current
2022-02-11	Ben Soares	JAL-3949 Complete new abstracted logging framework...	blob \| commitdiff \| diff to current
2022-01-11	Ben Soares	JAL-3703 fix Gff3 shared InputStream with embedded...	blob \| commitdiff \| diff to current
2020-08-21	Jim Procter	JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615...	blob \| commitdiff \| diff to current
2020-08-21	Jim Procter	JAL-3615 code tidy, improve unit test	blob \| commitdiff \| diff to current
2020-08-20	Ben Soares	JAL-2656 better read of (potential) gzip magic bytes	blob \| commitdiff \| diff to current
2020-08-18	gmungoc	JAL-2656 Java 8 compatible test for gzipped, refactored...	blob \| commitdiff \| diff to current
2020-07-28	Jim Procter	JAL-3615 JAL-2656 missing import after cherrypick	blob \| commitdiff \| diff to current
2020-07-28	Jim Procter	JAL-2656 recognise non-HTTP URI input streams as gzippe...	blob \| commitdiff \| diff to current
2020-07-28	Jim Procter	JAL-2656 recognise Gzipped file input streams by their...	blob \| commitdiff \| diff to current
2020-07-28	Jim Procter	JAL-2656 recognise non-HTTP URI input streams as gzippe...	blob \| commitdiff \| diff to current
2020-07-28	Jim Procter	JAL-2656 recognise Gzipped file input streams by their...	blob \| commitdiff \| diff to current
2020-07-27	gmungoc	JAL-2656 JAL-3615 check response headers to test for...	blob \| commitdiff \| diff to current
2020-07-27	gmungoc	JAL-3615 used gzip endpoints for Pfam and Rfam	blob \| commitdiff \| diff to current
2020-07-02	gmungoc	JAL-2656 JAL-3615 check response headers to test for...	blob \| commitdiff \| diff to current
2020-07-02	gmungoc	JAL-3615 used gzip endpoints for Pfam and Rfam	blob \| commitdiff \| diff to current
2020-04-21	gmungoc	JAL-3603 load annotation file from RELATIVE_URL in...	blob \| commitdiff \| diff to current
2019-03-27	hansonr	consolidation of Platform isJS calls	blob \| commitdiff \| diff to current
2018-07-20	gmungoc	JAL-3048 revised AlignExportSettings dialog with respon...	blob \| commitdiff \| diff to current
2018-06-28	hansonr	FileAsBytes	blob \| commitdiff \| diff to current
2018-06-28	hansonr	JAL-3032 FileChooser missing correct call to JSToolkit...	blob \| commitdiff \| diff to current
2018-06-28	hansonr	JAL-3032 DND enabled; additional io changes for File...	blob \| commitdiff \| diff to current
2018-06-27	hansonr	JAL-3026 FileParser for JFileChooser results as ByteArr...	blob \| commitdiff \| diff to current
2018-06-27	hansonr	JAL-3032 part2 local file reading by JFileChooser	blob \| commitdiff \| diff to current
2018-06-23	hansonr	JAL-3026 JDesktop/JInternalFrames support + relative...	blob \| commitdiff \| diff to current
2018-06-22	hansonr	fix for no access-control-origin on jalview site	blob \| commitdiff \| diff to current
2018-05-24	gmungoc	JAL-2997 additional tests	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	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
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-03-23	tcofoegbu	JAL-2009 added programmatic custom feature setting...	blob \| commitdiff \| diff to current
2016-01-05	gmungoc	Merge remote-tracking branch 'origin/features/JAL-1705_...	blob \| commitdiff \| diff to current
2015-11-21	gmungoc	JAL-653 JAL-1968 FeaturesFile now handles Jalview or...	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-1705_ensembl	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	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
2015-09-02	gmungoc	JAL-1544 spelling	blob \| commitdiff \| diff to current
2015-06-26	Jim Procter	JAL-1705 - allow a FileParse to be constructed directly...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-18	Jim Procter	JAL-653 JAL-1780 JAL-1543 javadoc and comment about...	blob \| commitdiff \| diff to current
2015-06-18	Jim Procter	JAL-1780 JAL-653 moved AlignExportSettings reference...	blob \| commitdiff \| diff to current
2015-05-19	tcofoegbu	JAL-1641 Further refactoring of JSON export option...	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
2015-01-23	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1286 don't print an exception if a non-gzip stream...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-10-06	Jim Procter	Merge branch 'Release_2_8_2_Branch' into JAL-429_phylip...	blob \| commitdiff \| diff to current
2014-10-03	Charles Ofoegbu	Integration of David Corsars Phylip File support	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	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
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-11-07	Jim Procter	JAL-1286 check if local file ends with .gz and opens...	blob \| commitdiff \| diff to current
2013-05-13	Jim Procter	JAL-1286 URL stream reader tries to use a GZIPInputStre...	blob \| commitdiff \| diff to current
2013-04-12	Jim Procter	JAL-1286 URL stream reader tries to use a GZIPInputStre...	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
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
2011-01-05	jprocter	JAL-727	blob \| commitdiff \| diff to current
2010-12-09	jprocter	dataIn.ready() is not a test of data source validity!	blob \| commitdiff \| diff to current
2010-11-14	jprocter	refactored to decouple dependencies due to FileParse...	blob \| commitdiff \| diff to current
2010-11-14	jprocter	refactored protocol parser and allow human readable...	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-04-10	jprocter	bug fix for Features/Annotations file parameter parsing...	blob \| commitdiff \| diff to current
2008-01-29	jprocter	FileParse object can be re-used to read different files...	blob \| commitdiff \| diff to current
2007-10-31	jprocter	error message associated with an alignment file loading...	blob \| commitdiff \| diff to current
2007-10-11	jprocter	pass up the errormessage in the exception when a dataso...	blob \| commitdiff \| diff to current
2007-08-22	jprocter	added facility for sending non-fatal warnings back...	blob \| commitdiff \| diff to current
2007-04-26	jprocter	fixed bug in prefix extraction for application	blob \| commitdiff \| diff to current
2007-04-17	jprocter	bugfix.	blob \| commitdiff \| diff to current
2007-04-17	jprocter	refactored to allow seeks on a FileParse datasource...	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-03-08	amwaterhouse	Able to read resources from Zip file	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Formatted source	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	GPL license added	blob \| commitdiff \| diff to current
2004-11-02	amwaterhouse	Jalview Imported Sources start	blob \| commitdiff \| diff to current

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