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JAL-4199 Fix cancel button not appearing on progress bar
[jalview.git] / src / jalview / io /
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their... tree | commitdiff
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-07-27 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description tree | commitdiff
2020-07-27 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... tree | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... tree | commitdiff
2020-07-24 gmungocJAL-3692 parse DE for description, and other refactoring... tree | commitdiff
2020-07-22 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote... tree | commitdiff
2020-07-21 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-07 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error... tree | commitdiff
2020-07-06 gmungocJAL-3311 JAL-3141 JAL-3144 tidying obsolete message... tree | commitdiff
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
2020-07-02 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-02 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-06-30 Ben SoaresJAL-3676 Added Log Level ComboBox and Copy to Clipboard... tree | commitdiff
2020-06-30 gmungocJAL-3446 unused imports removed tree | commitdiff
2020-06-29 Jim ProcterMerge branch 'bug/JAL-3490findSpanHiddenGaps' into... 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
2020-06-14 BobHansonJAL-3445 BSML BBB file format. tree | commitdiff
2020-06-12 BobHansonJAL-3446 from applet -- reload; also fixes some repaint... tree | commitdiff
2020-06-10 BobHansonJAL-3446 from applet, JAL-3584 tooltip fixes <br> and... tree | commitdiff
2020-06-08 Ben SoaresJAL-3628 Changed all file1.renameTo(file2) calls to... tree | commitdiff
2020-06-03 BobHansonJAL-3664 support for user.home, user.dir, user tree | commitdiff
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider... tree | commitdiff
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider tree | commitdiff
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider... tree | commitdiff
2020-06-02 BobHansonJAL-3446 from JAL-3253 AppletFormatAdapter not fixed tree | commitdiff
2020-06-02 BobHansonthis was supposed to go on a separate branch. Didn... tree | commitdiff
2020-06-02 BobHansonJAL-3446 JAL-3253 JAL-3445 BSML bbb XML format reader... tree | commitdiff
2020-06-02 BobHansonJAL-3446 from JAL-3253-applet StockholmFile updated... tree | commitdiff
2020-06-02 BobHansonJAL-3626 from JAL-3253-applet web page embedding tree | commitdiff
2020-06-01 BobHansonJAL-3626 Regex optimization from JAL-3253-applet; also... tree | commitdiff
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop tree | commitdiff
2020-04-23 Jim ProcterMerge branch 'develop' into alpha/JAL-3362_Jalview_212_... 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
2020-04-21 gmungocJAL-3603 load annotation file from RELATIVE_URL in... 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
2020-04-14 gmungocJAL-3583 remove debug logging, Javadoc added tree | commitdiff
2020-03-31 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2020-03-30 Jim ProcterJAL-3407 JAL-3130 back out java 9+ syntax that breaks... tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop 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
2020-02-06 gmungocJAL-3509 JAL-1842 minor tidying of code tree | commitdiff
2020-02-06 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin... 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
2019-12-11 gmungocJAL-3490 revised layout and search algorithm (more... 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
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop 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
2019-08-13 Jim ProcterJAL-3362 keep Java 1.8 build happy by specifying generi... tree | commitdiff
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... 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
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... 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
2019-07-03 tvaJAL-2629 removed empty line produced under sequence... tree | commitdiff
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit... tree | commitdiff
2019-07-02 tvaJAL-2629 add simple jackhmmer functionality tree | commitdiff
2019-06-28 tvaJAL-2629 add ability to add background frequencies... 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
2019-06-06 tvaJAL-3285 fix FileLoader failing to load HMMER file tree | commitdiff
2019-06-05 tvaJAL-3285 add methods and small changes to StockholmFile... tree | commitdiff
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer 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
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