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JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API
[jalview.git] / src / jalview / io /
2022-06-06 Jim ProcterJAL-4023 store distances as doubles tree | commitdiff
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu... tree | commitdiff
2022-04-05 Jim ProcterJAL-3981 patch tests and remove errant imports tree | commitdiff
2022-04-05 Jim ProcterJAL-3990 gradle spotlessApply tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 defensive copy - inefficient but fixes bug tree | commitdiff
2022-03-25 Jim ProcterJAL-3981 Additional line breaks - sort of helps tree | commitdiff
2022-03-24 Jim ProcterJAL-3981 strategic newlines to help speed up Java's... tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... tree | commitdiff
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop... tree | commitdiff
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2022-01-17 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... tree | commitdiff
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... tree | commitdiff
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... tree | commitdiff
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting... tree | commitdiff
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-09-30 Ben SoaresJAL-1260 Added .gbk to GenBank extensions. Added GenBa... tree | commitdiff
2021-09-23 Jim ProcterJAL-3821 less ambiguous base class name for EMBL and... tree | commitdiff
2021-09-23 Jim ProcterJAL-3821 ported to refactored FlatFile parser tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-21 Jim ProcterMerge branch 'doc/JAL-3746_Release_2_11_2' into develop tree | commitdiff
2021-09-21 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format... tree | commitdiff
2021-09-17 Ben SoaresJAL-1260 rudimentary parsing of LOCUS line to at least... tree | commitdiff
2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators tree | commitdiff
2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for... tree | commitdiff
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser tree | commitdiff
2021-09-17 Jim ProcterJAL-1260 FileFormat entry for EMBL/GENBANK: TODO: creat... tree | commitdiff
2021-09-16 gmungocJAL-3779 apply properties to all groups with given... tree | commitdiff
2021-09-16 Jim ProcterMerge branch 'develop' into doc/JAL-3746_Release_2_11_2 tree | commitdiff
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable... tree | commitdiff
2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray tree | commitdiff
2021-09-15 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-02 gmungocJAL-3509 JAL-1842 minor tidying of code tree | commitdiff
2021-09-02 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin... tree | commitdiff
2021-02-17 Jim ProcterJAL-3821 patch for 2.11.2 to retrieve RNA ENA records... patch/for2.11.2/JAL-3821_ena_rna_moltype tree | commitdiff
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch... tree | commitdiff
2020-11-13 Ben SoaresJAL-3775 Eclipse re-formatting commit tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 Small changes to allow future fitting with... tree | commitdiff
2020-11-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Fix for slightly incorrect boolean usage to... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Even more Cache.log.debug statements tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 More Cache.log.debug statements tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed all file1.renameTo(file2) calls to... tree | commitdiff
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... tree | commitdiff
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon... tree | commitdiff
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2020-09-21 Jim ProcterMerge branch 'merge_review/JAL-3490_2_11_2_develop... tree | commitdiff
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2020-09-14 Ben SoaresMerge branch 'feature/JAL-3615gzipXfam' into develop tree | commitdiff
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch tree | commitdiff
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615... tree | commitdiff
2020-08-21 Jim ProcterJAL-3615 code tidy, improve unit test tree | commitdiff
2020-08-20 Ben SoaresJAL-2656 better read of (potential) gzip magic bytes tree | commitdiff
2020-08-18 gmungocJAL-2656 Java 8 compatible test for gzipped, refactored... tree | commitdiff
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3691_No_score_models_available... tree | commitdiff
2020-08-17 Jim ProcterJAL-3490 don't init the combo box's history cache for... tree | commitdiff
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... tree | commitdiff
2020-08-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... tree | commitdiff
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard... tree | commitdiff
2020-08-10 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-08-10 Jim ProcterJAL-3628 JAL-3708 call Cache.initLogger() before using... tree | commitdiff
2020-08-09 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... tree | commitdiff
2020-08-05 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL... tree | commitdiff
2020-08-03 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description tree | commitdiff
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 parse DE for description, and other refactoring... tree | commitdiff
2020-08-03 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-07-28 Jim ProcterMerge branch 'feature/JAL-3615gzipXfam' into develop tree | commitdiff
2020-07-28 Jim ProcterJAL-3615 JAL-2656 missing import after cherrypick 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
2020-07-28 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
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