JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
[jalview.git] / src / jalview / io /
2022-10-06 Jim ProcterJAL-1551 formatting
2022-10-06 Jim ProcterPatch for JAL-4074 - any content ending in ‘gzip’ recog...
2022-06-06 Jim ProcterJAL-4023 store distances as doubles
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu...
2022-04-05 Jim ProcterJAL-3981 patch tests and remove errant imports
2022-04-05 Jim ProcterJAL-3990 gradle spotlessApply
2022-03-25 Jim ProcterJAL-3980 defensive copy - inefficient but fixes bug
2022-03-25 Jim ProcterJAL-3981 Additional line breaks - sort of helps
2022-03-24 Jim ProcterJAL-3981 strategic newlines to help speed up Java's...
2022-03-08 Jim ProcterJAL-3746 apply copyright to source
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti...
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual...
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache...
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_...
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no...
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop...
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to...
2022-01-17 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded...
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting...
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded...
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting...
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-09-30 Ben SoaresJAL-1260 Added .gbk to GenBank extensions. Added GenBa...
2021-09-23 Jim ProcterJAL-3821 less ambiguous base class name for EMBL and...
2021-09-23 Jim ProcterJAL-3821 ported to refactored FlatFile parser
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-21 Jim ProcterMerge branch 'doc/JAL-3746_Release_2_11_2' into develop
2021-09-21 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'...
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format...
2021-09-17 Ben SoaresJAL-1260 rudimentary parsing of LOCUS line to at least...
2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators
2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for...
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser
2021-09-17 Jim ProcterJAL-1260 FileFormat entry for EMBL/GENBANK: TODO: creat...
2021-09-16 gmungocJAL-3779 apply properties to all groups with given...
2021-09-16 Jim ProcterMerge branch 'develop' into doc/JAL-3746_Release_2_11_2
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable...
2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray
2021-09-15 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile...
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2
2021-09-02 gmungocJAL-3509 JAL-1842 minor tidying of code
2021-09-02 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin...
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
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch...
2020-11-13 Ben SoaresJAL-3775 Eclipse re-formatting commit
2020-11-13 Ben SoaresJAL-3633 Small changes to allow future fitting with...
2020-11-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for...
2020-11-10 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error...
2020-11-10 Ben SoaresJAL-3628 Fix for slightly incorrect boolean usage to...
2020-11-10 Ben SoaresJAL-3628 Even more Cache.log.debug statements
2020-11-10 Ben SoaresJAL-3628 More Cache.log.debug statements
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF...
2020-11-06 Ben SoaresJAL-3628 Changed all file1.renameTo(file2) calls to...
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon...
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to...
2020-09-21 Jim ProcterMerge branch 'merge_review/JAL-3490_2_11_2_develop...
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile...
2020-09-14 Ben SoaresMerge branch 'feature/JAL-3615gzipXfam' into develop
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615...
2020-08-21 Jim ProcterJAL-3615 code tidy, improve unit test
2020-08-20 Ben SoaresJAL-2656 better read of (potential) gzip magic bytes
2020-08-18 gmungocJAL-2656 Java 8 compatible test for gzipped, refactored...
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3691_No_score_models_available...
2020-08-17 Jim ProcterJAL-3490 don't init the combo box's history cache for...
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL...
2020-08-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for...
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard...
2020-08-10 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' into...
2020-08-10 Jim ProcterJAL-3628 JAL-3708 call Cache.initLogger() before using...
2020-08-09 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to...
2020-08-05 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to...
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into...
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped...
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped...
2020-08-05 Jim ProcterMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL...
2020-08-03 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test...
2020-08-03 gmungocJAL-3692 parse DE for description, and other refactoring...
2020-08-03 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote...
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into...
2020-07-28 Jim ProcterMerge branch 'feature/JAL-3615gzipXfam' into develop
2020-07-28 Jim ProcterJAL-3615 JAL-2656 missing import after cherrypick
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe...
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their...
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe...
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their...
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for...
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam
2020-07-27 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description
2020-07-27 gmungocJAL-3692 refactor/complete parsing, more unit test...
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to...
next