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JAL-1601 Read full file before passing to FileParse
[jalview.git] / src / jalview / ws /
2023-07-28 Mateusz WarownyJAL-4241 Create sequence mapping before adjusting annot... tree | commitdiff
2023-07-14 Mateusz WarownyMerge branch 'feature/JAL-3954-ebi-phmmer' into mmw... mmw/JAL-4199-task-execution-update tree | commitdiff
2023-06-14 Mateusz WarownyJAL-4199 Update slivka client tree | commitdiff
2023-05-08 Mateusz WarownyJAL-3954 Add value parsers for double, int and bool... tree | commitdiff
2023-03-28 Mateusz WarownyMerge branch 'JAL-4152-typed-singleton-provider' into... tree | commitdiff
2023-03-24 Mateusz WarownyJAL-4152 Remove redundant casts from getInstance usages. JAL-4152-typed-singleton-provider tree | commitdiff
2023-02-17 Mateusz WarownyJAL-4131 Replace usages of requireNonNullElse tree | commitdiff
2023-02-06 Mateusz WarownyMerge branch 'JAL-3878_ws-overhaul-3' into mmw/Release_... tree | commitdiff
2023-01-20 Jim ProcterJAL-4102 update 2.12 from 2.11.2.6 patch release -... tree | commitdiff
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch tree | commitdiff
2023-01-06 Jim ProcterMerge branch 'improvement/JAL-4111_suffixed_DEVELOP_cha... tree | commitdiff
2022-12-16 Jim ProcterJAL-4107 fix merge and avoid NPE tree | commitdiff
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2... tree | commitdiff
2022-12-13 Jim ProcterMerge branch 'alpha/origin_2022_JAL-3066_Jalview_212_sl... tree | commitdiff
2022-11-30 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL tree | commitdiff
2022-11-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... tree | commitdiff
2022-11-29 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL tree | commitdiff
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge... tree | commitdiff
2022-10-11 Jim ProcterJAL-4073 fix PEBCAK failure tree | commitdiff
2022-10-06 Jim Procterstable url for PFAM retrieval via interpro api :) JAL... tree | commitdiff
2022-10-06 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-06 Jim ProcterJAL-4073 Pfam retrieval now works via a template includ... tree | commitdiff
2022-03-25 Mateusz WarownyJAL-3878 Fix NullPointerExceptions caused by nulls... tree | commitdiff
2022-03-25 Mateusz WarownyJAL-3878 Add builders to each service parameter class tree | commitdiff
2022-03-11 Mateusz WarownyJAL-3878 Add hasPresets and hasParameters utility metho... 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
2022-03-04 Jim ProcterJAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab... tree | commitdiff
2022-02-17 Jim ProcterJAL-3959 add key retrieval urls that support CORS neede... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2021-12-13 Jim ProcterJAL-3855 JAL-3829 don’t need to make up alphafold model... tree | commitdiff
2021-12-08 Jim ProcterJAL-3929 URLencode pdbid to remove problematic characte... tree | commitdiff
2021-11-18 Mateusz WarownyJAL-3066 Remove redundant throws declaration from Slivk... tree | commitdiff
2021-11-16 Mateusz WarownyMerge branch 'JAL-3866_RNAalifold-slivka-client' into... tree | commitdiff
2021-10-06 Mateusz WarownyJAL-3899 Update usages of uniquify and deuniquify. tree | commitdiff
2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2021-09-29 Jim ProcterJAL-3884 squish alarming but harmless errors when unipr... tree | commitdiff
2021-09-29 Jim ProcterJAL-3881 split on any nonalphanumeric symbol (plus... tree | commitdiff
2021-09-23 Jim ProcterJAL-3692 JAL-3861 remove extra call to .parse() so... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-16 Ben SoaresJAL-3739 (combined) commits from feature/JAL-3739_useFo... tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 JAL-3855 ignore case when detecting alphafold ID tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 3d-beacons doesn’t work as a sequence source... tree | commitdiff
2021-09-02 Mateusz WarownyAdd RNAalifold service instance to slivka web services. JAL-3866_RNAalifold-slivka-client tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 generalised Alphafold retrieval mechanism... tree | commitdiff
2021-08-30 Jim ProcterJAL-3863 mark first accession retrieved from Uniprot... tree | commitdiff
2021-08-30 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import... tree | commitdiff
2021-08-30 arngucciJAL-3829_spike minor changes tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 forgot to add in the dummy 3d-beacons db proxy tree | commitdiff
2021-07-29 Mateusz WarownyMerge branch 'improvement/JAL-3848_slivka_0.8' into... tree | commitdiff
2021-07-27 Mateusz WarownyMerge branch 'bug/JAL-3807_jpred-with-slivka' into... tree | commitdiff
2021-07-27 Jim ProcterJAL-3855 ALPHAFOLD database source based on the PDB... tree | commitdiff
2021-07-22 Jim ProcterJAL-3848 ensure annotation from a service gets a calcId... tree | commitdiff
2021-07-22 Jim ProcterJAL-3848 don’t include sequence limits in sequence... tree | commitdiff
2021-07-21 Mateusz WarownyJAL-3848 print exception for failed align jobs tree | commitdiff
2021-07-09 Mateusz WarownyMerge branch 'jpred-fix' into bug/JAL-3807_jpred-with... bug/JAL-3807_jpred-with-slivka tree | commitdiff
2021-07-09 Mateusz WarownyJAL-3807 Fix SlivkaWSInstance not fetching alignments. tree | commitdiff
2021-07-09 Mateusz WarownyMerge branch 'bug/JAL-3849_aacon-parameters' into impro... tree | commitdiff
2021-07-08 Mateusz WarownyJAL-3848 SlivkaParamSet: reformat code and add service... tree | commitdiff
2021-07-08 Mateusz WarownyJAL-3848 Update slivka client library. tree | commitdiff
2021-07-08 Mateusz WarownyJAL-3849 Remove join() which blocked the ui. tree | commitdiff
2021-05-12 Mateusz WarownyRevert "Merge branch 'bug/JAL-3807_jpred-with-slivka... tree | commitdiff
2021-04-06 Jim ProcterJAL-3832 dummy 3d-beacons database client and code... tree | commitdiff
2021-02-22 Mateusz WarownyMerge branch 'bug/JAL-3807_jpred-with-slivka' into... tree | commitdiff
2021-02-22 Mateusz WarownyJAL-3807 - Add single sequence capabilities to jws2... tree | commitdiff
2021-02-22 Mateusz WarownyJAL-3807 - Move new JPred client to the jws2 package. tree | commitdiff
2021-02-22 Mateusz WarownyJAL-3807 - Re-implement results processing. tree | commitdiff
2021-02-22 MateuszJAL-3807 JPred can now successfully submit and track... tree | commitdiff
2021-02-22 Mateusz WarownyMerge branch 'bug/JAL-3809_ws_params_dialog_fix' into... tree | commitdiff
2021-02-22 Mateusz WarownyMerge branch 'bug/JAL-3810_annotation_ws_stopping_abrup... bug/JAL-3809_ws_params_dialog_fix tree | commitdiff
2021-02-22 Mateusz WarownyJAL-3809 - Fixed param edit dialog for jalviewjs. tree | commitdiff
2021-02-22 MateuszMerge branch 'feature/JAL-3690_callback-based-web-servi... tree | commitdiff
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch... tree | commitdiff
2021-02-05 Jim ProcterJAL-3813 NOIDENTIFIERSSERVICE preference disables jalvi... tree | commitdiff
2021-02-05 Mateusz WarownyJAL-3810 - Replace log.trace() calls with log.debug() tree | commitdiff
2021-01-22 MateuszJAL-3690 AACon ws menu entry fix. tree | commitdiff
2021-01-22 MateuszJAL-3690 Fix typo in enum name in slivka client. tree | commitdiff
2021-01-22 MateuszJAL-3690 Fixed slivka wsmenu categories. tree | commitdiff
2020-12-18 Jim ProcterJAL-3690 recoded AWSThread to use javax.swing.Timer... merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services tree | commitdiff
2020-12-17 Jim ProcterJAL-3690 patch out use of java.streams/spliterator... tree | commitdiff
2020-12-15 Jim ProcterJAL-3690 patch out need for java.time in j2s (see https... tree | commitdiff
2020-12-14 Jim ProcterMerge branch 'Jalview-JS/develop' into merge_js_develop tree | commitdiff
2020-11-13 Mateusz WaronwyJAL-3690 separate startup and poll code in SeqAnnotatio... tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2020-10-21 Mateusz WarownyJAL - 3690 AlignCalc rebuilt - FutureTask-based manager tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 recover complement alignment from complement... 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 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... 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 refactor/complete parsing, more unit test... tree | commitdiff
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