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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / ws /
2023-11-20 James ProcterJAL-4343 patch for JAL-4347 uniprot non-pos feature... tree | commitdiff
2023-11-15 James ProcterMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatur... tree | commitdiff
2023-11-15 James ProcterJAL-4090 JAL-4334 position status when start, end or... bug/JAL-4334_unknownstartenduniprotfeatures tree | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... tree | commitdiff
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence... tree | commitdiff
2023-08-31 James ProcterJAL-4124 MappableContactMatrix equivalence and hashCode... tree | commitdiff
2023-08-29 James ProcterJAL-4124 decouple mappable contact matrix mapping logic... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from... tree | commitdiff
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download... tree | commitdiff
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into... tree | commitdiff
2023-06-01 James ProcterJAL-4134 properly resolve positions in associated align... features/JAL-4134_use_annotation_row_for_colours_and_groups tree | commitdiff
2023-05-29 James ProcterJAL-4134 JAL-2349 test & fixed implementation(ish)... tree | commitdiff
2023-05-22 James ProcterJAL-4134 only build tree when showing it in the tree... tree | commitdiff
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-18 James ProcterJAL-4134 support recovery of mapped positions for raw... tree | commitdiff
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... tree | commitdiff
2023-05-18 James ProcterJAL-4134 formatting tree | commitdiff
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... tree | commitdiff
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje... tree | commitdiff
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... tree | commitdiff
2023-05-01 James ProcterJAL-3858 report errors when trying to parse JSON to... tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... tree | commitdiff
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#' tree | commitdiff
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... tree | commitdiff
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact... tree | commitdiff
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! tree | commitdiff
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... tree | commitdiff
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... tree | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... tree | commitdiff
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 slight tidy up tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa... tree | commitdiff
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on... tree | commitdiff
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... tree | commitdiff
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error tree | commitdiff
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... tree | commitdiff
2023-02-22 James ProcterJAL-3858 construct a PAE direct from float array tree | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT... tree | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... tree | commitdiff
2023-02-03 James ProcterJAL-1551 remove temp file in src tree | commitdiff
2023-02-02 James ProcterJAL-4119 use split_xml directories rather than the... tree | commitdiff
2023-01-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855 tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... tree | commitdiff
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options 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
2022-10-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... tree | commitdiff
2022-10-28 Jim ProcterJAL-2349 allow contact matrix to provide labels for... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 ContactListI.getPosition() to recover... tree | commitdiff
2022-10-17 Jim ProcterJAL-3855 bump AF version to 3 - keep contact renderer... tree | commitdiff
2022-10-17 Jim ProcterJAL-3855 report download errors as errors! tree | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... tree | commitdiff
2022-10-15 Jim ProcterJAL-3855 import pAE when StructureSelectionManager... tree | commitdiff
2022-10-15 Jim ProcterJAL-3855 pAE v2 import tree | commitdiff
2022-10-14 Jim ProcterJAL-3855 refactor the pAE retrieval code so it can... tree | commitdiff
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into... 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
2022-06-24 Jim ProcterJAL-2349 JAL-3855 formatting tree | commitdiff
2022-06-24 Jim ProcterJAL-3855 update EBI Alphafold barcoded URL generation... tree | commitdiff
2022-06-24 Jim ProcterJAL-2349 JAL-3855 resolve sequence position for contact... tree | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... 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
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... 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
2021-10-01 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
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