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JAL-4059 Converting Pattern/Matcher methods that are possibly incompatible with JS...
[jalview.git]
/
src
/
jalview
/
ws
/
2023-09-21
James Procter
JAL-3855 disable the AlphaFold DB entry in Sequence...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2023-07-18
James Procter
JAL-3855 PAE matrices are transposed on import from...
tree
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commitdiff
2023-07-17
James Procter
JAL-4119 TRACE level console message reporting download...
tree
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commitdiff
2023-07-07
James Procter
Merge branch 'patch/JAL-4119_sifts_ftp_split' into...
tree
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commitdiff
2023-06-01
James Procter
JAL-4134 properly resolve positions in associated align...
features/JAL-4134_use_annotation_row_for_colours_and_groups
tree
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commitdiff
2023-05-29
James Procter
JAL-4134 JAL-2349 test & fixed implementation(ish)...
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 only build tree when showing it in the tree...
tree
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commitdiff
2023-05-19
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 support recovery of mapped positions for raw...
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 column grouping model and methods moved to...
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 formatting
tree
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commitdiff
2023-05-14
James Procter
JAL-2349 fix up tests for Java 11 compatibility and...
tree
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commitdiff
2023-05-14
James Procter
JAL-2349 store/restore mappable contact matrix in proje...
tree
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commitdiff
2023-05-12
James Procter
JAL-2349 allow PAE or other contact matrices to hold...
tree
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commitdiff
2023-05-01
James Procter
JAL-3858 report errors when trying to parse JSON to...
tree
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commitdiff
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
tree
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commitdiff
2023-04-14
Ben Soares
JAL-629 Adding PAE and TFType at structure loading...
tree
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commitdiff
2023-04-12
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 allow comments in argfiles '#'
tree
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commitdiff
2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
tree
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commitdiff
2023-03-24
James Procter
JAL-4158 first attempt at stashing colours for contact...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 override default hasTree so PAE tree is saved!
tree
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commitdiff
2023-03-17
James Procter
JAL-4134 store/restore Newick tree for PAE annotation row
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...
tree
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commitdiff
2023-03-15
James Procter
JAL-4134 JAL-3855 store/restore groups, tree and thresh...
tree
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commitdiff
2023-03-09
Ben Soares
JAL-629 --argfile=glob implemented. Remove reference...
tree
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commitdiff
2023-03-08
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-03-06
Ben Soares
JAL-629 Fix null AlignPanel. More descriptive label...
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 slight tidy up
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 Removal of unnecessary methods. Set pLTTD tempf...
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
tree
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commitdiff
2023-02-27
Ben Soares
JAL-629 add AF examples for FER1_SPIOL. Link and displa...
tree
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commitdiff
2023-02-27
James Procter
JAL-4134 allow tree groups to be stored/recovered on...
tree
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commitdiff
2023-02-27
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-27
Ben Soares
JAL-629 removed debug prints. added .cif. added some...
tree
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commitdiff
2023-02-24
James Procter
JAL-629 JAL-4124 JAL-3855 test to check we can import...
tree
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commitdiff
2023-02-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
features/JAL-3858_PAEsInProjects
tree
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commitdiff
2023-02-23
Ben Soares
JAL-629 fix a PAEMatrix casting error
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 persist PAE matrix (only so far) as serialised...
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 construct a PAE direct from float array
tree
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-22
James Procter
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT...
tree
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-02-03
James Procter
JAL-1551 remove temp file in src
tree
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commitdiff
2023-02-02
James Procter
JAL-4119 use split_xml directories rather than the...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release...
features/r2_11_2_alphafold/JAL-2349_JAL-3855
tree
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commitdiff
2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-2353 primary ref candidates that should be promoted...
patch/Release_2_11_2_6_Branch
tree
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 Allow attachment of pAE file to a particular...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-11-30
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
tree
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commitdiff
2022-11-30
Jim Procter
JAL-2353 patch for Ensembl refs from uniprot - needs...
tree
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commitdiff
2022-11-29
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
tree
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commitdiff
2022-10-30
Jim Procter
JAL-2353 patch for Ensembl refs from uniprot - needs...
tree
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commitdiff
2022-10-28
Jim Procter
JAL-2349 allow contact matrix to provide labels for...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 ContactListI.getPosition() to recover...
tree
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commitdiff
2022-10-17
Jim Procter
JAL-3855 bump AF version to 3 - keep contact renderer...
tree
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commitdiff
2022-10-17
Jim Procter
JAL-3855 report download errors as errors!
tree
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
tree
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commitdiff
2022-10-15
Jim Procter
JAL-3855 import pAE when StructureSelectionManager...
tree
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commitdiff
2022-10-15
Jim Procter
JAL-3855 pAE v2 import
tree
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commitdiff
2022-10-14
Jim Procter
JAL-3855 refactor the pAE retrieval code so it can...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-10-11
Jim Procter
JAL-4073 fix PEBCAK failure
tree
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commitdiff
2022-10-06
Jim Procter
stable url for PFAM retrieval via interpro api :) JAL...
tree
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-06
Jim Procter
JAL-4073 Pfam retrieval now works via a template includ...
tree
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commitdiff
2022-06-24
Jim Procter
JAL-2349 JAL-3855 formatting
tree
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commitdiff
2022-06-24
Jim Procter
JAL-3855 update EBI Alphafold barcoded URL generation...
tree
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commitdiff
2022-06-24
Jim Procter
JAL-2349 JAL-3855 resolve sequence position for contact...
tree
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab...
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3959 add key retrieval urls that support CORS neede...
tree
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-01-28
Jim Procter
Merge branch 'merge/develop_JAL-3725' into develop
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 exclude stop codon from CDS-to-protein mapping
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3855 JAL-3829 don’t need to make up alphafold model...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3929 URLencode pdbid to remove problematic characte...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 exclude stop codon from CDS-to-protein mapping
tree
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commitdiff
2021-09-29
Jim Procter
JAL-3884 squish alarming but harmless errors when unipr...
tree
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commitdiff
2021-09-29
Jim Procter
JAL-3881 split on any nonalphanumeric symbol (plus...
tree
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commitdiff
2021-09-23
Jim Procter
JAL-3692 JAL-3861 remove extra call to .parse() so...
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2021-09-16
Ben Soares
JAL-3739 (combined) commits from feature/JAL-3739_useFo...
tree
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commitdiff
2021-09-15
Ben Soares
Merge branch 'develop' into merge/develop_ben2
tree
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commitdiff
2021-09-14
Jim Procter
JAL-3829 JAL-3855 ignore case when detecting alphafold ID
tree
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commitdiff
2021-09-14
Jim Procter
JAL-3829 3d-beacons doesn’t work as a sequence source...
tree
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commitdiff
2021-08-30
Jim Procter
JAL-3829 generalised Alphafold retrieval mechanism...
tree
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commitdiff
2021-08-30
Jim Procter
JAL-3863 mark first accession retrieved from Uniprot...
tree
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commitdiff
2021-08-30
Jim Procter
Merge branch 'feature/JAL-3855_ebi_alphafold_import...
tree
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commitdiff
2021-08-30
arngucci
JAL-3829_spike minor changes
tree
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commitdiff
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