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JAL-4059 Converting Pattern/Matcher methods that are possibly incompatible with JS...
[jalview.git]
/
src
/
jalview
/
datamodel
/
2023-10-17
James Procter
JAL-4089 selected columns are reported in absolute...
tree
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commitdiff
2023-10-03
James Procter
Merge branch 'patch/JAL-4062_sort_and_merge_contiguousr...
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 don’t divide if we only had one value to count
tree
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commitdiff
2023-09-26
James Procter
JAL-3858 JAL-4090 avoid NPE when given out of bound...
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 revert to ArrayList and integrate check for...
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 fix up imports
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 appendResult(seq,start,end) called by structur...
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
2023-07-20
James Procter
JAL-3855 auto select clusters and fix up colouring...
tree
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commitdiff
2023-07-18
James Procter
JAL-3858 fix off-by-one in matrix visualisation and...
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
2023-07-07
James Procter
JAL-4221 update description when transferring annotatio...
tree
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commitdiff
2023-05-25
James Procter
JAL-4134 popup menu and annotation row property to...
tree
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commitdiff
2023-05-25
James Procter
JAL-2381 don’t need to set description, dbrefs etc...
tree
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commitdiff
2023-05-25
James Procter
JAL-2381 copy and paste sequence also copies contact...
tree
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
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
2023-05-19
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 colour by annotation needs distinct annotation...
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
2023-05-18
James Procter
JAL-4134 properly specify BinaryNode as a typed generic...
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
2023-05-13
James Procter
JAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp...
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
2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
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
2023-03-25
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-2349 fix off by one when resolving columns for...
tree
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commitdiff
2023-03-15
James Procter
JAL-2349 don’t clobber existing label/description...
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
2023-03-08
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 Some refactoring to allow more flexible use...
tree
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commitdiff
2023-02-27
James Procter
JAL-2349 TODO consider caching contactRanges from getCo...
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
2023-02-23
James Procter
JAL-4134 tidied up refactoring and fix compilation...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - refactor tree calculation code to work with...
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
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
James Procter
JAL-1551 remove temp file in src
tree
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commitdiff
2023-02-02
James Procter
JAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null versi...
patch/JAL-4119_sifts_ftp_split
tree
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-10-29
Jim Procter
Merge branch 'features/JAL-4061_and_JAL-4062_findselect...
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
2022-10-21
Jim Procter
JAL-4033 - heuristic threshold for pAE matrix - mark...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 formatting/pick correct exception
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 off by one and daft return
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
2022-10-20
Jim Procter
JAL-2349 JAL-3855 experimenting with filtering columns...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-3855 JAL-2349 AlignmentI.getContactList takes care...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 adjusted range calculation to be inclusive...
tree
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 column selection highlighting
tree
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commitdiff
2022-10-17
Jim Procter
JAL-1551 formatting
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-2349 reusable contact map holder for SequenceI...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-06
Jim Procter
JAL-3895 alphafold colours via pluggable annotation...
tree
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commitdiff
2022-09-15
Jim Procter
JAL-4062 avc operation and model method for copying...
tree
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commitdiff
2022-06-10
Jim Procter
JAL-4027 getter for contact matrices on the Alignment.
tree
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commitdiff
2022-06-10
Jim Procter
JAL-1551 formatting
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
2022-06-06
Jim Procter
JAL-4023 store distances as doubles
tree
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commitdiff
2022-04-16
Jim Procter
JAL-3365 expand range of allowed DSSP secondary structu...
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 JAL-3979 TODOs
bug/JAL-3980_JAL-3981_tooltips_sequence_details
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
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2022-02-14
Jim Procter
JAL-3956 - PDBEntry objects constructed from 3D-Beacons...
tree
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commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
tree
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commitdiff
2022-02-04
Jim Procter
JAL-3806 require mapping extent covers both sequence...
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
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3806 (2.11.2 version) more lax allowance (3 positio...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3829 isCanonical should by default be false - ensur...
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3919 use model format field to ensure we get the...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 restrict mapped virtual feature location to...
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
2021-09-21
Jim Procter
JAL-3829 ignore the fake ID generated when a PDB format...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 ensure nulls are not wildcards when retrieving...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 store 3db metadata on PDBEntry so it can be...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 allow PDBEntry with file and ID with mismatchi...
tree
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commitdiff
2021-09-17
Jim Procter
JAL-2226 new method to search for annotation matching...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom/To revised with tests; unused...
tree
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commitdiff
2021-09-03
Jim Procter
JAL-3863 promote non-canonical version of dbref to...
tree
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commitdiff
2021-09-03
Jim Procter
JAL-3863 passing test to verify a uniprot accession...
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
Jim Procter
JAL-3829 3d-beacons structure chooser logic (not yet...
tree
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commitdiff
2021-08-18
Jim Procter
JAL-2349 allow contact map to be associated with a...
tree
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commitdiff
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