JAL-629 javadoc on new setMapping variant for structureselectionmanager
[jalview.git] / src / jalview / datamodel /
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring...
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and...
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into...
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio...
2023-05-25 James ProcterJAL-4134 popup menu and annotation row property to...
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc...
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact...
2023-05-22 James ProcterJAL-1551 spotless
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot...
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-05-18 James ProcterJAL-4134 support recovery of mapped positions for raw...
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation...
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to...
2023-05-18 James ProcterJAL-4134 formatting
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic...
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and...
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje...
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp...
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold...
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac...
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement...
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact...
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for...
2023-03-15 James ProcterJAL-2349 don’t clobber existing label/description...
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh...
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label...
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use...
2023-02-27 James ProcterJAL-2349 TODO consider caching contactRanges from getCo...
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on...
2023-02-23 James ProcterJAL-4134 tidied up refactoring and fix compilation...
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with...
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised...
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT...
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-02-03 James ProcterJAL-1551 remove temp file in src
2023-02-02 James ProcterJAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null versi... patch/JAL-4119_sifts_ftp_split
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification...
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options
2022-10-29 Jim ProcterMerge branch 'features/JAL-4061_and_JAL-4062_findselect...
2022-10-28 Jim ProcterJAL-2349 allow contact matrix to provide labels for...
2022-10-21 Jim ProcterJAL-4033 - heuristic threshold for pAE matrix - mark...
2022-10-20 Jim ProcterJAL-2349 formatting/pick correct exception
2022-10-20 Jim ProcterJAL-2349 JAL-3855 off by one and daft return
2022-10-20 Jim ProcterJAL-2349 JAL-3855 ContactListI.getPosition() to recover...
2022-10-20 Jim ProcterJAL-2349 JAL-3855 experimenting with filtering columns...
2022-10-20 Jim ProcterJAL-3855 JAL-2349 AlignmentI.getContactList takes care...
2022-10-20 Jim ProcterJAL-2349 adjusted range calculation to be inclusive...
2022-10-17 Jim ProcterJAL-2349 JAL-3855 column selection highlighting
2022-10-17 Jim ProcterJAL-1551 formatting
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
2022-10-15 Jim ProcterJAL-2349 reusable contact map holder for SequenceI...
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into...
2022-10-06 Jim ProcterJAL-1551 formatting
2022-10-06 Jim ProcterJAL-3895 alphafold colours via pluggable annotation...
2022-09-15 Jim ProcterJAL-4062 avc operation and model method for copying...
2022-06-10 Jim ProcterJAL-4027 getter for contact matrices on the Alignment.
2022-06-10 Jim ProcterJAL-1551 formatting
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
2022-06-06 Jim ProcterJAL-4023 store distances as doubles
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu...
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details
2022-03-08 Jim ProcterJAL-3746 apply copyright to source
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold...
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons...
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into...
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio...
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur...
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the...
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format...
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving...
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be...
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi...
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching...
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused...
2021-09-03 Jim ProcterJAL-3863 promote non-canonical version of dbref to...
2021-09-03 Jim ProcterJAL-3863 passing test to verify a uniprot accession...
2021-08-30 Jim ProcterJAL-3829 generalised Alphafold retrieval mechanism...
2021-08-30 Jim ProcterJAL-3863 mark first accession retrieved from Uniprot...
2021-08-30 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import...
2021-08-30 Jim ProcterJAL-3829 3d-beacons structure chooser logic (not yet...
2021-08-18 Jim ProcterJAL-2349 allow contact map to be associated with a...
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature...
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_2
2021-06-09 Jim Procterfixes JAL-3840
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_1_4
2021-06-09 Jim Procterfixes JAL-3840
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows
next