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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / datamodel /
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-11-02 James ProcterJAL-1551 formatting tree | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... tree | commitdiff
2023-10-17 James ProcterJAL-4089 selected columns are reported in absolute... tree | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... tree | commitdiff
2023-09-28 James ProcterJAL-3858 don’t divide if we only had one value to count tree | commitdiff
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... tree | commitdiff
2023-09-01 James ProcterJAL-4124 matrix is saved in dataset, with forward refer... tree | commitdiff
2023-09-01 James ProcterJAL-4124 add strategic newlines in matrix stringified... 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
2023-08-21 James ProcterJAL-4062 revert to ArrayList and integrate check for... tree | commitdiff
2023-08-21 James ProcterJAL-4062 fix up imports tree | commitdiff
2023-08-21 James ProcterJAL-4062 appendResult(seq,start,end) called by structur... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... tree | commitdiff
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and... tree | commitdiff
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into... tree | commitdiff
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio... tree | commitdiff
2023-05-25 James ProcterJAL-4134 popup menu and annotation row property to... tree | commitdiff
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc... tree | commitdiff
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact... tree | commitdiff
2023-05-22 James ProcterJAL-1551 spotless 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
2023-05-19 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 colour by annotation needs distinct annotation... 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
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic... 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
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... tree | commitdiff
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... tree | commitdiff
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... 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-2349 fix off by one when resolving columns for... tree | commitdiff
2023-03-15 James ProcterJAL-2349 don’t clobber existing label/description... tree | commitdiff
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... 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 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-27 James ProcterJAL-2349 TODO consider caching contactRanges from getCo... tree | commitdiff
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on... tree | commitdiff
2023-02-23 James ProcterJAL-4134 tidied up refactoring and fix compilation... tree | commitdiff
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... tree | commitdiff
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... 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 James ProcterJAL-1551 remove temp file in src tree | commitdiff
2023-02-02 James ProcterJAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null versi... patch/JAL-4119_sifts_ftp_split tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options tree | commitdiff
2022-10-29 Jim ProcterMerge branch 'features/JAL-4061_and_JAL-4062_findselect... tree | commitdiff
2022-10-28 Jim ProcterJAL-2349 allow contact matrix to provide labels for... tree | commitdiff
2022-10-21 Jim ProcterJAL-4033 - heuristic threshold for pAE matrix - mark... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 formatting/pick correct exception tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 off by one and daft return tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 ContactListI.getPosition() to recover... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 experimenting with filtering columns... tree | commitdiff
2022-10-20 Jim ProcterJAL-3855 JAL-2349 AlignmentI.getContactList takes care... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 adjusted range calculation to be inclusive... tree | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 column selection highlighting tree | commitdiff
2022-10-17 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... tree | commitdiff
2022-10-15 Jim ProcterJAL-2349 reusable contact map holder for SequenceI... tree | commitdiff
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into... tree | commitdiff
2022-10-06 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-06 Jim ProcterJAL-3895 alphafold colours via pluggable annotation... tree | commitdiff
2022-09-15 Jim ProcterJAL-4062 avc operation and model method for copying... tree | commitdiff
2022-06-10 Jim ProcterJAL-4027 getter for contact matrices on the Alignment. tree | commitdiff
2022-06-10 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2022-06-06 Jim ProcterJAL-4023 store distances as doubles tree | commitdiff
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu... tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details 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
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons... tree | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 tree | commitdiff
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... tree | commitdiff
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio... tree | commitdiff
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur... tree | commitdiff
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the... tree | commitdiff
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi... tree | commitdiff
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... tree | commitdiff
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