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jalview.git
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff | tree | snapshot
2023-02-03 Ben SoaresJAL-629 "updated" json-simple commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-629 example files from nf-core commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-629 helper eclipse CLI run commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 need to delay call to AlignFile.parse() if... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 don’t complain for Unary args commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone commit | commitdiff | tree | snapshot
2023-01-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855 commit | commitdiff | tree | snapshot
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... commit | commitdiff | tree | snapshot
2023-01-23 James ProcterJAL-4104 JAL-4102 update help docs with script to add... Release_2_11_2_6 commit | commitdiff | tree | snapshot
2023-01-23 Jim ProcterJAL-4102 whatsNew for 2.11.2.6 commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 model_page_url not required in v2.0 response patch/JAL-4114_updated_3dbeacons_api commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4102 update date and release notes for 2.11.2.6 commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterMerge branch 'patch/Release_2_11_2_6_Branch' into develop commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 missing mock server response commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 only rank model qualities that are computed... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 alphafold now marked as AB-INITIO so adjust... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 additional warnings when PDBe doesn’t return... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 patch REST client for changed JSON schema... commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 formatting commit | commitdiff | tree | snapshot
2023-01-20 Jim ProcterJAL-4114 updated mock tests and responses for v2.0 api commit | commitdiff | tree | snapshot
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' commit | commitdiff | tree | snapshot
2023-01-11 Ben SoaresJAL-629 added Alphafold cif, pdb and PAE json files... commit | commitdiff | tree | snapshot
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... commit | commitdiff | tree | snapshot
2022-12-19 Ben SoaresJAL-629 Add image output and quit commit | commitdiff | tree | snapshot
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... commit | commitdiff | tree | snapshot
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline commit | commitdiff | tree | snapshot
2022-12-09 Ben SoaresJAL-629 null check, fixed tests! commit | commitdiff | tree | snapshot
2022-12-08 Ben SoaresJAL-629 fix opening files commit | commitdiff | tree | snapshot
2022-12-08 Ben SoaresJAL-629 stray code deleted commit | commitdiff | tree | snapshot
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... commit | commitdiff | tree | snapshot
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options commit | commitdiff | tree | snapshot
2022-11-30 Jim ProcterJAL-4102 bump version number commit | commitdiff | tree | snapshot
2022-11-30 Jim ProcterJAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL... commit | commitdiff | tree | snapshot
2022-11-30 Ben SoaresJAL-4101 Updated Rfam* tests commit | commitdiff | tree | snapshot
2022-11-30 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL commit | commitdiff | tree | snapshot
2022-11-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... commit | commitdiff | tree | snapshot
2022-11-29 Ben SoaresJAL-4101 Updated Rfam* tests commit | commitdiff | tree | snapshot
2022-11-29 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL commit | commitdiff | tree | snapshot
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments commit | commitdiff | tree | snapshot
2022-11-03 Jim ProcterJAL-3855 JAL-4095 simple picking of ranges adjacent... commit | commitdiff | tree | snapshot
2022-10-30 Jim ProcterJAL-2349 JAL-3855 bizarre resizing exception when resiz... commit | commitdiff | tree | snapshot
2022-10-30 Jim ProcterJAL-4091 lines to associate rows sharing same sequence... commit | commitdiff | tree | snapshot
2022-10-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... commit | commitdiff | tree | snapshot
2022-10-29 Jim ProcterJAL-4094 shift+click drag up/down to resize all annotat... commit | commitdiff | tree | snapshot
2022-10-29 Jim ProcterJAL-4091 - noodling about including the names for seque... commit | commitdiff | tree | snapshot
2022-10-29 Jim ProcterJAL-4090 bump version and set up release notes for... commit | commitdiff | tree | snapshot
2022-10-29 Jim ProcterMerge branch 'features/JAL-4061_and_JAL-4062_findselect... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterMerge branch 'bug/JAL-4083_exceptions_for_multiple_resi... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterJAL-2349 allow contact matrix to provide labels for... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterJAL-4086 commented out attempt to create measurement... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterJAL-4089 use column selection to superpose if 4 or... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterJAL-2961 centerViewOn command for structure viewers... commit | commitdiff | tree | snapshot
2022-10-28 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... commit | commitdiff | tree | snapshot
2022-10-27 Ben SoaresJAL-4083 don't need globalUseScriptWait after all,... bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol commit | commitdiff | tree | snapshot
2022-10-27 Ben SoaresJAL-4083 only set globalUseScriptWait if needed commit | commitdiff | tree | snapshot
2022-10-27 Ben SoaresJAL-4083 Use jmolViewer.scriptWait instead of jmolViewe... commit | commitdiff | tree | snapshot
2022-10-26 Jim ProcterJAL-4086 quick and dirty mouseovers on ruler highlighti... commit | commitdiff | tree | snapshot
2022-10-26 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... commit | commitdiff | tree | snapshot
2022-10-26 Ben SoaresJAL-3416 (and others) increasing number of STDERR lines... commit | commitdiff | tree | snapshot
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl... commit | commitdiff | tree | snapshot
2022-10-22 Jim ProcterJAL-2349 JAL-3855 highlight residues associated with... commit | commitdiff | tree | snapshot
2022-10-21 Jim ProcterJAL-2349 JAL-3855 fix failing tests commit | commitdiff | tree | snapshot
2022-10-21 Jim ProcterJAL-2349 JAL-3855 experiment masking hidden columns... commit | commitdiff | tree | snapshot
2022-10-21 Jim ProcterJAL-4033 - heuristic threshold for pAE matrix - mark... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 formatting/pick correct exception commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 JAL-3855 off by one and daft return commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 avoid div-by-zero when annotation height is... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 JAL-3855 adapt renderer for AlignmentI.getCont... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 JAL-3855 ContactListI.getPosition() to recover... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 JAL-3855 experimenting with filtering columns... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-3855 JAL-2349 AlignmentI.getContactList takes care... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-4033 fix drag selections and distinguish row/column... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 (still buggy) interactive selection - time... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 tooltip reports value from contact range commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 adjusted range calculation to be inclusive... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 debugged click/drag and added yellow rubber... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-2349 JAL-3855 - interactive point-wise row/column... commit | commitdiff | tree | snapshot
2022-10-20 Jim ProcterJAL-3855 RGB colours from the alphafold paE scale. commit | commitdiff | tree | snapshot
2022-10-19 Jim ProcterJAL-2349 JAL-4033 refactored contact matrix geom calc... commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-2349 JAL-3855 column selection highlighting commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-3855 bump AF version to 3 - keep contact renderer... commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-2349 JAL-3855 tests that probably should be part... commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-3855 report download errors as errors! commit | commitdiff | tree | snapshot
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... commit | commitdiff | tree | snapshot
2022-10-15 Jim ProcterJAL-2349 reusable contact map holder for SequenceI... commit | commitdiff | tree | snapshot
2022-10-15 Jim ProcterJAL-3855 2349 TODO commit | commitdiff | tree | snapshot
2022-10-15 Jim ProcterJAL-3855 import pAE when StructureSelectionManager... commit | commitdiff | tree | snapshot
2022-10-15 Jim ProcterJAL-3855 pAE v2 import commit | commitdiff | tree | snapshot
2022-10-14 Jim ProcterJAL-3855 refactor the pAE retrieval code so it can... commit | commitdiff | tree | snapshot
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