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JAL-629 example files from nf-core
[jalview.git] / src /
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... tree | commitdiff
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... tree | commitdiff
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... tree | commitdiff
2023-01-24 James ProcterJAL-629 need to delay call to AlignFile.parse() if... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t complain for Unary args tree | commitdiff
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone tree | commitdiff
2023-01-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855 tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... tree | commitdiff
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api... tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 model_page_url not required in v2.0 response patch/JAL-4114_updated_3dbeacons_api tree | commitdiff
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api... tree | commitdiff
2023-01-20 Jim ProcterMerge branch 'patch/Release_2_11_2_6_Branch' into develop tree | commitdiff
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 only rank model qualities that are computed... tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 alphafold now marked as AB-INITIO so adjust... tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 additional warnings when PDBe doesn’t return... tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 patch REST client for changed JSON schema... tree | commitdiff
2023-01-20 Jim ProcterJAL-4114 formatting tree | commitdiff
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2022-12-19 Ben SoaresJAL-629 Add image output and quit tree | commitdiff
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... tree | commitdiff
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline tree | commitdiff
2022-12-09 Ben SoaresJAL-629 null check, fixed tests! tree | commitdiff
2022-12-08 Ben SoaresJAL-629 fix opening files tree | commitdiff
2022-12-08 Ben SoaresJAL-629 stray code deleted tree | commitdiff
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options tree | commitdiff
2022-11-30 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL tree | commitdiff
2022-11-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... tree | commitdiff
2022-11-29 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL tree | commitdiff
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments tree | commitdiff
2022-11-03 Jim ProcterJAL-3855 JAL-4095 simple picking of ranges adjacent... tree | commitdiff
2022-10-30 Jim ProcterJAL-2349 JAL-3855 bizarre resizing exception when resiz... tree | commitdiff
2022-10-30 Jim ProcterJAL-4091 lines to associate rows sharing same sequence... tree | commitdiff
2022-10-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs... tree | commitdiff
2022-10-29 Jim ProcterJAL-4094 shift+click drag up/down to resize all annotat... tree | commitdiff
2022-10-29 Jim ProcterJAL-4091 - noodling about including the names for seque... 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
2022-10-28 Jim ProcterJAL-4086 commented out attempt to create measurement... tree | commitdiff
2022-10-28 Jim ProcterJAL-4089 use column selection to superpose if 4 or... tree | commitdiff
2022-10-28 Jim ProcterJAL-2961 centerViewOn command for structure viewers... tree | commitdiff
2022-10-28 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2022-10-27 Ben SoaresJAL-4083 don't need globalUseScriptWait after all,... bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol tree | commitdiff
2022-10-27 Ben SoaresJAL-4083 only set globalUseScriptWait if needed tree | commitdiff
2022-10-27 Ben SoaresJAL-4083 Use jmolViewer.scriptWait instead of jmolViewe... tree | commitdiff
2022-10-26 Jim ProcterJAL-4086 quick and dirty mouseovers on ruler highlighti... tree | commitdiff
2022-10-26 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl... tree | commitdiff
2022-10-22 Jim ProcterJAL-2349 JAL-3855 highlight residues associated with... tree | commitdiff
2022-10-21 Jim ProcterJAL-2349 JAL-3855 fix failing tests tree | commitdiff
2022-10-21 Jim ProcterJAL-2349 JAL-3855 experiment masking hidden columns... 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 avoid div-by-zero when annotation height is... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 adapt renderer for AlignmentI.getCont... 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-4033 fix drag selections and distinguish row/column... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 (still buggy) interactive selection - time... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 tooltip reports value from contact range tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 adjusted range calculation to be inclusive... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 debugged click/drag and added yellow rubber... tree | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 - interactive point-wise row/column... tree | commitdiff
2022-10-20 Jim ProcterJAL-3855 RGB colours from the alphafold paE scale. tree | commitdiff
2022-10-19 Jim ProcterJAL-2349 JAL-4033 refactored contact matrix geom calc... tree | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 column selection highlighting tree | commitdiff
2022-10-17 Jim ProcterJAL-3855 bump AF version to 3 - keep contact renderer... tree | commitdiff
2022-10-17 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-17 Jim ProcterJAL-3855 report download errors as errors! 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
2022-10-15 Jim ProcterJAL-3855 2349 TODO tree | commitdiff
2022-10-15 Jim ProcterJAL-3855 import pAE when StructureSelectionManager... tree | commitdiff
2022-10-15 Jim ProcterJAL-3855 pAE v2 import tree | commitdiff
2022-10-14 Jim ProcterJAL-3855 refactor the pAE retrieval code so it can... tree | commitdiff
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into... tree | commitdiff
2022-10-14 Jim ProcterMerge branch 'develop' into features/JAL-3895_alphafold... features/JAL-3895_alphafoldcolours tree | commitdiff
2022-10-11 Jim ProcterJAL-4073 fix PEBCAK failure tree | commitdiff
2022-10-07 Jim ProcterFix for JAL-4075 - don’t write a label in secondary... tree | commitdiff
2022-10-06 Jim Procterstable url for PFAM retrieval via interpro api :) JAL... tree | commitdiff
2022-10-06 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-06 Jim ProcterJAL-3895 alphafold colours via pluggable annotation... tree | commitdiff
2022-10-06 Jim ProcterJAL-1551 formatting tree | commitdiff
2022-10-06 Jim ProcterJAL-4073 Pfam retrieval now works via a template includ... tree | commitdiff
2022-10-06 Jim ProcterPatch for JAL-4074 - any content ending in ‘gzip’ recog... tree | commitdiff
2022-09-16 Jim ProcterJAL-4062 copy highlighted region docs, new Alignment... tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 use alignment panel’s feature renderer to... tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 support incremental search of features tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 tests, bugfixes and TODOs for matching feature... tree | commitdiff
2022-09-15 Jim ProcterJAL-4062 avc operation and model method for copying... tree | commitdiff
2022-09-15 Jim ProcterMerge branch 'develop' into features/JAL-4061_and_JAL... tree | commitdiff
2022-09-14 Jim ProcterMerge branch 'bug/JAL-3612_overviewFeatureOrdering... tree | commitdiff
2022-09-14 Jim ProcterJAL-4061 JAL-4062 button in Find dialog to copy highlig... tree | commitdiff
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