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jalview.git
2023-02-23 James ProcterJAL-4134 - brutal hack to build a tree clustering colum... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 tidied up refactoring and fix compilation... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4133 update validChar width when font is changed... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4133 store/restore alignment view’s charWidth and... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-1551 source formatting commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 simple test for PAE matrix recovery commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 construct a PAE direct from float array commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-629 make sure we show GUI when not driven programma... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4095 slightly better threshold setting and todos... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4095 magic fill behaviour is PAE specific commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 JAL-2381 allow different linear shading scheme... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT... commit | commitdiff | tree | snapshot
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview... commit | commitdiff | tree | snapshot
2023-02-15 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff | tree | snapshot
2023-02-15 James ProcterPassing test for JAL-4127 failing on the JAL-1713 branch commit | commitdiff | tree | snapshot
2023-02-15 James ProcterJAL-4090 move 2.11.3 series release notes to 2.11.3... commit | commitdiff | tree | snapshot
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-3077 broken conflict resolve resulted in failing... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterFix for JAL-4126 - don’t automatically create a thresho... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-4126 comment out closeAll - so we can visually... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-4126 failing test - colour scheme appears to be... commit | commitdiff | tree | snapshot
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
2023-02-03 James ProcterJAL-1551 remove temp file in src commit | commitdiff | tree | snapshot
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-4118 remove unnecessary sleep from QuitHandlerTest commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-4118 fix a small buglet in BackupFiles exhibited... commit | commitdiff | tree | snapshot
2023-01-26 Ben SoaresJAL-1988 Add a sleep to file save test to give time... 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
2023-01-25 James ProcterJAL-4116 relegate the failed to promote warning to... commit | commitdiff | tree | snapshot
2023-01-25 James ProcterMerge branch 'new_feature/JAL-4019_ambiguous_base_colou... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterJAL-4090 Release 2.11.3.0 release notes and version... commit | commitdiff | tree | snapshot
2023-01-24 James ProcterMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... 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
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme commit | commitdiff | tree | snapshot
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme... commit | commitdiff | tree | snapshot
2023-01-06 Ben SoaresJAL-3416 remove a missed panel titlebar icon in TreePanel commit | commitdiff | tree | snapshot
2023-01-06 Ben SoaresJAL-3416 Fix file permissions on bundled macOS JREs 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
2022-11-17 Ben SoaresJAL-4019 Clarification of position on 'X' in help text commit | commitdiff | tree | snapshot
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... commit | commitdiff | tree | snapshot
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf commit | commitdiff | tree | snapshot
2022-11-16 Ben SoaresJAL-4019 finalised a boolean option and tidied some... commit | commitdiff | tree | snapshot
2022-11-14 Ben SoaresJAL-4019 Put original test back commit | commitdiff | tree | snapshot
2022-11-14 Ben SoaresJAL-4019 Make diagnostic message debug level commit | commitdiff | tree | snapshot
2022-11-13 Ben SoaresJAL-4019 small colour fix for X in the documentation commit | commitdiff | tree | snapshot
2022-11-13 Ben SoaresJAL-4019 attribution to Suzanne commit | commitdiff | tree | snapshot
2022-11-13 Ben SoaresJAL-4019 Help pages for Nucleotide Ambiguity colour... commit | commitdiff | tree | snapshot
2022-11-13 Ben SoaresJAL-4019 small but important corrections to array order... commit | commitdiff | tree | snapshot
2022-11-13 Ben SoaresJAL-4019 Added tests for new Nucleotide sequence detection commit | commitdiff | tree | snapshot
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