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Merge branch 'features/JAL-3858_PAEsInProjects' into features/JAL-4134_treeviewerforc...
[jalview.git] / src / jalview /
2023-02-23 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... tree | commitdiff
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO tree | commitdiff
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... tree | commitdiff
2023-02-23 James ProcterJAL-4133 update validChar width when font is changed... tree | commitdiff
2023-02-22 James ProcterJAL-4133 store/restore alignment view’s charWidth and... tree | commitdiff
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... tree | commitdiff
2023-02-22 James ProcterJAL-3858 construct a PAE direct from float array tree | commitdiff
2023-02-22 James ProcterJAL-629 make sure we show GUI when not driven programma... tree | commitdiff
2023-02-22 James ProcterJAL-4095 slightly better threshold setting and todos... tree | commitdiff
2023-02-22 James ProcterJAL-4095 magic fill behaviour is PAE specific tree | commitdiff
2023-02-22 James ProcterJAL-3858 JAL-2381 allow different linear shading scheme... 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
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview... tree | commitdiff
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... tree | commitdiff
2023-02-10 James ProcterFix for JAL-4126 - don’t automatically create a thresho... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... tree | commitdiff
2023-02-03 James ProcterJAL-1551 remove temp file in src tree | commitdiff
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop tree | commitdiff
2023-01-26 Ben SoaresJAL-4118 fix a small buglet in BackupFiles exhibited... tree | commitdiff
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... tree | commitdiff
2023-01-25 James ProcterJAL-4116 relegate the failed to promote warning to... tree | commitdiff
2023-01-25 James ProcterMerge branch 'new_feature/JAL-4019_ambiguous_base_colou... tree | commitdiff
2023-01-24 James ProcterMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... 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
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme... tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 remove a missed panel titlebar icon in TreePanel 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
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... tree | commitdiff
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf tree | commitdiff
2022-11-16 Ben SoaresJAL-4019 finalised a boolean option and tidied some... tree | commitdiff
2022-11-14 Ben SoaresJAL-4019 Make diagnostic message debug level tree | commitdiff
2022-11-13 Ben SoaresJAL-4019 small but important corrections to array order... tree | commitdiff
2022-11-13 Ben SoaresJAL-4019 improvement to short sequence nucleotide detec... tree | commitdiff
2022-11-10 Ben SoaresJAL-4019 Nucleotide Ambiguity Colour Scheme added.... tree | commitdiff
2022-11-09 Ben SoaresJAL-3416 Add necessary logo to non-internal Frames tree | commitdiff
2022-11-09 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... tree | commitdiff
2022-11-09 Ben SoaresJAL-3416 Add necessary logo to non-internal Frames tree | commitdiff
2022-11-09 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... tree | commitdiff
2022-11-09 Ben SoaresJAL-3416 Remove all JFrame/JInternalFrame icons (set... tree | commitdiff
2022-11-09 Ben SoaresMerge branch 'bug/JAL-1988_JAL-3772_improved_quit_handl... tree | commitdiff
2022-11-09 Ben SoaresJAL-1988 JAL-3772 Test for FORCE_QUIT whilst saving... bug/JAL-1988_JAL-3772_improved_quit_handling tree | commitdiff
2022-11-08 Ben SoaresMerge branch 'bug/JAL-1988_JAL-3772_improved_quit_handl... tree | commitdiff
2022-11-08 Ben SoaresJAL-1988 JAL-3776 Formatting JvOptionPane tree | commitdiff
2022-11-08 Ben SoaresJAL-1988 JAL-3772 Fixes highlighted by tests tree | commitdiff
2022-11-04 Ben SoaresJAL-3416 Added logoIcon to quit (and potentially other... tree | commitdiff
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution... tree | commitdiff
2022-11-03 Ben SoaresJAL-3416 File Chooser iconified, JvOptionPanes iconifie... tree | commitdiff
2022-11-03 Jim ProcterJAL-3855 JAL-4095 simple picking of ranges adjacent... tree | commitdiff
2022-11-03 Ben SoaresJAL-1988 JAL-3772 Allow other window closing dialogs... tree | commitdiff
2022-11-03 Ben SoaresJAL-3416 More JInternalFrame icons tree | commitdiff
2022-11-03 Ben SoaresJAL-1988 JAL-3772 Tidying of unspecified Callable decla... tree | commitdiff
2022-11-03 Ben SoaresJAL-3416 Start to add JInternalFrame icons (to replace... tree | commitdiff
2022-11-02 Ben SoaresJAL-1988 JAL-3772 Moving packages to somewhere more... tree | commitdiff
2022-11-01 Ben SoaresJAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE tree | commitdiff
2022-11-01 Ben SoaresJAL-1988 JAL-3772 Change default alignmentviewport... 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 Ben SoaresJAL-1988 JAL-3772 removed a debugging log line 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 Ben SoaresJAL-1988 JAL-3772 Removed 'Wait' button from waitDialog... 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
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