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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / io /
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-13 James ProcterJAL-4336 set preferred dimensions for JTextBox workarou... tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-10-30 James ProcterJAL-4315 identify feature settings file from its xml... tree | commitdiff
2023-10-23 James ProcterJAL-4308 reduce number of refs to 5, always have canoni... tree | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... tree | commitdiff
2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded... tree | commitdiff
2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... tree | commitdiff
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches... tree | commitdiff
2023-06-15 Ben SoaresJAL-4206 Use All Known Alignment Files as default until... tree | commitdiff
2023-06-14 Ben SoaresJAL-4026 if relative path in recently opened exists... tree | commitdiff
2023-06-14 Ben SoaresJAL-4206 unified dimensions tree | commitdiff
2023-06-14 Ben SoaresJAL-4206 Added recentlyOpenedCellRenderer to better... tree | commitdiff
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... tree | commitdiff
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-25 Ben SoaresJAL-4186 Turn JvOptionPane Callable<Void> handlers... 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 properly specify BinaryNode as a typed generic... tree | commitdiff
2023-05-17 Ben SoaresJAL-629 Tidy up tests and replaced methods before merge... tree | commitdiff
2023-05-17 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-05-17 James ProcterJAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... tree | commitdiff
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... tree | commitdiff
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... tree | commitdiff
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact... tree | commitdiff
2023-03-24 Ben SoaresJAL-629 Test tidyup tree | commitdiff
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... tree | commitdiff
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-27 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-23 James ProcterJAL-4134 - brutal hack to build a tree clustering colum... 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
2023-02-20 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha... bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly tree | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... tree | commitdiff
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... 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
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064 tree | commitdiff
2023-01-26 Ben SoaresJAL-4118 fix a small buglet in BackupFiles exhibited... tree | commitdiff
2023-01-24 James ProcterJAL-629 need to delay call to AlignFile.parse() if... tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... 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
2022-11-09 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
2022-11-04 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
2022-11-01 Ben SoaresJAL-1988 JAL-3772 Change default alignmentviewport... tree | commitdiff
2022-10-27 Ben SoaresJAL-1988 Allow generic Container object in JvOptionPane... tree | commitdiff
2022-10-27 Ben SoaresMerge branch 'develop' into bug/JAL-1988_JAL-3772_impro... tree | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 wait timer working first time but... tree | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave... 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 ProcterPatch for JAL-4074 - any content ending in ‘gzip’ recog... tree | commitdiff
2022-09-02 Ben SoaresJAL-1988 Added a saves in progress check for quit tree | commitdiff
2022-08-31 Ben SoaresJAL-1988 added a saveInProgress stack to BackupFiles 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
2022-04-05 Jim ProcterJAL-3981 patch tests and remove errant imports tree | commitdiff
2022-04-05 Jim ProcterJAL-3990 gradle spotlessApply tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 defensive copy - inefficient but fixes bug tree | commitdiff
2022-03-25 Jim ProcterJAL-3981 Additional line breaks - sort of helps tree | commitdiff
2022-03-24 Jim ProcterJAL-3981 strategic newlines to help speed up Java's... 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
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti... tree | commitdiff
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... tree | commitdiff
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-07 Jim ProcterMerge branch 'feature/JAL-1713_overviewInProject' into... tree | commitdiff
2022-02-07 Jim ProcterJAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTit... bug/JAL-3785autoOverviewTitle tree | commitdiff
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop... tree | commitdiff
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