jalview.git
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil...
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr...
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar...
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label...
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ...
2023-03-02 Ben SoaresJAL-629 slight tidy up
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf...
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use...
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in...
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa...
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless
2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file
2023-02-27 Ben SoaresJAL-629 JAL-4124 JAL-3855 remove deleted debugging...
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some...
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename
2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options....
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import...
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import...
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac...
2023-02-24 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into...
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure...
2023-02-24 Ben SoaresJAL-629 better test fixes. --props=... instead of ...
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies...
2023-02-23 Ben SoaresJAL-629 test fixing
2023-02-23 Ben SoaresJAL-629 Add debug messages for more failing tests
2023-02-23 Ben SoaresJAL-629 fixed a Log4j test by adding --debug arg
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index...
2023-02-23 Ben SoaresJAL-629 nf-core sample alignment files and a2m versions
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO
2023-02-23 James ProcterJAL-4133 update validChar width when font is changed...
2023-02-22 James ProcterJAL-4133 store/restore alignment view’s charWidth and...
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised...
2023-02-22 James ProcterJAL-1551 source formatting
2023-02-22 James ProcterJAL-3858 simple test for PAE matrix recovery
2023-02-22 James ProcterJAL-3858 construct a PAE direct from float array
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-22 Ben SoaresJAL-4064 JAL-4054 Corrected the tgz top-level dir from...
2023-02-22 James ProcterJAL-629 make sure we show GUI when not driven programma...
2023-02-22 James ProcterJAL-4095 slightly better threshold setting and todos...
2023-02-22 James ProcterJAL-4095 magic fill behaviour is PAE specific
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-22 James ProcterJAL-3858 JAL-2381 allow different linear shading scheme...
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT...
2023-02-21 Ben SoaresJAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
2023-02-20 Ben SoaresJAL-4064 JAL-4054 Correct names of mac arch installer...
2023-02-20 Ben SoaresMerge branch 'develop' into improvement/JAL-4111_suffix... improvement/JAL-4111_suffixed_DEVELOP_channels
2023-02-20 Ben SoaresJAL-4128 Catch RasterFormatException caused whilst... bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception
2023-02-20 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha... bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview...
2023-02-15 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn...
2023-02-15 James ProcterPassing test for JAL-4127 failing on the JAL-1713 branch
2023-02-15 James ProcterJAL-4090 move 2.11.3 series release notes to 2.11.3...
2023-02-13 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha...
2023-02-13 Ben SoaresJAL-4125 Spanish translations
2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
2023-02-13 Ben SoaresJAL-4125 Move confirmation of closing external viewer...
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn...
2023-02-10 James ProcterJAL-3077 broken conflict resolve resulted in failing...
2023-02-10 James ProcterFix for JAL-4126 - don’t automatically create a thresho...
2023-02-10 James ProcterJAL-4126 comment out closeAll - so we can visually...
2023-02-10 James ProcterJAL-4126 failing test - colour scheme appears to be...
2023-02-09 Ben SoaresJAL-4125 Additions to JvOptionPane and QuitHandler...
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi...
2023-02-03 Ben SoaresJAL-629 "updated" json-simple
2023-02-03 James ProcterJAL-1551 remove temp file in src
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold...
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
2023-01-26 Ben SoaresJAL-4118 remove unnecessary sleep from QuitHandlerTest
2023-01-26 Ben SoaresJAL-4118 fix a small buglet in BackupFiles exhibited...
2023-01-26 Ben SoaresJAL-1988 Add a sleep to file save test to give time...
2023-01-26 Ben SoaresJAL-629 example files from nf-core
2023-01-26 Ben SoaresJAL-629 helper eclipse CLI run
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was...
2023-01-25 James ProcterJAL-4116 relegate the failed to promote warning to...
2023-01-25 James ProcterMerge branch 'new_feature/JAL-4019_ambiguous_base_colou...
2023-01-24 James ProcterJAL-4090 Release 2.11.3.0 release notes and version...
2023-01-24 James ProcterMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to...
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce...
2023-01-24 James ProcterJAL-629 need to delay call to AlignFile.parse() if...
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already...
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when...
2023-01-24 James ProcterJAL-629 don’t complain for Unary args
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone
2023-01-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless...
2023-01-23 James ProcterJAL-4104 JAL-4102 update help docs with script to add... Release_2_11_2_6
2023-01-23 Jim ProcterJAL-4102 whatsNew for 2.11.2.6
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api...
2023-01-20 Jim ProcterJAL-4114 model_page_url not required in v2.0 response patch/JAL-4114_updated_3dbeacons_api
2023-01-20 Jim ProcterJAL-4102 update date and release notes for 2.11.2.6
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