jalview.git
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution...
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being...
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with...
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args...
2023-03-30 Ben SoaresJAL-629 fix SubVals npe
2023-03-29 Ben SoaresJAL-629 extensive tests for ArgParser features
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added...
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in...
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement...
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-03-24 Ben SoaresJAL-629 Test tidyup
2023-03-23 James ProcterMerge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTe...
2023-03-23 Ben SoaresJAL-629 don't clear appProps in tests
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to...
2023-03-21 Ben SoaresJAL-629 null checks for Desktop.instance.closeAll(...
2023-03-20 James ProcterJAL-4153 longer Thread.sleep() calls in the hope that...
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr...
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage
2023-03-18 Ben SoaresJAL-629 Back to forking tests
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through...
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
2023-03-17 Ben SoaresJAL-629 more memory to tests task
2023-03-17 Ben SoaresJAL-629 add in jvmArgs for memory for tests and keep...
2023-03-17 Ben SoaresJAL-629 remove jvmArgs for memory for tests. Increase...
2023-03-17 Ben SoaresJAL-629 Add in jvmArgs for memory for tests
2023-03-16 Ben SoaresJAL-629 closer to normal gradle settings with just...
2023-03-16 Ben SoaresJAL-629 increase test JVM size
2023-03-16 Ben SoaresJAL-629 failFast and new threads for each test
2023-03-16 Ben SoaresJAL-629 increased memory for clover
2023-03-16 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-03-16 Ben SoaresJAL-629 revert metal laf
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests
2023-03-16 Ben SoaresJAL-629 fixed a test failing when run without a Jalview...
2023-03-15 Ben SoaresJAL-3833 fixed HiDPI test for macOS
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader...
2023-03-13 Ben SoaresJAL-629 teardown in CommandsTest
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter...
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -...
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags...
2023-03-11 Ben SoaresJAL-629 start of CommandsTest. More ArgParserTests.
2023-03-10 Ben SoaresJAL-629 start of tests and more examples
2023-03-09 Ben SoaresJAL-629 start of tests
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference...
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened...
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
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