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jalview.git
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 fix SubVals npe commit | commitdiff | tree | snapshot
2023-03-29 Ben SoaresJAL-629 extensive tests for ArgParser features commit | commitdiff | tree | snapshot
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... commit | commitdiff | tree | snapshot
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet commit | commitdiff | tree | snapshot
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in... commit | commitdiff | tree | snapshot
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... commit | commitdiff | tree | snapshot
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-03-24 Ben SoaresJAL-629 Test tidyup commit | commitdiff | tree | snapshot
2023-03-23 James ProcterMerge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTe... commit | commitdiff | tree | snapshot
2023-03-23 Ben SoaresJAL-629 don't clear appProps in tests commit | commitdiff | tree | snapshot
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... commit | commitdiff | tree | snapshot
2023-03-21 Ben SoaresJAL-629 null checks for Desktop.instance.closeAll(... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4153 longer Thread.sleep() calls in the hope that... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 Back to forking tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 more memory to tests task commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 add in jvmArgs for memory for tests and keep... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 remove jvmArgs for memory for tests. Increase... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 Add in jvmArgs for memory for tests commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 closer to normal gradle settings with just... commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 increase test JVM size commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 failFast and new threads for each test commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 increased memory for clover commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 revert metal laf commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 fixed a test failing when run without a Jalview... commit | commitdiff | tree | snapshot
2023-03-15 Ben SoaresJAL-3833 fixed HiDPI test for macOS commit | commitdiff | tree | snapshot
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... commit | commitdiff | tree | snapshot
2023-03-13 Ben SoaresJAL-629 teardown in CommandsTest commit | commitdiff | tree | snapshot
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 start of CommandsTest. More ArgParserTests. commit | commitdiff | tree | snapshot
2023-03-10 Ben SoaresJAL-629 start of tests and more examples commit | commitdiff | tree | snapshot
2023-03-09 Ben SoaresJAL-629 start of tests commit | commitdiff | tree | snapshot
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry commit | commitdiff | tree | snapshot
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... commit | commitdiff | tree | snapshot
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 slight tidy up commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... commit | commitdiff | tree | snapshot
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 JAL-4124 JAL-3855 remove deleted debugging... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... commit | commitdiff | tree | snapshot
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options.... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 better test fixes. --props=... instead of ... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 test fixing commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 Add debug messages for more failing tests commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 fixed a Log4j test by adding --debug arg commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 nf-core sample alignment files and a2m versions commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO 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 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-22 Ben SoaresJAL-4064 JAL-4054 Corrected the tgz top-level dir from... 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 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... 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
2023-02-21 Ben SoaresJAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... commit | commitdiff | tree | snapshot
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