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JAL-629 allow comments in argfiles '#'
[jalview.git] / src /
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#' tree | commitdiff
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 more info in usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Start of Usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Remove debugging comment tree | commitdiff
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix SubVals npe tree | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... tree | commitdiff
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet tree | commitdiff
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in... tree | commitdiff
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... tree | commitdiff
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... 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
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... tree | commitdiff
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit tree | commitdiff
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-16 Ben SoaresJAL-629 revert metal laf tree | commitdiff
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests tree | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... tree | commitdiff
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags... tree | commitdiff
2023-03-10 Ben SoaresJAL-629 start of tests and more examples tree | commitdiff
2023-03-09 Ben SoaresJAL-629 start of tests tree | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry tree | commitdiff
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... tree | commitdiff
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 slight tidy up 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
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file tree | commitdiff
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... tree | commitdiff
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options.... tree | commitdiff
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... tree | commitdiff
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error tree | commitdiff
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO 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 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... 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
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... tree | commitdiff
2023-02-20 Ben SoaresJAL-4128 Catch RasterFormatException caused whilst... bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception 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
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview... tree | commitdiff
2023-02-13 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha... tree | commitdiff
2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... tree | commitdiff
2023-02-13 Ben SoaresJAL-4125 Move confirmation of closing external viewer... 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
2023-02-09 Ben SoaresJAL-4125 Additions to JvOptionPane and QuitHandler... 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
2023-01-30 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
2023-01-26 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
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