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JAL-4159 implement bounds for PASIMAP calculation - from 9 to 20000 sequences.
[jalview.git]
/
src
/
jalview
/
util
/
2024-05-13
Renia Correya
JAL-4386 - Implementation of substitution matrix and...
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 re-used random color code
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 Preserve the user given 'linkedId' with ArgVal...
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 Add a 'random' colour to produce a random...
tree
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commitdiff
2023-11-13
James Procter
JAL-4090 JAL-1551 source license
tree
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commitdiff
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 report PAE range with sensible precision
tree
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commitdiff
2023-09-21
James Procter
JAL-1551 javadoc for mapUtils
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4274 Use Cache BITMAP_* if no other image restricti...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4262 Made deprecation warning properly modal
bug/JAL-4277_dirname_substitution_always_absolute
tree
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commitdiff
2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4277 --mkdirs with cautious refusal for paths with ..
tree
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commitdiff
2023-09-08
Ben Soares
Merge branch 'bug/JAL-4277_dirname_substitution_always_...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
tree
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commitdiff
2023-09-07
Ben Soares
Merge branch 'develop' into bug/JAL-4277_dirname_substi...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-4277 Corrected choice of all or last opened linkedI...
tree
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commitdiff
2023-09-07
James Procter
JAL-4090 JAL-4160 JAL-4274 image export dimensions...
tree
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commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-23
Ben Soares
JAL-4250 Simplification of polygons and adjustments...
tree
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commitdiff
2023-08-17
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-08-16
Ben Soares
Merge branch 'develop' into improvement/JAL-3830_remove...
tree
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commitdiff
2023-08-16
Ben Soares
JAL-3820 JAL-4189 Move checks for java executable symli...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Move more stdout messages to stderr when output...
tree
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commitdiff
2023-07-20
James Procter
JAL-3855 auto select clusters and fix up colouring...
tree
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commitdiff
2023-06-22
Ben Soares
Merge branch 'develop' into task/JAL-4001_Plausible_API
tree
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commitdiff
2023-06-22
Ben Soares
JAL-4019 corrected to '>' to '>=' for percentage compar...
bug/JAL-4125_flatlaf_quithandler_external_structureviewers_not_closed
tree
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commitdiff
2023-06-21
Ben Soares
JAL-4001 Rationalise user-agent string into HttpUtils
tree
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commitdiff
2023-05-25
Ben Soares
JAL-4186 Turn JvOptionPane Callable<Void> handlers...
tree
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commitdiff
2023-05-22
Ben Soares
JAL-629 --structureimage with formatting args.
tree
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commitdiff
2023-05-19
Ben Soares
JAL-629 Added Arg.Types and additional --help-type...
tree
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commitdiff
2023-05-14
Ben Soares
JAL-629 add an {extension} substitution
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
tree
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commitdiff
2023-04-23
Ben Soares
JAL-629 Change --open to --append and --opennew to...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 Add substituteHomeDir to getDirname(). Tighten...
tree
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commitdiff
2023-04-03
Ben Soares
JAL-629 sort files from java glob for predictability...
tree
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commitdiff
2023-04-03
Ben Soares
JAL-629 added setprop. More filename based substitution...
tree
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commitdiff
2023-03-30
Ben Soares
JAL-629 More extensive tests with real files being...
tree
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commitdiff
2023-03-29
Ben Soares
JAL-629 Added --opennew --nonews --nosplash. Added...
tree
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commitdiff
2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
tree
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commitdiff
2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
tree
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commitdiff
2023-03-10
Ben Soares
JAL-629 start of tests and more examples
tree
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commitdiff
2023-03-09
Ben Soares
JAL-629 --argfile=glob implemented. Remove reference...
tree
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commitdiff
2023-03-08
Ben Soares
JAL-629 improved comment and return speed of StringUtil...
tree
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commitdiff
2023-02-26
Ben Soares
JAL-629 PAE matrix file guesstimate from filename
tree
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-02-03
James Procter
JAL-1551 remove temp file in src
tree
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commitdiff
2023-02-03
James Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-01-25
James Procter
JAL-4116 relegate the failed to promote warning to...
tree
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commitdiff
2023-01-25
James Procter
JAL-4116 relegate the failed to promote warning to...
tree
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commitdiff
2023-01-25
James Procter
Merge branch 'new_feature/JAL-4019_ambiguous_base_colou...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release...
features/r2_11_2_alphafold/JAL-2349_JAL-3855
tree
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commitdiff
2023-01-20
Jim Procter
JAL-2353 primary ref candidates that should be promoted...
patch/Release_2_11_2_6_Branch
tree
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commitdiff
2022-11-16
Ben Soares
JAL-4019 finalised a boolean option and tidied some...
tree
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commitdiff
2022-11-14
Ben Soares
JAL-4019 Make diagnostic message debug level
tree
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commitdiff
2022-11-13
Ben Soares
JAL-4019 improvement to short sequence nucleotide detec...
tree
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commitdiff
2022-11-10
Ben Soares
JAL-4019 Nucleotide Ambiguity Colour Scheme added....
tree
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commitdiff
2022-11-03
Ben Soares
JAL-1988 JAL-3772 Tidying of unspecified Callable decla...
tree
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commitdiff
2022-10-24
Ben Soares
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
tree
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 JAVA_COMPILE_VERSION put into build_properties...
tree
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commitdiff
2022-03-18
Ben Soares
JAL-3978 New tasks to build archive 'old' dir with...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Put jalview.jar first in getdown for .properti...
tree
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commitdiff
2022-03-07
Ben Soares
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3691 patch toUpper/toLower to use Locale.ROOT for...
tree
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'develop' into update/JAL-3949_abstracted_...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-02-04
Ben Soares
JAL-3949 An attempt at converting to Log4j 2 -- no...
tree
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commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
tree
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commitdiff
2022-02-04
Jim Procter
JAL-3806 require mapping extent covers both sequence...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 use the covers() test for each selected sequen...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 use same logic as for mouse over highlighting...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 todo - problem seems to be Protein:Many CDS...
tree
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commitdiff
2022-01-28
Jim Procter
Merge branch 'merge/develop_JAL-3725' into develop
tree
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commitdiff
2022-01-27
Jim Procter
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jal...
tree
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commitdiff
2022-01-26
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2021-09-17
gmungoc
JAL-1260 refactored GenBank (and EMBL) flat file parser
tree
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commitdiff
2021-09-16
Jim Procter
JAL-3794 X and N are counted as DNA characters, but...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 more consistent parameter naming
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 helper method reinstated to avoid code duplication
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom/To revised with tests; unused...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 debugged and working (but not tidied) locateIn...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom2 work in progress commit
tree
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commitdiff
2021-09-15
gmungoc
JAL-3761 failing test, formatting, method renamed
tree
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commitdiff
2021-09-15
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2021-09-15
Ben Soares
Merge branch 'develop' into merge/develop_ben2
tree
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commitdiff
2021-09-15
Jim Procter
Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride...
tree
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commitdiff
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