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Merge branch 'develop' into releases/Release_2_11_3_Branch
[jalview.git]
/
src
/
jalview
/
2023-06-01
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-06-01
Ben Soares
JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt...
tree
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commitdiff
2023-06-01
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-06-01
James Procter
JAL-4134 properly resolve positions in associated align...
features/JAL-4134_use_annotation_row_for_colours_and_groups
tree
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commitdiff
2023-05-30
James Procter
JAL-4134 repaint the tree or alignment view(s) when...
tree
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commitdiff
2023-05-30
James Procter
JAL-4134 highlight selected column nodes on the linked...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-629 JAL-4121 Added documentation to Help docs and...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-629 Better formatting of Arg.Opt options in usage...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-4121 slight refactoring of method name and added...
tree
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commitdiff
2023-05-29
James Procter
JAL-4190 - escape clears selected nodes
tree
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commitdiff
2023-05-29
James Procter
JAL-4134 JAL-2349 test & fixed implementation(ish)...
tree
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commitdiff
2023-05-29
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-27
Ben Soares
JAL-4121 Added a NPE check caught in tests. Added ...
tree
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commitdiff
2023-05-27
Ben Soares
JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...
tree
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commitdiff
2023-05-26
Ben Soares
JAL-4125 Fixed non-closing external viewers, also added...
tree
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commitdiff
2023-05-26
James Procter
JAL-4134 internationalise popup menu entries and show...
tree
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commitdiff
2023-05-26
James Procter
JAL-1556 fix bad import
tree
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commitdiff
2023-05-26
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-26
James Procter
JAL-1556 initial implementation - no tests as yet but...
tree
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commitdiff
2023-05-26
Ben Soares
JAL-629 dispose of non-displaying StructureChooser...
tree
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commitdiff
2023-05-26
Ben Soares
Merge branch 'develop' into feature/JAL-3416_update_to_...
feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_native_libraries
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3416 JAL-3820 FlatLaf default for everyone, includi...
tree
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commitdiff
2023-05-25
James Procter
JAL-4134 popup menu and annotation row property to...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3820 JAL-3830 improvements to script launching...
tree
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commitdiff
2023-05-25
James Procter
JAL-2381 don’t need to set description, dbrefs etc...
tree
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commitdiff
2023-05-25
James Procter
JAL-2381 copy and paste sequence also copies contact...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3820 Create and use 'Jalview app' symblinks to...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-4186 Turn JvOptionPane Callable<Void> handlers...
tree
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commitdiff
2023-05-24
Ben Soares
JAL-4186 attempts to work in jalviewjs, still not working
tree
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commitdiff
2023-05-24
Ben Soares
JAL-4186 fix dialog. broken in JalviewJS
tree
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commitdiff
2023-05-24
Ben Soares
JAL-3416 slightly improved colours for tabber pane...
tree
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commitdiff
2023-05-23
Ben Soares
JAL-629 Updated help docs and fixed structure image...
tree
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commitdiff
2023-05-23
Ben Soares
JAL-629 Added --structureimage code and formatting...
tree
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commitdiff
2023-05-22
Ben Soares
JAL-629 --structureimage with formatting args.
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 map between column and node selections better...
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 efficiency improvement
tree
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commitdiff
2023-05-22
James Procter
JAL-629 javadoc on StructureSelectionManager.computeMapping
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 only build tree when showing it in the tree...
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 catch NPE - though in principle this should...
tree
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commitdiff
2023-05-22
James Procter
Merge branch 'JAL-1551_2_11_3_spotlett' into features...
tree
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
tree
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commitdiff
2023-05-21
Ben Soares
JAL-629 Clarify sections of arguments with --help-all...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4187 JAL-629 JAL-3830 small adjustments after furth...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-3416 Ensure setFrameIcon(null) is set for remaining...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-3416 Removed another internal Frame icon from title bar
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
tree
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commitdiff
2023-05-19
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-19
Ben Soares
JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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
2023-05-18
James Procter
JAL-4134 support recovery of mapped positions for raw...
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 colour by annotation needs distinct annotation...
tree
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commitdiff
2023-05-18
Ben Soares
JAL-629 fixes to typed args
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 column grouping model and methods moved to...
tree
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commitdiff
2023-05-18
Ben Soares
JAL-629 Added 'Type' to args and argvalues
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 formatting
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 properly specify BinaryNode as a typed generic...
tree
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commitdiff
2023-05-17
Ben Soares
JAL-629 Tidy up tests and replaced methods before merge...
tree
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commitdiff
2023-05-17
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-05-17
James Procter
JAL-4184 export description line in stockholm
patch/JAL-4184_description_stockholm
tree
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commitdiff
2023-05-16
Ben Soares
JAL-629 Ensure precedence of named linked ID values...
tree
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commitdiff
2023-05-16
James Procter
JAL-4089 - if no centerViewOn commands are given, don...
tree
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commitdiff
2023-05-15
James Procter
JAL-4182 patch - map selection group onto sequence...
tree
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commitdiff
2023-05-15
Ben Soares
Revert "JAL-629 Add a --threads argument to allow a...
tree
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commitdiff
2023-05-15
Ben Soares
JAL-629 Add a --threads argument to allow a limited...
tree
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commitdiff
2023-05-14
James Procter
JAL-2349 fix up tests for Java 11 compatibility and...
tree
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commitdiff
2023-05-14
James Procter
JAL-2349 store/restore mappable contact matrix in proje...
tree
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commitdiff
2023-05-14
Ben Soares
JAL-629 add an {extension} substitution
tree
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commitdiff
2023-05-13
James Procter
JAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp...
tree
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commitdiff
2023-05-13
James Procter
JAL-2349 JAL-3855 helper method to make it easy to...
tree
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commitdiff
2023-05-13
Ben Soares
JAL-629 launcher shell script uses jalview.bin.Launcher...
tree
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commitdiff
2023-05-12
James Procter
JAL-2349 allow PAE or other contact matrices to hold...
tree
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commitdiff
2023-05-12
Ben Soares
JAL-629 Added --opened arg which is like limiting ...
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Add some shortnames to args. Add Opt.OUTPUT...
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
2023-05-11
Ben Soares
JAL-629 Added linkedId to ArgValuesMap for reference...
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 Check Arg options for obtaining boolean or...
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 Catch a NPE, fix a test
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 More docs. Usage statement. Adjust some logging...
tree
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commitdiff
2023-05-09
Ben Soares
JAL-629 Add --seqid for non-subval use, make arg value...
tree
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commitdiff
2023-05-09
Ben Soares
JAL-629 change --renderer to --textrenderer to be more...
tree
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commitdiff
2023-05-05
Ben Soares
JAL-629 test fixes
tree
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commitdiff
2023-05-04
Ben Soares
JAL-629 More NG arguments: --features, --annotations...
tree
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commitdiff
2023-05-03
Ben Soares
JAL-629 added eps and imagemap. Added --output and...
tree
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commitdiff
2023-05-02
Ben Soares
JAL-629 Changed --newframe and --allframes to --new...
tree
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commitdiff
2023-05-02
Ben Soares
JAL-629 Add --renderer arg/subval for vector output...
tree
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commitdiff
2023-05-01
James Procter
Merge branch 'features/JAL-4134_treeviewerforcolumns...
tree
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commitdiff
2023-05-01
James Procter
JAL-4177 disable ‘Cancel’ as well - since we as yet...
features/JAL-4134_treeviewerforcolumns
tree
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commitdiff
2023-05-01
James Procter
JAL-4177 disable add/new view when an import is started.
tree
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commitdiff
2023-05-01
James Procter
JAL-4123 JAL-3914 JAL-3858 tweak wording and layout...
tree
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commitdiff
2023-05-01
James Procter
JAL-4134 double click to select column groups
tree
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commitdiff
2023-05-01
James Procter
JAL-3858 report errors when trying to parse JSON to...
tree
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commitdiff
2023-04-30
Ben Soares
JAL-629 Change behaviour of --open GLOB to increment...
tree
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commitdiff
2023-04-29
Ben Soares
JAL-629 Added --all arg, [*] linkedId and functionality...
tree
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commitdiff
2023-04-28
Ben Soares
JAL-629 Change colour scheme shortnames to something...
tree
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commitdiff
2023-04-27
Ben Soares
JAL-629 Fixed appending URLs
tree
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commitdiff
2023-04-27
Ben Soares
JAL-629 Changed --increment to --newframe to make sense...
tree
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commitdiff
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