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Cleanup, note: rectangular selection works by holding mouse wheel and s (see line...
[jalview.git]
/
src
/
jalview
/
gui
/
2023-12-05
MorellThomas
Cleanup, note: rectangular selection works by holding...
tree
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commitdiff
2023-12-05
MorellThomas
Enable rectangular selection for PaSiMap
tree
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commitdiff
2023-12-04
MorellThomas
New independent jbgui Panel for PaSiMap. Revert the...
tree
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commitdiff
2023-12-04
MorellThomas
New GPCAPanel button : output pairwise alignments ...
tree
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commitdiff
2023-12-01
MorellThomas
Applying adjustablenw_params.patch (JAL-4159)
tree
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commitdiff
2023-09-16
MorellThomas
Almost working
tree
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commitdiff
2023-09-08
MorellThomas
Properly integrated endGaps option for AlignSeq.traceAl...
tree
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commitdiff
2023-09-07
MorellThomas
Merge branch 'hardcode'
tree
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commitdiff
2023-08-04
MorellThomas
Fix alignment and score calculation for cc_analysis
tree
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commitdiff
2023-07-22
MorellThomas
Implement MSA, scoring and counting the connections
tree
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commitdiff
2023-07-20
James Procter
JAL-3855 tree title for PAE matrix tree is PAE Matrix...
patch/JAL-3855_fixup_pae
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
2023-07-18
James Procter
JAL-3858 fix off-by-one in matrix visualisation and...
tree
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commitdiff
2023-07-18
James Procter
JAL-3858 flip diagonal so matrix visualisation is top...
tree
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commitdiff
2023-07-09
MorellThomas
Copied PCA files to PaSiMap analogues and changed all...
tree
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commitdiff
2023-07-08
MorellThomas
Includes the PaSiMap button in the CalculationChooser
tree
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commitdiff
2023-07-06
James Procter
JAL-629 make —structure image work again after threadin...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 catch case when the structure viewer doesn...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 wrap imageExport CLI method's call to imageExp...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 wrap imageExport CLI method's call to imageExp...
tree
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commitdiff
2023-07-05
James Procter
Merge branch 'patch/JAL-4213_addref_with_selection...
tree
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commitdiff
2023-06-30
James Procter
JAL-4217 try really hard to shut down and dispose of...
tree
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commitdiff
2023-06-22
James Procter
JAL-4213 don’t pass active selection when actioning...
patch/JAL-4213_addref_with_selection
tree
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commitdiff
2023-06-21
James Procter
Merge branch 'patch/JAL-4196_structure_viewer_synchroni...
patch/JAL-4196_structure_viewer_synchronising
tree
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commitdiff
2023-06-14
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-09
Ben Soares
JAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest...
tree
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commitdiff
2023-06-09
Ben Soares
JAL-3599 Deliberate NPE to see if build plan fails
tree
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commitdiff
2023-06-08
Ben Soares
JAL-3599 gradle tasks to test JalviewJS launches in...
tree
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commitdiff
2023-06-08
James Procter
JAL-4196 structure view cli tests wait using new jalvie...
tree
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commitdiff
2023-06-08
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-07
James Procter
JAL-4195 add exception handling for all image output...
tree
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commitdiff
2023-06-07
James Procter
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...
tree
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commitdiff
2023-06-07
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-07
Ben Soares
JAL-4001 GA4 tracking is now ENABLED. Currently loggin...
tree
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commitdiff
2023-06-07
James Procter
JAL-4195 tidy up desktop instances after creating them
tree
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commitdiff
2023-06-06
James Procter
JAL-4195 report full stack trace for exceptions raised...
tree
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commitdiff
2023-06-01
Ben Soares
Merge branch 'develop' into improvement/JAL-4193_cl_arg...
tree
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commitdiff
2023-06-01
Ben Soares
JAL-4193 JAL-4194 sessionProperties layer in Cache...
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
2023-05-29
James Procter
JAL-4190 - escape clears selected nodes
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
2023-05-26
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
James Procter
JAL-4134 popup menu and annotation row property to...
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
2023-05-23
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-4134 only build tree when showing it in the tree...
tree
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
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
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
2023-05-18
James Procter
JAL-4134 support recovery of mapped positions for raw...
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 column grouping model and methods moved to...
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
2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
tree
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commitdiff
2023-05-05
Ben Soares
JAL-629 test fixes
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-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
2023-04-22
Ben Soares
JAL-629 Test and fix --annotation --ssannotation args...
tree
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commitdiff
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
tree
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commitdiff
2023-04-14
Ben Soares
JAL-629 Adding PAE and TFType at structure loading...
tree
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commitdiff
2023-04-12
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
tree
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commitdiff
2023-03-24
James Procter
JAL-4134 - store colours in annotation row, so colour...
tree
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commitdiff
2023-03-24
James Procter
JAL-4158 first attempt at stashing colours for contact...
tree
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commitdiff
2023-03-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-03-24
Ben Soares
JAL-629 Test tidyup
tree
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commitdiff
2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
tree
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commitdiff
2023-03-20
James Procter
Merge branch 'develop' into features/JAL-4134_treeviewe...
tree
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commitdiff
2023-03-20
James Procter
JAL-4150 test and quick patch copying code from AlignFr...
tree
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commitdiff
2023-03-20
James Procter
JAL-2349 JAL-4134 Console log messages for contact...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 propagate column selection changes in tree...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 fix off-by-one in selection
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 fix NPEs when matrix not resolved or alignment...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 better popup menu name ‘Tree for Contact Matrix’
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
2023-03-17
James Procter
JAL-4134 fix up column selection when hidden regions...
tree
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commitdiff
2023-03-17
James Procter
JAL-4134 store/restore Newick tree for PAE annotation row
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-4147 - revised annotation label display...
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
2023-03-08
James Procter
JAL-2349 handle matrix_clicked on mouse_release rather...
tree
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commitdiff
2023-03-08
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
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