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OrthoMCL - Custom tree-table for OrthoGroup page #904

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OrthoMCL - Custom tree-table for OrthoGroup page #904

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Commits on Mar 1, 2024

  1. made a start - WIP

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Commits on Mar 4, 2024

  1. re-render sequence table with Mesa

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  2. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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    bobular committed Mar 4, 2024
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  3. tweak comments

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    bobular committed Mar 4, 2024
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  4. WIP

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Commits on Mar 5, 2024

  1. loosely wire in TreeTable and get shimmimg working

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  2. add patristic and basic type support

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Commits on Mar 8, 2024

  1. made a start with controlling table row height but should investigate… 

    … the Mesa inline option
    @bobular
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  2. added Mesa table tooltips for td contents when in 'inline' mode (basi… 

    …cally fixed-height mode)
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  3. use Mesa's inline option and tidy up

    @bobular
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  4. Revert "added Mesa table tooltips for td contents when in 'inline' mo… 

    …de (basically fixed-height mode)"

This reverts commit f215762.
    @bobular
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  5. remove placeholder td title

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  6. restore whitespace in DataCell.tsx

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  7. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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Commits on Mar 15, 2024

  1. upgrade tidytree and use new interactive option

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  2. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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  3. table and tree order are the same

    @bobular
    bobular committed Mar 15, 2024
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  4. added basic checkboxes

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Commits on Mar 19, 2024

  1. WIP clustal form

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  2. that's hopefully clustal sorted - but can't test with local ortho-site

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Commits on Mar 20, 2024

  1. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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  2. improve 'must select two proteins' verbiage

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  3. de-complicate .DataTable margin-bottom override

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  4. rename TreeResponse to GroupTreeResponse

    @bobular
    bobular committed Mar 20, 2024
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  5. add PFam domain architecture column

    @bobular
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  6. ugly search working as a demo on description column

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Commits on Mar 25, 2024

  1. add warning banner for data issue and tweak pfam column heading

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  2. used RealTimeSearchBox and made regexps safer and reorganised so we c… 

    …an useMemo for the table filtering
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  3. more memo and remove some commented code

    @bobular
    bobular committed Mar 25, 2024
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  4. add tree filtering

    @bobular
    bobular committed Mar 25, 2024
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  5. tree highlighting works with filtering now, dependency issues fixed

    @bobular
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  6. add core/peripheral filtering

    @bobular
    bobular committed Mar 25, 2024
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  7. added pfam legend - needs wiring still

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    bobular committed Mar 25, 2024
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  8. wired up pfam checkboxes to table search

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Commits on Mar 26, 2024

  1. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

    @bobular
    bobular committed Mar 26, 2024
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  2. added the row count

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  3. conditionally render pfam legend and add heading

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    bobular committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. Remove vert scrollbar from tidytree table

    @dmfalke
    dmfalke committed Mar 27, 2024
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Commits on May 29, 2024

  1. Merge branch 'main' into orthogroup-tree-table

    @bobular
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  2. remove code that collapsed the main section of the orthogroup page

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  3. no longer request trees for 1 or 2 sequences; fix RowCounter props ch… 

    …ange; fix some imports
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Commits on Jun 4, 2024

  1. fudge to sort table based on dodgy colon-containing full_ids

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Commits on Jun 6, 2024

  1. make tree darker and make tree/table check more robust

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  2. provide PFam descriptions in domain cartoon tooltips

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  3. sort out row counts

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  4. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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Commits on Jun 11, 2024

  1. add better console logging for tree/table mismatches

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  2. made tree-table comparison for console more robust

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Commits on Jun 19, 2024

  1. add inlineUseTooltips options prop but not working fully yet

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  2. attempted better handling of very large groups

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Commits on Jun 21, 2024

  1. looks good now

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Commits on Jun 24, 2024

  1. removed full_id column (from display only) and added Accession aka se… 

    …quence_link column and enabled the link
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  2. Merge pull request #1115 from VEuPathDB/mesa-inline-changes 

    New optional Mesa inline table behaviour using tooltips
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Commits on Jun 28, 2024

  1. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

    @dmfalke
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  2. Use flex for label to allow for block children

    @dmfalke
    dmfalke committed Jun 28, 2024
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  3. Use SelectList for Pfam filter

    @dmfalke
    dmfalke committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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  2. Explicit empty PFam legend

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  3. Merge branch 'main' into orthogroup-tree-table

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Commits on Jul 12, 2024

  1. Use similar style for core/peripheral filter

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  2. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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  3. Merge branch 'orthogroup-tree-table' into orthogroup-tree-table__pfam… 

    …-filter
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Commits on Jul 16, 2024

  1. Add species filter to protein table

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Commits on Jul 17, 2024

  1. prevent overflow in SelectTree button with many items selected; also … 

    …use flex-wrap to prevent large buttons crowding the search box
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  2. add shouldOnlyUpdateOnClose option to SelectTree

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  3. remove some unused imports

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  4. add MAX_SEQUENCES_FOR_TREE logic

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    bobular committed Jul 17, 2024
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  5. selected row highlighting

    @bobular
    bobular committed Jul 17, 2024
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  6. tone down the row background color

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Commits on Jul 18, 2024

  1. Merge pull request #1140 from VEuPathDB/orthogroup-tree-table__pfam-f… 

    …ilter

Orthogroup tree table  pfam filter
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  2. Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

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Commits on Jul 19, 2024

  1. don't indent search bar and filters

    @bobular
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  2. add instantUpdate option to SelectList

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  3. Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth… 

    …o-instant-filters
    @bobular
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  4. revert taxon filter to instant-update

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  5. instantUpdate for core/peripheral filter

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  6. Pfam architectures are now scaled by protein length

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  7. removed core-only filter for larger groups

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Commits on Aug 1, 2024

  1. improved table sort and filter performance - added comments about fur… 

    …ther optimisations
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Commits on Aug 2, 2024

  1. rename shouldOnlyUpdateOnClose to instantUpdate

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  2. remove an effect

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  3. Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth… 

    …o-instant-filters
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  4. missed a setSelected and dependency

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    bobular committed Aug 2, 2024
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  5. final tweaks to button label behaviour

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  6. Merge pull request #1144 from VEuPathDB/ortho-instant-filters 

    Instant filters for the orthogroup page
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Commits on Aug 3, 2024

  1. add reset button, revisit filter button layout

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