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OrthoMCL - Custom tree-table for OrthoGroup page #904
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7ac2d3e
made a start - WIP
bobular 2f4bc1f
re-render sequence table with Mesa
bobular 4340f10
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 3498348
tweak comments
bobular dc1731f
WIP
bobular 785a9ed
loosely wire in TreeTable and get shimmimg working
bobular 8c3d330
add patristic and basic type support
bobular adb464a
made a start with controlling table row height but should investigate…
bobular f215762
added Mesa table tooltips for td contents when in 'inline' mode (basi…
bobular 1abea4b
use Mesa's inline option and tidy up
bobular ded7a66
Revert "added Mesa table tooltips for td contents when in 'inline' mo…
bobular a7c0e1b
remove placeholder td title
bobular a19369e
restore whitespace in DataCell.tsx
bobular 5c04215
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 5f908bd
upgrade tidytree and use new interactive option
bobular 89d17a7
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular ea9283d
table and tree order are the same
bobular 76bfe05
added basic checkboxes
bobular cdc9d49
WIP clustal form
bobular 1495c07
that's hopefully clustal sorted - but can't test with local ortho-site
bobular 57f6a10
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 8831695
improve 'must select two proteins' verbiage
bobular 5c896a0
de-complicate .DataTable margin-bottom override
bobular fd446f8
rename TreeResponse to GroupTreeResponse
bobular a36c6ad
add PFam domain architecture column
bobular f489066
ugly search working as a demo on description column
bobular c06178d
add warning banner for data issue and tweak pfam column heading
bobular 2599155
used RealTimeSearchBox and made regexps safer and reorganised so we c…
bobular 7668085
more memo and remove some commented code
bobular 95ac689
add tree filtering
bobular 0a15ccb
tree highlighting works with filtering now, dependency issues fixed
bobular 0c8639b
add core/peripheral filtering
bobular f137fa2
added pfam legend - needs wiring still
bobular b4e30ed
wired up pfam checkboxes to table search
bobular c97bcc1
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 0599d1b
added the row count
bobular 6bef0de
conditionally render pfam legend and add heading
bobular 4f1e80e
Remove vert scrollbar from tidytree table
dmfalke 8a27952
Merge branch 'main' into orthogroup-tree-table
bobular c0cb043
remove code that collapsed the main section of the orthogroup page
bobular 3e47e2c
no longer request trees for 1 or 2 sequences; fix RowCounter props ch…
bobular 40eacc1
fudge to sort table based on dodgy colon-containing full_ids
bobular 8ff24e2
make tree darker and make tree/table check more robust
bobular fcdddbd
provide PFam descriptions in domain cartoon tooltips
bobular 032c479
sort out row counts
bobular 9f3d563
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 7bf58f4
add better console logging for tree/table mismatches
bobular e6904a1
made tree-table comparison for console more robust
bobular 06f4959
add inlineUseTooltips options prop but not working fully yet
bobular 9ecec3d
attempted better handling of very large groups
bobular 30da70a
looks good now
bobular 443528c
removed full_id column (from display only) and added Accession aka se…
bobular e7abcb9
Merge pull request #1115 from VEuPathDB/mesa-inline-changes
bobular 9567b62
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
dmfalke 5de59a6
Use flex for label to allow for block children
dmfalke 2e33989
Use SelectList for Pfam filter
dmfalke f33f711
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 5e04d5f
Explicit empty PFam legend
bobular 5a49184
Merge branch 'main' into orthogroup-tree-table
bobular 5cf07bf
Use similar style for core/peripheral filter
dmfalke 0cbb71d
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
dmfalke 592ef2d
Merge branch 'orthogroup-tree-table' into orthogroup-tree-table__pfam…
dmfalke b316022
Add species filter to protein table
dmfalke a422072
prevent overflow in SelectTree button with many items selected; also …
bobular c50a85e
add shouldOnlyUpdateOnClose option to SelectTree
bobular 96056a2
remove some unused imports
bobular 8c05b0c
add MAX_SEQUENCES_FOR_TREE logic
bobular 0620543
selected row highlighting
bobular 871583e
tone down the row background color
bobular f00a872
Merge pull request #1140 from VEuPathDB/orthogroup-tree-table__pfam-f…
bobular 6d50fca
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular 11deb34
don't indent search bar and filters
bobular a718914
add instantUpdate option to SelectList
bobular d168e75
Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth…
bobular 9c5ff46
revert taxon filter to instant-update
bobular de9d761
instantUpdate for core/peripheral filter
bobular 9281471
Pfam architectures are now scaled by protein length
bobular 789629b
removed core-only filter for larger groups
bobular 209fd02
improved table sort and filter performance - added comments about fur…
bobular 3874c5a
rename shouldOnlyUpdateOnClose to instantUpdate
bobular d45f975
remove an effect
bobular f9a19b7
Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth…
bobular eb238e5
missed a setSelected and dependency
bobular 66e13f2
final tweaks to button label behaviour
bobular 969db0d
Merge pull request #1144 from VEuPathDB/ortho-instant-filters
bobular febb312
add reset button, revisit filter button layout
bobular 58711a0
placeholder wrapper for image next to group stats
bobular 5e310a1
restore the buttonless phyletic distribution
bobular 700e277
improved comment/documentation
bobular 3c75ebd
Merge pull request #1171 from VEuPathDB/ortho-restore-phyletic-section
bobular 46d8b26
merge origin/main and resolve conflicts
bobular 39da8f7
Merge branch 'orthogroup-tree-table' into ortho-stats-wrapper
bobular 8c8f3a3
Adding update evalue histogram
704acd0
Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth…
bobular 15f0df3
static histogram image now shows, with elaborate width-setting for ca…
bobular eff237e
make caption rendering smoother - no horizontal shifting of the figure
bobular 144c838
moved png file again
bobular 65b065d
simplified to hardcoded dimensions
bobular 0452f8d
Merge branch 'main' into orthogroup-tree-table
dmfalke 9e6d939
Address typescript errors
dmfalke 3a68137
Merge pull request #1169 from VEuPathDB/ortho-stats-wrapper
bobular 7508ad7
remove taxon_abbrev column
bobular 7f758f4
rename Taxon column to Clade
bobular 0eb1a70
rename Species filter button to Organism
bobular c368e92
improve filter button layout, especially when buttons have expanded c…
bobular dd0c40a
fix Omit prop typo that wasn't detected because only consumer so far …
bobular d3f421b
main proteins table now has fully-fledged search box with column sele…
bobular 6f0cad6
moved styling to .scss file
bobular 0e09962
revert column changes now that model is updated OrthoMCLModel#5
bobular dacbd81
Merge pull request #1194 from VEuPathDB/ortho-table-tweaks
bobular 4cce0b1
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
bobular c02d237
added new WDK record scope - record-collapsed
bobular 5121654
added Dave's suggestions
bobular 8b79cb6
Merge pull request #1199 from VEuPathDB/wdk-record-collapsed-scope
bobular 506dd66
merge in npm action change
bobular 07934e8
cherry picking missed this line
bobular 85dc60e
Orthogroup tree table perf (#1233)
dmfalke d79d21c
Only call anchorNode.scrollIntoView() if the position has changed
dmfalke 083d7e6
Update note to handle MIN_SEQUENCES_FOR_TREE
dmfalke fa46c14
useDeferredValue partially working
bobular 4b73e5a
onSpeciesSelected wasn't stable, is now
bobular 981507f
replace debouncing with deferred value for CheckboxTree searchTerm
bobular b1c0891
tidy up
bobular 09d935b
new useDeferredState hook
bobular 4638fed
Use fixed dimensions for organism filter of protein table
dmfalke 8b024bc
Merge pull request #1243 from VEuPathDB/orthogroup-tree-table__useDef…
bobular 355d5a4
the very basics
bobular f5ee686
straw man ready
bobular fccec4c
forgot the reset button
bobular ca400d5
DRYed up a bit
bobular ab88a2a
fixed the edge case as described in PR, improved search box responsiv…
bobular 2f60de7
text search field selectors now more responsive
bobular 72e4740
added asterisk and improved filter positioning
bobular c22b905
fixed broken logic with corePeripheral filter
bobular f6f9153
memoized rowsByAccession and mesaState and fixed some logic errors
bobular 337348e
memoize treeProps just for tidiness
bobular 2520735
replaced the key hack with ref approach
bobular 07a9a6d
Merge pull request #1252 from VEuPathDB/orthogroup-tree-table__protei…
bobular 4e825c0
Orthogroup tree table - tooltips (#1253)
dmfalke 5e04a76
new warning added, no new component, sorry
bobular bbd65ea
improved tree error warning with link to contact form
bobular 564f453
use display names in SelectList button labels
bobular 6907790
standardised search behaviour with help text
bobular 5bd7d1c
fixed broken protein popover with useImperativeHandle deps array
bobular 494e55d
Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth…
bobular 25def36
protein filter and paged table interaction fixed
bobular 075fff3
fixed label display issue in EDA
bobular 470ff89
Convert to function component with simple debounce logic using setTim…
dmfalke 07a8363
Make callbacks stable across renders
dmfalke 0c382ac
Merge remote-tracking branch 'origin/orthogroup-tree-table' into orth…
bobular 997837d
target _blank
bobular 2e76120
fix import path
bobular 6b8f7f4
show table for 1 or 2 protein groups, not the error. Changes to Check…
bobular 5deced2
changes to CheckboxList/SelectList generics 2 of 2
bobular 4557b84
reset button also cancels text search
bobular 2fa75aa
error banner was showing instead of loading spinner for large groups,…
bobular 7ef7b0e
use const for min seqs in tree
bobular d24c342
Merge pull request #1259 from VEuPathDB/orthogroup-tree-table__1254-f…
bobular 81ed37c
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
dmfalke 655c269
Remove style override that is no longer necessary
dmfalke 4a83f7d
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
dmfalke 8abb5d6
Merge remote-tracking branch 'origin/main' into orthogroup-tree-table
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Not using
delayMs
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We should fix and test this before merging, @dmfalke