From 8856770e425bb21f70a63187faf94e7125bddccc Mon Sep 17 00:00:00 2001 From: Colin Date: Tue, 9 Jul 2024 17:21:25 -0400 Subject: [PATCH] Don't show highlight/alignment if exact match --- package.json | 2 +- .../components/AlphaFoldDBSearch.tsx | 23 +- src/LaunchProteinView/index.ts | 2 +- src/ProteinView/components/Header.tsx | 12 +- src/ProteinView/model.ts | 20 +- yarn.lock | 349 ++++++++++-------- 6 files changed, 236 insertions(+), 172 deletions(-) diff --git a/package.json b/package.json index 0740008..d5446f0 100644 --- a/package.json +++ b/package.json @@ -28,7 +28,7 @@ "pako": "^2.1.0" }, "devDependencies": { - "@eslint/compat": "^1.1.0", + "@eslint/compat": "^1.1.1", "@fal-works/esbuild-plugin-global-externals": "^2.1.2", "@jbrowse/core": "^2.0.0", "@jbrowse/plugin-linear-genome-view": "^2.4.2", diff --git a/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx b/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx index 3a2c021..bcba746 100644 --- a/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx +++ b/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx @@ -63,7 +63,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, view, }) - const protein = isoformSequences?.[userSelection ?? ''] + const userSelectedProteinSequence = isoformSequences?.[userSelection ?? ''] const { uniprotId, isLoading: isMyGeneLoading, @@ -116,6 +116,20 @@ const AlphaFoldDBSearch = observer(function ({ variant="h6" message="Looking up UniProt ID from mygene.info" /> + ) : !uniprotId ? ( +
+ UniProt ID not found. Search sequence on AlphaFoldDB{' '} + + here + {' '} +
+ After visiting the above link, then paste the structure URL into the + Manual tab +
) : null} {isIsoformProteinSequencesLoading ? ( { session.addView('ProteinView', { type: 'ProteinView', url, - seq2: protein?.seq, + seq2: userSelectedProteinSequence?.seq, feature: selectedTranscript?.toJSON(), - completeMatch: connectedViewId: view.id, displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`, }) diff --git a/src/LaunchProteinView/index.ts b/src/LaunchProteinView/index.ts index 134def9..3aaae23 100644 --- a/src/LaunchProteinView/index.ts +++ b/src/LaunchProteinView/index.ts @@ -26,7 +26,7 @@ function extendStateModel(stateModel: IAnyModelType) { ...(feature ? [ { - label: 'Launch protein view', + label: 'Launch 3-D protein view', icon: AddIcon, onClick: () => { getSession(track).queueDialog(handleClose => [ diff --git a/src/ProteinView/components/Header.tsx b/src/ProteinView/components/Header.tsx index 7914940..4b6d775 100644 --- a/src/ProteinView/components/Header.tsx +++ b/src/ProteinView/components/Header.tsx @@ -20,11 +20,13 @@ const ProteinViewHeader = observer(function ({ return (
- {showAlignment && alignment ? ( - - ) : ( - - )} + {showAlignment ? ( + alignment ? ( + + ) : ( + + ) + ) : null}
) }) diff --git a/src/ProteinView/model.ts b/src/ProteinView/model.ts index b36b253..9f34fd2 100644 --- a/src/ProteinView/model.ts +++ b/src/ProteinView/model.ts @@ -93,15 +93,15 @@ function stateModelFactory() { /** * #property */ - showHighlight: true, + showHighlight: false, /** * #property */ - zoomToBaseLevel: false, + zoomToBaseLevel: true, /** * #property */ - showAlignment: true, + showAlignment: false, }), ) .volatile(() => ({ @@ -317,6 +317,12 @@ function stateModelFactory() { get structureSeqHoverPos(): number | undefined { return self.hoverPosition?.structureSeqPos }, + + get exactMatch() { + const r1 = self.seq1?.replaceAll('*', '') + const r2 = self.seq2?.replaceAll('*', '') + return r1 === r2 + }, })) .actions(self => ({ afterAttach() { @@ -325,13 +331,13 @@ function stateModelFactory() { self, autorun(async () => { try { - const { seq1, seq2 } = self + const { seq1, seq2, exactMatch } = self if (!!self.alignment || !seq1 || !seq2) { return } const r1 = seq1.replaceAll('*', '') const r2 = seq2.replaceAll('*', '') - if (r1 !== r2) { + if (!exactMatch) { const alignment = await launchPairwiseAlignment({ seq1: r1, seq2: r2, @@ -339,6 +345,10 @@ function stateModelFactory() { onProgress: arg => self.setProgress(arg), }) self.setAlignment(alignment.alignment) + + // showHighlight when we are + self.setShowHighlight(true) + self.setShowAlignment(true) } else { let consensus = '' // eslint-disable-next-line @typescript-eslint/prefer-for-of diff --git a/yarn.lock b/yarn.lock index d6023f4..e947a58 100644 --- a/yarn.lock +++ b/yarn.lock @@ -18,50 +18,50 @@ "@babel/highlight" "^7.24.7" picocolors "^1.0.0" -"@babel/compat-data@^7.24.7": - version "7.24.7" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.24.7.tgz#d23bbea508c3883ba8251fb4164982c36ea577ed" - integrity sha512-qJzAIcv03PyaWqxRgO4mSU3lihncDT296vnyuE2O8uA4w3UHWI4S3hgeZd1L8W1Bft40w9JxJ2b412iDUFFRhw== +"@babel/compat-data@^7.24.8": + version "7.24.8" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.24.8.tgz#f9196455334c38d059ac8b1a16a51decda9d30d3" + integrity sha512-c4IM7OTg6k1Q+AJ153e2mc2QVTezTwnb4VzquwcyiEzGnW0Kedv4do/TrkU98qPeC5LNiMt/QXwIjzYXLBpyZg== "@babel/core@^7.11.6", "@babel/core@^7.12.3", "@babel/core@^7.23.9": - 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version "0.4.7" - resolved "https://registry.yarnpkg.com/eslint-plugin-react-refresh/-/eslint-plugin-react-refresh-0.4.7.tgz#1f597f9093b254f10ee0961c139a749acb19af7d" - integrity sha512-yrj+KInFmwuQS2UQcg1SF83ha1tuHC1jMQbRNyuWtlEzzKRDgAl7L4Yp4NlDUZTZNlWvHEzOtJhMi40R7JxcSw== + version "0.4.8" + resolved "https://registry.yarnpkg.com/eslint-plugin-react-refresh/-/eslint-plugin-react-refresh-0.4.8.tgz#3b1db9188844101213ca637f181e84a016e36732" + integrity sha512-MIKAclwaDFIiYtVBLzDdm16E+Ty4GwhB6wZlCAG1R3Ur+F9Qbo6PRxpA5DK7XtDgm+WlCoAY2WxAwqhmIDHg6Q== eslint-plugin-react@^7.20.3: version "7.34.3" @@ -2860,6 +2872,13 @@ file-saver@^2.0.0: resolved "https://registry.yarnpkg.com/file-saver/-/file-saver-2.0.5.tgz#d61cfe2ce059f414d899e9dd6d4107ee25670c38" integrity sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA== +filelist@^1.0.4: + version "1.0.4" + resolved "https://registry.yarnpkg.com/filelist/-/filelist-1.0.4.tgz#f78978a1e944775ff9e62e744424f215e58352b5" + integrity sha512-w1cEuf3S+DrLCQL7ET6kz+gmlJdbq9J7yXCSjK/OZCPA+qEN1WyF4ZAf0YYJa4/shHJra2t/d/r8SV4Ji+x+8Q== + dependencies: + minimatch "^5.0.1" + fill-range@^7.1.1: version "7.1.1" resolved "https://registry.yarnpkg.com/fill-range/-/fill-range-7.1.1.tgz#44265d3cac07e3ea7dc247516380643754a05292" @@ -3042,9 +3061,9 @@ glob-parent@^6.0.2: is-glob "^4.0.3" glob@^10.3.7: - 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version "10.4.2" - resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-10.4.2.tgz#78c38f194b747174cff90e60afabcae40c3619f2" - integrity sha512-voV4dDrdVZVNz84n39LFKDaRzfwhdzJ7akpyXfTMxCgRUp07U3lcJUXRlhTKP17rgt09sUzLi5iCitpEAr+6ug== + version "10.4.3" + resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-10.4.3.tgz#410fc8a17b70e598013df257c2446b7f3383f119" + integrity sha512-JNAzZcXrCt42VGLuYz0zfAzDfAvJWW6AfYlDBQyDV5DClI2m5sAmK+OIO7s59XfsRsWHp02jAJrRadPRGTt6SQ== lru-cache@^5.1.1: version "5.1.1" @@ -4566,6 +4595,13 @@ minimatch@^3.0.4, minimatch@^3.1.1, minimatch@^3.1.2: dependencies: brace-expansion "^1.1.7" +minimatch@^5.0.1: + version "5.1.6" + resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-5.1.6.tgz#1cfcb8cf5522ea69952cd2af95ae09477f122a96" + integrity sha512-lKwV/1brpG6mBUFHtb7NUmtABCb2WZZmm2wNiOA5hAb8VdCS4B3dtMWyvcoViccwAW/COERjXLt0zP1zXUN26g== + dependencies: + brace-expansion "^2.0.1" + minimatch@^9.0.4: version "9.0.5" resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-9.0.5.tgz#d74f9dd6b57d83d8e98cfb82133b03978bc929e5" @@ -5147,7 +5183,7 @@ react-is@^16.13.1: resolved "https://registry.yarnpkg.com/react-is/-/react-is-16.13.1.tgz#789729a4dc36de2999dc156dd6c1d9c18cea56a4" integrity sha512-24e6ynE2H+OKt4kqsOvNd8kBpV65zoxbA4BVsEOB3ARVWQki/DHzaUoC5KuON/BiccDaCCTZBuOcfZs70kR8bQ== -react-is@^18.0.0, react-is@^18.2.0: +react-is@^18.0.0, react-is@^18.3.1: version "18.3.1" resolved "https://registry.yarnpkg.com/react-is/-/react-is-18.3.1.tgz#e83557dc12eae63a99e003a46388b1dcbb44db7e" integrity sha512-/LLMVyas0ljjAtoYiPqYiL8VWXzUUdThrmU5+n20DZv+a+ClRoevUzw5JxU+Ieh5/c87ytoTBV9G1FiKfNJdmg== @@ -5864,11 +5900,12 @@ ts-api-utils@^1.3.0: integrity sha512-UQMIo7pb8WRomKR1/+MFVLTroIvDVtMX3K6OUir8ynLyzB8Jeriont2bTAtmNPa1ekAgN7YPDyf6V+ygrdU+eQ== ts-jest@^29.1.2: - 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