jbrowse-plugin-protein3d 0.0.4 → 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/AddHighlightModel/HighlightComponents.d.ts +1 -2
- package/dist/AddHighlightModel/HighlightComponents.js.map +1 -1
- package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js +7 -8
- package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map +1 -1
- package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js +8 -4
- package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js.map +1 -1
- package/dist/LaunchProteinView/components/ManualUniProtIDEntry.d.ts +8 -0
- package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js +225 -0
- package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js.map +1 -0
- package/dist/LaunchProteinView/components/UserProvidedStructure.js +1 -1
- package/dist/LaunchProteinView/components/UserProvidedStructure.js.map +1 -1
- package/dist/ProteinView/components/ProteinView.js +1 -1
- package/dist/ProteinView/components/ProteinView.js.map +1 -1
- package/dist/ProteinView/model.d.ts +26 -30
- package/dist/ProteinView/model.js +1 -0
- package/dist/ProteinView/model.js.map +1 -1
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js +1181 -318
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js.map +4 -4
- package/package.json +6 -6
- package/src/AddHighlightModel/HighlightComponents.tsx +1 -3
- package/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx +8 -9
- package/src/LaunchProteinView/components/LaunchProteinViewDialog.tsx +12 -3
- package/src/LaunchProteinView/components/ManualUniProtIDEntry.tsx +332 -0
- package/src/LaunchProteinView/components/UserProvidedStructure.tsx +1 -1
- package/src/ProteinView/components/ProteinView.tsx +1 -1
- package/src/ProteinView/model.ts +1 -0
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@@ -1,7 +1,6 @@
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import React from 'react';
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import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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type LGV = LinearGenomeViewModel;
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declare const HighlightComponents: ({ model, }: {
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model:
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model: LinearGenomeViewModel;
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}) => React.JSX.Element;
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export default HighlightComponents;
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@@ -1 +1 @@
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-
{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS;AACT,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;
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{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS;AACT,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;AAEjE,MAAM,mBAAmB,GAAG,QAAQ,CAAC,SAAS,SAAS,CAAC,EACtD,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,wBAAwB,IAAC,KAAK,EAAE,KAAK,GAAI,CACzC,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,mBAAmB,CAAA"}
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@@ -56,8 +56,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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React.createElement(DialogContent, { className: classes.dialogContent },
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e ? React.createElement(ErrorMessage, { error: e }) : null,
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React.createElement(Typography, null,
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"Automatically find AlphaFoldDB entry for given transcript",
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' ',
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"Automatically find AlphaFoldDB entry for given transcript via gene ID lookup ",
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React.createElement(HelpButton, null)),
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isRemoteStructureSequenceLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading sequence from remote structure file" })) : null,
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isMyGeneLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Looking up UniProt ID from mygene.info" })) : uniprotId ? null : (React.createElement("div", null,
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@@ -146,7 +145,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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assemblyNames: [uniprotId],
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displays: [
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{
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displayId: `${
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displayId: `${s}-LinearBasicDisplay`,
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type: 'LinearBasicDisplay',
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jexlFilters: [`get(feature,'type')=='${type}'`],
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},
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@@ -155,7 +154,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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});
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session.addTrackConf({
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type: 'FeatureTrack',
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trackId:
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trackId: `${uniprotId}-Antigen`,
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name: 'Antigen',
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adapter: {
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type: 'Gff3Adapter',
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@@ -167,7 +166,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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});
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session.addTrackConf({
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type: 'FeatureTrack',
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trackId:
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trackId: `${uniprotId}-Variation`,
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name: 'Variation',
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adapter: {
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type: 'UniProtVariationAdapter',
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@@ -179,7 +178,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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});
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session.addTrackConf({
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type: 'QuantitativeTrack',
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trackId:
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trackId: `${uniprotId}-AlphaFold-confidence`,
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name: 'AlphaFold confidence',
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adapter: {
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type: 'AlphaFoldConfidenceAdapter',
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@@ -191,7 +190,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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});
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session.addTrackConf({
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type: 'MultiQuantitativeTrack',
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trackId:
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trackId: `${uniprotId}-AlphaMissense-scores`,
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name: 'AlphaMissense scores',
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assemblyNames: [uniprotId],
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adapter: {
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@@ -203,7 +202,7 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
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displays: [
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{
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type: 'MultiLinearWiggleDisplay',
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displayId:
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displayId: `${uniprotId}-AlphaMissense-scores-MultiLinearWiggleDisplay`,
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defaultRendering: 'multirowdensity',
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renderers: {
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MultiDensityRenderer: {
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@@ -1 +1 @@
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{"version":3,"file":"AlphaFoldDBSearch.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/AlphaFoldDBSearch.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAGL,iBAAiB,EACjB,UAAU,EACV,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAGhE,SAAS;AACT,OAAO,EACL,cAAc,EACd,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,QAAQ,CAAA;AAEf,aAAa;AACb,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAE/D,QAAQ;AACR,OAAO,4BAA4B,MAAM,gCAAgC,CAAA;AACzE,OAAO,8BAA8B,MAAM,kCAAkC,CAAA;AAC7E,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AAErE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,EACL,WAAW,GAKZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAEjC,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC5D,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,EACJ,gBAAgB,EAChB,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,0BAA0B,CAAC;QAC7B,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,2BAA2B,GAAG,gBAAgB,EAAE,CAAC,aAAa,IAAI,EAAE,CAAC,CAAA;IAC3E,MAAM,EACJ,SAAS,EACT,SAAS,EAAE,eAAe,EAC1B,KAAK,EAAE,WAAW,GACnB,GAAG,4BAA4B,CAAC;QAC/B,EAAE,EAAE,kBAAkB;YACpB,CAAC,CAAC,cAAc,CAAC,kBAAkB,CAAC;YACpC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC;KAC5B,CAAC,CAAA;IAEF,MAAM,GAAG,GAAG,SAAS;QACnB,CAAC,CAAC,wCAAwC,SAAS,kBAAkB;QACrE,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,EACJ,SAAS,EAAE,kBAAkB,EAC7B,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,8BAA8B,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;IAC3C,MAAM,CAAC,GACL,WAAW,IAAI,4BAA4B,IAAI,4BAA4B,CAAA;IAE7E,MAAM,iBAAiB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;IACjD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,gBAAgB,KAAK,SAAS,EAAE,CAAC;YACnC,MAAM,GAAG,GACP,OAAO,CAAC,IAAI,CACV,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;gBACjD,iBAAiB,CACpB,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;YACpD,gBAAgB,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAA;QAC7B,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,CAAC,CAAC,CAAA;IAElD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU;;
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{"version":3,"file":"AlphaFoldDBSearch.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/AlphaFoldDBSearch.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAGL,iBAAiB,EACjB,UAAU,EACV,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAGhE,SAAS;AACT,OAAO,EACL,cAAc,EACd,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,QAAQ,CAAA;AAEf,aAAa;AACb,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAE/D,QAAQ;AACR,OAAO,4BAA4B,MAAM,gCAAgC,CAAA;AACzE,OAAO,8BAA8B,MAAM,kCAAkC,CAAA;AAC7E,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AAErE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,EACL,WAAW,GAKZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAEjC,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC5D,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,EACJ,gBAAgB,EAChB,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,0BAA0B,CAAC;QAC7B,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,2BAA2B,GAAG,gBAAgB,EAAE,CAAC,aAAa,IAAI,EAAE,CAAC,CAAA;IAC3E,MAAM,EACJ,SAAS,EACT,SAAS,EAAE,eAAe,EAC1B,KAAK,EAAE,WAAW,GACnB,GAAG,4BAA4B,CAAC;QAC/B,EAAE,EAAE,kBAAkB;YACpB,CAAC,CAAC,cAAc,CAAC,kBAAkB,CAAC;YACpC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC;KAC5B,CAAC,CAAA;IAEF,MAAM,GAAG,GAAG,SAAS;QACnB,CAAC,CAAC,wCAAwC,SAAS,kBAAkB;QACrE,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,EACJ,SAAS,EAAE,kBAAkB,EAC7B,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,8BAA8B,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;IAC3C,MAAM,CAAC,GACL,WAAW,IAAI,4BAA4B,IAAI,4BAA4B,CAAA;IAE7E,MAAM,iBAAiB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;IACjD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,gBAAgB,KAAK,SAAS,EAAE,CAAC;YACnC,MAAM,GAAG,GACP,OAAO,CAAC,IAAI,CACV,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;gBACjD,iBAAiB,CACpB,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;YACpD,gBAAgB,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAA;QAC7B,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,CAAC,CAAC,CAAA;IAElD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU;;gBAEF,oBAAC,UAAU,OAAG,CACV;YACZ,gCAAgC,CAAC,CAAC,CAAC,CAClC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAC,6CAA6C,GACrD,CACH,CAAC,CAAC,CAAC,IAAI;YACP,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAC,wCAAwC,GAChD,CACH,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACrB;;gBACuD,GAAG;gBACxD,2BACE,IAAI,EAAE,+CAA+C,2BAA2B,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAC3G,MAAM,EAAC,QAAQ,EACf,GAAG,EAAC,YAAY,WAGd;gBAAC,GAAG;gBACR,+BAAM;kGAGF,CACP;YACA,gCAAgC,CAAC,CAAC,CAAC,CAClC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAC,oDAAoD,GAC5D,CACH,CAAC,CAAC,CAAC,IAAI;YACP,gBAAgB,IAAI,iBAAiB,IAAI,kBAAkB,CAAC,CAAC,CAAC,CAC7D;gBACE,oBAAC,kBAAkB,IACjB,GAAG,EAAE,aAAa,IAAI,EAAE,EACxB,MAAM,EAAE,gBAAgB,EACxB,iBAAiB,EAAE,iBAAiB,EACpC,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,OAAO,EACjB,gBAAgB,EAAE,gBAAgB,GAClC;gBACF,oBAAC,uBAAuB,IACtB,SAAS,EAAE,SAAS,EACpB,kBAAkB,EAAE,kBAAkB,EACtC,iBAAiB,EAAE,iBAAiB,EACpC,gBAAgB,EAAE,gBAAgB,GAClC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EACN,CAAC,SAAS,IAAI,CAAC,2BAA2B,IAAI,CAAC,kBAAkB,EAEnE,OAAO,EAAE,GAAG,EAAE;oBACZ,OAAO,CAAC,OAAO,CAAC,aAAa,EAAE;wBAC7B,IAAI,EAAE,aAAa;wBACnB,UAAU,EAAE,IAAI;wBAChB,UAAU,EAAE;4BACV;gCACE,GAAG;gCACH,8BAA8B,EAC5B,2BAA2B,EAAE,GAAG;gCAClC,OAAO,EAAE,kBAAkB,EAAE,MAAM,EAAE;gCACrC,eAAe,EAAE,IAAI,CAAC,EAAE;6BACzB;yBACF;wBACD,WAAW,EAAE;4BACX,cAAc;4BACd,SAAS;4BACT,kBAAkB,CAAC,OAAO,CAAC;4BAC3B,wBAAwB,CAAC,kBAAkB,CAAC;yBAC7C,CAAC,IAAI,CAAC,KAAK,CAAC;qBACd,CAAC,CAAA;oBACF,WAAW,EAAE,CAAA;gBACf,CAAC,wCAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,SAAS,IAAI,CAAC,2BAA2B,IAAI,CAAC,kBAAkB,EAEnE,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,SAAS,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACjD,mEAAmE;wBACnE,CAAC;wBAAA,CAAC,KAAK,IAAI,EAAE;4BACX,IAAI,CAAC;gCACH,OAAO,CAAC,oBAAoB,EAAE,CAAC;oCAC7B,IAAI,EAAE,SAAS;oCACf,QAAQ,EAAE;wCACR,IAAI,EAAE,wBAAwB;wCAC9B,OAAO,EAAE,GAAG,SAAS,yBAAyB;wCAC9C,YAAY,EAAE,KAAK;wCACnB,OAAO,EAAE;4CACP,IAAI,EAAE,uBAAuB;4CAC7B,eAAe,EAAE,4BAA4B;4CAC7C,aAAa,EAAE;gDACb,GAAG,EAAE,sCAAsC,SAAS,QAAQ;6CAC7D;yCACF;qCACF;iCACF,CAAC,CAAA;gCACF,MAAM,GAAG,GAAG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@@ -4,20 +4,24 @@ import { Tab, Tabs } from '@mui/material';
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4
4
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// locals
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5
5
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import AlphaFoldDBSearch from './AlphaFoldDBSearch';
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6
6
|
import UserProvidedStructure from './UserProvidedStructure';
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7
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+
import ManualUniProtIDEntry from './ManualUniProtIDEntry';
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7
8
|
import TabPanel from './TabPanel';
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8
9
|
export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
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9
10
|
const [choice, setChoice] = useState(0);
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10
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-
return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () => {
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11
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+
return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", open: true, onClose: () => {
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11
12
|
handleClose();
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12
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-
}
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13
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+
} },
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13
14
|
React.createElement(Tabs, { value: choice, onChange: (_, val) => {
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setChoice(val);
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} },
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16
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-
React.createElement(Tab, { value: 0, label: "Automatic lookup" }),
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17
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-
React.createElement(Tab, { value: 1, label: "Manual" })
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17
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+
React.createElement(Tab, { value: 0, label: "Automatic UniProt lookup" }),
|
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18
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+
React.createElement(Tab, { value: 1, label: "Manual UniProt entry" }),
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19
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+
React.createElement(Tab, { value: 2, label: "Open file manually" })),
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18
20
|
React.createElement(TabPanel, { value: choice, index: 0 },
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19
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React.createElement(AlphaFoldDBSearch, { model: model, feature: feature, handleClose: handleClose })),
|
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20
22
|
React.createElement(TabPanel, { value: choice, index: 1 },
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23
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+
React.createElement(ManualUniProtIDEntry, { model: model, feature: feature, handleClose: handleClose })),
|
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24
|
+
React.createElement(TabPanel, { value: choice, index: 2 },
|
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21
25
|
React.createElement(UserProvidedStructure, { model: model, feature: feature, handleClose: handleClose }))));
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22
26
|
}
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23
27
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//# sourceMappingURL=LaunchProteinViewDialog.js.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"LaunchProteinViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/LaunchProteinViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAGzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC
|
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1
|
+
{"version":3,"file":"LaunchProteinViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/LaunchProteinViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAGzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC;QAED,oBAAC,IAAI,IACH,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,SAAS,CAAC,GAAG,CAAC,CAAA;YAChB,CAAC;YAED,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,0BAA0B,GAAG;YAClD,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,sBAAsB,GAAG;YAC9C,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,oBAAoB,GAAG,CACvC;QACP,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,iBAAiB,IAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO;QACX,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,oBAAoB,IACnB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO;QACX,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,qBAAqB,IACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO,CACJ,CACV,CAAA;AACH,CAAC"}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
|
|
3
|
+
declare const ManualUniProtIDEntry: ({ feature, model, handleClose, }: {
|
|
4
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+
feature: Feature;
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model: AbstractTrackModel;
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handleClose: () => void;
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}) => React.JSX.Element;
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export default ManualUniProtIDEntry;
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import React, { useEffect, useState } from 'react';
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import { observer } from 'mobx-react';
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import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
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import { makeStyles } from 'tss-react/mui';
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import { getContainingView, getSession, isSessionWithAddTracks, } from '@jbrowse/core/util';
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import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
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// locals
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import { getId, getGeneDisplayName, getTranscriptDisplayName, getTranscriptFeatures, } from './util';
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// components
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import TranscriptSelector from './TranscriptSelector';
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import AlphaFoldDBSearchStatus from './AlphaFoldDBSearchStatus';
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// hooks
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import useRemoteStructureFileSequence from './useRemoteStructureFileSequence';
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import useIsoformProteinSequences from './useIsoformProteinSequences';
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const useStyles = makeStyles()(theme => ({
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dialogContent: {
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marginTop: theme.spacing(6),
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width: '80em',
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},
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}));
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const ManualUniProtIDEntry = observer(function ({ feature, model, handleClose, }) {
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const { classes } = useStyles();
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const session = getSession(model);
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// check if we are looking at a 'two-level' or 'three-level' feature by
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// finding exon/CDS subfeatures. we want to select from transcript names
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const options = getTranscriptFeatures(feature);
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const [userSelection, setUserSelection] = useState();
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const view = getContainingView(model);
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const selectedTranscript = options.find(val => getId(val) === userSelection);
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const { isoformSequences, isLoading: isIsoformProteinSequencesLoading, error: isoformProteinSequencesError, } = useIsoformProteinSequences({
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feature,
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view,
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});
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const userSelectedProteinSequence = isoformSequences?.[userSelection ?? ''];
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const [uniprotId, setUniprotId] = useState('');
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const url = uniprotId
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? `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_v4.cif`
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: undefined;
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const { sequences: structureSequences, isLoading: isRemoteStructureSequenceLoading, error: remoteStructureSequenceError, } = useRemoteStructureFileSequence({ url });
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const e = isoformProteinSequencesError || remoteStructureSequenceError;
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const structureSequence = structureSequences?.[0];
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useEffect(() => {
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if (isoformSequences !== undefined) {
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const ret = options.find(f => isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
|
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structureSequence) ?? options.find(f => !!isoformSequences[f.id()]);
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setUserSelection(ret?.id());
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}
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}, [options, structureSequence, isoformSequences]);
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return (React.createElement(React.Fragment, null,
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React.createElement(DialogContent, { className: classes.dialogContent },
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e ? React.createElement(ErrorMessage, { error: e }) : null,
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React.createElement(Typography, null, "Manually enter a UniProt ID"),
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isRemoteStructureSequenceLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading sequence from remote structure file" })) : null,
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React.createElement(TextField, { label: "UniProt ID", value: uniprotId, onChange: event => {
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setUniprotId(event.target.value);
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} }),
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isIsoformProteinSequencesLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading protein sequences from transcript isoforms" })) : null,
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58
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isoformSequences && structureSequence && selectedTranscript ? (React.createElement(React.Fragment, null,
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React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, structureSequence: structureSequence, feature: feature, isoforms: options, isoformSequences: isoformSequences }),
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React.createElement(AlphaFoldDBSearchStatus, { uniprotId: uniprotId, selectedTranscript: selectedTranscript, structureSequence: structureSequence, isoformSequences: isoformSequences }))) : null),
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React.createElement(DialogActions, null,
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React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
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handleClose();
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} }, "Cancel"),
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React.createElement(Button, { variant: "contained", color: "primary", disabled: !uniprotId || !userSelectedProteinSequence || !selectedTranscript, onClick: () => {
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session.addView('ProteinView', {
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type: 'ProteinView',
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isFloating: true,
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structures: [
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{
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url,
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userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
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feature: selectedTranscript?.toJSON(),
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connectedViewId: view.id,
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},
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],
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displayName: [
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'Protein view',
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uniprotId,
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getGeneDisplayName(feature),
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81
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+
getTranscriptDisplayName(selectedTranscript),
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].join(' - '),
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83
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+
});
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+
handleClose();
|
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85
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+
} }, "Launch 3-D protein structure view"),
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86
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+
React.createElement(Button, { variant: "contained", disabled: !uniprotId || !userSelectedProteinSequence || !selectedTranscript, onClick: () => {
|
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87
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+
if (uniprotId && isSessionWithAddTracks(session)) {
|
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88
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+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
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89
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+
;
|
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90
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+
(async () => {
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try {
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session.addTemporaryAssembly?.({
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name: uniprotId,
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sequence: {
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type: 'ReferenceSequenceTrack',
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96
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+
trackId: `${uniprotId}-ReferenceSequenceTrack`,
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+
sequenceType: 'pep',
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+
adapter: {
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+
type: 'UnindexedFastaAdapter',
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100
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+
rewriteRefNames: "jexl:split(refName,'|')[1]",
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101
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+
fastaLocation: {
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102
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+
uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.fasta`,
|
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103
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+
},
|
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104
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+
},
|
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105
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+
},
|
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106
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+
});
|
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107
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+
const url = `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
|
|
108
|
+
const res = await fetch(url);
|
|
109
|
+
if (!res.ok) {
|
|
110
|
+
throw new Error(`HTTP ${res.status} fetching ${url}`);
|
|
111
|
+
}
|
|
112
|
+
const data = await res.text();
|
|
113
|
+
const types = [
|
|
114
|
+
...new Set(data
|
|
115
|
+
.split('\n')
|
|
116
|
+
.filter(f => !f.startsWith('#'))
|
|
117
|
+
.map(f => f.trim())
|
|
118
|
+
.filter(f => !!f)
|
|
119
|
+
.map(f => f.split('\t')[2])),
|
|
120
|
+
];
|
|
121
|
+
types.forEach(type => {
|
|
122
|
+
const s = `${uniprotId}-${type}`;
|
|
123
|
+
session.addTrackConf({
|
|
124
|
+
type: 'FeatureTrack',
|
|
125
|
+
trackId: s,
|
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126
|
+
name: type,
|
|
127
|
+
adapter: {
|
|
128
|
+
type: 'Gff3Adapter',
|
|
129
|
+
gffLocation: {
|
|
130
|
+
uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`,
|
|
131
|
+
},
|
|
132
|
+
},
|
|
133
|
+
assemblyNames: [uniprotId],
|
|
134
|
+
displays: [
|
|
135
|
+
{
|
|
136
|
+
displayId: `${type}-LinearBasicDisplay`,
|
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137
|
+
type: 'LinearBasicDisplay',
|
|
138
|
+
jexlFilters: [`get(feature,'type')=='${type}'`],
|
|
139
|
+
},
|
|
140
|
+
],
|
|
141
|
+
});
|
|
142
|
+
});
|
|
143
|
+
session.addTrackConf({
|
|
144
|
+
type: 'FeatureTrack',
|
|
145
|
+
trackId: 'Antigen',
|
|
146
|
+
name: 'Antigen',
|
|
147
|
+
adapter: {
|
|
148
|
+
type: 'Gff3Adapter',
|
|
149
|
+
gffLocation: {
|
|
150
|
+
uri: `https://www.ebi.ac.uk/proteins/api/antigen/${uniprotId}?format=gff`,
|
|
151
|
+
},
|
|
152
|
+
},
|
|
153
|
+
assemblyNames: [uniprotId],
|
|
154
|
+
});
|
|
155
|
+
session.addTrackConf({
|
|
156
|
+
type: 'FeatureTrack',
|
|
157
|
+
trackId: 'Variation',
|
|
158
|
+
name: 'Variation',
|
|
159
|
+
adapter: {
|
|
160
|
+
type: 'UniProtVariationAdapter',
|
|
161
|
+
location: {
|
|
162
|
+
uri: `https://www.ebi.ac.uk/proteins/api/variation/${uniprotId}.json`,
|
|
163
|
+
},
|
|
164
|
+
},
|
|
165
|
+
assemblyNames: [uniprotId],
|
|
166
|
+
});
|
|
167
|
+
session.addTrackConf({
|
|
168
|
+
type: 'QuantitativeTrack',
|
|
169
|
+
trackId: 'AlphaFold confidence',
|
|
170
|
+
name: 'AlphaFold confidence',
|
|
171
|
+
adapter: {
|
|
172
|
+
type: 'AlphaFoldConfidenceAdapter',
|
|
173
|
+
location: {
|
|
174
|
+
uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_v4.json`,
|
|
175
|
+
},
|
|
176
|
+
},
|
|
177
|
+
assemblyNames: [uniprotId],
|
|
178
|
+
});
|
|
179
|
+
session.addTrackConf({
|
|
180
|
+
type: 'MultiQuantitativeTrack',
|
|
181
|
+
trackId: 'AlphaMissense scores',
|
|
182
|
+
name: 'AlphaMissense scores',
|
|
183
|
+
assemblyNames: [uniprotId],
|
|
184
|
+
adapter: {
|
|
185
|
+
type: 'AlphaMissensePathogenicityAdapter',
|
|
186
|
+
location: {
|
|
187
|
+
uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
|
|
188
|
+
},
|
|
189
|
+
},
|
|
190
|
+
displays: [
|
|
191
|
+
{
|
|
192
|
+
type: 'MultiLinearWiggleDisplay',
|
|
193
|
+
displayId: 'AlphaMissense scores-MultiLinearWiggleDisplay',
|
|
194
|
+
defaultRendering: 'multirowdensity',
|
|
195
|
+
renderers: {
|
|
196
|
+
MultiDensityRenderer: {
|
|
197
|
+
type: 'MultiDensityRenderer',
|
|
198
|
+
bicolorPivotValue: 0.5,
|
|
199
|
+
},
|
|
200
|
+
},
|
|
201
|
+
},
|
|
202
|
+
],
|
|
203
|
+
});
|
|
204
|
+
const view = session.addView('LinearGenomeView', {
|
|
205
|
+
type: 'LinearGenomeView',
|
|
206
|
+
displayName: [
|
|
207
|
+
'Protein view',
|
|
208
|
+
uniprotId,
|
|
209
|
+
getGeneDisplayName(feature),
|
|
210
|
+
getTranscriptDisplayName(selectedTranscript),
|
|
211
|
+
].join(' - '),
|
|
212
|
+
});
|
|
213
|
+
await view.navToLocString(uniprotId, uniprotId);
|
|
214
|
+
}
|
|
215
|
+
catch (e) {
|
|
216
|
+
console.error(e);
|
|
217
|
+
session.notifyError(`${e}`, e);
|
|
218
|
+
}
|
|
219
|
+
})();
|
|
220
|
+
}
|
|
221
|
+
handleClose();
|
|
222
|
+
} }, "Launch linear protein annotation view"))));
|
|
223
|
+
});
|
|
224
|
+
export default ManualUniProtIDEntry;
|
|
225
|
+
//# sourceMappingURL=ManualUniProtIDEntry.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ManualUniProtIDEntry.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/ManualUniProtIDEntry.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAGL,iBAAiB,EACjB,UAAU,EACV,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAGhE,SAAS;AACT,OAAO,EACL,KAAK,EACL,kBAAkB,EAClB,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,QAAQ,CAAA;AAEf,aAAa;AACb,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAE/D,QAAQ;AACR,OAAO,8BAA8B,MAAM,kCAAkC,CAAA;AAC7E,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AAErE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,OAAO,EACP,KAAK,EACL,WAAW,GAKZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAEjC,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC5D,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,EACJ,gBAAgB,EAChB,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,0BAA0B,CAAC;QAC7B,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,2BAA2B,GAAG,gBAAgB,EAAE,CAAC,aAAa,IAAI,EAAE,CAAC,CAAA;IAC3E,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC9C,MAAM,GAAG,GAAG,SAAS;QACnB,CAAC,CAAC,wCAAwC,SAAS,kBAAkB;QACrE,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,EACJ,SAAS,EAAE,kBAAkB,EAC7B,SAAS,EAAE,gCAAgC,EAC3C,KAAK,EAAE,4BAA4B,GACpC,GAAG,8BAA8B,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;IAC3C,MAAM,CAAC,GAAG,4BAA4B,IAAI,4BAA4B,CAAA;IAEtE,MAAM,iBAAiB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;IACjD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,gBAAgB,KAAK,SAAS,EAAE,CAAC;YACnC,MAAM,GAAG,GACP,OAAO,CAAC,IAAI,CACV,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;gBACjD,iBAAiB,CACpB,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;YACpD,gBAAgB,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAA;QAC7B,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,CAAC,CAAC,CAAA;IAElD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU,sCAAyC;YACnD,gCAAgC,CAAC,CAAC,CAAC,CAClC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAC,6CAA6C,GACrD,CACH,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,SAAS,IACR,KAAK,EAAC,YAAY,EAClB,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAClC,CAAC,GACD;YACD,gCAAgC,CAAC,CAAC,CAAC,CAClC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAC,oDAAoD,GAC5D,CACH,CAAC,CAAC,CAAC,IAAI;YACP,gBAAgB,IAAI,iBAAiB,IAAI,kBAAkB,CAAC,CAAC,CAAC,CAC7D;gBACE,oBAAC,kBAAkB,IACjB,GAAG,EAAE,aAAa,IAAI,EAAE,EACxB,MAAM,EAAE,gBAAgB,EACxB,iBAAiB,EAAE,iBAAiB,EACpC,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,OAAO,EACjB,gBAAgB,EAAE,gBAAgB,GAClC;gBACF,oBAAC,uBAAuB,IACtB,SAAS,EAAE,SAAS,EACpB,kBAAkB,EAAE,kBAAkB,EACtC,iBAAiB,EAAE,iBAAiB,EACpC,gBAAgB,EAAE,gBAAgB,GAClC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EACN,CAAC,SAAS,IAAI,CAAC,2BAA2B,IAAI,CAAC,kBAAkB,EAEnE,OAAO,EAAE,GAAG,EAAE;oBACZ,OAAO,CAAC,OAAO,CAAC,aAAa,EAAE;wBAC7B,IAAI,EAAE,aAAa;wBACnB,UAAU,EAAE,IAAI;wBAChB,UAAU,EAAE;4BACV;gCACE,GAAG;gCACH,8BAA8B,EAC5B,2BAA2B,EAAE,GAAG;gCAClC,OAAO,EAAE,kBAAkB,EAAE,MAAM,EAAE;gCACrC,eAAe,EAAE,IAAI,CAAC,EAAE;6BACzB;yBACF;wBACD,WAAW,EAAE;4BACX,cAAc;4BACd,SAAS;4BACT,kBAAkB,CAAC,OAAO,CAAC;4BAC3B,wBAAwB,CAAC,kBAAkB,CAAC;yBAC7C,CAAC,IAAI,CAAC,KAAK,CAAC;qBACd,CAAC,CAAA;oBACF,WAAW,EAAE,CAAA;gBACf,CAAC,wCAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,SAAS,IAAI,CAAC,2BAA2B,IAAI,CAAC,kBAAkB,EAEnE,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,SAAS,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACjD,mEAAmE;wBACnE,CAAC;wBAAA,CAAC,KAAK,IAAI,EAAE;4BACX,IAAI,CAAC;gCACH,OAAO,CAAC,oBAAoB,EAAE,CAAC;oCAC7B,IAAI,EAAE,SAAS;oCACf,QAAQ,EAAE;wCACR,IAAI,EAAE,wBAAwB;wCAC9B,OAAO,EAAE,GAAG,SAAS,yBAAyB;wCAC9C,YAAY,EAAE,KAAK;wCACnB,OAAO,EAAE;4CACP,IAAI,EAAE,uBAAuB;4CAC7B,eAAe,EAAE,4BAA4B;4CAC7C,aAAa,EAAE;gDACb,GAAG,EAAE,sCAAsC,SAAS,QAAQ;6CAC7D;yCACF;qCACF;iCACF,CAAC,CAAA;gCACF,MAAM,GAAG,GAAG,sCAAsC,SAAS,MAAM,CAAA;gCACjE,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;gCAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oCACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,EAAE,CAAC,CAAA;gCACvD,CAAC;gCACD,MAAM,IAAI,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;gCAE7B,MAAM,KAAK,GAAG;oCACZ,GAAG,IAAI,GAAG,CACR,IAAI;yCACD,KAAK,CAAC,IAAI,CAAC;yCACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC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@@ -132,7 +132,7 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
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setError(e);
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}
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})();
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-
} }, "
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+
} }, "Launch 3-D protein structure view"))));
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});
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export default UserProvidedStructure;
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//# sourceMappingURL=UserProvidedStructure.js.map
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@@ -1 +1 @@
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1
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-
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@@ -30,7 +30,7 @@ const ProteinViewContainer = observer(function ({ model, parentRef, }) {
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30
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height,
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31
31
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} }),
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32
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React.createElement(ResizeHandle, { style: { height: 4, background: 'grey' }, onDrag: delta => {
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33
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-
model.setHeight(model.height + delta);
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33
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+
return model.setHeight(model.height + delta);
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34
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} })));
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35
35
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});
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36
36
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export default ProteinView;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"ProteinView.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAI7D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AAEnD,QAAQ;AACR,OAAO,cAAc,MAAM,mBAAmB,CAAA;AAE9C,MAAM;AACN,OAAO,GAAG,MAAM,gBAAgB,CAAA;AAEhC,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;AAC7C,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACjB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;AAE3B,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC9B,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,cAAc,CAAC;QAClD,YAAY;KACb,CAAC,CAAA;IAEF,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC,CAAA;IACvC,CAAC,EAAE,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAA;IAEnB,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,GAAI,CAC7D,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,EACL,SAAS,GAIV;IACC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEtC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,MAAM,EAAE;QAC/B,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI;QACnC,6BACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,KAAK;gBACL,MAAM;aACP,GACD;QACF,oBAAC,YAAY,IACX,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,UAAU,EAAE,MAAM,EAAE,EACxC,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"ProteinView.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAI7D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AAEnD,QAAQ;AACR,OAAO,cAAc,MAAM,mBAAmB,CAAA;AAE9C,MAAM;AACN,OAAO,GAAG,MAAM,gBAAgB,CAAA;AAEhC,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;AAC7C,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACjB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;AAE3B,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC9B,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,cAAc,CAAC;QAClD,YAAY;KACb,CAAC,CAAA;IAEF,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC,CAAA;IACvC,CAAC,EAAE,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAA;IAEnB,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,GAAI,CAC7D,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,EACL,SAAS,GAIV;IACC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEtC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,MAAM,EAAE;QAC/B,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI;QACnC,6BACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,KAAK;gBACL,MAAM;aACP,GACD;QACF,oBAAC,YAAY,IACX,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,UAAU,EAAE,MAAM,EAAE,EACxC,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,OAAO,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;YAC9C,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
|