react-msaview 5.3.0 → 5.4.1
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/bundle/index.js +22 -22
- package/bundle/index.js.LICENSE.txt +1 -1
- package/bundle/index.js.map +1 -1
- package/dist/components/Checkbox2.js +3 -1
- package/dist/components/Checkbox2.js.map +1 -1
- package/dist/components/Loading.js +6 -4
- package/dist/components/Loading.js.map +1 -1
- package/dist/components/MSAViewer.d.ts +3 -1
- package/dist/components/MSAViewer.js +3 -4
- package/dist/components/MSAViewer.js.map +1 -1
- package/dist/components/dialogs/InterProScanDialog.js +2 -1
- package/dist/components/dialogs/InterProScanDialog.js.map +1 -1
- package/dist/components/msa/renderMSABlock.js +4 -6
- package/dist/components/msa/renderMSABlock.js.map +1 -1
- package/dist/components/renderCtx.d.ts +1 -1
- package/dist/components/tracks/renderTracksSvg.js +1 -1
- package/dist/components/tracks/renderTracksSvg.js.map +1 -1
- package/dist/components/tree/TreeNodeMenu.js +1 -1
- package/dist/components/tree/TreeNodeMenu.js.map +1 -1
- package/dist/components/tree/renderTreeCanvas.d.ts +10 -0
- package/dist/components/tree/renderTreeCanvas.js +84 -12
- package/dist/components/tree/renderTreeCanvas.js.map +1 -1
- package/dist/fetchUtils.d.ts +19 -0
- package/dist/fetchUtils.js +28 -0
- package/dist/fetchUtils.js.map +1 -1
- package/dist/hierarchy.d.ts +9 -1
- package/dist/hierarchy.js +37 -0
- package/dist/hierarchy.js.map +1 -1
- package/dist/model/msaModel.d.ts +7 -0
- package/dist/model/msaModel.js +14 -0
- package/dist/model/msaModel.js.map +1 -1
- package/dist/model.d.ts +9 -4
- package/dist/model.js +95 -32
- package/dist/model.js.map +1 -1
- package/dist/neighborJoining.js +44 -30
- package/dist/neighborJoining.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +5 -5
- package/src/components/Checkbox2.tsx +7 -1
- package/src/components/Loading.tsx +15 -5
- package/src/components/MSAViewer.tsx +5 -3
- package/src/components/dialogs/InterProScanDialog.tsx +2 -1
- package/src/components/msa/renderMSABlock.ts +2 -8
- package/src/components/renderCtx.ts +1 -0
- package/src/components/tracks/renderTracksSvg.ts +1 -1
- package/src/components/tree/TreeNodeMenu.tsx +1 -1
- package/src/components/tree/renderTreeCanvas.ts +117 -11
- package/src/fetchUtils.test.ts +66 -0
- package/src/fetchUtils.ts +48 -0
- package/src/hierarchy.test.ts +56 -0
- package/src/hierarchy.ts +44 -1
- package/src/impgRender.test.tsx +125 -0
- package/src/model/msaModel.ts +21 -0
- package/src/model.ts +99 -55
- package/src/neighborJoining.ts +44 -31
- package/src/version.ts +1 -1
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@@ -2,6 +2,8 @@ import React from 'react';
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import { Checkbox, FormControlLabel } from '@mui/material';
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export default function Checkbox2({ checked, label, disabled, onChange, }) {
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return (React.createElement("div", null,
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React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { disabled: disabled, checked: checked, onChange:
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React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { disabled: disabled, checked: checked, onChange: () => {
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onChange();
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} }), label: label })));
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}
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//# sourceMappingURL=Checkbox2.js.map
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@@ -1 +1 @@
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{"version":3,"file":"Checkbox2.js","sourceRoot":"","sources":["../../src/components/Checkbox2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAA;AAE1D,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,OAAO,EACP,KAAK,EACL,QAAQ,EACR,QAAQ,GAMT;IACC,OAAO,CACL;QACE,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,
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{"version":3,"file":"Checkbox2.js","sourceRoot":"","sources":["../../src/components/Checkbox2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAA;AAE1D,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,OAAO,EACP,KAAK,EACL,QAAQ,EACR,QAAQ,GAMT;IACC,OAAO,CACL;QACE,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,QAAQ,EAAE,QAAQ,EAClB,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,GAAG,EAAE;oBACb,QAAQ,EAAE,CAAA;gBACZ,CAAC,GACD,EAEJ,KAAK,EAAE,KAAK,GACZ,CACE,CACP,CAAA;AACH,CAAC"}
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@@ -5,7 +5,8 @@ import { Button, Typography } from '@mui/material';
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import { observer } from 'mobx-react';
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import MSAView from "./MSAView.js";
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import ImportForm from "./import/ImportForm.js";
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const LoadingSpinner = observer(function ({ model }) {
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const { status } = model;
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return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 12, padding: 20 } },
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React.createElement("svg", { width: "24", height: "24", viewBox: "0 0 24 24", xmlns: "http://www.w3.org/2000/svg" },
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React.createElement("style", null, `@keyframes spinner { to { transform: rotate(360deg); } }`),
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@@ -14,8 +15,9 @@ function LoadingSpinner() {
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animation: 'spinner 1s linear infinite',
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transformOrigin: 'center',
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} })),
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React.createElement(Typography, { variant: "h6" },
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}
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React.createElement(Typography, { variant: "h6" }, status?.msg ?? 'Loading...'),
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status?.onCancel ? (React.createElement(Button, { variant: "outlined", size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null));
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});
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const Reset = observer(function ({ model, error, }) {
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return (React.createElement("div", null,
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React.createElement(ErrorMessage, { error: error }),
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@@ -27,7 +29,7 @@ const Loading = observer(function ({ model }) {
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const { isLoading, dataInitialized, msaFilehandle, treeFilehandle } = model;
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const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
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return (React.createElement("div", null,
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React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner,
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React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
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});
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export default Loading;
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//# sourceMappingURL=Loading.js.map
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@@ -1 +1 @@
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{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,
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{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,OAAO,CACL,6BACE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;QAEtE,6BACE,KAAK,EAAC,IAAI,EACV,MAAM,EAAC,IAAI,EACX,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,4BAA4B;YAElC,mCACG,0DAA0D,CACrD;YACR,gCACE,EAAE,EAAC,IAAI,EACP,EAAE,EAAC,IAAI,EACP,CAAC,EAAC,IAAI,EACN,MAAM,EAAC,MAAM,EACb,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,GACX;YACF,8BACE,CAAC,EAAC,yBAAyB,EAC3B,MAAM,EAAC,SAAS,EAChB,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,EACX,aAAa,EAAC,OAAO,EACrB,KAAK,EAAE;oBACL,SAAS,EAAE,4BAA4B;oBACvC,eAAe,EAAE,QAAQ;iBAC1B,GACD,CACE;QACN,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IAAE,MAAM,EAAE,GAAG,IAAI,YAAY,CAAc;QAClE,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAClB,oBAAC,MAAM,IACL,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAG3B,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,4BAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,aAAa,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAC3E,MAAM,oBAAoB,GAAG,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,CAAC,CAAA;IAEhE,OAAO,CACL;QACE,oBAAC,aAAa,IACZ,iBAAiB,EAAE,CAAC,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,GAAI,IAE9D,eAAe,CAAC,CAAC,CAAC,CACjB,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,oBAAoB,IAAI,SAAS,CAAC,CAAC,CAAC,CACtC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
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@@ -9,6 +9,8 @@ interface MSAViewerProps {
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gffFilehandle?: FileLocationType;
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height?: number;
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/** row name to diff every other row against (matches render as ".") */
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relativeTo?: string;
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}
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export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, }: MSAViewerProps): React.JSX.Element;
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export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, relativeTo, }: MSAViewerProps): React.JSX.Element;
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@@ -4,7 +4,7 @@ import useMeasure from '@jbrowse/core/util/useMeasure';
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import { ThemeProvider } from '@mui/material/styles';
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import MSAModelF from "../model.js";
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import Loading from "./Loading.js";
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export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, }) {
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export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, relativeTo, }) {
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const theme = useMemo(() => createJBrowseTheme(), []);
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const model = useMemo(() => MSAModelF().create({
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...(gffFilehandle ? { gffFilehandle } : {}),
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...(colorScheme ? { colorSchemeName: colorScheme } : {}),
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...(relativeTo ? { relativeTo } : {}),
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}),
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// eslint-disable-next-line react-hooks/exhaustive-deps
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[]);
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});
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}
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{"version":3,"file":"MSAViewer.js","sourceRoot":"","sources":["../../src/components/MSAViewer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,OAAO,CAAA;AAEjD,OAAO,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAA;AAC3D,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AAEpD,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,OAAO,MAAM,cAAe,CAAA;
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{"version":3,"file":"MSAViewer.js","sourceRoot":"","sources":["../../src/components/MSAViewer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,OAAO,CAAA;AAEjD,OAAO,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAA;AAC3D,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AAEpD,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,OAAO,MAAM,cAAe,CAAA;AAiBnC,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,GAAG,EACH,IAAI,EACJ,GAAG,EACH,aAAa,EACb,cAAc,EACd,aAAa,EACb,WAAW,EACX,MAAM,EACN,UAAU,GACK;IACf,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,EAAE,EAAE,EAAE,CAAC,CAAA;IACrD,MAAM,KAAK,GAAG,OAAO,CACnB,GAAG,EAAE,CACH,SAAS,EAAE,CAAC,MAAM,CAAC;QACjB,IAAI,EAAE,SAAS;QACf,GAAG,CAAC,GAAG,IAAI,IAAI,IAAI,GAAG;YACpB,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,EAAE,IAAI,IAAI,EAAE,EAAE,GAAG,EAAE,EAAE;YACrD,CAAC,CAAC,EAAE,CAAC;QACP,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3C,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC7C,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3C,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,eAAe,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACxD,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC7B,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KACtC,CAAC;IACJ,uDAAuD;IACvD,EAAE,CACH,CAAA;IAED,MAAM,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACrC,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;QACvB,CAAC;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IAElB,OAAO,CACL,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK;QACzB,6BAAK,GAAG,EAAE,GAAG;YACX,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrB,CACQ,CACjB,CAAA;AACH,CAAC"}
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import { launchInterProScan } from "../../launchInterProScan.js";
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const InterProScanDialog = observer(function ({ handleClose, model, }) {
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.map(row => [row[0], row[1]
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.map(row => [row[0], getUngappedSequence(row[1])])
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.filter(f => !!f[1])
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.join('\n'),
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-
{"version":3,"file":"InterProScanDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/InterProScanDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;
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1
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{"version":3,"file":"InterProScanDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/InterProScanDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AAEjD,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAA;AAIhE,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC;QAC/B;YACE,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,qCAAqC;YAClD,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,MAAM;YACZ,WAAW,EAAE,qCAAqC;YAClD,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,WAAW,EACT,gEAAgE;YAClE,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,aAAa;YACnB,QAAQ,EAAE,gBAAgB;YAC1B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,uBAAuB;YAC7B,QAAQ,EAAE,gBAAgB;YAC1B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,uBAAuB;YAC7B,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,aAAa;YACnB,QAAQ,EAAE,oBAAoB;YAC9B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,oBAAoB;YAC9B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,iBAAiB;YACvB,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,iBAAiB;YACvB,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,yBAAyB;YACnC,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,KAAK;YACX,WAAW,EAAE,4BAA4B;YACzC,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,YAAY;YAClB,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QAED;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,oCAAoC;SAC/C;KACF,CAAC,CAAA;IAEF,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC7D,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,oCAAoC,EAC1C,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,aAAa;YACZ,oBAAC,UAAU,6FAGE;YACb,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,OAAO,CAAC,CAAC,IAAI,CAAC,CAAA;gBAChB,CAAC;gBAEA,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM;oCAChB;YACR,IAAI,CAAC,CAAC,CAAC,CACN;gBACE,oBAAC,UAAU,oDAAuD;gBAClE;oBACE,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;wBACpD,CAAC,kBAGM;oBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;4BACZ,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;wBACnD,CAAC,iBAGM,CACL;gBACN;oBACE,mCACG,IAAI;yBACF,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;yBACxD,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,CACpC,4BAAI,GAAG,EAAE,IAAI;wBACX;4BACE,+BACE,IAAI,EAAC,UAAU,EACf,GAAG,EAAE,IAAI,EACT,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,GAAG,EAAE;oCACb,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACX,CAAC,CAAC,IAAI,KAAK,IAAI;wCACb,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,OAAO,EAAE;wCAC/B,CAAC,CAAC,CAAC,CACN,CACF,CAAA;gCACH,CAAC,GACD,CACC;wBACL,gCAAK,IAAI,CAAM;wBACf,gCAAK,QAAQ,CAAM,CAChB,CACN,CAAC,CACE,CACF,CACJ,CACP,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,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAEvC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;4BACtB,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;gCACtB,MAAM,IAAI,KAAK,CACb,qDAAqD,CACtD,CAAA;4BACH,CAAC;4BACD,MAAM,kBAAkB,CAAC;gCACvB,SAAS,EAAE,cAAc;gCACzB,QAAQ,EAAE,QAAQ;gCAClB,GAAG,EAAE,IAAI;qCACN,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;qCACjD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;qCACnB,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;qCACnC,IAAI,CAAC,IAAI,CAAC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@@ -28,7 +28,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
|
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28
28
|
ctx,
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29
29
|
theme,
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30
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contrastScheme,
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31
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-
offsetX,
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xStart,
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xEnd,
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visibleLeaves,
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@@ -39,7 +38,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
|
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drawText({
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model,
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ctx,
|
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-
offsetX,
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xStart,
|
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44
42
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xEnd,
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visibleLeaves,
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@@ -55,7 +53,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
|
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55
53
|
});
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54
|
ctx.resetTransform();
|
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55
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}
|
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58
|
-
function drawTilesAndText({ model,
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|
+
function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xStart, xEnd, referenceSeq, }) {
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59
57
|
const { bgColor, colorSchemeName, colorScheme, columns, colWidth, rowHeight, relativeTo, showMsaLetters, colClustalX, colConsensus, } = model;
|
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60
58
|
const isClustalX = colorSchemeName === 'clustalx_protein_dynamic';
|
|
61
59
|
const isPercentIdentity = colorSchemeName === 'percent_identity_dynamic';
|
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@@ -63,7 +61,7 @@ function drawTilesAndText({ model, offsetX, ctx, theme, contrastScheme, visibleL
|
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|
63
61
|
if (!drawBgTiles && !showMsaLetters) {
|
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64
62
|
return;
|
|
65
63
|
}
|
|
66
|
-
const offsetXAligned =
|
|
64
|
+
const offsetXAligned = xStart * colWidth;
|
|
67
65
|
const halfColWidth = colWidth / 2;
|
|
68
66
|
const quarterRowHeight = rowHeight / 4;
|
|
69
67
|
for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
|
|
@@ -110,12 +108,12 @@ function drawTilesAndText({ model, offsetX, ctx, theme, contrastScheme, visibleL
|
|
|
110
108
|
}
|
|
111
109
|
// When domains are shown the background tiles come from renderBoxFeatureCanvasBlock,
|
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112
110
|
// so we only need to draw text here.
|
|
113
|
-
function drawText({ model,
|
|
111
|
+
function drawText({ model, ctx, visibleLeaves, xStart, xEnd, referenceSeq, }) {
|
|
114
112
|
const { showMsaLetters, columns, colWidth, rowHeight, relativeTo } = model;
|
|
115
113
|
if (!showMsaLetters) {
|
|
116
114
|
return;
|
|
117
115
|
}
|
|
118
|
-
const offsetXAligned =
|
|
116
|
+
const offsetXAligned = xStart * colWidth;
|
|
119
117
|
const halfColWidth = colWidth / 2;
|
|
120
118
|
const quarterRowHeight = rowHeight / 4;
|
|
121
119
|
// note: -rowHeight/4 matches +rowHeight/4 in tree
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AACtD,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,sBAAsB,EAAE,MAAM,eAAe,CAAA;AAQtD,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,WAAW,CAAC,GAAG,EAAE,QAAQ,EAAE,CAAC,OAAO,CAAC,CAAA;IAEpC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,EAAE;QACd,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,aAAa,GAAG,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC,CAAA;IAC1E,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACrC,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC9C,CAAC,CAAC,IAAI,CAAA;IAER,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,gBAAgB,CAAC;YACf,KAAK;YACL,GAAG;YACH,KAAK;YACL,cAAc;YACd,MAAM;YACN,IAAI;YACJ,aAAa;YACb,YAAY;SACb,CAAC,CAAA;IACJ,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC;YACP,KAAK;YACL,GAAG;YACH,MAAM;YACN,IAAI;YACJ,aAAa;YACb,YAAY;SACb,CAAC,CAAA;IACJ,CAAC;IACD,uBAAuB,CAAC;QACtB,KAAK;QACL,GAAG;QACH,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,gBAAgB,CAAC,EACxB,KAAK,EACL,GAAG,EACH,KAAK,EACL,cAAc,EACd,aAAa,EACb,MAAM,EACN,IAAI,EACJ,YAAY,GAUb;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,EACT,UAAU,EACV,cAAc,EACd,WAAW,EACX,YAAY,GACb,GAAG,KAAK,CAAA;IAET,MAAM,UAAU,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACjE,MAAM,iBAAiB,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACxE,MAAM,WAAW,GAAG,OAAO,IAAI,UAAU,IAAI,iBAAiB,CAAA;IAC9D,IAAI,CAAC,WAAW,IAAI,CAAC,cAAc,EAAE,CAAC;QACpC,OAAM;IACR,CAAC;IACD,MAAM,cAAc,GAAG,MAAM,GAAG,QAAQ,CAAA;IACxC,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;IACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;IAEtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,IAAI,CAAA;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,SAAQ;QACV,CAAC;QACD,MAAM,KAAK,GAAG,CAAC,GAAG,SAAS,CAAA;QAC3B,MAAM,KAAK,GAAG,CAAC,GAAG,gBAAgB,CAAA;QAElC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;YACtB,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,cAAc,CAAA;YACvC,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;YAEnE,IAAI,KAAyB,CAAA;YAC7B,IAAI,UAAU,EAAE,CAAC;gBACf,KAAK,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,MAAM,CAAC,CAAA;YAC1C,CAAC;iBAAM,IAAI,iBAAiB,EAAE,CAAC;gBAC7B,MAAM,SAAS,GAAG,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;gBAC3C,KAAK,GAAG,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;YACnE,CAAC;iBAAM,CAAC;gBACN,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;YAC7B,CAAC;YAED,IAAI,WAAW,EAAE,CAAC;gBAChB,GAAG,CAAC,SAAS,GAAG,mBAAmB;oBACjC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;oBAC5B,CAAC,CAAC,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;gBAC7C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YAC7C,CAAC;YAED,IAAI,cAAc,EAAE,CAAC;gBACnB,GAAG,CAAC,SAAS,GAAG,OAAO;oBACrB,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,IAAI,OAAO,CAAC;oBACrC,CAAC,CAAC,KAAK;wBACL,CAAC,CAAC,sBAAsB,CAAC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAC;wBACjE,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAA;gBAChC,GAAG,CAAC,QAAQ,CACV,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAClC,CAAC,GAAG,YAAY,EAChB,KAAK,CACN,CAAA;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,qFAAqF;AACrF,qCAAqC;AACrC,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,EACJ,YAAY,GAQb;IACC,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAE1E,IAAI,CAAC,cAAc,EAAE,CAAC;QACpB,OAAM;IACR,CAAC;IACD,MAAM,cAAc,GAAG,MAAM,GAAG,QAAQ,CAAA;IACxC,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;IACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;IACtC,kDAAkD;IAClD,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;IAEvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,IAAI,CAAA;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,GAAG,gBAAgB,CAAA;QACpC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,SAAQ;QACV,CAAC;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,E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@@ -4,4 +4,4 @@
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4
4
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* SVG export) satisfy this, so renderers can be typed against it without an
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5
5
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* `as any` cast at the SVG-export boundary.
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6
6
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*/
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7
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-
export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'clearRect' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'resetTransform' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'translate'>;
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7
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+
export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'clearRect' | 'closePath' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'resetTransform' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'translate'>;
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@@ -25,7 +25,7 @@ export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, b
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25
25
|
const letter = str[i];
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26
26
|
const color = colorScheme[letter.toUpperCase()];
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27
27
|
if (bgColor) {
|
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28
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-
const x =
|
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28
|
+
const x = (xStart + i) * colWidth;
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29
29
|
ctx.fillStyle = color || 'white';
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30
30
|
ctx.fillRect(x, 0, colWidth, rowHeight);
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31
31
|
if (rowHeight >= 10 && colWidth >= rowHeight / 2) {
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"renderTracksSvg.js","sourceRoot":"","sources":["../../../src/components/tracks/renderTracksSvg.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAM3D,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,GAQV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IAEF,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;IACtB,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9D,MAAM,KAAK,GAAG,YAAY,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAA;QACrC,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAA;QACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;IAC/D,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,IAAI,EACJ,WAAW,EACX,cAAc,EACd,OAAO,EACP,QAAQ,EACR,SAAS,EACT,OAAO,EACP,SAAS,GAWV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAErC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;QAC/C,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,CAAC,GAAG,CAAC,
|
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1
|
+
{"version":3,"file":"renderTracksSvg.js","sourceRoot":"","sources":["../../../src/components/tracks/renderTracksSvg.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAM3D,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,GAQV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IAEF,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;IACtB,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9D,MAAM,KAAK,GAAG,YAAY,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAA;QACrC,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAA;QACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;IAC/D,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,IAAI,EACJ,WAAW,EACX,cAAc,EACd,OAAO,EACP,QAAQ,EACR,SAAS,EACT,OAAO,EACP,SAAS,GAWV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAErC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;QAC/C,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAA;YACjC,GAAG,CAAC,SAAS,GAAG,KAAK,IAAI,OAAO,CAAA;YAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACvC,IAAI,SAAS,IAAI,EAAE,IAAI,QAAQ,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;gBACjD,GAAG,CAAC,SAAS,GAAG,cAAc,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,OAAO,CAAA;gBAC/D,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;YAC3D,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,EACtC,KAAK,EACL,GAAG,EACH,OAAO,EACP,OAAO,EACP,WAAW,EACX,kBAAkB,EAClB,0BAA0B,GAS3B;IACC,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,kBAAkB,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAE1D,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;IAEhC,oBAAoB,CAAC;QACnB,GAAG;QACH,YAAY;QACZ,QAAQ;QACR,WAAW;QACX,OAAO;QACP,SAAS,EAAE,EAAE;KACd,CAAC,CAAA;IAEF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAC9B,KAAK,EACL,GAAG,EACH,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,kBAAkB,EAClB,0BAA0B,GAU3B;IACC,MAAM,EACJ,SAAS,EACT,OAAO,EACP,WAAW,EAAE,gBAAgB,EAC7B,QAAQ,EACR,QAAQ,EACR,SAAS,EACT,kBAAkB,GACnB,GAAG,KAAK,CAAA;IAET,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAC/C,MAAM,WAAW,GAAG,iBAAiB,IAAI,gBAAgB,CAAA;IACzD,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAE1D,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;IAChC,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IAE1B,oBAAoB,CAAC;QACnB,GAAG;QACH,IAAI;QACJ,WAAW;QACX,cAAc;QACd,OAAO;QACP,QAAQ;QACR,SAAS;QACT,OAAO;QACP,SAAS,EAAE,EAAE;KACd,CAAC,CAAA;IAEF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAC9B,KAAK,EACL,GAAG,EACH,OAAO,EACP,cAAc,EACd,kBAAkB,EAClB,0BAA0B,GAQ3B;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;IAEhB,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE,CAAC;QACnC,MAAM,WAAW,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAA;QAEtC,IAAI,KAAK,CAAC,KAAK,CAAC,EAAE,KAAK,cAAc,EAAE,CAAC;YACtC,uBAAuB,CAAC;gBACtB,KAAK;gBACL,GAAG;gBACH,OAAO;gBACP,OAAO,EAAE,QAAQ;gBACjB,WAAW;gBACX,kBAAkB;gBAClB,0BAA0B;aAC3B,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,eAAe,CAAC;gBACd,KAAK;gBACL,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO,EAAE,QAAQ;gBACjB,cAAc;gBACd,kBAAkB;gBAClB,0BAA0B;aAC3B,CAAC,CAAA;QACJ,CAAC;QAED,QAAQ,IAAI,WAAW,CAAA;IACzB,CAAC;AACH,CAAC"}
|
|
@@ -27,7 +27,7 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
|
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|
27
27
|
React.createElement(MenuItem, { dense: true, onClick: () => {
|
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model.toggleCollapsed(id);
|
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|
onClose();
|
|
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|
-
} }, isCollapsed ? '
|
|
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|
+
} }, isCollapsed ? 'Expand subtree' : 'Collapse subtree'),
|
|
31
31
|
React.createElement(MenuItem, { dense: true, onClick: () => {
|
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|
model.drawRelativeTo(node.name);
|
|
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onClose();
|
|
@@ -1 +1 @@
|
|
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1
|
-
{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC3B,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IACzB,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC3B,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IACzB,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,kBAAkB,CAC3C;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
|
|
@@ -31,6 +31,16 @@ export declare function renderTree({ offsetY, ctx, model, theme, maxBranchLen, m
|
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|
31
31
|
maxDepthToLeaf: number;
|
|
32
32
|
blockSizeYOverride?: number;
|
|
33
33
|
}): void;
|
|
34
|
+
export declare function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
|
|
35
|
+
ctx: RenderCtx;
|
|
36
|
+
clickMap?: ClickMapIndex;
|
|
37
|
+
offsetY: number;
|
|
38
|
+
model: MsaViewModel;
|
|
39
|
+
theme: Theme;
|
|
40
|
+
maxBranchLen: number;
|
|
41
|
+
maxDepthToLeaf: number;
|
|
42
|
+
blockSizeYOverride?: number;
|
|
43
|
+
}): void;
|
|
34
44
|
export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
|
|
35
45
|
ctx: RenderCtx;
|
|
36
46
|
clickMap?: ClickMapIndex;
|
|
@@ -12,6 +12,9 @@ function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
|
|
|
12
12
|
if (showBranchLen) {
|
|
13
13
|
return node.len;
|
|
14
14
|
}
|
|
15
|
+
if (maxDepthToLeaf === 0) {
|
|
16
|
+
return 0;
|
|
17
|
+
}
|
|
15
18
|
const depthToLeaf = calcDepthToLeaf(node);
|
|
16
19
|
return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * maxBranchLen;
|
|
17
20
|
}
|
|
@@ -41,6 +44,55 @@ export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthT
|
|
|
41
44
|
}
|
|
42
45
|
});
|
|
43
46
|
}
|
|
47
|
+
export function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
|
|
48
|
+
const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, rowHeight, fontSize, marginLeft: ml, } = model;
|
|
49
|
+
const by = blockSizeYOverride ?? blockSize;
|
|
50
|
+
const halfHeight = Math.max(2, rowHeight * 0.42);
|
|
51
|
+
forEachDescendant(hierarchy, node => {
|
|
52
|
+
const { id, name } = node.data;
|
|
53
|
+
if (collapsed.includes(id)) {
|
|
54
|
+
const apexX = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
|
|
55
|
+
const y = node.x;
|
|
56
|
+
const inBlock = y > offsetY - extendBounds && y < offsetY + by + extendBounds;
|
|
57
|
+
// in cladogram mode the hidden tips align at the right edge, otherwise use
|
|
58
|
+
// the branch-length extent recorded in the model's hierarchy getter
|
|
59
|
+
const baseX = showBranchLen
|
|
60
|
+
? (node.collapsedTipXFar ?? maxBranchLen)
|
|
61
|
+
: maxBranchLen;
|
|
62
|
+
if (apexX !== undefined && inBlock && baseX > apexX) {
|
|
63
|
+
ctx.beginPath();
|
|
64
|
+
ctx.moveTo(apexX, y);
|
|
65
|
+
ctx.lineTo(baseX, y - halfHeight);
|
|
66
|
+
ctx.lineTo(baseX, y + halfHeight);
|
|
67
|
+
ctx.closePath();
|
|
68
|
+
ctx.fillStyle = theme.palette.action.disabled;
|
|
69
|
+
ctx.fill();
|
|
70
|
+
ctx.strokeStyle = theme.palette.text.primary;
|
|
71
|
+
ctx.stroke();
|
|
72
|
+
// node.value carries the leaf count from the pre-collapse sum() pass
|
|
73
|
+
const count = node.value;
|
|
74
|
+
if (count !== undefined && rowHeight >= 8) {
|
|
75
|
+
ctx.fillStyle = theme.palette.text.primary;
|
|
76
|
+
ctx.textAlign = 'left';
|
|
77
|
+
ctx.fillText(`${count}`, baseX + 3, y + fontSize / 4);
|
|
78
|
+
}
|
|
79
|
+
// the whole triangle is a click/hover target that opens the
|
|
80
|
+
// branch menu (Expand this node); the apex bubble's own click entry is
|
|
81
|
+
// skipped for collapsed nodes so this descriptive label wins
|
|
82
|
+
const label = name === id ? 'Collapsed clade' : name;
|
|
83
|
+
clickMap?.insert({
|
|
84
|
+
minX: apexX + ml,
|
|
85
|
+
maxX: baseX + ml,
|
|
86
|
+
minY: y - halfHeight,
|
|
87
|
+
maxY: y + halfHeight,
|
|
88
|
+
branch: true,
|
|
89
|
+
id,
|
|
90
|
+
name: count === undefined ? label : `${label} (${count} tips)`,
|
|
91
|
+
});
|
|
92
|
+
}
|
|
93
|
+
}
|
|
94
|
+
});
|
|
95
|
+
}
|
|
44
96
|
export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
|
|
45
97
|
const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
|
|
46
98
|
const by = blockSizeYOverride ?? blockSize;
|
|
@@ -55,26 +107,31 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
|
|
|
55
107
|
if (node.height >= 1 &&
|
|
56
108
|
y > offsetY - extendBounds &&
|
|
57
109
|
y < offsetY + by + extendBounds) {
|
|
110
|
+
const isCollapsed = collapsed.includes(id);
|
|
58
111
|
ctx.strokeStyle = 'black';
|
|
59
|
-
ctx.fillStyle =
|
|
112
|
+
ctx.fillStyle = isCollapsed ? 'black' : 'white';
|
|
60
113
|
ctx.beginPath();
|
|
61
114
|
ctx.arc(x, y, radius, 0, 2 * Math.PI);
|
|
62
115
|
ctx.fill();
|
|
63
116
|
ctx.stroke();
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
117
|
+
// collapsed nodes get their click/hover target from the triangle pass,
|
|
118
|
+
// which covers the apex bubble and carries a descriptive label
|
|
119
|
+
if (!isCollapsed) {
|
|
120
|
+
clickMap?.insert({
|
|
121
|
+
minX: x - radius + ml,
|
|
122
|
+
maxX: x - radius + d + ml,
|
|
123
|
+
minY: y - radius,
|
|
124
|
+
maxY: y - radius + d,
|
|
125
|
+
branch: true,
|
|
126
|
+
id,
|
|
127
|
+
name,
|
|
128
|
+
});
|
|
129
|
+
}
|
|
73
130
|
}
|
|
74
131
|
});
|
|
75
132
|
}
|
|
76
133
|
export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
|
|
77
|
-
const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, labelWidthMap, } = model;
|
|
134
|
+
const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, labelWidthMap, collapsed, } = model;
|
|
78
135
|
const by = blockSizeYOverride ?? blockSize;
|
|
79
136
|
const emHeight = ctx.measureText('M').width;
|
|
80
137
|
if (labelsAlignRight) {
|
|
@@ -88,7 +145,12 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
|
|
|
88
145
|
const { data: { name, id }, } = node;
|
|
89
146
|
const y = node.x;
|
|
90
147
|
const displayName = treeMetadata[name]?.genome || name;
|
|
91
|
-
|
|
148
|
+
// a collapsed clade is drawn as a triangle + tip count; suppress its leaf
|
|
149
|
+
// label when the "name" is just the auto-generated internal-node id
|
|
150
|
+
const isAnonymousCollapsed = collapsed.includes(id) && name === id;
|
|
151
|
+
if (!isAnonymousCollapsed &&
|
|
152
|
+
y > offsetY - extendBounds &&
|
|
153
|
+
y < offsetY + by + extendBounds) {
|
|
92
154
|
// note: +rowHeight/4 matches with -rowHeight/4 in msa
|
|
93
155
|
const yp = y + fontSize / 4;
|
|
94
156
|
let xp = 0;
|
|
@@ -156,6 +218,16 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
|
|
|
156
218
|
maxDepthToLeaf,
|
|
157
219
|
blockSizeYOverride,
|
|
158
220
|
});
|
|
221
|
+
renderCollapsedTriangles({
|
|
222
|
+
ctx,
|
|
223
|
+
clickMap,
|
|
224
|
+
offsetY,
|
|
225
|
+
model,
|
|
226
|
+
theme,
|
|
227
|
+
maxBranchLen,
|
|
228
|
+
maxDepthToLeaf,
|
|
229
|
+
blockSizeYOverride,
|
|
230
|
+
});
|
|
159
231
|
if (drawNodeBubbles) {
|
|
160
232
|
renderNodeBubbles({
|
|
161
233
|
ctx,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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1
|
+
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|
package/dist/fetchUtils.d.ts
CHANGED
|
@@ -1,5 +1,24 @@
|
|
|
1
|
+
import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
|
|
2
|
+
export interface FetchStatus {
|
|
3
|
+
msg: string;
|
|
4
|
+
url?: string;
|
|
5
|
+
onCancel?: () => void;
|
|
6
|
+
}
|
|
7
|
+
type Filehandle = Parameters<typeof fetchAndMaybeUnzipText>[0];
|
|
8
|
+
type ProgressFetcher = (loc: Filehandle, opts: {
|
|
9
|
+
signal: AbortSignal;
|
|
10
|
+
statusCallback: (msg: string) => void;
|
|
11
|
+
}) => Promise<string>;
|
|
12
|
+
/**
|
|
13
|
+
* Fetch text from a filehandle while reporting download/unzip progress through
|
|
14
|
+
* setStatus, and wiring a Cancel handler that aborts the underlying request.
|
|
15
|
+
* The status is always cleared once the fetch settles. The fetcher is injectable
|
|
16
|
+
* for testing.
|
|
17
|
+
*/
|
|
18
|
+
export declare function fetchTextWithProgress(loc: Filehandle, setStatus: (status?: FetchStatus) => void, fetcher?: ProgressFetcher): Promise<string>;
|
|
1
19
|
export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
|
|
2
20
|
export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
|
|
3
21
|
export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
|
|
4
22
|
export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;
|
|
5
23
|
export declare function isAbortError(e: unknown): boolean;
|
|
24
|
+
export {};
|
package/dist/fetchUtils.js
CHANGED
|
@@ -1,3 +1,31 @@
|
|
|
1
|
+
import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
|
|
2
|
+
/**
|
|
3
|
+
* Fetch text from a filehandle while reporting download/unzip progress through
|
|
4
|
+
* setStatus, and wiring a Cancel handler that aborts the underlying request.
|
|
5
|
+
* The status is always cleared once the fetch settles. The fetcher is injectable
|
|
6
|
+
* for testing.
|
|
7
|
+
*/
|
|
8
|
+
export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMaybeUnzipText) {
|
|
9
|
+
const controller = new AbortController();
|
|
10
|
+
try {
|
|
11
|
+
return await fetcher(loc, {
|
|
12
|
+
signal: controller.signal,
|
|
13
|
+
statusCallback: msg => {
|
|
14
|
+
setStatus(msg
|
|
15
|
+
? {
|
|
16
|
+
msg,
|
|
17
|
+
onCancel: () => {
|
|
18
|
+
controller.abort();
|
|
19
|
+
},
|
|
20
|
+
}
|
|
21
|
+
: undefined);
|
|
22
|
+
},
|
|
23
|
+
});
|
|
24
|
+
}
|
|
25
|
+
finally {
|
|
26
|
+
setStatus(undefined);
|
|
27
|
+
}
|
|
28
|
+
}
|
|
1
29
|
export async function myfetch(url, args) {
|
|
2
30
|
const response = await fetch(url, args);
|
|
3
31
|
if (!response.ok) {
|
package/dist/fetchUtils.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/dist/hierarchy.d.ts
CHANGED
|
@@ -11,6 +11,8 @@ export interface HierarchyNode<T = NodeWithIds> {
|
|
|
11
11
|
len?: number;
|
|
12
12
|
depthToLeaf?: number;
|
|
13
13
|
_children?: HierarchyNode<T>[] | null;
|
|
14
|
+
collapsedTipXNear?: number;
|
|
15
|
+
collapsedTipXFar?: number;
|
|
14
16
|
}
|
|
15
17
|
export interface HierarchyLink<T = NodeWithIds> {
|
|
16
18
|
source: HierarchyNode<T>;
|
|
@@ -27,7 +29,13 @@ export declare function forEachLink<T>(node: HierarchyNode<T>, cb: (source: Hier
|
|
|
27
29
|
export declare function forEachDescendant<T>(node: HierarchyNode<T>, cb: (n: HierarchyNode<T>) => void): void;
|
|
28
30
|
export declare function clusterLayout<T>(root: HierarchyNode<T>, sizeX: number, sizeY: number): void;
|
|
29
31
|
export declare function collapse<T>(node: HierarchyNode<T>): void;
|
|
30
|
-
export declare function
|
|
32
|
+
export declare function collapsedSubtreeLengthExtent<T extends {
|
|
33
|
+
length?: number;
|
|
34
|
+
}>(node: HierarchyNode<T>): {
|
|
35
|
+
min: number;
|
|
36
|
+
max: number;
|
|
37
|
+
};
|
|
38
|
+
export declare function calcDepthToLeaf<T>(node: HierarchyNode<T>): number;
|
|
31
39
|
export declare function findMaxBranchLen(node: HierarchyNode): number;
|
|
32
40
|
export declare function maxLength(d: HierarchyNode): number;
|
|
33
41
|
export declare function setBrLength(d: HierarchyNode, y0: number, k: number): void;
|