@jbrowse/plugin-sequence 2.4.0 → 2.4.1
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/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +1 -2
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +4 -5
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +2 -2
- package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js.map +1 -1
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +1 -2
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +4 -5
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/model.d.ts +2 -2
- package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map +1 -1
- package/package.json +2 -2
- package/src/DivSequenceRenderer/components/DivSequenceRendering.tsx +21 -9
- package/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap +21 -21
- package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts +1 -1
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@@ -1,7 +1,6 @@
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/// <reference types="react" />
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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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3
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-
import { Feature } from '@jbrowse/core/util';
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4
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-
import { Region } from '@jbrowse/core/util/types';
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3
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+
import { Feature, Region } from '@jbrowse/core/util';
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declare function Sequence(props: {
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exportSVG?: {
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rasterizeLayers: boolean;
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@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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Object.defineProperty(exports, "__esModule", { value: true });
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/* eslint-disable @typescript-eslint/no-explicit-any */
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const react_1 = __importDefault(require("react"));
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-
const color_1 = require("@jbrowse/core/util/color");
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const ui_1 = require("@jbrowse/core/ui");
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const mobx_react_1 = require("mobx-react");
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const util_1 = require("@jbrowse/core/util");
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@@ -39,9 +38,9 @@ function Translation(props) {
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const { letter, codon } = element;
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return (react_1.default.createElement(react_1.default.Fragment, { key: `${index}-${letter}` },
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react_1.default.createElement("rect", { x: x, y: y, width: render ? w : w + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: render ? '#555' : 'none', fill: util_1.defaultStarts.includes(codon)
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-
? theme.palette.startCodon
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? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
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: util_1.defaultStops.includes(codon)
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44
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-
? theme.palette.stopCodon
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+
? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
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: map[Math.abs(frame)] }),
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render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
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})));
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@@ -58,7 +57,7 @@ function DNA(props) {
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const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
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return (react_1.default.createElement(react_1.default.Fragment, { key: index },
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react_1.default.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
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-
render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ?
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render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
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})));
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}
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const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
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@@ -87,7 +86,7 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
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? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
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: null));
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};
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-
const Wrapper = ({ exportSVG, width, totalHeight, children }) => {
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+
const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
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return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
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};
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function Sequence(props) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"DivSequenceRendering.js","sourceRoot":"","sources":["../../../src/DivSequenceRenderer/components/DivSequenceRendering.tsx"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,kDAAyB;AAEzB,
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+
{"version":3,"file":"DivSequenceRendering.js","sourceRoot":"","sources":["../../../src/DivSequenceRenderer/components/DivSequenceRendering.tsx"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,kDAAyB;AAEzB,yCAAqD;AACrD,2CAAqC;AACrC,6CAU2B;AAG3B,SAAS,WAAW,CAAC,KAUpB;IACC,MAAM,EACJ,UAAU,EACV,GAAG,EACH,KAAK,EACL,OAAO,EACP,MAAM,EACN,MAAM,EACN,CAAC,EACD,OAAO,GAAG,KAAK,EACf,KAAK,GACN,GAAG,KAAK,CAAA;IACT,MAAM,KAAK,GAAG,OAAO,CAAA;IAErB,wEAAwE;IACxE,4CAA4C;IAC5C,MAAM,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;IAEnC,qEAAqE;IACrE,2EAA2E;IAC3E,4CAA4C;IAC5C,MAAM,cAAc,GAAG,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;IAE7C,MAAM,SAAS,GAAG,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,CAAA;IAE3C,MAAM,UAAU,GAAwC,EAAE,CAAA;IAC1D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAC5C,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACvC,MAAM,eAAe,GAAG,OAAO,CAAC,CAAC,CAAC,IAAA,aAAM,EAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;QACvD,MAAM,SAAS,GAAG,UAAU,CAAC,eAAe,CAAC,IAAI,EAAE,CAAA;QACnD,UAAU,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,eAAe,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;KAC7E;IAED,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,CAAC,GAAG,OAAO,IAAI,EAAE,CAAA;IAChC,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IAEnD,MAAM,GAAG,GAAG,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC,CAAC,OAAO,EAAE,CAAA;IACvD,OAAO,CACL,8DACG,UAAU,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,KAAK,EAAE,EAAE;QACjC,MAAM,CAAC,GAAG,MAAM,CAAC,QAAQ;YACvB,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,cAAc,GAAG,KAAK,GAAG,IAAI,CAAC;YAC3D,CAAC,CAAC,CAAC,GAAG,KAAK,GAAG,cAAc,GAAG,KAAK,GAAG,IAAI,CAAA;QAC7C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;QACjC,OAAO,CACL,8BAAC,eAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,KAAK,IAAI,MAAM,EAAE;YACvC,wCACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EACH,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,uCAAuC,EAE9D,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAChC,IAAI,EACF,oBAAa,CAAC,QAAQ,CAAC,KAAK,CAAC;oBAC3B,CAAC,CAAC,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,OAAO,CAAC,UAAU;oBAC3B,CAAC,CAAC,mBAAY,CAAC,QAAQ,CAAC,KAAK,CAAC;wBAC9B,CAAC,CAAC,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,OAAO,CAAC,SAAS;wBAC1B,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,GAE1B;YACD,MAAM,CAAC,CAAC,CAAC,CACR,wCACE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EACZ,CAAC,EAAE,CAAC,GAAG,MAAM,GAAG,CAAC,EACjB,gBAAgB,EAAC,QAAQ,EACzB,UAAU,EAAC,QAAQ,IAElB,MAAM,CACF,CACR,CAAC,CAAC,CAAC,IAAI,CACO,CAClB,CAAA;IACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,GAAG,CAAC,KAQZ;IACC,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,KAAK,CAAA;IACjE,MAAM,MAAM,GAAG,CAAC,GAAG,OAAO,IAAI,EAAE,CAAA;IAEhC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,eAAQ,EAChC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,EACpB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAClB,MAAM,EACN,OAAO,CACR,CAAA;IACD,MAAM,OAAO,GAAG,MAAM,CAAC,QAAQ,CAAA;IAC/B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACrD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,OAAO,GAAG,MAAM,CAAC,GAAG,GAAG,EAAE,GAAG,CAAC,CAAA;IAEjD,OAAO,CACL,8DACG,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;QACnC,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;QACvD,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;QAClE,OAAO,CACL,8BAAC,eAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,KAAK;YACxB,wCACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,EACjC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAChC;YACD,MAAM,CAAC,CAAC,CAAC,CACR,wCACE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EACZ,CAAC,EAAE,CAAC,GAAG,MAAM,GAAG,CAAC,EACjB,gBAAgB,EAAC,QAAQ,EACzB,UAAU,EAAC,QAAQ,EACnB,IAAI,EACF,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,IAG5D,MAAM,CACF,CACR,CAAC,CAAC,CAAC,IAAI,CACO,CAClB,CAAA;IACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,MAAM,WAAW,GAAG,CAAC,EACnB,OAAO,EACP,KAAK,EAAE,WAAW,EAClB,QAAQ,GAAG,IAAI,GAAG,EAAE,EACpB,WAAW,GAAG,IAAI,EAClB,WAAW,GAAG,IAAI,EAClB,eAAe,GAAG,IAAI,EACtB,OAAO,GACH,EAAE,EAAE;IACR,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;IACxB,MAAM,KAAK,GAAG,IAAA,uBAAkB,EAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,UAAU,GAAG,IAAA,yBAAkB,EAAC,wBAAiB,CAAC,CAAA;IACxD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IACxC,IAAI,CAAC,OAAO,EAAE;QACZ,OAAO,IAAI,CAAA;KACZ;IACD,MAAM,GAAG,GAAW,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IACtC,IAAI,CAAC,GAAG,EAAE;QACR,OAAO,IAAI,CAAA;KACZ;IAED,wEAAwE;IACxE,kDAAkD;IAClD,IAAI,KAAK,GAAG,CAAC,EAAE,CAAA;IAEf,OAAO,CACL;QAGG,eAAe,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC;YAC/D,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACrB,8BAAC,WAAW,IACV,GAAG,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@@ -132,7 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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} & {
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readonly height:
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readonly height: number;
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readonly blockType: "dynamicBlocks" | "staticBlocks";
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readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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} & {
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setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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clearRegionStats(): void;
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setHeight(displayHeight: number):
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setHeight(displayHeight: number): number;
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resizeHeight(distance: number): number;
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setScrollTop(scrollTop: number): void;
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updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
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-
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|
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1
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+
{"version":3,"file":"SequenceSearchAdapter.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/SequenceSearchAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,kDAA0D;AAC1D,6CAM2B;AAC3B,8CAAwC;AACxC,+BAAqC;AAErC,eAAqB,SAAQ,oCAAsB;IAC1C,KAAK,CAAC,SAAS;;QACpB,MAAM,OAAO,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAC,CAAA,CAAA;QAC3E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,OAAO,OAAO,CAAC,WAAqC,CAAA;IACtD,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,IAAiB;QACjD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,EAAE,GAAG,IAAI,CAAA;YACf,IAAI,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;YAChD,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,UAAU,GAAG,EAAE,CAAC,CAAA;YACzC,QAAQ,IAAI,EAAE,CAAA;YAEd,IAAI,QAAQ,GAAG,CAAC,IAAI,UAAU,GAAG,QAAQ,EAAE;gBACzC,QAAQ,CAAC,QAAQ,EAAE,CAAA;gBACnB,OAAM;aACP;YAED,MAAM,GAAG,GAAG,eAAe,CAAC,WAAW,CACrC;gBACE,GAAG,KAAK;gBACR,KAAK,EAAE,UAAU;gBACjB,GAAG,EAAE,QAAQ;aACd,EACD,IAAI,CACL,CAAA;YACD,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAAC,GAAG,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;YACvD,MAAM,QAAQ,GAAW,CAAA,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,KAAI,EAAE,CAAA;YACnD,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAW,CAAA;YAC/C,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;YACnD,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;YACvD,MAAM,EAAE,GAAG,IAAI,MAAM,CAAC,MAAM,EAAE,GAAG,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;YAEjE,IAAI,MAAM,EAAE;gBACV,IAAI,aAAa,EAAE;oBACjB,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;oBACrC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE;wBAC3B,MAAM,CAAC,GAAG,UAAU,GAAG,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAA;wBAEzC,IAAI,IAAA,qBAAc,EAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;gCAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,UAAU,CAAC,IAAI;gCACnC,OAAO,EAAE,KAAK,CAAC,OAAO;gCACtB,KAAK,EAAE,CAAC;gCACR,GAAG,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;gCACxB,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC;gCACd,MAAM,EAAE,CAAC;6BACV,CAAC,CACH,CAAA;yBACF;qBACF;iBACF;gBACD,IAAI,aAAa,EAAE;oBACjB,MAAM,OAAO,GAAG,IAAA,aAAM,EAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;oBAC7C,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE;wBAC3B,MAAM,CAAC,GAAG,QAAQ,GAAG,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAA;wBACvC,IAAI,IAAA,qBAAc,EAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;gCAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,UAAU,CAAC,IAAI;gCACnC,OAAO,EAAE,KAAK,CAAC,OAAO;gCACtB,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;gCAC1B,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC;gCACd,GAAG,EAAE,CAAC;gCACN,MAAM,EAAE,CAAC,CAAC;6BACX,CAAC,CACH,CAAA;yBACF;qBACF;iBACF;aACF;YAED,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,KAAI,CAAC;CAC1B;AAxFD,4BAwFC"}
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@@ -1,7 +1,6 @@
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1
1
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/// <reference types="react" />
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2
2
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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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3
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-
import { Feature } from '@jbrowse/core/util';
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4
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-
import { Region } from '@jbrowse/core/util/types';
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3
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+
import { Feature, Region } from '@jbrowse/core/util';
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5
4
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declare function Sequence(props: {
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6
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exportSVG?: {
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7
6
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rasterizeLayers: boolean;
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@@ -1,6 +1,5 @@
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1
1
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/* eslint-disable @typescript-eslint/no-explicit-any */
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2
2
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import React from 'react';
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3
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-
import { contrastingTextColor } from '@jbrowse/core/util/color';
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4
3
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import { createJBrowseTheme } from '@jbrowse/core/ui';
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5
4
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import { observer } from 'mobx-react';
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6
5
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import { bpSpanPx, revcom, complement, defaultStarts, defaultStops, defaultCodonTable, generateCodonTable, } from '@jbrowse/core/util';
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@@ -34,9 +33,9 @@ function Translation(props) {
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34
33
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const { letter, codon } = element;
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35
34
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return (React.createElement(React.Fragment, { key: `${index}-${letter}` },
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36
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React.createElement("rect", { x: x, y: y, width: render ? w : w + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: render ? '#555' : 'none', fill: defaultStarts.includes(codon)
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37
|
-
? theme.palette.startCodon
|
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36
|
+
? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
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38
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|
: defaultStops.includes(codon)
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39
|
-
? theme.palette.stopCodon
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38
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+
? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
|
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40
39
|
: map[Math.abs(frame)] }),
|
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41
40
|
render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
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42
41
|
})));
|
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@@ -53,7 +52,7 @@ function DNA(props) {
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53
52
|
const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
|
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54
53
|
return (React.createElement(React.Fragment, { key: index },
|
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55
54
|
React.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
|
|
56
|
-
render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ?
|
|
55
|
+
render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
|
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57
56
|
})));
|
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58
57
|
}
|
|
59
58
|
const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
|
|
@@ -82,7 +81,7 @@ const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showRe
|
|
|
82
81
|
? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
|
|
83
82
|
: null));
|
|
84
83
|
};
|
|
85
|
-
const Wrapper = ({ exportSVG, width, totalHeight, children }) => {
|
|
84
|
+
const Wrapper = ({ exportSVG, width, totalHeight, children, }) => {
|
|
86
85
|
return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
|
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87
86
|
};
|
|
88
87
|
function Sequence(props) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"DivSequenceRendering.js","sourceRoot":"","sources":["../../../src/DivSequenceRenderer/components/DivSequenceRendering.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,
|
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1
|
+
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@@ -132,7 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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133
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estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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} & {
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135
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-
readonly height:
|
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135
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+
readonly height: number;
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|
readonly blockType: "dynamicBlocks" | "staticBlocks";
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137
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readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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138
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|
} & {
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@@ -162,7 +162,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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162
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setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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164
164
|
clearRegionStats(): void;
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165
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-
setHeight(displayHeight: number):
|
|
165
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+
setHeight(displayHeight: number): number;
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166
166
|
resizeHeight(distance: number): number;
|
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167
167
|
setScrollTop(scrollTop: number): void;
|
|
168
168
|
updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
|
|
@@ -1 +1 @@
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1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-sequence",
|
|
3
|
-
"version": "2.4.
|
|
3
|
+
"version": "2.4.1",
|
|
4
4
|
"description": "JBrowse 2 sequence adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -58,5 +58,5 @@
|
|
|
58
58
|
"distModule": "esm/index.js",
|
|
59
59
|
"srcModule": "src/index.ts",
|
|
60
60
|
"module": "esm/index.js",
|
|
61
|
-
"gitHead": "
|
|
61
|
+
"gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
|
|
62
62
|
}
|
|
@@ -1,12 +1,11 @@
|
|
|
1
1
|
/* eslint-disable @typescript-eslint/no-explicit-any */
|
|
2
2
|
import React from 'react'
|
|
3
3
|
import { AnyConfigurationModel } from '@jbrowse/core/configuration'
|
|
4
|
-
import { contrastingTextColor } from '@jbrowse/core/util/color'
|
|
5
|
-
import { Feature } from '@jbrowse/core/util'
|
|
6
|
-
import { Region } from '@jbrowse/core/util/types'
|
|
7
4
|
import { createJBrowseTheme } from '@jbrowse/core/ui'
|
|
8
5
|
import { observer } from 'mobx-react'
|
|
9
6
|
import {
|
|
7
|
+
Feature,
|
|
8
|
+
Region,
|
|
10
9
|
bpSpanPx,
|
|
11
10
|
revcom,
|
|
12
11
|
complement,
|
|
@@ -15,9 +14,10 @@ import {
|
|
|
15
14
|
defaultCodonTable,
|
|
16
15
|
generateCodonTable,
|
|
17
16
|
} from '@jbrowse/core/util'
|
|
17
|
+
import { Theme } from '@mui/material'
|
|
18
18
|
|
|
19
19
|
function Translation(props: {
|
|
20
|
-
codonTable:
|
|
20
|
+
codonTable: Record<string, string>
|
|
21
21
|
seq: string
|
|
22
22
|
frame: number
|
|
23
23
|
bpPerPx: number
|
|
@@ -25,7 +25,7 @@ function Translation(props: {
|
|
|
25
25
|
reverse?: boolean
|
|
26
26
|
height: number
|
|
27
27
|
y: number
|
|
28
|
-
theme?:
|
|
28
|
+
theme?: Theme
|
|
29
29
|
}) {
|
|
30
30
|
const {
|
|
31
31
|
codonTable,
|
|
@@ -84,9 +84,9 @@ function Translation(props: {
|
|
|
84
84
|
stroke={render ? '#555' : 'none'}
|
|
85
85
|
fill={
|
|
86
86
|
defaultStarts.includes(codon)
|
|
87
|
-
? theme
|
|
87
|
+
? theme?.palette.startCodon
|
|
88
88
|
: defaultStops.includes(codon)
|
|
89
|
-
? theme
|
|
89
|
+
? theme?.palette.stopCodon
|
|
90
90
|
: map[Math.abs(frame)]
|
|
91
91
|
}
|
|
92
92
|
/>
|
|
@@ -150,7 +150,9 @@ function DNA(props: {
|
|
|
150
150
|
y={y + height / 2}
|
|
151
151
|
dominantBaseline="middle"
|
|
152
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|
textAnchor="middle"
|
|
153
|
-
fill={
|
|
153
|
+
fill={
|
|
154
|
+
color ? theme.palette.getContrastText(color.main) : 'black'
|
|
155
|
+
}
|
|
154
156
|
>
|
|
155
157
|
{letter}
|
|
156
158
|
</text>
|
|
@@ -255,7 +257,17 @@ const SequenceSVG = ({
|
|
|
255
257
|
)
|
|
256
258
|
}
|
|
257
259
|
|
|
258
|
-
const Wrapper = ({
|
|
260
|
+
const Wrapper = ({
|
|
261
|
+
exportSVG,
|
|
262
|
+
width,
|
|
263
|
+
totalHeight,
|
|
264
|
+
children,
|
|
265
|
+
}: {
|
|
266
|
+
exportSVG?: { rasterizeLayers: boolean }
|
|
267
|
+
width: number
|
|
268
|
+
totalHeight: number
|
|
269
|
+
children: React.ReactNode
|
|
270
|
+
}) => {
|
|
259
271
|
return exportSVG ? (
|
|
260
272
|
<>{children}</>
|
|
261
273
|
) : (
|
|
@@ -144,7 +144,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
144
144
|
/>
|
|
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|
<text
|
|
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|
dominant-baseline="middle"
|
|
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|
-
fill="
|
|
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|
+
fill="#fff"
|
|
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|
text-anchor="middle"
|
|
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149
|
x="19970"
|
|
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|
y="70"
|
|
@@ -169,7 +169,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
169
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|
B
|
|
170
170
|
</text>
|
|
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|
<rect
|
|
172
|
-
fill="#
|
|
172
|
+
fill="#ff9800"
|
|
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173
|
height="20"
|
|
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|
stroke="#555"
|
|
175
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|
width="20"
|
|
@@ -178,7 +178,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
178
178
|
/>
|
|
179
179
|
<text
|
|
180
180
|
dominant-baseline="middle"
|
|
181
|
-
fill="
|
|
181
|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
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|
text-anchor="middle"
|
|
183
183
|
x="19930"
|
|
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|
y="70"
|
|
@@ -246,7 +246,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
246
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|
/>
|
|
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|
<text
|
|
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|
dominant-baseline="middle"
|
|
249
|
-
fill="
|
|
249
|
+
fill="#fff"
|
|
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|
text-anchor="middle"
|
|
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|
x="19850"
|
|
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252
|
y="70"
|
|
@@ -297,7 +297,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
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|
/>
|
|
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|
<text
|
|
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|
dominant-baseline="middle"
|
|
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|
-
fill="
|
|
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|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
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|
text-anchor="middle"
|
|
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|
x="19970"
|
|
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|
y="90"
|
|
@@ -331,7 +331,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
331
331
|
/>
|
|
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332
|
<text
|
|
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|
dominant-baseline="middle"
|
|
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|
-
fill="
|
|
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|
+
fill="#fff"
|
|
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|
text-anchor="middle"
|
|
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|
x="19930"
|
|
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337
|
y="90"
|
|
@@ -390,7 +390,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
390
390
|
F
|
|
391
391
|
</text>
|
|
392
392
|
<rect
|
|
393
|
-
fill="#
|
|
393
|
+
fill="#ff9800"
|
|
394
394
|
height="20"
|
|
395
395
|
stroke="#555"
|
|
396
396
|
width="20"
|
|
@@ -399,7 +399,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
|
|
|
399
399
|
/>
|
|
400
400
|
<text
|
|
401
401
|
dominant-baseline="middle"
|
|
402
|
-
fill="
|
|
402
|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
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403
|
text-anchor="middle"
|
|
404
404
|
x="19850"
|
|
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|
y="90"
|
|
@@ -714,7 +714,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
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|
/>
|
|
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|
<text
|
|
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|
dominant-baseline="middle"
|
|
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|
-
fill="
|
|
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|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
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|
text-anchor="middle"
|
|
719
719
|
x="30"
|
|
720
720
|
y="70"
|
|
@@ -748,7 +748,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
748
748
|
/>
|
|
749
749
|
<text
|
|
750
750
|
dominant-baseline="middle"
|
|
751
|
-
fill="
|
|
751
|
+
fill="#fff"
|
|
752
752
|
text-anchor="middle"
|
|
753
753
|
x="70"
|
|
754
754
|
y="70"
|
|
@@ -807,7 +807,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
807
807
|
F
|
|
808
808
|
</text>
|
|
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809
|
<rect
|
|
810
|
-
fill="#
|
|
810
|
+
fill="#ff9800"
|
|
811
811
|
height="20"
|
|
812
812
|
stroke="#555"
|
|
813
813
|
width="20"
|
|
@@ -816,7 +816,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
816
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|
/>
|
|
817
817
|
<text
|
|
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|
dominant-baseline="middle"
|
|
819
|
-
fill="
|
|
819
|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
820
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|
text-anchor="middle"
|
|
821
821
|
x="150"
|
|
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|
y="70"
|
|
@@ -867,7 +867,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
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|
/>
|
|
868
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|
<text
|
|
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869
|
dominant-baseline="middle"
|
|
870
|
-
fill="
|
|
870
|
+
fill="#fff"
|
|
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|
text-anchor="middle"
|
|
872
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|
x="30"
|
|
873
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|
y="90"
|
|
@@ -892,7 +892,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
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|
B
|
|
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|
</text>
|
|
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|
<rect
|
|
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|
-
fill="#
|
|
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|
+
fill="#ff9800"
|
|
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|
height="20"
|
|
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|
stroke="#555"
|
|
898
898
|
width="20"
|
|
@@ -901,7 +901,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
901
901
|
/>
|
|
902
902
|
<text
|
|
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903
|
dominant-baseline="middle"
|
|
904
|
-
fill="
|
|
904
|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
905
905
|
text-anchor="middle"
|
|
906
906
|
x="70"
|
|
907
907
|
y="90"
|
|
@@ -969,7 +969,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
|
|
|
969
969
|
/>
|
|
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970
|
<text
|
|
971
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|
dominant-baseline="middle"
|
|
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|
-
fill="
|
|
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|
+
fill="#fff"
|
|
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|
text-anchor="middle"
|
|
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|
x="150"
|
|
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|
y="90"
|
|
@@ -1200,7 +1200,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
|
|
|
1200
1200
|
/>
|
|
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|
<text
|
|
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1202
|
dominant-baseline="middle"
|
|
1203
|
-
fill="
|
|
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|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
1204
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|
text-anchor="middle"
|
|
1205
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|
x="30"
|
|
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|
y="70"
|
|
@@ -1234,7 +1234,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
|
|
|
1234
1234
|
/>
|
|
1235
1235
|
<text
|
|
1236
1236
|
dominant-baseline="middle"
|
|
1237
|
-
fill="
|
|
1237
|
+
fill="#fff"
|
|
1238
1238
|
text-anchor="middle"
|
|
1239
1239
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x="70"
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1240
1240
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y="70"
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@@ -1251,7 +1251,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
|
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1251
1251
|
/>
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1252
1252
|
<text
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|
1253
1253
|
dominant-baseline="middle"
|
|
1254
|
-
fill="
|
|
1254
|
+
fill="#fff"
|
|
1255
1255
|
text-anchor="middle"
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1256
1256
|
x="30"
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1257
1257
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y="90"
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@@ -1276,7 +1276,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
|
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1276
1276
|
B
|
|
1277
1277
|
</text>
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1278
1278
|
<rect
|
|
1279
|
-
fill="#
|
|
1279
|
+
fill="#ff9800"
|
|
1280
1280
|
height="20"
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1281
1281
|
stroke="#555"
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1282
1282
|
width="20"
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@@ -1285,7 +1285,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
|
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1285
1285
|
/>
|
|
1286
1286
|
<text
|
|
1287
1287
|
dominant-baseline="middle"
|
|
1288
|
-
fill="
|
|
1288
|
+
fill="rgba(0, 0, 0, 0.87)"
|
|
1289
1289
|
text-anchor="middle"
|
|
1290
1290
|
x="70"
|
|
1291
1291
|
y="90"
|
|
@@ -50,7 +50,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
50
50
|
)
|
|
51
51
|
const feats = await firstValueFrom(ret.pipe(toArray()))
|
|
52
52
|
const residues: string = feats[0]?.get('seq') || ''
|
|
53
|
-
const search = this.getConf('search')
|
|
53
|
+
const search = this.getConf('search') as string
|
|
54
54
|
const searchForward = this.getConf('searchForward')
|
|
55
55
|
const searchReverse = this.getConf('searchReverse')
|
|
56
56
|
const caseInsensitive = this.getConf('caseInsensitive')
|