@jbrowse/plugin-sequence 2.4.0 → 2.4.2
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 +27 -32
- package/dist/LinearReferenceSequenceDisplay/model.js +2 -2
- package/dist/LinearReferenceSequenceDisplay/model.js.map +1 -1
- 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 +27 -32
- package/esm/LinearReferenceSequenceDisplay/model.js +2 -2
- package/esm/LinearReferenceSequenceDisplay/model.js.map +1 -1
- 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/LinearReferenceSequenceDisplay/model.ts +7 -4
- 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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-
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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-
? 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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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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};
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}[];
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|
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|
} & {
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|
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
|
|
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/**
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|
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|
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|
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|
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|
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|
|
@@ -274,7 +267,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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|
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|
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|
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|
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|
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|
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|
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*/
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|
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|
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|
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|
|
@@ -41,11 +41,11 @@ function modelFactory(configSchema) {
|
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|
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|
* #method
|
|
42
42
|
*/
|
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|
renderProps() {
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|
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const { showForward, showReverse, showTranslation } = self;
|
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|
+
const { showForward, rpcDriverName, showReverse, showTranslation } = self;
|
|
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45
|
return {
|
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|
...superRenderProps(),
|
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|
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|
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47
|
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|
|
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|
+
rpcDriverName,
|
|
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49
|
showForward,
|
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50
|
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|
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|
showTranslation,
|
|
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|
|
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1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":";;;AAAA,qDAAoD;AACpD,kFAG2C;AAC3C,+DAGoC;AACpC,6CAAsD;AACtD,+BAA8B;
|
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1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":";;;AAAA,qDAAoD;AACpD,kFAG2C;AAC3C,+DAGoC;AACpC,6CAAsD;AACtD,+BAA8B;AAI9B;;;GAGG;AACH,SAAgB,YAAY,CAAC,YAAwC;IACnE,OAAO,uBAAK;SACT,OAAO,CACN,gCAAgC,EAChC,6CAAiB,EACjB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,gCAAgC,CAAC;QACrD;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QACnD;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,EAAE,eAAe,EAAE,GAChE,IAAI,CAAA;gBACN,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,aAAa;oBACb,WAAW;oBACX,WAAW;oBACX,eAAe;iBAChB,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,sBAAsB,EAAC,YAAY;YACjC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;YAC3C,OAAO,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,SAAS,CAAA;QACnE,CAAC;QACD;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,qBAAqB;YACnB,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QAC9C,CAAC;QACD,WAAW;YACT,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EAAC,GAAG,EAAE;gBACX,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;gBAC3C,IAAI,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,EAAE;oBACtB,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;iBACnB;qBAAM;oBACL,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBAC1D,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;oBACjB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC1B;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,cAAc;YACZ,OAAO;gBACL;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,qBAAqB,EAAE;iBAC5C;aACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAjID,oCAiIC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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
|
declare function Sequence(props: {
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6
5
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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
|
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
|
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
|
const { letter, codon } = element;
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35
34
|
return (React.createElement(React.Fragment, { key: `${index}-${letter}` },
|
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36
35
|
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
|
|
36
|
+
? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
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38
37
|
: defaultStops.includes(codon)
|
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39
|
-
? theme.palette.stopCodon
|
|
38
|
+
? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
|
|
40
39
|
: map[Math.abs(frame)] }),
|
|
41
40
|
render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
|
|
42
41
|
})));
|
|
@@ -53,7 +52,7 @@ function DNA(props) {
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53
52
|
const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
|
|
54
53
|
return (React.createElement(React.Fragment, { key: index },
|
|
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));
|
|
57
56
|
})));
|
|
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));
|
|
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,
|
|
1
|
+
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muiName: string;
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|
-
};
|
|
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|
-
onClick: () => void;
|
|
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|
-
}[];
|
|
183
|
+
contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
194
184
|
renderProps(): any;
|
|
195
185
|
} & {
|
|
196
186
|
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
|
|
@@ -260,6 +250,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
260
250
|
isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
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251
|
}, {
|
|
262
252
|
renderInProgress: AbortController | undefined;
|
|
253
|
+
/**
|
|
254
|
+
* #method
|
|
255
|
+
*/
|
|
263
256
|
filled: boolean;
|
|
264
257
|
reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
|
|
265
258
|
features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
|
|
@@ -274,7 +267,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
274
267
|
renderProps: any;
|
|
275
268
|
} & {
|
|
276
269
|
doReload(): void;
|
|
277
|
-
afterAttach(): void;
|
|
270
|
+
afterAttach(): void; /**
|
|
271
|
+
* #action
|
|
272
|
+
*/
|
|
278
273
|
setStatus(message: string): void;
|
|
279
274
|
setLoading(abortController: AbortController): void;
|
|
280
275
|
setMessage(messageText: string): void;
|
|
@@ -38,11 +38,11 @@ export function modelFactory(configSchema) {
|
|
|
38
38
|
* #method
|
|
39
39
|
*/
|
|
40
40
|
renderProps() {
|
|
41
|
-
const { showForward, showReverse, showTranslation } = self;
|
|
41
|
+
const { showForward, rpcDriverName, showReverse, showTranslation } = self;
|
|
42
42
|
return {
|
|
43
43
|
...superRenderProps(),
|
|
44
|
-
rpcDriverName: self.rpcDriverName,
|
|
45
44
|
config: self.configuration.renderer,
|
|
45
|
+
rpcDriverName,
|
|
46
46
|
showForward,
|
|
47
47
|
showReverse,
|
|
48
48
|
showTranslation,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EACL,iBAAiB,GAElB,MAAM,oCAAoC,CAAA;AAC3C,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EACL,iBAAiB,GAElB,MAAM,oCAAoC,CAAA;AAC3C,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9B;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,YAAwC;IACnE,OAAO,KAAK;SACT,OAAO,CACN,gCAAgC,EAChC,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,gCAAgC,CAAC;QACrD;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,EAAE,eAAe,EAAE,GAChE,IAAI,CAAA;gBACN,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,aAAa;oBACb,WAAW;oBACX,WAAW;oBACX,eAAe;iBAChB,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,sBAAsB,EAAC,YAAY;YACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;YAC3C,OAAO,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,SAAS,CAAA;QACnE,CAAC;QACD;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,qBAAqB;YACnB,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QAC9C,CAAC;QACD,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;gBAC3C,IAAI,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,EAAE;oBACtB,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;iBACnB;qBAAM;oBACL,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBAC1D,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;oBACjB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC1B;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,cAAc;YACZ,OAAO;gBACL;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,qBAAqB,EAAE;iBAC5C;aACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SequenceSearchAdapter.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/SequenceSearchAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EACL,aAAa,EAGb,MAAM,EACN,cAAc,GACf,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;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,gBAAgB,CAAU,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,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,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,
|
|
1
|
+
{"version":3,"file":"SequenceSearchAdapter.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/SequenceSearchAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EACL,aAAa,EAGb,MAAM,EACN,cAAc,GACf,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;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,gBAAgB,CAAU,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,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,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,cAAc,CAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,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,MAAM,CAAC,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,cAAc,CAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,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"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-sequence",
|
|
3
|
-
"version": "2.4.
|
|
3
|
+
"version": "2.4.2",
|
|
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": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
|
|
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
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+
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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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@@ -10,6 +10,8 @@ import {
|
|
|
10
10
|
import { getContainingView } from '@jbrowse/core/util'
|
|
11
11
|
import { autorun } from 'mobx'
|
|
12
12
|
|
|
13
|
+
type LGV = LinearGenomeViewModel
|
|
14
|
+
|
|
13
15
|
/**
|
|
14
16
|
* #stateModel LinearReferenceSequenceDisplay
|
|
15
17
|
* base model `BaseLinearDisplay`
|
|
@@ -49,11 +51,12 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
|
|
|
49
51
|
* #method
|
|
50
52
|
*/
|
|
51
53
|
renderProps() {
|
|
52
|
-
const { showForward, showReverse, showTranslation } =
|
|
54
|
+
const { showForward, rpcDriverName, showReverse, showTranslation } =
|
|
55
|
+
self
|
|
53
56
|
return {
|
|
54
57
|
...superRenderProps(),
|
|
55
|
-
rpcDriverName: self.rpcDriverName,
|
|
56
58
|
config: self.configuration.renderer,
|
|
59
|
+
rpcDriverName,
|
|
57
60
|
showForward,
|
|
58
61
|
showReverse,
|
|
59
62
|
showTranslation,
|
|
@@ -66,7 +69,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
|
|
|
66
69
|
* #method
|
|
67
70
|
*/
|
|
68
71
|
regionCannotBeRendered(/* region */) {
|
|
69
|
-
const view = getContainingView(self) as
|
|
72
|
+
const view = getContainingView(self) as LGV
|
|
70
73
|
return view?.bpPerPx >= 1 ? 'Zoom in to see sequence' : undefined
|
|
71
74
|
},
|
|
72
75
|
/**
|
|
@@ -99,7 +102,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
|
|
|
99
102
|
addDisposer(
|
|
100
103
|
self,
|
|
101
104
|
autorun(() => {
|
|
102
|
-
const view = getContainingView(self) as
|
|
105
|
+
const view = getContainingView(self) as LGV
|
|
103
106
|
if (view?.bpPerPx >= 1) {
|
|
104
107
|
self.setHeight(50)
|
|
105
108
|
} else {
|
|
@@ -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')
|
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56
56
|
const caseInsensitive = this.getConf('caseInsensitive')
|