@jbrowse/plugin-sequence 2.3.2 → 2.3.4
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 +8 -10
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +1 -1
- package/dist/DivSequenceRenderer/components/DivSequenceRendering.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +1 -3
- package/dist/LinearReferenceSequenceDisplay/model.js +13 -5
- package/dist/LinearReferenceSequenceDisplay/model.js.map +1 -1
- package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js +2 -1
- package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js.map +1 -1
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +8 -10
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +1 -1
- package/esm/DivSequenceRenderer/components/DivSequenceRendering.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/model.d.ts +1 -3
- package/esm/LinearReferenceSequenceDisplay/model.js +13 -5
- package/esm/LinearReferenceSequenceDisplay/model.js.map +1 -1
- package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js +2 -1
- package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map +1 -1
- package/package.json +3 -3
- package/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx +161 -0
- package/src/DivSequenceRenderer/components/DivSequenceRendering.tsx +16 -19
- package/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap +1426 -0
- package/src/IndexedFastaAdapter/IndexedFastaAdapter.test.ts +4 -3
- package/src/LinearReferenceSequenceDisplay/model.ts +12 -5
- package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts +2 -1
- package/src/TwoBitAdapter/TwoBitAdapter.test.ts +4 -3
- package/src/__snapshots__/{index.test.js.snap → index.test.ts.snap} +0 -0
- package/src/{index.test.js → index.test.ts} +5 -10
- package/src/DivSequenceRenderer/components/DivSequenceRendering.test.js +0 -211
- package/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.js.snap +0 -67
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@@ -1,8 +1,8 @@
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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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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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import { Feature } from '@jbrowse/core/util';
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import { Region } from '@jbrowse/core/util/types';
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-
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5
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declare function Sequence(props: {
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exportSVG?: {
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rasterizeLayers: boolean;
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};
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@@ -10,12 +10,10 @@ interface MyProps {
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regions: Region[];
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bpPerPx: number;
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config: AnyConfigurationModel;
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}
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declare function Sequence(props: MyProps): JSX.Element;
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theme?: any;
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showForward?: boolean;
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showReverse?: boolean;
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showTranslation?: boolean;
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}): JSX.Element;
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declare const _default: typeof Sequence;
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export default _default;
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@@ -61,7 +61,7 @@ function DNA(props) {
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render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? (0, color_1.contrastingTextColor)(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, showForward, showTranslation, bpPerPx, }) => {
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const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
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const [region] = regions;
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const theme = (0, ui_1.createJBrowseTheme)(configTheme);
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const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
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@@ -1 +1 @@
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-
{"version":3,"file":"DivSequenceRendering.js","sourceRoot":"","sources":["../../../src/DivSequenceRenderer/components/DivSequenceRendering.tsx"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,kDAAyB;AAEzB,oDAA+D;AAG/D,yCAAqD;AACrD,2CAAqC;AACrC,6CAQ2B;
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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,oDAA+D;AAG/D,yCAAqD;AACrD,2CAAqC;AACrC,6CAQ2B;AAE3B,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,CAAC,OAAO,CAAC,UAAU;oBAC1B,CAAC,CAAC,mBAAY,CAAC,QAAQ,CAAC,KAAK,CAAC;wBAC9B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,SAAS;wBACzB,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,EAAE,KAAK,CAAC,CAAC,CAAC,IAAA,4BAAoB,EAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,IAEvD,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,EAAE,eAAe,KAAK,EAAE,EAC3B,GAAG,EAAE,GAAG,EACR,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,EAChB,UAAU,EAAE,UAAU,EACtB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,CAAC,QAAQ,GACxB,CACH,CAAC;YACJ,CAAC,CAAC,IAAI;QAEP,WAAW,CAAC,CAAC,CAAC,CACb,8BAAC,GAAG,IACF,MAAM,EAAE,MAAM,EACd,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,EAChB,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,GAAG,EAAE,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAA,iBAAU,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,EAC5C,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,WAAW,CAAC,CAAC,CAAC,CACb,8BAAC,GAAG,IACF,MAAM,EAAE,MAAM,EACd,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,EAChB,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,GAAG,EAAE,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAU,EAAC,GAAG,CAAC,EAC5C,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI;QAIP,eAAe,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC;YAC/D,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACvB,8BAAC,WAAW,IACV,GAAG,EAAE,mBAAmB,KAAK,EAAE,EAC/B,GAAG,EAAE,GAAG,EACR,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,EAChB,UAAU,EAAE,UAAU,EACtB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,CAAC,MAAM,CAAC,QAAQ,GACzB,CACH,CAAC;YACJ,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAA;AAED,MAAM,OAAO,GAAG,CAAC,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,EAAE,QAAQ,EAAO,EAAE,EAAE;IACnE,OAAO,SAAS,CAAC,CAAC,CAAC,CACjB,8DAAG,QAAQ,CAAI,CAChB,CAAC,CAAC,CAAC,CACF,sDACc,gBAAgB,EAC5B,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,WAAW,EACnB,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,IAEpC,QAAQ,CACL,CACP,CAAA;AACH,CAAC,CAAA;AAED,SAAS,QAAQ,CAAC,KAUjB;IACC,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAClC,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;IACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IACnD,MAAM,WAAW,GAAG,GAAG,CAAA;IAEvB,OAAO,CACL,8BAAC,OAAO,OAAK,KAAK,EAAE,WAAW,EAAE,WAAW,EAAE,KAAK,EAAE,KAAK;QACxD,8BAAC,WAAW,OAAK,KAAK,GAAI,CAClB,CACX,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,QAAQ,CAAC,CAAA"}
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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const { showTranslation, showReverse, showForward } = self;
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const r1 = showReverse && showTranslation ? 60 : 0;
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const r2 = showForward && showTranslation ? 60 : 0;
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self.setHeight(t + r + s);
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}
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-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":";;;AAAA,qDAAoD;AACpD,kFAG2C;AAC3C,+DAGoC;AACpC,6CAAsD;AACtD,+BAA8B;AAE9B;;;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,WAAW,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;gBAC1D,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,aAAa,EAAE,IAAI,CAAC,aAAa;oBACjC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,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,CAA0B,CAAA;YAC7D,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,
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":";;;AAAA,qDAAoD;AACpD,kFAG2C;AAC3C,+DAGoC;AACpC,6CAAsD;AACtD,+BAA8B;AAE9B;;;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,WAAW,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;gBAC1D,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,aAAa,EAAE,IAAI,CAAC,aAAa;oBACjC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,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,CAA0B,CAAA;YAC7D,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,CAA0B,CAAA;gBAC7D,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;AAhID,oCAgIC"}
|
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@@ -4,6 +4,7 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const util_1 = require("@jbrowse/core/util");
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const operators_1 = require("rxjs/operators");
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const rxjs_2 = require("rxjs");
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class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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async configure() {
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var _a;
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@@ -34,7 +35,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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start: queryStart,
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end: queryEnd,
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}, opts);
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const feats = await ret.pipe((0, operators_1.toArray)())
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const feats = await (0, rxjs_2.firstValueFrom)(ret.pipe((0, operators_1.toArray)()));
|
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|
const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
|
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|
const search = this.getConf('search');
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|
const searchForward = this.getConf('searchForward');
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"SequenceSearchAdapter.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/SequenceSearchAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,kDAA0D;AAC1D,6CAM2B;AAC3B,8CAAwC;
|
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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,CAAC,CAAA;YACrC,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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|
@@ -1,8 +1,8 @@
|
|
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1
1
|
/// <reference types="react" />
|
|
2
|
-
import { AnyConfigurationModel } from '@jbrowse/core/configuration
|
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3
|
-
import { Feature } from '@jbrowse/core/util
|
|
2
|
+
import { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
|
+
import { Feature } from '@jbrowse/core/util';
|
|
4
4
|
import { Region } from '@jbrowse/core/util/types';
|
|
5
|
-
|
|
5
|
+
declare function Sequence(props: {
|
|
6
6
|
exportSVG?: {
|
|
7
7
|
rasterizeLayers: boolean;
|
|
8
8
|
};
|
|
@@ -10,12 +10,10 @@ interface MyProps {
|
|
|
10
10
|
regions: Region[];
|
|
11
11
|
bpPerPx: number;
|
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12
12
|
config: AnyConfigurationModel;
|
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13
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-
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|
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17
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-
|
|
18
|
-
}
|
|
19
|
-
declare function Sequence(props: MyProps): JSX.Element;
|
|
13
|
+
theme?: any;
|
|
14
|
+
showForward?: boolean;
|
|
15
|
+
showReverse?: boolean;
|
|
16
|
+
showTranslation?: boolean;
|
|
17
|
+
}): JSX.Element;
|
|
20
18
|
declare const _default: typeof Sequence;
|
|
21
19
|
export default _default;
|
|
@@ -56,7 +56,7 @@ function DNA(props) {
|
|
|
56
56
|
render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? contrastingTextColor(color.main) : 'black' }, letter)) : null));
|
|
57
57
|
})));
|
|
58
58
|
}
|
|
59
|
-
const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse, showForward, showTranslation, bpPerPx, }) => {
|
|
59
|
+
const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) => {
|
|
60
60
|
const [region] = regions;
|
|
61
61
|
const theme = createJBrowseTheme(configTheme);
|
|
62
62
|
const codonTable = generateCodonTable(defaultCodonTable);
|
|
@@ -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,oBAAoB,EAAE,MAAM,0BAA0B,CAAA;AAG/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,QAAQ,EACR,MAAM,EACN,UAAU,EACV,aAAa,EACb,YAAY,EACZ,iBAAiB,EACjB,kBAAkB,GACnB,MAAM,oBAAoB,CAAA;
|
|
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,oBAAoB,EAAE,MAAM,0BAA0B,CAAA;AAG/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,QAAQ,EACR,MAAM,EACN,UAAU,EACV,aAAa,EACb,YAAY,EACZ,iBAAiB,EACjB,kBAAkB,GACnB,MAAM,oBAAoB,CAAA;AAE3B,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,MAAM,CAAC,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,0CACG,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,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,KAAK,IAAI,MAAM,EAAE;YACvC,8BACE,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,aAAa,CAAC,QAAQ,CAAC,KAAK,CAAC;oBAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,UAAU;oBAC1B,CAAC,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,CAAC;wBAC9B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,SAAS;wBACzB,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,GAE1B;YACD,MAAM,CAAC,CAAC,CAAC,CACR,8BACE,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,QAAQ,CAChC,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,0CACG,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,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,KAAK;YACxB,8BACE,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,8BACE,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,EAAE,KAAK,CAAC,CAAC,CAAC,oBAAoB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,IAEvD,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,kBAAkB,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,UAAU,GAAG,kBAAkB,CAAC,iBAAiB,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,C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|
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@@ -108,9 +108,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
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|
108
108
|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
109
109
|
}, {
|
|
110
110
|
rendererTypeName: string;
|
|
111
|
-
error: unknown;
|
|
112
|
-
* #method
|
|
113
|
-
*/
|
|
111
|
+
error: unknown;
|
|
114
112
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
115
113
|
}> | null;
|
|
116
114
|
readonly adapterConfig: any;
|
|
@@ -85,12 +85,20 @@ export function modelFactory(configSchema) {
|
|
|
85
85
|
self.showTranslation = !self.showTranslation;
|
|
86
86
|
},
|
|
87
87
|
afterAttach() {
|
|
88
|
-
// auto-adjust height depending on settings
|
|
89
88
|
addDisposer(self, autorun(() => {
|
|
90
|
-
const
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
89
|
+
const view = getContainingView(self);
|
|
90
|
+
if ((view === null || view === void 0 ? void 0 : view.bpPerPx) >= 1) {
|
|
91
|
+
self.setHeight(50);
|
|
92
|
+
}
|
|
93
|
+
else {
|
|
94
|
+
const { showTranslation, showReverse, showForward } = self;
|
|
95
|
+
const r1 = showReverse && showTranslation ? 60 : 0;
|
|
96
|
+
const r2 = showForward && showTranslation ? 60 : 0;
|
|
97
|
+
const t = r1 + r2;
|
|
98
|
+
const r = showReverse ? 20 : 0;
|
|
99
|
+
const s = showForward ? 20 : 0;
|
|
100
|
+
self.setHeight(t + r + s);
|
|
101
|
+
}
|
|
94
102
|
}));
|
|
95
103
|
},
|
|
96
104
|
}))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
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;AAE9B;;;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,WAAW,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;gBAC1D,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,aAAa,EAAE,IAAI,CAAC,aAAa;oBACjC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,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,CAA0B,CAAA;YAC7D,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,CAA0B,CAAA;gBAC7D,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"}
|
|
@@ -2,6 +2,7 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
|
|
|
2
2
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
3
3
|
import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
|
|
4
4
|
import { toArray } from 'rxjs/operators';
|
|
5
|
+
import { firstValueFrom } from 'rxjs';
|
|
5
6
|
export default class extends BaseFeatureDataAdapter {
|
|
6
7
|
async configure() {
|
|
7
8
|
var _a;
|
|
@@ -32,7 +33,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
32
33
|
start: queryStart,
|
|
33
34
|
end: queryEnd,
|
|
34
35
|
}, opts);
|
|
35
|
-
const feats = await ret.pipe(toArray())
|
|
36
|
+
const feats = await firstValueFrom(ret.pipe(toArray()));
|
|
36
37
|
const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
|
|
37
38
|
const search = this.getConf('search');
|
|
38
39
|
const searchForward = this.getConf('searchForward');
|
|
@@ -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;
|
|
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,CAAC,CAAA;YACrC,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": "2.3.
|
|
3
|
+
"version": "2.3.4",
|
|
4
4
|
"description": "JBrowse 2 sequence adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -50,7 +50,7 @@
|
|
|
50
50
|
"mobx-react": "^7.0.0",
|
|
51
51
|
"mobx-state-tree": "^5.0.0",
|
|
52
52
|
"react": ">=16.8.0",
|
|
53
|
-
"rxjs": "^
|
|
53
|
+
"rxjs": "^7.0.0"
|
|
54
54
|
},
|
|
55
55
|
"publishConfig": {
|
|
56
56
|
"access": "public"
|
|
@@ -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": "98ae48be91ee2371e1b2768a907b4997995e9915"
|
|
62
62
|
}
|
|
@@ -0,0 +1,161 @@
|
|
|
1
|
+
import React from 'react'
|
|
2
|
+
import { render } from '@testing-library/react'
|
|
3
|
+
import SimpleFeature from '@jbrowse/core/util/simpleFeature'
|
|
4
|
+
import DivSequenceRendering from './DivSequenceRendering'
|
|
5
|
+
import DivRenderingConfigSchema from '../configSchema'
|
|
6
|
+
|
|
7
|
+
// This just keeps our testing logs clean by not displaying `console.error`s
|
|
8
|
+
// from errors we intentionally throw in our tests. Hopefully React will
|
|
9
|
+
// someday provide a way for error boundaries to prevent error logging so we
|
|
10
|
+
// won't have to do this: https://github.com/facebook/react/issues/15069
|
|
11
|
+
const originalError = console.error
|
|
12
|
+
beforeAll(() => {
|
|
13
|
+
console.error = (...args) => {
|
|
14
|
+
if (
|
|
15
|
+
args[0].includes('feature one did not contain a valid `seq` attribute') ||
|
|
16
|
+
args[0].includes(
|
|
17
|
+
'The above error occurred in the <SequenceDivs> component',
|
|
18
|
+
)
|
|
19
|
+
) {
|
|
20
|
+
return
|
|
21
|
+
}
|
|
22
|
+
originalError.call(console, ...args)
|
|
23
|
+
}
|
|
24
|
+
})
|
|
25
|
+
|
|
26
|
+
afterAll(() => {
|
|
27
|
+
console.error = originalError
|
|
28
|
+
})
|
|
29
|
+
|
|
30
|
+
test('renders with one, zoomed way out', () => {
|
|
31
|
+
const { container } = render(
|
|
32
|
+
<DivSequenceRendering
|
|
33
|
+
regions={[
|
|
34
|
+
{ assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
|
|
35
|
+
]}
|
|
36
|
+
features={
|
|
37
|
+
new Map([
|
|
38
|
+
[
|
|
39
|
+
'one',
|
|
40
|
+
new SimpleFeature({
|
|
41
|
+
uniqueId: 'one',
|
|
42
|
+
start: 1,
|
|
43
|
+
end: 3,
|
|
44
|
+
seq: 'AB',
|
|
45
|
+
}),
|
|
46
|
+
],
|
|
47
|
+
])
|
|
48
|
+
}
|
|
49
|
+
config={DivRenderingConfigSchema.create({})}
|
|
50
|
+
bpPerPx={3}
|
|
51
|
+
/>,
|
|
52
|
+
)
|
|
53
|
+
|
|
54
|
+
expect(container).toMatchSnapshot()
|
|
55
|
+
})
|
|
56
|
+
|
|
57
|
+
test('renders with one feature with no seq, zoomed in, should throw', () => {
|
|
58
|
+
const { container } = render(
|
|
59
|
+
<DivSequenceRendering
|
|
60
|
+
regions={[
|
|
61
|
+
{ assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
|
|
62
|
+
]}
|
|
63
|
+
features={
|
|
64
|
+
new Map([
|
|
65
|
+
['one', new SimpleFeature({ uniqueId: 'one', start: 1, end: 3 })],
|
|
66
|
+
])
|
|
67
|
+
}
|
|
68
|
+
config={DivRenderingConfigSchema.create({})}
|
|
69
|
+
bpPerPx={0.05}
|
|
70
|
+
/>,
|
|
71
|
+
)
|
|
72
|
+
|
|
73
|
+
expect(container).toMatchSnapshot()
|
|
74
|
+
})
|
|
75
|
+
|
|
76
|
+
test('renders with one feature with an incorrect seq, zoomed in, should throw', () => {
|
|
77
|
+
const { container } = render(
|
|
78
|
+
<DivSequenceRendering
|
|
79
|
+
regions={[
|
|
80
|
+
{ assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
|
|
81
|
+
]}
|
|
82
|
+
features={
|
|
83
|
+
new Map([
|
|
84
|
+
[
|
|
85
|
+
'one',
|
|
86
|
+
new SimpleFeature({
|
|
87
|
+
uniqueId: 'one',
|
|
88
|
+
start: 1,
|
|
89
|
+
end: 3,
|
|
90
|
+
seq: 'ABC',
|
|
91
|
+
}),
|
|
92
|
+
],
|
|
93
|
+
])
|
|
94
|
+
}
|
|
95
|
+
config={DivRenderingConfigSchema.create({})}
|
|
96
|
+
bpPerPx={0.05}
|
|
97
|
+
/>,
|
|
98
|
+
)
|
|
99
|
+
|
|
100
|
+
expect(container).toMatchSnapshot()
|
|
101
|
+
})
|
|
102
|
+
|
|
103
|
+
test('renders with one feature with a correct seq, zoomed in, should render nicely', () => {
|
|
104
|
+
const { container } = render(
|
|
105
|
+
<DivSequenceRendering
|
|
106
|
+
regions={[
|
|
107
|
+
{ assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
|
|
108
|
+
]}
|
|
109
|
+
features={
|
|
110
|
+
new Map([
|
|
111
|
+
[
|
|
112
|
+
'one',
|
|
113
|
+
new SimpleFeature({
|
|
114
|
+
uniqueId: 'one',
|
|
115
|
+
start: 1,
|
|
116
|
+
end: 10,
|
|
117
|
+
seq: 'ABCDEFGHI',
|
|
118
|
+
}),
|
|
119
|
+
],
|
|
120
|
+
])
|
|
121
|
+
}
|
|
122
|
+
config={DivRenderingConfigSchema.create({})}
|
|
123
|
+
bpPerPx={0.05}
|
|
124
|
+
/>,
|
|
125
|
+
)
|
|
126
|
+
|
|
127
|
+
expect(container).toMatchSnapshot()
|
|
128
|
+
})
|
|
129
|
+
|
|
130
|
+
test('renders with one feature reversed with a correct seq, zoomed in, should render nicely', () => {
|
|
131
|
+
const { container } = render(
|
|
132
|
+
<DivSequenceRendering
|
|
133
|
+
regions={[
|
|
134
|
+
{
|
|
135
|
+
assemblyName: 'volvox',
|
|
136
|
+
refName: 'zonk',
|
|
137
|
+
start: 0,
|
|
138
|
+
end: 1000,
|
|
139
|
+
reversed: true,
|
|
140
|
+
},
|
|
141
|
+
]}
|
|
142
|
+
features={
|
|
143
|
+
new Map([
|
|
144
|
+
[
|
|
145
|
+
'one',
|
|
146
|
+
new SimpleFeature({
|
|
147
|
+
uniqueId: 'one',
|
|
148
|
+
start: 1,
|
|
149
|
+
end: 10,
|
|
150
|
+
seq: 'ABCDEFGHI',
|
|
151
|
+
}),
|
|
152
|
+
],
|
|
153
|
+
])
|
|
154
|
+
}
|
|
155
|
+
config={DivRenderingConfigSchema.create({})}
|
|
156
|
+
bpPerPx={0.05}
|
|
157
|
+
/>,
|
|
158
|
+
)
|
|
159
|
+
|
|
160
|
+
expect(container).toMatchSnapshot()
|
|
161
|
+
})
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
/* eslint-disable @typescript-eslint/no-explicit-any */
|
|
2
2
|
import React from 'react'
|
|
3
|
-
import { AnyConfigurationModel } from '@jbrowse/core/configuration
|
|
3
|
+
import { AnyConfigurationModel } from '@jbrowse/core/configuration'
|
|
4
4
|
import { contrastingTextColor } from '@jbrowse/core/util/color'
|
|
5
|
-
import { Feature } from '@jbrowse/core/util
|
|
5
|
+
import { Feature } from '@jbrowse/core/util'
|
|
6
6
|
import { Region } from '@jbrowse/core/util/types'
|
|
7
7
|
import { createJBrowseTheme } from '@jbrowse/core/ui'
|
|
8
8
|
import { observer } from 'mobx-react'
|
|
@@ -16,19 +16,6 @@ import {
|
|
|
16
16
|
generateCodonTable,
|
|
17
17
|
} from '@jbrowse/core/util'
|
|
18
18
|
|
|
19
|
-
interface MyProps {
|
|
20
|
-
exportSVG?: { rasterizeLayers: boolean }
|
|
21
|
-
features: Map<string, Feature>
|
|
22
|
-
regions: Region[]
|
|
23
|
-
bpPerPx: number
|
|
24
|
-
config: AnyConfigurationModel
|
|
25
|
-
highResolutionScaling: number
|
|
26
|
-
theme: any
|
|
27
|
-
showForward: boolean
|
|
28
|
-
showReverse: boolean
|
|
29
|
-
showTranslation: boolean
|
|
30
|
-
}
|
|
31
|
-
|
|
32
19
|
function Translation(props: {
|
|
33
20
|
codonTable: any
|
|
34
21
|
seq: string
|
|
@@ -179,9 +166,9 @@ const SequenceSVG = ({
|
|
|
179
166
|
regions,
|
|
180
167
|
theme: configTheme,
|
|
181
168
|
features = new Map(),
|
|
182
|
-
showReverse,
|
|
183
|
-
showForward,
|
|
184
|
-
showTranslation,
|
|
169
|
+
showReverse = true,
|
|
170
|
+
showForward = true,
|
|
171
|
+
showTranslation = true,
|
|
185
172
|
bpPerPx,
|
|
186
173
|
}: any) => {
|
|
187
174
|
const [region] = regions
|
|
@@ -283,7 +270,17 @@ const Wrapper = ({ exportSVG, width, totalHeight, children }: any) => {
|
|
|
283
270
|
)
|
|
284
271
|
}
|
|
285
272
|
|
|
286
|
-
function Sequence(props:
|
|
273
|
+
function Sequence(props: {
|
|
274
|
+
exportSVG?: { rasterizeLayers: boolean }
|
|
275
|
+
features: Map<string, Feature>
|
|
276
|
+
regions: Region[]
|
|
277
|
+
bpPerPx: number
|
|
278
|
+
config: AnyConfigurationModel
|
|
279
|
+
theme?: any
|
|
280
|
+
showForward?: boolean
|
|
281
|
+
showReverse?: boolean
|
|
282
|
+
showTranslation?: boolean
|
|
283
|
+
}) {
|
|
287
284
|
const { regions, bpPerPx } = props
|
|
288
285
|
const [region] = regions
|
|
289
286
|
const width = (region.end - region.start) / bpPerPx
|