jbrowse-plugin-msaview 2.0.3 → 2.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +1 -1
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/HighlightComponents.js +1 -1
- package/dist/AddHighlightModel/HighlightComponents.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +2 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/AddHighlightModel/index.js.map +1 -1
- package/dist/AddHighlightModel/util.d.ts +2 -2
- package/dist/AddHighlightModel/util.js +1 -1
- package/dist/AddHighlightModel/util.js.map +1 -1
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +8 -3
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +17 -9
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js +51 -30
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +9 -5
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/TabUtils.d.ts +1 -5
- package/dist/LaunchMsaView/components/TabUtils.js +1 -7
- package/dist/LaunchMsaView/components/TabUtils.js.map +1 -1
- package/dist/LaunchMsaView/components/tabUtil.d.ts +4 -0
- package/dist/LaunchMsaView/components/tabUtil.js +7 -0
- package/dist/LaunchMsaView/components/tabUtil.js.map +1 -0
- package/dist/LaunchMsaView/index.js +4 -5
- package/dist/LaunchMsaView/index.js.map +1 -1
- package/dist/LaunchMsaView/util.d.ts +1 -1
- package/dist/LaunchMsaView/util.js +1 -1
- package/dist/LaunchMsaView/util.js.map +1 -1
- package/dist/MsaViewPanel/components/LoadingBLAST.js +2 -2
- package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/components/RIDLink.js.map +1 -1
- package/dist/MsaViewPanel/doLaunchBlast.js +18 -5
- package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
- package/dist/MsaViewPanel/genomeToMSA.js.map +1 -1
- package/dist/MsaViewPanel/index.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +39 -35
- package/dist/MsaViewPanel/model.js +7 -5
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js +4 -4
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +1 -1
- package/dist/OpenInNewIcon.js.map +1 -1
- package/dist/TextField2.js.map +1 -1
- package/dist/index.js +2 -2
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +84 -30
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/msa.js +4 -0
- package/dist/utils/msa.js.map +1 -1
- package/dist/utils/ncbiBlast.js +8 -5
- package/dist/utils/ncbiBlast.js.map +1 -1
- package/package.json +24 -22
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +4 -2
- package/src/AddHighlightModel/HighlightComponents.tsx +3 -2
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +9 -6
- package/src/AddHighlightModel/index.tsx +1 -0
- package/src/AddHighlightModel/util.ts +1 -1
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +13 -4
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +22 -13
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.ts +2 -2
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts +1 -0
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts +69 -34
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +19 -14
- package/src/LaunchMsaView/components/TabUtils.tsx +2 -7
- package/src/LaunchMsaView/components/tabUtil.ts +6 -0
- package/src/LaunchMsaView/index.ts +39 -33
- package/src/LaunchMsaView/util.ts +2 -2
- package/src/MsaViewPanel/components/LoadingBLAST.tsx +6 -4
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +1 -0
- package/src/MsaViewPanel/components/RIDLink.tsx +2 -0
- package/src/MsaViewPanel/doLaunchBlast.ts +25 -7
- package/src/MsaViewPanel/genomeToMSA.ts +2 -1
- package/src/MsaViewPanel/index.ts +1 -0
- package/src/MsaViewPanel/model.ts +10 -7
- package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +4 -4
- package/src/OpenInNewIcon.tsx +1 -0
- package/src/TextField2.tsx +1 -0
- package/src/index.ts +2 -2
- package/src/utils/msa.ts +3 -0
- package/src/utils/ncbiBlast.ts +22 -10
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import React from 'react';
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import { observer } from 'mobx-react';
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import { getSession } from '@jbrowse/core/util';
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import { observer } from 'mobx-react';
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import { useStyles } from './util';
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const GenomeMouseoverHighlight = observer(function GenomeMouseoverHighlight2({ model, }) {
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const { hovered } = getSession(model);
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{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
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{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAElC,MAAM,wBAAwB,GAAG,QAAQ,CAAC,SAAS,yBAAyB,CAAC,EAC3E,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,OAAO,OAAO;QACZ,OAAO,OAAO,KAAK,QAAQ;QAC3B,eAAe,IAAI,OAAO,CAAC,CAAC,CAAC,CAC7B,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,IAAI,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,EAAE,CAAC;QAClD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QAC3B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QAC1B,mBAAmB;QACnB,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QAEhD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GAAI,CAAA;QACtE,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}
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import React from 'react';
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import { observer } from 'mobx-react';
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// locals
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import MsaToGenomeHighlight from './MsaToGenomeHighlight';
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import GenomeMouseoverHighlight from './GenomeMouseoverHighlight';
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import MsaToGenomeHighlight from './MsaToGenomeHighlight';
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const HighlightComponents = observer(function HighlightComponents2({ model, }) {
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return (React.createElement(React.Fragment, null,
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React.createElement(MsaToGenomeHighlight, { model: model }),
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{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
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{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAGzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,SAAS;AACT,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;AACjE,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AAIzD,MAAM,mBAAmB,GAAG,QAAQ,CAAC,SAAS,oBAAoB,CAAC,EACjE,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,wBAAwB,IAAC,KAAK,EAAE,KAAK,GAAI,CACzC,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,mBAAmB,CAAA"}
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import React from 'react';
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import { observer } from 'mobx-react';
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import { getSession } from '@jbrowse/core/util';
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// locals
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import { useStyles } from './util';
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function getCanonicalName(assembly, s) {
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{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
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{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAGzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS;AACT,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAKlC,SAAS,gBAAgB,CAAC,QAAkB,EAAE,CAAS;IACrD,OAAO,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAC7C,CAAC;AAED,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEjC,CAAA;IACb,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACrC,MAAM,OAAO,GAAG,gBAAgB,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;YAC9D,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAKzB,SAAS;AACT,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAEvD,MAAM,CAAC,OAAO,UAAU,4BAA4B,CAClD,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,2CAA2C;IAC3C,mBAAmB;IACnB,CACE,OAA0B,EAAE,EAC5B,EAAE,KAAK,EAAoC,EAC3C,EAAE;QACF,OAAO;YACL,GAAG,IAAI;YACP,oBAAC,mBAAmB,IAClB,GAAG,EAAC,kCAAkC,EACtC,KAAK,EAAE,KAAK,GACZ;SACH,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}
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} | undefined) => {
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classes: Record<"highlight", string>;
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theme: import("@mui/material").Theme;
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css: import("tss-react").Css;
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cx: import("tss-react").Cx;
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css: import("tss-react/types").Css;
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cx: import("tss-react/types").Cx;
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};
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}
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import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
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import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
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export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
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{"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;
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{"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAE9C,SAAS;AAET,OAAO,sBAAsB,MAAM,qBAAqB,CAAA;AACxD,OAAO,YAAY,MAAM,sCAAsC,CAAA;AAC/D,OAAO,cAAc,MAAM,YAAY,CAAA;AACvC,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAErC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IAErC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,iBAAiB,EACvB,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;YAClD,oBAAC,IAAI,IACH,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC;gBAED,oBAAC,GAAG,IAAC,KAAK,EAAC,kBAAkB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI;gBAClD,oBAAC,GAAG,IAAC,KAAK,EAAC,sBAAsB,KAAK,SAAS,CAAC,CAAC,CAAC,GAAI,CACjD,CACH;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,sBAAsB,IACrB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,GACZ,CACa;QACjB,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YACpC,oBAAC,YAAY,IACX,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACa,CACV,CACV,CAAA;AACH,CAAC"}
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@@ -1,15 +1,15 @@
|
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1
1
|
import React, { useState } from 'react';
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2
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-
import {
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2
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+
import { ErrorMessage } from '@jbrowse/core/ui';
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3
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+
import { getContainingView, } from '@jbrowse/core/util';
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3
4
|
import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
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+
import { observer } from 'mobx-react';
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4
6
|
import { makeStyles } from 'tss-react/mui';
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-
import { getContainingView, } from '@jbrowse/core/util';
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-
import { ErrorMessage } from '@jbrowse/core/ui';
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7
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// locals
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8
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-
import { getId, getTranscriptDisplayName, getTranscriptFeatures, getGeneDisplayName, } from '../../util';
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8
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import { getProteinSequence } from './calculateProteinSequence';
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+
import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
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10
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import { useFeatureSequence } from './useFeatureSequence';
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11
|
import TextField2 from '../../../TextField2';
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import {
|
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12
|
+
import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
|
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const useStyles = makeStyles()({
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|
dialogContent: {
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width: '80em',
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@@ -40,9 +40,15 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature,
|
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40
40
|
const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
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|
return (React.createElement(DialogContent, { className: classes.dialogContent },
|
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|
error ? React.createElement(ErrorMessage, { error: error }) : null,
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React.createElement(TextField2, { value: blastDatabase, onChange: event =>
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-
|
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43
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+
React.createElement(TextField2, { value: blastDatabase, onChange: event => {
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+
setBlastDatabase(event.target.value);
|
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45
|
+
}, label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
|
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+
React.createElement(TextField2, { value: msaAlgorithm, onChange: event => {
|
|
47
|
+
setMsaAlgorithm(event.target.value);
|
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48
|
+
}, label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
|
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|
+
React.createElement(TextField2, { value: userSelection, onChange: event => {
|
|
50
|
+
setUserSelection(event.target.value);
|
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|
+
}, label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
|
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46
52
|
getGeneDisplayName(feature),
|
|
47
53
|
" - ",
|
|
48
54
|
getTranscriptDisplayName(val))))),
|
|
@@ -70,7 +76,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature,
|
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|
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76
|
});
|
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77
|
handleClose();
|
|
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|
}, disabled: !proteinSequence }, "Submit"),
|
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-
React.createElement(Button, { color: "secondary", variant: "contained", onClick: () =>
|
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79
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+
React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
|
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80
|
+
handleClose();
|
|
81
|
+
} }, "Cancel"))));
|
|
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82
|
});
|
|
75
83
|
export default NcbiBlastPanel;
|
|
76
84
|
//# sourceMappingURL=NcbiBlastPanel.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"NcbiBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;
|
|
1
|
+
{"version":3,"file":"NcbiBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAA;AAC/D,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,UAAU,MAAM,qBAAqB,CAAA;AAC5C,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,YAAY,CAAA;AAEnB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACvD,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IACxD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;IAE5D,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAE,CAAA;IAC7E,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,kBAAkB,CAAC;QAC7C,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IACF,MAAM,eAAe,GACnB,QAAQ,IAAI,CAAC,CAAC,OAAO,IAAI,QAAQ,CAAC;QAChC,CAAC,CAAC,kBAAkB,CAAC;YACjB,GAAG,EAAE,QAAQ,CAAC,GAAG;YACjB,kBAAkB;SACnB,CAAC;QACJ,CAAC,CAAC,EAAE,CAAA;IAER,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACrD,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;IAC/D,OAAO,CACL,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;QAC5C,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,UAAU,IACT,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACtC,CAAC,EACD,KAAK,EAAC,qBAAqB,EAC3B,MAAM,UAEL,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;QAEb,oBAAC,UAAU,IACT,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACrC,CAAC,EACD,KAAK,EAAC,eAAe,EACrB,MAAM,UAEL,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;QAEb,oBAAC,UAAU,IACT,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACtC,CAAC,EACD,KAAK,EAAC,yBAAyB,EAC/B,MAAM,UAEL,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;YACvC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,GAAG,CAAC,CACrD,CACZ,CAAC,CACS;QACb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,EAElB,UAAU,EAAE;gBACV,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF,GACD;QAEF,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,OAAO,GAAG,mBAAmB,CAAC;wBAClC,OAAO,EAAE,kBAAkB;wBAC3B,IAAI;wBACJ,YAAY,EAAE,gBAAgB,kBAAkB,CAAC,OAAO,CAAC,MAAM,wBAAwB,CAAC,kBAAkB,CAAC,MAAM,YAAY,EAAE;qBAChI,CAAC,CAAA;oBACF,OAAO,CAAC,cAAc,CAAC;wBACrB,YAAY,EAAE,QAAQ;wBACtB,aAAa;wBACb,YAAY;wBACZ,kBAAkB;wBAClB,eAAe;qBAChB,CAAC,CAAA;oBACF,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,QAAQ,EAAE,CAAC,eAAe,aAGnB;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACF,CACjB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
|
|
@@ -7,7 +7,7 @@ export function calculateProteinSequence({ cds, sequence, codonTable, }) {
|
|
|
7
7
|
let protein = '';
|
|
8
8
|
for (let i = 0; i < str.length; i += 3) {
|
|
9
9
|
// use & symbol for undefined codon, or partial slice
|
|
10
|
-
protein += codonTable[str.slice(i, i + 3)]
|
|
10
|
+
protein += codonTable[str.slice(i, i + 3)] ?? '&';
|
|
11
11
|
}
|
|
12
12
|
return protein;
|
|
13
13
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CACrB,IAAoD,EACpD,MAAc;IAEd,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,
|
|
1
|
+
{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CACrB,IAAoD,EACpD,MAAc;IAEd,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,CACzE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,kBAAkB,EAClB,GAAG,GAIJ;IACC,mBAAmB;IACnB,MAAM,CAAC,GAAG,kBAAkB,CAAC,MAAM,EAMlC,CAAA;IACD,MAAM,GAAG,GAAG,MAAM,CAChB,CAAC,CAAC,WAAW;SACV,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACjC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK;QAC1B,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK;KACvB,CAAC,CAAC;SACF,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,CACjC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACrD,QAAQ,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC7C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;
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1
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+
{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAMxD,MAAM,UAAU,mBAAmB,CAAC,EAClC,YAAY,EACZ,IAAI,EACJ,OAAO,GAKR;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,aAAa,EAAE,GAAG;QAClB,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,IAAI;QACrB,gBAAgB,EAAE,IAAI;QACtB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;KAC5C,CAA8B,CAAA;AACjC,CAAC"}
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@@ -1,43 +1,45 @@
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1
1
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import { useEffect, useState } from 'react';
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2
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-
import { getSession } from '@jbrowse/core/util';
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3
2
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import { getConf } from '@jbrowse/core/configuration';
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import { getSession } from '@jbrowse/core/util';
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4
|
const BPLIMIT = 500_000;
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async function fetchSeq({ start, end, refName, session, assemblyName, }) {
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const { assemblyManager, rpcManager } = session;
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const assembly = await assemblyManager.waitForAssembly(assemblyName);
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if (!assembly) {
|
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9
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throw new Error('assembly not found');
|
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}
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11
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const sessionId = 'getSequence';
|
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12
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+
const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
|
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+
adapterConfig: getConf(assembly, ['sequence', 'adapter']),
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sessionId,
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regions: [
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{
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start,
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end,
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refName: assembly.getCanonicalRefName(refName),
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assemblyName,
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},
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],
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}));
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return feats[0]?.get('seq') ?? '';
|
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}
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5
26
|
export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
|
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6
27
|
const [sequence, setSequence] = useState();
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const [error, setError] = useState();
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+
const assemblyName = view?.assemblyNames?.[0];
|
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30
|
useEffect(() => {
|
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9
31
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if (view) {
|
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10
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-
const { assemblyManager, rpcManager } = getSession(view);
|
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11
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-
const [assemblyName] = view?.assemblyNames || [];
|
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12
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-
async function fetchSeq(start, end, refName) {
|
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13
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-
const assembly = await assemblyManager.waitForAssembly(assemblyName);
|
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14
|
-
if (!assembly) {
|
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15
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-
throw new Error('assembly not found');
|
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16
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-
}
|
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17
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-
const sessionId = 'getSequence';
|
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18
|
-
const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
|
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|
-
adapterConfig: getConf(assembly, ['sequence', 'adapter']),
|
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sessionId,
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-
regions: [
|
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-
{
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start,
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end,
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-
refName: assembly.getCanonicalRefName(refName),
|
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-
assemblyName,
|
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27
|
-
},
|
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|
-
],
|
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|
-
});
|
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30
|
-
const [feat] = feats;
|
|
31
|
-
return feat?.get('seq') || '';
|
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|
-
}
|
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32
|
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
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|
;
|
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34
|
(async () => {
|
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|
try {
|
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36
|
setError(undefined);
|
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37
|
setSequence(undefined);
|
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|
-
|
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38
|
+
const session = getSession(view);
|
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40
39
|
const { start, end, refName } = feature.toJSON();
|
|
40
|
+
if (!assemblyName) {
|
|
41
|
+
throw new Error('No assembly found');
|
|
42
|
+
}
|
|
41
43
|
if (!forceLoad && end - start > BPLIMIT) {
|
|
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44
|
setSequence({
|
|
43
45
|
error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
|
|
@@ -46,10 +48,29 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
|
|
|
46
48
|
else {
|
|
47
49
|
const b = start - upDownBp;
|
|
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50
|
const e = end + upDownBp;
|
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|
-
|
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-
|
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-
|
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-
|
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51
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+
setSequence({
|
|
52
|
+
seq: await fetchSeq({
|
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53
|
+
start,
|
|
54
|
+
end,
|
|
55
|
+
refName,
|
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56
|
+
assemblyName,
|
|
57
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+
session,
|
|
58
|
+
}),
|
|
59
|
+
upstream: await fetchSeq({
|
|
60
|
+
start: Math.max(0, b),
|
|
61
|
+
end: start,
|
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refName,
|
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+
assemblyName,
|
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64
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+
session,
|
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65
|
+
}),
|
|
66
|
+
downstream: await fetchSeq({
|
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|
+
start: end,
|
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68
|
+
end: e,
|
|
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|
+
refName,
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+
assemblyName,
|
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+
session,
|
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72
|
+
}),
|
|
73
|
+
});
|
|
53
74
|
}
|
|
54
75
|
}
|
|
55
76
|
catch (e) {
|
|
@@ -58,7 +79,7 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
|
|
|
58
79
|
}
|
|
59
80
|
})();
|
|
60
81
|
}
|
|
61
|
-
}, [feature, view, upDownBp, forceLoad]);
|
|
82
|
+
}, [feature, view, upDownBp, assemblyName, forceLoad]);
|
|
62
83
|
return { sequence, error };
|
|
63
84
|
}
|
|
64
85
|
//# sourceMappingURL=useFeatureSequence.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3C,OAAO,
|
|
1
|
+
{"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAiC,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAW9E,MAAM,OAAO,GAAG,OAAO,CAAA;AAEvB,KAAK,UAAU,QAAQ,CAAC,EACtB,KAAK,EACL,GAAG,EACH,OAAO,EACP,OAAO,EACP,YAAY,GAOb;IACC,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IACpE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;IACvC,CAAC;IACD,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,MAAM,KAAK,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACjE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACzD,SAAS;QACT,OAAO,EAAE;YACP;gBACE,KAAK;gBACL,GAAG;gBACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;gBAC9C,YAAY;aACb;SACF;KACF,CAAC,CAAc,CAAA;IAChB,OAAQ,KAAK,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAwB,IAAI,EAAE,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,GAAG,CAAC,EACZ,SAAS,GAAG,IAAI,GAMjB;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAyB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,IAAI,EAAE,CAAC;YACT,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,WAAW,CAAC,SAAS,CAAC,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAI7C,CAAA;oBACD,IAAI,CAAC,YAAY,EAAE,CAAC;wBAClB,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;oBACtC,CAAC;oBACD,IAAI,CAAC,SAAS,IAAI,GAAG,GAAG,KAAK,GAAG,OAAO,EAAE,CAAC;wBACxC,WAAW,CAAC;4BACV,KAAK,EAAE,gCAAgC,OAAO,wCAAwC;yBACvF,CAAC,CAAA;oBACJ,CAAC;yBAAM,CAAC;wBACN,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,CAAA;wBAC1B,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;wBACxB,WAAW,CAAC;4BACV,GAAG,EAAE,MAAM,QAAQ,CAAC;gCAClB,KAAK;gCACL,GAAG;gCACH,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,QAAQ,EAAE,MAAM,QAAQ,CAAC;gCACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gCACrB,GAAG,EAAE,KAAK;gCACV,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,UAAU,EAAE,MAAM,QAAQ,CAAC;gCACzB,KAAK,EAAE,GAAG;gCACV,GAAG,EAAE,CAAC;gCACN,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;yBACH,CAAC,CAAA;oBACJ,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,YAAY,EAAE,SAAS,CAAC,CAAC,CAAA;IACtD,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;AAC5B,CAAC"}
|
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
import React, { useEffect, useState } from 'react';
|
|
2
|
-
import { observer } from 'mobx-react';
|
|
3
2
|
import { ErrorMessage } from '@jbrowse/core/ui';
|
|
4
|
-
import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
|
|
5
3
|
import { getContainingView, getSession, } from '@jbrowse/core/util';
|
|
4
|
+
import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
|
|
5
|
+
import { observer } from 'mobx-react';
|
|
6
6
|
import { makeStyles } from 'tss-react/mui';
|
|
7
7
|
// locals
|
|
8
|
-
import { getTranscriptDisplayName, getId, getTranscriptFeatures, getGeneDisplayName, } from '../../util';
|
|
9
8
|
import { fetchGeneList } from './fetchGeneList';
|
|
10
9
|
import { preCalculatedLaunchView } from './preCalculatedLaunchView';
|
|
10
|
+
import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
|
|
11
11
|
const useStyles = makeStyles()({
|
|
12
12
|
dialogContent: {
|
|
13
13
|
width: '80em',
|
|
@@ -51,7 +51,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
|
|
|
51
51
|
React.createElement("a", { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
|
|
52
52
|
error ? React.createElement(ErrorMessage, { error: error }) : null,
|
|
53
53
|
geneNameList && !ret ? (React.createElement("div", { style: { color: 'red' } }, "No MSA data for this gene found")) : null,
|
|
54
|
-
React.createElement(TextField, { value: userSelection, onChange: event =>
|
|
54
|
+
React.createElement(TextField, { value: userSelection, onChange: event => {
|
|
55
|
+
setUserSelection(event.target.value);
|
|
56
|
+
}, label: "Choose isoform to view MSA for", select: true },
|
|
55
57
|
options
|
|
56
58
|
.filter(val => set.has(getId(val)))
|
|
57
59
|
.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
|
|
@@ -84,7 +86,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
|
|
|
84
86
|
}
|
|
85
87
|
})();
|
|
86
88
|
} }, "Submit"),
|
|
87
|
-
React.createElement(Button, { color: "secondary", variant: "contained", onClick: () =>
|
|
89
|
+
React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
|
|
90
|
+
handleClose();
|
|
91
|
+
} }, "Cancel"))));
|
|
88
92
|
});
|
|
89
93
|
export default PreLoadedMSA;
|
|
90
94
|
//# sourceMappingURL=PreLoadedMSADataPanel.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;
|
|
1
|
+
{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AACnE,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,YAAY,CAAA;AAEnB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAY,CAAA;IAC5D,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,IAAI,GAAG,MAAM,aAAa,EAAE,CAAA;gBAClC,eAAe,CAAC,IAAI,CAAC,CAAA;gBACrB,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,CAAA;gBACzB,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;gBAC9C,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;gBACpD,IAAI,GAAG,EAAE,CAAC;oBACR,gBAAgB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC9B,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IACb,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,YAAY,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;IACpD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAErE,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC7C,oBAAC,UAAU;;gBACsD,GAAG;gBAClE,2BAAG,IAAI,EAAC,0EAA0E,+CAE9E,CACO;YACZ,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC7C,YAAY,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CACtB,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,sCAAuC,CACpE,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,SAAS,IACR,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACtC,CAAC,EACD,KAAK,EAAC,gCAAgC,EACtC,MAAM;gBAEL,OAAO;qBACL,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;qBAClC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACV,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;oBACvC,wBAAwB,CAAC,GAAG,CAAC;kCACrB,CACZ,CAAC;gBACH,OAAO;qBACL,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;qBACnC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACV,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,UACjD,wBAAwB,CAAC,GAAG,CAAC,CACrB,CACZ,CAAC,CACM,CACE;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,IAAI,CAAC,GAAG,EAAE,CAAC;gCACT,OAAM;4BACR,CAAC;4BACD,MAAM,uBAAuB,CAAC;gCAC5B,aAAa;gCACb,OAAO;gCACP,YAAY,EAAE,kBAAkB,CAAC,GAAG,CAAC;gCACrC,IAAI;gCACJ,OAAO,EAAE,GAAG;6BACb,CAAC,CAAA;4BACF,WAAW,EAAE,CAAA;wBACf,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACb,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;gBACN,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
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@@ -4,9 +4,5 @@ interface TabPanelProps {
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4
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index: number;
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value: number;
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}
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export
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-
export declare function a11yProps(index: number): {
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id: string;
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'aria-controls': string;
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};
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+
export default function CustomTabPanel(props: TabPanelProps): React.JSX.Element;
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export {};
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@@ -1,13 +1,7 @@
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1
1
|
import React from 'react';
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2
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import { Box } from '@mui/material';
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-
export function CustomTabPanel(props) {
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+
export default function CustomTabPanel(props) {
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const { children, value, index, ...other } = props;
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return (React.createElement("div", { role: "tabpanel", hidden: value !== index, id: `gtabpanel-${index}`, "aria-labelledby": `gtab-${index}`, ...other }, value === index && React.createElement(Box, { sx: { p: 3 } }, children)));
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}
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export function a11yProps(index) {
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return {
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id: `gtab-${index}`,
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'aria-controls': `gtabpanel-${index}`,
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};
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}
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//# sourceMappingURL=TabUtils.js.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
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1
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+
{"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,GAAG,EAAE,MAAM,eAAe,CAAA;AAQnC,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAoB;IACzD,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,EAAE,GAAG,KAAK,CAAA;IAElD,OAAO,CACL,6BACE,IAAI,EAAC,UAAU,EACf,MAAM,EAAE,KAAK,KAAK,KAAK,EACvB,EAAE,EAAE,aAAa,KAAK,EAAE,qBACP,QAAQ,KAAK,EAAE,KAC5B,KAAK,IAER,KAAK,KAAK,KAAK,IAAI,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAO,CACnD,CACP,CAAA;AACH,CAAC"}
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@@ -0,0 +1 @@
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1
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+
{"version":3,"file":"tabUtil.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/tabUtil.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO;QACL,EAAE,EAAE,QAAQ,KAAK,EAAE;QACnB,eAAe,EAAE,aAAa,KAAK,EAAE;KACtC,CAAA;AACH,CAAC"}
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@@ -1,13 +1,13 @@
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1
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-
import {
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-
// icons
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1
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+
import { getContainingTrack, getSession } from '@jbrowse/core/util';
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3
2
|
import AddIcon from '@mui/icons-material/Add';
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3
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+
// icons
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// locals
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5
|
import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
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6
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function isDisplay(elt) {
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return elt.name === 'LinearBasicDisplay';
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}
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function extendStateModel(stateModel) {
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return stateModel.views(self => {
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return stateModel.views((self) => {
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const superContextMenuItems = self.contextMenuItems;
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return {
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contextMenuItems() {
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@@ -21,8 +21,7 @@ function extendStateModel(stateModel) {
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label: 'Launch MSA view',
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icon: AddIcon,
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onClick: () => {
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session.queueDialog(handleClose => [
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getSession(track).queueDialog(handleClose => [
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LaunchMsaViewDialog,
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{
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model: track,
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchMsaView/index.ts"],"names":[],"mappings":"AAIA,OAAO,
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1
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+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchMsaView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAW,kBAAkB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5E,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAG7C,QAAQ;AAER,SAAS;AACT,OAAO,mBAAmB,MAAM,kCAAkC,CAAA;AAGlE,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CACrB,CAAC,IAGA,EAAE,EAAE;QACH,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,iBAAiB;gCACxB,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,mBAAmB;wCACnB;4CACE,KAAK,EAAE,KAAK;4CACZ,WAAW;4CACX,OAAO;yCACR;qCACF,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}
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@@ -1,5 +1,5 @@
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1
1
|
import { Feature } from '@jbrowse/core/util';
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2
2
|
export declare function getTranscriptFeatures(feature: Feature): Feature[];
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3
|
-
export declare function getId(val?: Feature):
|
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3
|
+
export declare function getId(val?: Feature): string;
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4
4
|
export declare function getTranscriptDisplayName(val?: Feature): string;
|
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5
5
|
export declare function getGeneDisplayName(val?: Feature): string;
|
|
@@ -8,7 +8,7 @@ export function getTranscriptFeatures(feature) {
|
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|
8
8
|
subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
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|
}
|
|
10
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|
export function getId(val) {
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return val
|
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11
|
+
return val?.get('name') || val?.get('id') || '';
|
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12
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|
}
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13
13
|
export function getTranscriptDisplayName(val) {
|
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14
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|
return val === undefined
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LaunchMsaView/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAA;IACpD,OAAO,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC;QACnD,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,oEAAoE;YACpE,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CACrB,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC,CACzD,CAAA;AACP,CAAC;AACD,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LaunchMsaView/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAA;IACpD,OAAO,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC;QACnD,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,oEAAoE;YACpE,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CACrB,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC,CACzD,CAAA;AACP,CAAC;AACD,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,GAAa;IACpD,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACjE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAa;IAC9C,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;aACrD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,GAAG,CAAC,CAAA;AAClB,CAAC"}
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
+
import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
|
|
2
3
|
import { Typography } from '@mui/material';
|
|
3
4
|
import { observer } from 'mobx-react';
|
|
4
5
|
import { makeStyles } from 'tss-react/mui';
|
|
5
|
-
import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
|
|
6
6
|
// locals
|
|
7
7
|
import RIDLink from './RIDLink';
|
|
8
8
|
const useStyles = makeStyles()(theme => ({
|
|
@@ -29,7 +29,7 @@ const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
|
|
|
29
29
|
const { classes } = useStyles();
|
|
30
30
|
return (React.createElement("div", { className: classes.margin },
|
|
31
31
|
React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
|
|
32
|
-
error ? (React.createElement(RIDError, { rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null,
|
|
32
|
+
error ? (React.createElement(RIDError, { rid: rid, error: error })) : (rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null),
|
|
33
33
|
React.createElement(Typography, null, processing || 'Initializing BLAST query')));
|
|
34
34
|
});
|
|
35
35
|
export default LoadingBLAST;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,
|
|
1
|
+
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