jbrowse-plugin-msaview 2.0.5 → 2.0.6
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.d.ts +1 -1
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/HighlightComponents.d.ts +1 -1
- package/dist/AddHighlightModel/HighlightComponents.js +0 -1
- package/dist/AddHighlightModel/HighlightComponents.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.d.ts +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +0 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/AddHighlightModel/index.js +0 -1
- package/dist/AddHighlightModel/index.js.map +1 -1
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +0 -1
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +6 -5
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.d.ts +2 -2
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +0 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/index.js +0 -2
- package/dist/LaunchMsaView/index.js.map +1 -1
- package/dist/LaunchMsaView/util.js +2 -2
- package/dist/MsaViewPanel/components/LoadingBLAST.js +0 -1
- package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/components/RIDLink.js +0 -1
- package/dist/MsaViewPanel/components/RIDLink.js.map +1 -1
- package/dist/MsaViewPanel/index.js +0 -1
- package/dist/MsaViewPanel/index.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +12 -3
- package/dist/MsaViewPanel/model.js +9 -1
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +1 -1
- package/dist/OpenInNewIcon.d.ts +1 -1
- package/dist/OpenInNewIcon.js.map +1 -1
- package/dist/TextField2.d.ts +1 -1
- package/dist/TextField2.js.map +1 -1
- package/dist/config.json +8 -0
- package/dist/index.js +0 -2
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +17 -17
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +2 -2
- package/package.json +2 -2
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +2 -1
- package/src/AddHighlightModel/HighlightComponents.tsx +2 -2
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +2 -3
- package/src/AddHighlightModel/index.tsx +2 -2
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +0 -2
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +8 -6
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts +2 -3
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +2 -2
- package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts +2 -1
- package/src/LaunchMsaView/index.ts +1 -4
- package/src/LaunchMsaView/util.ts +2 -2
- package/src/MsaViewPanel/components/LoadingBLAST.tsx +0 -2
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +0 -1
- package/src/MsaViewPanel/components/RIDLink.tsx +0 -1
- package/src/MsaViewPanel/index.ts +0 -1
- package/src/MsaViewPanel/model.ts +14 -4
- package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +0 -1
- package/src/OpenInNewIcon.tsx +3 -1
- package/src/TextField2.tsx +3 -1
- package/src/index.ts +0 -3
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@@ -1,5 +1,5 @@
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import React from 'react';
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import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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declare const GenomeMouseoverHighlight: ({ model, }: {
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model: LinearGenomeViewModel;
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}) => React.JSX.Element | null;
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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;
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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;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIlC,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 { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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type LGV = LinearGenomeViewModel;
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declare const HighlightComponents: ({ model, }: {
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model: LGV;
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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 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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{"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;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;AACjE,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AAMzD,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 { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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type LGV = LinearGenomeViewModel;
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declare const MsaToGenomeHighlight: ({ model, }: {
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model: LGV;
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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;
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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;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOlC,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;AAIzB,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAIvD,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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import React, { useState } from 'react';
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import { Dialog } from '@jbrowse/core/ui';
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import { Box, Tab, Tabs } from '@mui/material';
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// locals
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import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
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import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
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import CustomTabPanel from './TabUtils';
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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,
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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,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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import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
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import { observer } from 'mobx-react';
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import { makeStyles } from 'tss-react/mui';
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import { getProteinSequence } from './calculateProteinSequence';
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import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
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import { useFeatureSequence } from './useFeatureSequence';
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getTranscriptDisplayName(val))))),
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React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: proteinSequence
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? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
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input: {
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readOnly: true,
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classes: {
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input: classes.textAreaFont,
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},
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{"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;
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{"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;AAC3B,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,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;AAInB,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,SAAS,EAAE;gBACT,KAAK,EAAE;oBACL,QAAQ,EAAE,IAAI;oBACd,OAAO,EAAE;wBACP,KAAK,EAAE,OAAO,CAAC,YAAY;qBAC5B;iBACF;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"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { Feature } from '@jbrowse/core/util';
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
2
|
+
import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
|
|
3
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
4
4
|
export declare function ncbiBlastLaunchView({ newViewTitle, view, feature, }: {
|
|
5
5
|
newViewTitle: string;
|
|
6
6
|
view: LinearGenomeViewModel;
|
|
@@ -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;
|
|
1
|
+
{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKxD,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"}
|
|
@@ -4,7 +4,6 @@ import { getContainingView, getSession, } from '@jbrowse/core/util';
|
|
|
4
4
|
import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
|
|
5
5
|
import { observer } from 'mobx-react';
|
|
6
6
|
import { makeStyles } from 'tss-react/mui';
|
|
7
|
-
// locals
|
|
8
7
|
import { fetchGeneList } from './fetchGeneList';
|
|
9
8
|
import { preCalculatedLaunchView } from './preCalculatedLaunchView';
|
|
10
9
|
import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
|
|
@@ -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;AAElD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,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;AAC3B,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,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;AAInB,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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@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
|
|
2
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
2
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
3
|
export declare function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }: {
|
|
4
4
|
session: AbstractSessionModel;
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5
5
|
userSelection: string;
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"preCalculatedLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"preCalculatedLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAE,MAAM,MAAM,CAAA;AAI7B,KAAK,UAAU,OAAO,CAAC,GAAW;IAChC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IACpE,CAAC;IACD,MAAM,IAAI,GAAG,MAAM,GAAG,CAAC,WAAW,EAAE,CAAA;IACpC,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAA;AAC/C,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,uBAAuB,CAAC,EAC5C,aAAa,EACb,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,GAOR;IACC,MAAM,CAAC,GAAG,MAAM,OAAO,CACrB,oDAAoD,aAAa,SAAS,CAC3E,CAAA;IAED,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,aAAa,EAAE,GAAG;QAClB,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,KAAK;QACtB,gBAAgB,EAAE,IAAI;QACtB,aAAa,EAAE,KAAK;QACpB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;QAC3C,cAAc,EAAE;YACd,GAAG,EAAE,6EAA6E;SACnF;QACD,sBAAsB,EAAE;YACtB,GAAG,EAAE,6DAA6D;SACnE;QACD,IAAI,EAAE;YACJ,GAAG,EAAE,CAAC;SACP;QACD,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;KACnC,CAAC,CAAA;AACJ,CAAC"}
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@@ -1,7 +1,5 @@
|
|
|
1
1
|
import { getContainingTrack, getSession } from '@jbrowse/core/util';
|
|
2
2
|
import AddIcon from '@mui/icons-material/Add';
|
|
3
|
-
// icons
|
|
4
|
-
// locals
|
|
5
3
|
import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
|
|
6
4
|
function isDisplay(elt) {
|
|
7
5
|
return elt.name === 'LinearBasicDisplay';
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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;AAE7C,OAAO,mBAAmB,MAAM,kCAAkC,CAAA;AAIlE,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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@@ -8,7 +8,7 @@ export function getTranscriptFeatures(feature) {
|
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8
8
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subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
|
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}
|
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export function getId(val) {
|
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-
return val?.get('name')
|
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+
return val?.get('name') ?? val?.get('id') ?? '';
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}
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export function getTranscriptDisplayName(val) {
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return val === undefined
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@@ -18,7 +18,7 @@ export function getTranscriptDisplayName(val) {
|
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export function getGeneDisplayName(val) {
|
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return val === undefined
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? ''
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: [val.get('gene_name')
|
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+
: [val.get('gene_name') ?? val.get('name'), val.get('id')]
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.filter(f => !!f)
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.join(' ');
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}
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@@ -3,7 +3,6 @@ import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
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3
3
|
import { Typography } from '@mui/material';
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4
4
|
import { observer } from 'mobx-react';
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|
import { makeStyles } from 'tss-react/mui';
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6
|
-
// locals
|
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6
|
import RIDLink from './RIDLink';
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|
const useStyles = makeStyles()(theme => ({
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margin: {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;
|
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1
|
+
{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,OAAO,OAAO,MAAM,WAAW,CAAA;AAE/B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,EAAE;KACZ;IACD,OAAO,EAAE;QACP,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;KAC3C;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,QAAQ,CAAC,EAAE,GAAG,EAAE,KAAK,EAAoC;IAChE,OAAO,CACL;QACG,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,GAAG,EAAE,GAAG,GAAI,CAAC,CAAC,CAAC,IAAI;QACnC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAqC;IACvE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC5B,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,GAAG,EAAE,GAAG,GAAI,CAAC,CAAC,CAAC,IAAI;QACnC,oBAAC,UAAU,QAAE,QAAQ,CAAc,CAC/B,CACP,CAAA;AACH,CAAC;AAED,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAClD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM;QAC5B,oBAAC,eAAe,IAAC,OAAO,EAAC,oBAAoB,EAAC,OAAO,EAAC,IAAI,GAAG;QAC5D,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,GAAI,CACrC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CACT,oBAAC,WAAW,IAAC,GAAG,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC9C,CAAC,CAAC,CAAC,IAAI,CAAC;QACT,oBAAC,UAAU,QAAE,UAAU,IAAI,0BAA0B,CAAc,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;
|
|
1
|
+
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAGvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAEhD,
|
|
1
|
+
{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAEhD,OAAO,aAAa,MAAM,qBAAqB,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAA;AAEjD,SAAS,OAAO,CAAC,EAAE,GAAG,EAAmB;IACvC,OAAO,CACL,oBAAC,UAAU;;QACJ,GAAG;QAAE,GAAG;QACb,oBAAC,IAAI,IAAC,MAAM,EAAC,QAAQ,EAAC,IAAI,EAAE,GAAG,SAAS,gBAAgB,GAAG,EAAE;;YACvC,oBAAC,aAAa,OAAG;gBAChC,CACI,CACd,CAAA;AACH,CAAC;AAED,eAAe,OAAO,CAAA"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MsaViewPanel/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAG5B,OAAO,QAAQ,MAAM,8CAA8C,CAAA;AAEnE,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MsaViewPanel/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAG5B,OAAO,QAAQ,MAAM,8CAA8C,CAAA;AAEnE,OAAO,iBAAiB,MAAM,SAAS,CAAA;AAEvC,SAAS;AACT,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AAEpE,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,WAAW,CAAC,GAAG,EAAE;QAC7B,OAAO,IAAI,QAAQ,CAAC;YAClB,IAAI,EAAE,SAAS;YACf,UAAU,EAAE,iBAAiB,EAAE;YAC/B,cAAc,EAAE,YAAY;SAC7B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { Feature } from '@jbrowse/core/util';
|
|
2
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
|
-
import { Instance } from 'mobx-state-tree';
|
|
1
|
+
import type { Feature } from '@jbrowse/core/util';
|
|
2
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
|
+
import type { Instance } from 'mobx-state-tree';
|
|
4
4
|
type LGV = LinearGenomeViewModel;
|
|
5
5
|
type MaybeLGV = LGV | undefined;
|
|
6
6
|
export interface IRegion {
|
|
@@ -457,8 +457,17 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
457
457
|
showEntire(): void;
|
|
458
458
|
afterCreate(): void;
|
|
459
459
|
} & {
|
|
460
|
+
/**
|
|
461
|
+
* #volatile
|
|
462
|
+
*/
|
|
460
463
|
rid: string | undefined;
|
|
464
|
+
/**
|
|
465
|
+
* #volatile
|
|
466
|
+
*/
|
|
461
467
|
progress: string;
|
|
468
|
+
/**
|
|
469
|
+
* #volatile
|
|
470
|
+
*/
|
|
462
471
|
error: unknown;
|
|
463
472
|
} & {
|
|
464
473
|
/**
|
|
@@ -4,7 +4,6 @@ import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
|
|
|
4
4
|
import { autorun } from 'mobx';
|
|
5
5
|
import { addDisposer, cast, types } from 'mobx-state-tree';
|
|
6
6
|
import { MSAModelF } from 'react-msaview';
|
|
7
|
-
// locals
|
|
8
7
|
import { doLaunchBlast } from './doLaunchBlast';
|
|
9
8
|
import { genomeToMSA } from './genomeToMSA';
|
|
10
9
|
import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
|
|
@@ -42,8 +41,17 @@ export default function stateModelFactory() {
|
|
|
42
41
|
zoomToBaseLevel: false,
|
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43
42
|
}))
|
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44
43
|
.volatile(() => ({
|
|
44
|
+
/**
|
|
45
|
+
* #volatile
|
|
46
|
+
*/
|
|
45
47
|
rid: undefined,
|
|
48
|
+
/**
|
|
49
|
+
* #volatile
|
|
50
|
+
*/
|
|
46
51
|
progress: '',
|
|
52
|
+
/**
|
|
53
|
+
* #volatile
|
|
54
|
+
*/
|
|
47
55
|
error: undefined,
|
|
48
56
|
}))
|
|
49
57
|
.views(self => ({
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,
|
|
1
|
+
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"msaCoordToGenomeCoord.js","sourceRoot":"","sources":["../../src/MsaViewPanel/msaCoordToGenomeCoord.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"msaCoordToGenomeCoord.js","sourceRoot":"","sources":["../../src/MsaViewPanel/msaCoordToGenomeCoord.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,qBAAqB,CAAC,EACpC,KAAK,EACL,KAAK,EAAE,QAAQ,GAIhB;IACC,MAAM,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACpC,IAAI,kBAAkB,KAAK,SAAS,EAAE,CAAC;QACrC,OAAM;IACR,CAAC;IAED,MAAM,CAAC,GAAG,QAAQ,CAAA;IAClB,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAA;IAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;IACtE,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;IAC3C,MAAM,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IACjB,MAAM,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IACjB,OAAO,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,SAAS;QACvC,CAAC,CAAC;YACE,OAAO;YACP,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;YACrB,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;SACpB;QACH,CAAC,CAAC,SAAS,CAAA;AACf,CAAC"}
|
package/dist/OpenInNewIcon.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"OpenInNewIcon.js","sourceRoot":"","sources":["../src/OpenInNewIcon.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,
|
|
1
|
+
{"version":3,"file":"OpenInNewIcon.js","sourceRoot":"","sources":["../src/OpenInNewIcon.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAIvC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,KAAmB;IACvD,OAAO,CACL,oBAAC,OAAO,OAAK,KAAK;QAChB,8BAAM,CAAC,EAAC,eAAe,EAAC,IAAI,EAAC,MAAM,GAAG;QACtC,8BAAM,CAAC,EAAC,oIAAoI,GAAG,CACvI,CACX,CAAA;AACH,CAAC"}
|
package/dist/TextField2.d.ts
CHANGED
package/dist/TextField2.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"TextField2.js","sourceRoot":"","sources":["../src/TextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,SAAS,
|
|
1
|
+
{"version":3,"file":"TextField2.js","sourceRoot":"","sources":["../src/TextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAIzC,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,eAAe,UAAU,CAAA"}
|
package/dist/config.json
ADDED
package/dist/index.js
CHANGED
|
@@ -1,8 +1,6 @@
|
|
|
1
1
|
import Plugin from '@jbrowse/core/Plugin';
|
|
2
2
|
import { isAbstractMenuManager } from '@jbrowse/core/util';
|
|
3
|
-
// icons
|
|
4
3
|
import GridOn from '@mui/icons-material/GridOn';
|
|
5
|
-
// locals
|
|
6
4
|
import { version } from '../package.json';
|
|
7
5
|
import AddHighlightModelF from './AddHighlightModel';
|
|
8
6
|
import LaunchMsaViewF from './LaunchMsaView';
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EAAwB,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EAAwB,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;AAChF,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAE/C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,QAAQ,MAAM,gBAAgB,CAAA;AAErC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,MAAM;IAAjD;;QACE,SAAI,GAAG,eAAe,CAAA;QACtB,YAAO,GAAG,OAAO,CAAA;IAmBnB,CAAC;IAjBC,OAAO,CAAC,aAA4B;QAClC,QAAQ,CAAC,aAAa,CAAC,CAAA;QACvB,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,aAA4B;QACpC,IAAI,qBAAqB,CAAC,aAAa,CAAC,SAAS,CAAC,EAAE,CAAC;YACnD,aAAa,CAAC,SAAS,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,KAAK,EAAE,kCAAkC;gBACzC,IAAI,EAAE,MAAM;gBACZ,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;gBAChC,CAAC;aACF,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;CACF"}
|