jbrowse-plugin-msaview 2.0.4 → 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 +1 -1
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/HighlightComponents.d.ts +1 -1
- package/dist/AddHighlightModel/HighlightComponents.js +1 -2
- package/dist/AddHighlightModel/HighlightComponents.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.d.ts +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +1 -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/AddHighlightModel/util.d.ts +2 -2
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +1 -2
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +11 -10
- 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/useFeatureSequence.js +1 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +3 -4
- 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/components/TabUtils.js.map +1 -1
- package/dist/LaunchMsaView/index.js +1 -3
- package/dist/LaunchMsaView/index.js.map +1 -1
- package/dist/LaunchMsaView/util.js +2 -2
- package/dist/MsaViewPanel/components/LoadingBLAST.js +1 -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 +0 -1
- package/dist/MsaViewPanel/components/RIDLink.js.map +1 -1
- package/dist/MsaViewPanel/doLaunchBlast.js +1 -1
- package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
- package/dist/MsaViewPanel/genomeToMSA.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 +34 -30
- package/dist/MsaViewPanel/model.js +13 -5
- 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 +2 -4
- 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/package.json +20 -18
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +5 -2
- package/src/AddHighlightModel/HighlightComponents.tsx +4 -3
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +5 -5
- package/src/AddHighlightModel/index.tsx +3 -2
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +3 -4
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +18 -15
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts +3 -3
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts +1 -1
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +14 -13
- package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts +2 -1
- package/src/LaunchMsaView/components/TabUtils.tsx +1 -0
- package/src/LaunchMsaView/index.ts +5 -7
- package/src/LaunchMsaView/util.ts +2 -2
- package/src/MsaViewPanel/components/LoadingBLAST.tsx +3 -3
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +1 -1
- package/src/MsaViewPanel/components/RIDLink.tsx +2 -1
- package/src/MsaViewPanel/doLaunchBlast.ts +3 -3
- package/src/MsaViewPanel/genomeToMSA.ts +2 -1
- package/src/MsaViewPanel/index.ts +1 -1
- package/src/MsaViewPanel/model.ts +17 -6
- package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +0 -1
- package/src/OpenInNewIcon.tsx +4 -1
- package/src/TextField2.tsx +4 -1
- package/src/index.ts +2 -5
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
2
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
3
|
declare const GenomeMouseoverHighlight: ({ model, }: {
|
|
4
4
|
model: LinearGenomeViewModel;
|
|
5
5
|
}) => React.JSX.Element | null;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { observer } from 'mobx-react';
|
|
3
2
|
import { getSession } from '@jbrowse/core/util';
|
|
3
|
+
import { observer } from 'mobx-react';
|
|
4
4
|
import { useStyles } from './util';
|
|
5
5
|
const GenomeMouseoverHighlight = observer(function GenomeMouseoverHighlight2({ model, }) {
|
|
6
6
|
const { hovered } = getSession(model);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
|
|
1
|
+
{"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"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
2
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
3
|
type LGV = LinearGenomeViewModel;
|
|
4
4
|
declare const HighlightComponents: ({ model, }: {
|
|
5
5
|
model: LGV;
|
|
@@ -1,8 +1,7 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
2
|
import { observer } from 'mobx-react';
|
|
3
|
-
// locals
|
|
4
|
-
import MsaToGenomeHighlight from './MsaToGenomeHighlight';
|
|
5
3
|
import GenomeMouseoverHighlight from './GenomeMouseoverHighlight';
|
|
4
|
+
import MsaToGenomeHighlight from './MsaToGenomeHighlight';
|
|
6
5
|
const HighlightComponents = observer(function HighlightComponents2({ model, }) {
|
|
7
6
|
return (React.createElement(React.Fragment, null,
|
|
8
7
|
React.createElement(MsaToGenomeHighlight, { model: model }),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
|
|
1
|
+
{"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"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
2
|
+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
|
|
3
3
|
type LGV = LinearGenomeViewModel;
|
|
4
4
|
declare const MsaToGenomeHighlight: ({ model, }: {
|
|
5
5
|
model: LGV;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { observer } from 'mobx-react';
|
|
3
2
|
import { getSession } from '@jbrowse/core/util';
|
|
3
|
+
import { observer } from 'mobx-react';
|
|
4
4
|
import { useStyles } from './util';
|
|
5
5
|
function getCanonicalName(assembly, s) {
|
|
6
6
|
return assembly.getCanonicalRefName(s) ?? s;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
|
|
1
|
+
{"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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAIzB,
|
|
1
|
+
{"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"}
|
|
@@ -4,6 +4,6 @@ export declare const useStyles: (params: void, muiStyleOverridesParams?: {
|
|
|
4
4
|
} | undefined) => {
|
|
5
5
|
classes: Record<"highlight", string>;
|
|
6
6
|
theme: import("@mui/material").Theme;
|
|
7
|
-
css: import("tss-react").Css;
|
|
8
|
-
cx: import("tss-react").Cx;
|
|
7
|
+
css: import("tss-react/types").Css;
|
|
8
|
+
cx: import("tss-react/types").Cx;
|
|
9
9
|
};
|
|
@@ -1,10 +1,9 @@
|
|
|
1
1
|
import React, { useState } from 'react';
|
|
2
2
|
import { Dialog } from '@jbrowse/core/ui';
|
|
3
3
|
import { Box, Tab, Tabs } from '@mui/material';
|
|
4
|
-
// locals
|
|
5
|
-
import CustomTabPanel from './TabUtils';
|
|
6
4
|
import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
|
|
7
5
|
import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
|
|
6
|
+
import CustomTabPanel from './TabUtils';
|
|
8
7
|
import { a11yProps } from './tabUtil';
|
|
9
8
|
export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
|
|
10
9
|
const [value, setValue] = useState(0);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LaunchMsaViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/LaunchMsaViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;
|
|
1
|
+
{"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"}
|
|
@@ -1,15 +1,14 @@
|
|
|
1
1
|
import React, { useState } from 'react';
|
|
2
|
-
import {
|
|
2
|
+
import { ErrorMessage } from '@jbrowse/core/ui';
|
|
3
|
+
import { getContainingView, } from '@jbrowse/core/util';
|
|
3
4
|
import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
|
|
5
|
+
import { observer } from 'mobx-react';
|
|
4
6
|
import { makeStyles } from 'tss-react/mui';
|
|
5
|
-
import { getContainingView, } from '@jbrowse/core/util';
|
|
6
|
-
import { ErrorMessage } from '@jbrowse/core/ui';
|
|
7
|
-
// locals
|
|
8
|
-
import { getId, getTranscriptDisplayName, getTranscriptFeatures, getGeneDisplayName, } from '../../util';
|
|
9
7
|
import { getProteinSequence } from './calculateProteinSequence';
|
|
8
|
+
import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
|
|
10
9
|
import { useFeatureSequence } from './useFeatureSequence';
|
|
11
10
|
import TextField2 from '../../../TextField2';
|
|
12
|
-
import {
|
|
11
|
+
import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
|
|
13
12
|
const useStyles = makeStyles()({
|
|
14
13
|
dialogContent: {
|
|
15
14
|
width: '80em',
|
|
@@ -54,10 +53,12 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature,
|
|
|
54
53
|
getTranscriptDisplayName(val))))),
|
|
55
54
|
React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: proteinSequence
|
|
56
55
|
? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
|
|
57
|
-
: 'Loading...',
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
|
|
56
|
+
: 'Loading...', slotProps: {
|
|
57
|
+
input: {
|
|
58
|
+
readOnly: true,
|
|
59
|
+
classes: {
|
|
60
|
+
input: classes.textAreaFont,
|
|
61
|
+
},
|
|
61
62
|
},
|
|
62
63
|
} }),
|
|
63
64
|
React.createElement(DialogActions, null,
|
|
@@ -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;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;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { useEffect, useState } from 'react';
|
|
2
|
-
import { getSession } from '@jbrowse/core/util';
|
|
3
2
|
import { getConf } from '@jbrowse/core/configuration';
|
|
3
|
+
import { getSession } from '@jbrowse/core/util';
|
|
4
4
|
const BPLIMIT = 500_000;
|
|
5
5
|
async function fetchSeq({ start, end, refName, session, assemblyName, }) {
|
|
6
6
|
const { assemblyManager, rpcManager } = session;
|
|
@@ -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 +1,12 @@
|
|
|
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
|
-
// locals
|
|
8
|
-
import { getTranscriptDisplayName, getId, getTranscriptFeatures, getGeneDisplayName, } from '../../util';
|
|
9
7
|
import { fetchGeneList } from './fetchGeneList';
|
|
10
8
|
import { preCalculatedLaunchView } from './preCalculatedLaunchView';
|
|
9
|
+
import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
|
|
11
10
|
const useStyles = makeStyles()({
|
|
12
11
|
dialogContent: {
|
|
13
12
|
width: '80em',
|
|
@@ -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;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"}
|
|
@@ -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;
|
|
5
5
|
userSelection: string;
|
|
@@ -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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
|
|
1
|
+
{"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"}
|
|
@@ -1,7 +1,5 @@
|
|
|
1
|
-
import {
|
|
2
|
-
// icons
|
|
1
|
+
import { getContainingTrack, getSession } from '@jbrowse/core/util';
|
|
3
2
|
import AddIcon from '@mui/icons-material/Add';
|
|
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,EAAE,UAAU,EAAE,
|
|
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"}
|
|
@@ -8,7 +8,7 @@ export function getTranscriptFeatures(feature) {
|
|
|
8
8
|
subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
|
|
9
9
|
}
|
|
10
10
|
export function getId(val) {
|
|
11
|
-
return val?.get('name')
|
|
11
|
+
return val?.get('name') ?? val?.get('id') ?? '';
|
|
12
12
|
}
|
|
13
13
|
export function getTranscriptDisplayName(val) {
|
|
14
14
|
return val === undefined
|
|
@@ -18,7 +18,7 @@ export function getTranscriptDisplayName(val) {
|
|
|
18
18
|
export function getGeneDisplayName(val) {
|
|
19
19
|
return val === undefined
|
|
20
20
|
? ''
|
|
21
|
-
: [val.get('gene_name')
|
|
21
|
+
: [val.get('gene_name') ?? val.get('name'), val.get('id')]
|
|
22
22
|
.filter(f => !!f)
|
|
23
23
|
.join(' ');
|
|
24
24
|
}
|
|
@@ -1,9 +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
|
-
// locals
|
|
7
6
|
import RIDLink from './RIDLink';
|
|
8
7
|
const useStyles = makeStyles()(theme => ({
|
|
9
8
|
margin: {
|
|
@@ -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
|
+
{"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;
|
|
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;
|
|
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"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
+
import { makeId, strip, } from '../LaunchMsaView/components/NewNCBIBlastQuery/util';
|
|
1
2
|
import { launchMSA } from '../utils/msa';
|
|
2
3
|
import { queryBlast } from '../utils/ncbiBlast';
|
|
3
|
-
import { makeId, strip, } from '../LaunchMsaView/components/NewNCBIBlastQuery/util';
|
|
4
4
|
export async function doLaunchBlast({ self, }) {
|
|
5
5
|
const { blastDatabase, blastProgram, msaAlgorithm, proteinSequence } = self.blastParams;
|
|
6
6
|
const query = proteinSequence.replaceAll('*', '').replaceAll('&', '');
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"AACA,OAAO,EACL,MAAM,EACN,KAAK,GACN,MAAM,oDAAoD,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,EAClC,IAAI,GAGL;IACC,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,GAClE,IAAI,CAAC,WAAY,CAAA;IACnB,MAAM,KAAK,GAAG,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;IACrE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,UAAU,CAAC;QAChC,KAAK;QACL,aAAa;QACb,YAAY;QACZ,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;QACD,KAAK,EAAE,GAAG,CAAC,EAAE;YACX,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;KACF,CAAC,CAAA;IAEF,MAAM,QAAQ,GAAG;QACf,WAAW,KAAK,EAAE;QAClB,GAAG,IAAI;aACJ,GAAG,CACF,CAAC,CAAC,EAAE,CACF;YACE,MAAM,CACJ,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI;gBAClB,SAAS,EAAE,SAAS;gBACpB,EAAE,EAAE,SAAS;gBACb,OAAO,EAAE,SAAS;aACnB,CACF;YACD,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,IAAI,EAAE,CAAC;SACpB,CACb;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;KACxC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAEZ,MAAM,IAAI,GAAG,MAAM,SAAS,CAAC;QAC3B,SAAS,EAAE,YAAY;QACvB,QAAQ;QACR,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"genomeToMSA.js","sourceRoot":"","sources":["../../src/MsaViewPanel/genomeToMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"genomeToMSA.js","sourceRoot":"","sources":["../../src/MsaViewPanel/genomeToMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAG/C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAErC,MAAM,UAAU,WAAW,CAAC,EAAE,KAAK,EAAwC;IACzE,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,kBAAkB,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IACnD,IACE,aAAa,EAAE,WAAW;QAC1B,kBAAkB;QAClB,YAAY,CAAC,OAAO,CAAC,EACrB,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QACnD,MAAM,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAClC,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,OAAO,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,GAAG,GAAG,CAAC,CAAC,CAAA;QACjE,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MsaViewPanel/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;
|
|
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 {
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
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 {
|
|
@@ -28,9 +28,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
28
28
|
drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
29
29
|
labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
30
30
|
treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
31
|
-
treeWidth: import("mobx-state-tree"
|
|
32
|
-
* #property
|
|
33
|
-
*/).IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
31
|
+
treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
34
32
|
treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
35
33
|
showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
36
34
|
drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
@@ -42,9 +40,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
42
40
|
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
43
41
|
showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
44
42
|
allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
45
|
-
contrastLettering: import("mobx-state-tree"
|
|
46
|
-
* #getter
|
|
47
|
-
*/).IType<boolean | undefined, boolean, boolean>;
|
|
43
|
+
contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
48
44
|
subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
49
45
|
type: import("mobx-state-tree").ISimpleType<"MsaView">;
|
|
50
46
|
drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
@@ -55,19 +51,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
55
51
|
scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
56
52
|
scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
57
53
|
colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
58
|
-
treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree"
|
|
59
|
-
* #action
|
|
60
|
-
*/).ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
54
|
+
treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
61
55
|
locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
|
|
62
56
|
uri: import("mobx-state-tree").ISimpleType<string>;
|
|
63
57
|
baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
64
58
|
internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
65
|
-
internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import(
|
|
66
|
-
/**
|
|
67
|
-
* #method
|
|
68
|
-
* overrides base
|
|
69
|
-
*/
|
|
70
|
-
"mobx-state-tree").IModelType<{
|
|
59
|
+
internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
|
|
71
60
|
internetAccountType: import("mobx-state-tree").ISimpleType<string>;
|
|
72
61
|
authInfo: import("mobx-state-tree").IType<any, any, any>;
|
|
73
62
|
}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
@@ -234,6 +223,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
234
223
|
treeMetadata: string | undefined;
|
|
235
224
|
}>, [undefined]>;
|
|
236
225
|
featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
226
|
+
relativeTo: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
237
227
|
} & {
|
|
238
228
|
connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
239
229
|
connectedFeature: import("mobx-state-tree").IType<any, any, any>;
|
|
@@ -298,6 +288,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
298
288
|
} | undefined;
|
|
299
289
|
interProAnnotations: undefined | Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>;
|
|
300
290
|
} & {
|
|
291
|
+
drawRelativeTo(id: string): void;
|
|
301
292
|
setHideGaps(arg: boolean): void;
|
|
302
293
|
setAllowedGappyness(arg: number): void;
|
|
303
294
|
setContrastLettering(arg: boolean): void;
|
|
@@ -336,13 +327,6 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
336
327
|
extraViewMenuItems(): never[];
|
|
337
328
|
readonly colorScheme: Record<string, string>;
|
|
338
329
|
readonly header: {};
|
|
339
|
-
getRowData(name: string): {
|
|
340
|
-
data: {
|
|
341
|
-
name: string;
|
|
342
|
-
accession: string | undefined;
|
|
343
|
-
dbxref: string | undefined;
|
|
344
|
-
} | undefined;
|
|
345
|
-
};
|
|
346
330
|
readonly alignmentNames: string[];
|
|
347
331
|
readonly noTree: boolean;
|
|
348
332
|
readonly noDomains: boolean;
|
|
@@ -359,6 +343,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
359
343
|
readonly blanks: number[];
|
|
360
344
|
readonly blanksSet: Set<number>;
|
|
361
345
|
readonly rows: [string, string][];
|
|
346
|
+
readonly numRows: number;
|
|
362
347
|
readonly rowMap: Map<string, string>;
|
|
363
348
|
readonly columns: {
|
|
364
349
|
[k: string]: string;
|
|
@@ -406,8 +391,8 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
406
391
|
readonly secondaryStructureConsensus: string | undefined;
|
|
407
392
|
readonly seqConsensus: string | undefined;
|
|
408
393
|
readonly conservation: string[];
|
|
409
|
-
readonly adapterTrackModels: import("react-msaview/dist/model").
|
|
410
|
-
readonly tracks: import("react-msaview/dist/model").
|
|
394
|
+
readonly adapterTrackModels: import("react-msaview/dist/model").BasicTrack[];
|
|
395
|
+
readonly tracks: import("react-msaview/dist/model").BasicTrack[];
|
|
411
396
|
readonly turnedOnTracks: import("react-msaview/dist/model").ITextTrack[];
|
|
412
397
|
readonly showHorizontalScrollbar: boolean;
|
|
413
398
|
readonly rowNamesSet: Map<string, number>;
|
|
@@ -450,6 +435,14 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
450
435
|
readonly strokePalette: {
|
|
451
436
|
[k: string]: string;
|
|
452
437
|
};
|
|
438
|
+
getRowData(name: string): {
|
|
439
|
+
data: {
|
|
440
|
+
name: string;
|
|
441
|
+
accession: string | undefined;
|
|
442
|
+
dbxref: string | undefined;
|
|
443
|
+
} | undefined;
|
|
444
|
+
treeMetadata: any;
|
|
445
|
+
};
|
|
453
446
|
} & {
|
|
454
447
|
setHeaderHeight(arg: number): void;
|
|
455
448
|
reset(): void;
|
|
@@ -461,10 +454,20 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
461
454
|
incrementRef(): void;
|
|
462
455
|
initFilter(arg: string): void;
|
|
463
456
|
setFilter(arg: string, flag: boolean): void;
|
|
457
|
+
showEntire(): void;
|
|
464
458
|
afterCreate(): void;
|
|
465
459
|
} & {
|
|
460
|
+
/**
|
|
461
|
+
* #volatile
|
|
462
|
+
*/
|
|
466
463
|
rid: string | undefined;
|
|
464
|
+
/**
|
|
465
|
+
* #volatile
|
|
466
|
+
*/
|
|
467
467
|
progress: string;
|
|
468
|
+
/**
|
|
469
|
+
* #volatile
|
|
470
|
+
*/
|
|
468
471
|
error: unknown;
|
|
469
472
|
} & {
|
|
470
473
|
/**
|
|
@@ -476,8 +479,8 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
476
479
|
* #getter
|
|
477
480
|
*/
|
|
478
481
|
readonly transcriptToMsaMap: {
|
|
479
|
-
g2p: Record<number, number
|
|
480
|
-
p2g: Record<number, number
|
|
482
|
+
g2p: Record<number, number>;
|
|
483
|
+
p2g: Record<number, number>;
|
|
481
484
|
refName: string;
|
|
482
485
|
strand: number;
|
|
483
486
|
} | undefined;
|
|
@@ -554,7 +557,6 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
554
557
|
} & {
|
|
555
558
|
afterCreate(): void;
|
|
556
559
|
}, import("mobx-state-tree")._NotCustomized, {
|
|
557
|
-
height: number;
|
|
558
560
|
drawLabels: boolean;
|
|
559
561
|
labelsAlignRight: boolean;
|
|
560
562
|
treeAreaWidth: number;
|
|
@@ -579,6 +581,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
579
581
|
colWidth: number;
|
|
580
582
|
currentAlignment: number;
|
|
581
583
|
type: "MsaView";
|
|
584
|
+
height: number;
|
|
582
585
|
treeFilehandle: {
|
|
583
586
|
locationType: "UriLocation";
|
|
584
587
|
uri: string;
|
|
@@ -632,6 +635,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
632
635
|
showOnly: string | undefined;
|
|
633
636
|
turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
|
|
634
637
|
featureFilters: import("mobx").IKeyValueMap<boolean>;
|
|
638
|
+
relativeTo: string | undefined;
|
|
635
639
|
data: {
|
|
636
640
|
treeMetadata?: string | undefined;
|
|
637
641
|
msa?: string | undefined;
|