jbrowse-plugin-msaview 2.2.2 → 2.2.3
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/MsaViewPanel/model.d.ts +10 -0
- package/dist/MsaViewPanel/model.js +36 -20
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts +6 -3
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +21 -21
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +3 -3
- package/dist/out.js +32 -18
- package/package.json +1 -1
- package/src/MsaViewPanel/model.ts +39 -27
- package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +1 -3
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@@ -546,6 +546,16 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
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* #action
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*/
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setBlastParams(args?: BlastParams): void;
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/**
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* #action
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*/
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handleMsaClick(coord: number): void;
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} & {
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/**
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* #action
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* overrides base setMouseClickPos to trigger navigation
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*/
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setMouseClickPos(col?: number, row?: number): void;
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} & {
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/**
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* #method
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@@ -166,7 +166,43 @@ export default function stateModelFactory() {
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setBlastParams(args) {
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self.blastParams = args;
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},
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/**
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* #action
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*/
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handleMsaClick(coord) {
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const { connectedView, zoomToBaseLevel } = self;
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const { assemblyManager } = getSession(self);
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const r2 = msaCoordToGenomeCoord({ model: self, coord });
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if (!r2 || !connectedView) {
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return;
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}
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if (zoomToBaseLevel) {
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connectedView.navTo(r2);
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}
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else {
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const r = assemblyManager
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.get(connectedView.assemblyNames[0])
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?.getCanonicalRefName(r2.refName) ?? r2.refName;
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connectedView.centerAt(r2.start, r);
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}
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},
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}))
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.actions(self => {
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// store reference to the original action from react-msaview
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const superSetMouseClickPos = self.setMouseClickPos;
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return {
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/**
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* #action
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* overrides base setMouseClickPos to trigger navigation
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*/
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setMouseClickPos(col, row) {
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superSetMouseClickPos(col, row);
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if (col !== undefined) {
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self.handleMsaClick(col);
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}
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},
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};
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})
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.views(self => ({
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/**
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* #method
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@@ -231,26 +267,6 @@ export default function stateModelFactory() {
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: msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
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self.setConnectedHighlights([r1, r2].filter(f => !!f));
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}));
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// nav to genome position after click
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addDisposer(self, autorun(() => {
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const { connectedView, zoomToBaseLevel, mouseClickCol } = self;
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const { assemblyManager } = getSession(self);
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const r2 = mouseClickCol === undefined
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? undefined
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: msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
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if (!r2 || !connectedView) {
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return;
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}
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if (zoomToBaseLevel) {
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connectedView.navTo(r2);
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}
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else {
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const r = assemblyManager
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.get(connectedView.assemblyNames[0])
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?.getCanonicalRefName(r2.refName) ?? r2.refName;
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connectedView.centerAt(r2.start, r);
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}
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}));
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},
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}));
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}
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@@ -1 +1 @@
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1
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+
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|
|
@@ -1,9 +1,12 @@
|
|
|
1
|
-
import { JBrowsePluginMsaViewModel } from './model';
|
|
2
1
|
export declare function msaCoordToGenomeCoord({ model, coord: mouseCol, }: {
|
|
3
|
-
model:
|
|
2
|
+
model: {
|
|
3
|
+
querySeqName: string;
|
|
4
|
+
transcriptToMsaMap: any;
|
|
5
|
+
rows: string[][];
|
|
6
|
+
};
|
|
4
7
|
coord: number;
|
|
5
8
|
}): {
|
|
6
|
-
refName:
|
|
9
|
+
refName: any;
|
|
7
10
|
start: number;
|
|
8
11
|
end: number;
|
|
9
12
|
} | undefined;
|
|
@@ -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":"AAAA;;;GAGG;AACH,SAAS,qBAAqB,CAAC,GAAW,EAAE,SAAiB;IAC3D,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,WAAW,EAAE,CAAA;QACf,CAAC;IACH,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,EACpC,KAAK,EACL,KAAK,EAAE,QAAQ,GAIhB;IACC,MAAM,EAAE,YAAY,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAClD,IAAI,kBAAkB,KAAK,SAAS,EAAE,CAAC;QACrC,OAAO,SAAS,CAAA;IAClB,CAAC;SAAM,CAAC;QACN,yBAAyB;QACzB,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,YAAY,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAA;QAC9B,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,uDAAuD;QACvD,IAAI,QAAQ,CAAC,QAAQ,CAAC,KAAK,GAAG,EAAE,CAAC;YAC/B,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,4DAA4D;QAC5D,MAAM,WAAW,GAAG,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAE7D,sDAAsD;QACtD,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAC3C,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAA;QAC1B,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,GAAG,CAAC,CAAC,CAAA;QAC9B,OAAO,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,SAAS;YACvC,CAAC,CAAC;gBACE,OAAO;gBACP,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACrB,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;aACpB;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;AACH,CAAC"}
|