@jbrowse/plugin-linear-genome-view 2.4.2 → 2.6.1

package/esm/LinearGenomeView/components/TracksContainer.js

@@ -12,6 +12,7 @@ import Gridlines from './Gridlines';
 import CenterLine from './CenterLine';
 import VerticalGuide from './VerticalGuide';
 import RubberbandSpan from './RubberbandSpan';
+import { getEnv } from '@jbrowse/core/util';
 const useStyles = makeStyles()({
     tracksContainer: {
         position: 'relative',
@@ -20,17 +21,13 @@ const useStyles = makeStyles()({
 });
 export default observer(function TracksContainer({ children, model, }) {
     const { classes } = useStyles();
+    const { pluginManager } = getEnv(model);
     const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model);
     const ref = useRef(null);
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, handleMenuItemClick, open, handleClose, mouseMove, mouseDown: mouseDown2, } = useRangeSelect(ref, model, true);
     useWheelScroll(ref, model);
-    return (React.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onClick: event => {
-            var _a;
-            if (event.detail === 2) {
-                const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
-                model.zoomTo(model.bpPerPx / 2, event.clientX - left, true);
-            }
-        }, onMouseDown: event => {
+    const additional = pluginManager.evaluateExtensionPoint('LinearGenomeView-TracksContainerComponent', undefined, { model });
+    return (React.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onMouseDown: event => {
             mouseDown1(event);
             mouseDown2(event);
         }, onMouseMove: mouseMove, onMouseUp: mouseUp },
@@ -42,6 +39,7 @@ export default observer(function TracksContainer({ children, model, }) {
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null,
         React.createElement(Rubberband, { model: model, ControlComponent: React.createElement(Scalebar, { model: model, style: { height: SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
+        additional,
         children));
 });
 //# sourceMappingURL=TracksContainer.js.map

package/esm/LinearGenomeView/components/TracksContainer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TracksContainer.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TracksContainer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AAEvC,cAAc;AACd,OAAO,EAAyB,gBAAgB,EAAE,MAAM,IAAI,CAAA;AAC5D,OAAO,EAAE,aAAa,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,SAAS,CAAA;AAEvE,mBAAmB;AACnB,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAE3C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,eAAe,EAAE;QACf,QAAQ,EAAE,UAAU;QACpB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA;AAIF,eAAe,QAAQ,CAAC,SAAS,eAAe,CAAC,EAC/C,QAAQ,EACR,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,aAAa,CAAC,KAAK,CAAC,CAAA;IAC/D,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EACJ,MAAM,EACN,YAAY,EACZ,YAAY,EACZ,aAAa,EACb,eAAe,EACf,KAAK,EACL,IAAI,EACJ,cAAc,EACd,mBAAmB,EACnB,IAAI,EACJ,WAAW,EACX,SAAS,EACT,SAAS,EAAE,UAAU,GACtB,GAAG,cAAc,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IACpC,cAAc,CAAC,GAAG,EAAE,KAAK,CAAC,CAAA;IAE1B,MAAM,UAAU,GAAG,aAAa,CAAC,sBAAsB,CACrD,2CAA2C,EAC3C,SAAS,EACT,EAAE,KAAK,EAAE,CACS,CAAA;IAEpB,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBACI,gBAAgB,EAC5B,SAAS,EAAE,OAAO,CAAC,eAAe,EAClC,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,UAAU,CAAC,KAAK,CAAC,CAAA;YACjB,UAAU,CAAC,KAAK,CAAC,CAAA;QACnB,CAAC,EACD,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO;QAEjB,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACxD,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC1D,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CACtB,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CAChD,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CACjB,oBAAC,cAAc,IACb,YAAY,EAAE,YAAY,EAC1B,aAAa,EAAE,aAAa,EAC5B,eAAe,EAAE,eAAe,EAChC,KAAK,EAAE,KAAK,EACZ,IAAI,EAAE,IAAI,GACV,CACH,CAAC,CAAC,CAAC,IAAI;QACP,cAAc,CAAC,CAAC,CAAC,CAChB,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;gBACd,IAAI,EAAE,cAAc,CAAC,OAAO;gBAC5B,GAAG,EAAE,cAAc,CAAC,OAAO;aAC5B,EACD,eAAe,EAAE,mBAAmB,EACpC,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,WAAW,EACpB,SAAS,EAAE,KAAK,CAAC,mBAAmB,EAAE,GACtC,CACH,CAAC,CAAC,CAAC,IAAI;QAER,oBAAC,UAAU,IACT,KAAK,EAAE,KAAK,EACZ,gBAAgB,EACd,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,EAAE,MAAM,EAAE,gBAAgB,EAAE,SAAS,EAAE,YAAY,EAAE,GAC5D,GAEJ;QACD,UAAU;QACV,QAAQ,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

package/esm/LinearGenomeView/components/VerticalGuide.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function VerticalGuide({ model, coordX }: {
     model: LGV;
     coordX: number;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof VerticalGuide;
 export default _default;

package/esm/LinearGenomeView/components/ZoomControls.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 declare function ZoomControls({ model }: {
     model: LinearGenomeViewModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof ZoomControls;
 export default _default;

package/esm/LinearGenomeView/components/util.js

@@ -30,7 +30,7 @@ export function getRelativeX(event, element) {
 export function getCytobands(assembly, refName) {
     var _a;
     return (((_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.map(f => ({
-        refName: assembly.getCanonicalRefName(f.get('refName')),
+        refName: assembly.getCanonicalRefName(f.get('refName')) || f.get('refName'),
         start: f.get('start'),
         end: f.get('end'),
         type: f.get('type'),

package/esm/LinearGenomeView/components/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/util.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,MAAM,EAAqB,MAAM,oBAAoB,CAAA;AAC9D,OAAO,UAAU,MAAM,sCAAsC,CAAA;AAE7D,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,EACjC,WAAW,EACX,UAAU,EACV,WAAW,EACX,iBAAiB,EACjB,iBAAiB,EACjB,QAAQ,GAQT;;IACC,IAAI,CAAC,iBAAiB,EAAE;QACtB,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;KACvC;IAED,MAAM,iBAAiB,GAAG,MAAM,CAAA,iBAAiB,aAAjB,iBAAiB,uBAAjB,iBAAiB,CAAE,MAAM,CACvD;QACE,WAAW;QACX,UAAU;KACX,EACD,WAAW,EACX,iBAAiB,CAClB,CAAA,CAAA;IAED,MAAM,cAAc,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,0CACxC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,EACtE,KAAK,CAAC,CAAC,EAAE,EAAE,EACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,UAAU,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAEzC,OAAO,MAAM,CACX,CAAC,GAAG,CAAC,cAAc,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,iBAAiB,IAAI,EAAE,CAAC,CAAC,EACzD,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CACnB,CAAA;AACH,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,SAAS,CAAC,GAAW,EAAE,KAAa;IAClD,MAAM,SAAS,GAAG,GAAG,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;IACxC,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE;QACpB,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;KACjB;SAAM;QACL,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QACtC,OAAO,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;KACvB;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAE1B,KAAQ,EAAE,OAA2B;IACrC,OAAO,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,qBAAqB,GAAG,IAAI,KAAI,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,QAA8B,EAAE,OAAe;;IAC1E,OAAO,CACL,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CACf,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;QACV,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;QACvD,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;QACrB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;QACjB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;KACpB,CAAC,EACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,OAAO,CAAC,KAAI,EAAE,CAC5C,CAAA;AACH,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/util.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,MAAM,EAAqB,MAAM,oBAAoB,CAAA;AAC9D,OAAO,UAAU,MAAM,sCAAsC,CAAA;AAE7D,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,EACjC,WAAW,EACX,UAAU,EACV,WAAW,EACX,iBAAiB,EACjB,iBAAiB,EACjB,QAAQ,GAQT;;IACC,IAAI,CAAC,iBAAiB,EAAE;QACtB,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;KACvC;IAED,MAAM,iBAAiB,GAAG,MAAM,CAAA,iBAAiB,aAAjB,iBAAiB,uBAAjB,iBAAiB,CAAE,MAAM,CACvD;QACE,WAAW;QACX,UAAU;KACX,EACD,WAAW,EACX,iBAAiB,CAClB,CAAA,CAAA;IAED,MAAM,cAAc,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,0CACxC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,EACtE,KAAK,CAAC,CAAC,EAAE,EAAE,EACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,UAAU,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAEzC,OAAO,MAAM,CACX,CAAC,GAAG,CAAC,cAAc,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,iBAAiB,IAAI,EAAE,CAAC,CAAC,EACzD,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CACnB,CAAA;AACH,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,SAAS,CAAC,GAAW,EAAE,KAAa;IAClD,MAAM,SAAS,GAAG,GAAG,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;IACxC,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE;QACpB,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;KACjB;SAAM;QACL,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QACtC,OAAO,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;KACvB;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAE1B,KAAQ,EAAE,OAA2B;IACrC,OAAO,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,qBAAqB,GAAG,IAAI,KAAI,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,QAA8B,EAAE,OAAe;;IAC1E,OAAO,CACL,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CACf,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;QACV,OAAO,EACL,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;QACpE,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;QACrB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;QACjB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;KACpB,CAAC,EACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,OAAO,CAAC,KAAI,EAAE,CAC5C,CAAA;AACH,CAAC"}

package/esm/LinearGenomeView/model.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
 import { Region } from '@jbrowse/core/util/types';
 import { MenuItem } from '@jbrowse/core/ui';
+import { ParsedLocString } from '@jbrowse/core/util';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
@@ -44,6 +45,7 @@ export declare const SPACING = 7;
 export declare const WIDGET_HEIGHT = 32;
 /**
  * #stateModel LinearGenomeView
+ * #category view
  */
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -89,15 +91,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     afterDisplayedRegionsSetCallbacks: Function[];
     scaleFactor: number;
     trackRefs: {
-        [key: string]: any;
+        [key: string]: HTMLDivElement;
     };
     coarseDynamicBlocks: BaseBlock[];
     coarseTotalBp: number;
     leftOffset: BpOffset | undefined;
     rightOffset: BpOffset | undefined;
-    searchResults: BaseResult[] | undefined;
-    searchQuery: string | undefined;
-    seqDialogDisplayed: boolean;
 } & {
     /**
      * #getter
@@ -136,10 +135,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly hasDisplayedRegions: boolean;
-    /**
-     * #getter
-     */
-    readonly isSearchDialogDisplayed: boolean;
     /**
      * #getter
      */
@@ -256,17 +251,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
     /**
      * #action
-     * sets offsets used in the get sequence dialog
+     * sets offsets of rubberband, used in the get sequence dialog can call
+     * view.getSelectedRegions(view.leftOffset,view.rightOffset) to compute
+     * the selected regions from the offsets
      */
     setOffsets(left?: BpOffset, right?: BpOffset): void;
     /**
      * #action
      */
-    setSearchResults(results?: BaseResult[], query?: string): void;
-    /**
-     * #action
-     */
-    setGetSequenceDialogOpen(open: boolean): void;
+    setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName?: string): void;
     /**
      * #action
      */
@@ -315,10 +308,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #method
      * Helper method for the fetchSequence.
-     * Retrieves the corresponding regions that were selected by the rubberband
+     * Retrieves the corresponding regions that were selected by the
+     * rubberband
      *
-     * @param leftOffset - `object as {start, end, index, offset}`, offset = start of user drag
-     * @param rightOffset - `object as {start, end, index, offset}`, offset = end of user drag
+     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
+     * of user drag
+     * @param rightOffset - `object as {start, end, index, offset}`,
+     * offset = end of user drag
      * @returns array of Region[]
      */
     getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
@@ -336,7 +332,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }[];
     /**
      * #action
-     * schedule something to be run after the next time displayedRegions is set
+     * schedule something to be run after the next time displayedRegions is
+     * set
      */
     afterDisplayedRegionsSet(cb: Function): void;
     /**
@@ -392,8 +389,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly anyCytobandsExist: boolean;
     /**
      * #getter
-     * the cytoband is displayed to the right of the chromosome name,
-     * and that offset is calculated manually with this method
+     * the cytoband is displayed to the right of the chromosome name, and
+     * that offset is calculated manually with this method
      */
     readonly cytobandOffset: number;
 } & {
@@ -407,17 +404,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      * static blocks are an important concept jbrowse uses to avoid
      * re-rendering when you scroll to the side. when you horizontally
-     * scroll to the right, old blocks to the left may be removed, and
-     * new blocks may be instantiated on the right. tracks may use the
-     * static blocks to render their data for the region represented by
-     * the block
+     * scroll to the right, old blocks to the left may be removed, and new
+     * blocks may be instantiated on the right. tracks may use the static
+     * blocks to render their data for the region represented by the block
      */
     readonly staticBlocks: BlockSet;
     /**
      * #getter
      * dynamic blocks represent the exact coordinates of the currently
      * visible genome regions on the screen. they are similar to static
-     * blocks, but statcic blocks can go offscreen while dynamic blocks
+     * blocks, but static blocks can go offscreen while dynamic blocks
      * represent exactly what is on screen
      */
     readonly dynamicBlocks: BlockSet;
@@ -428,8 +424,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly roundedDynamicBlocks: BaseBlock[];
     /**
      * #getter
-     * a single "combo-locstring" representing all the regions visible
-     * on the screen
+     * a single "combo-locstring" representing all the regions visible on
+     * the screen
      */
     readonly visibleLocStrings: string;
     /**
@@ -446,8 +442,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     /**
      * #action
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
+     * offset is the base-pair-offset in the displayed region, index is the
+     * index of the displayed region in the linear genome view
      *
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`
@@ -455,19 +451,28 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     moveTo(start?: BpOffset, end?: BpOffset): void;
     /**
      * #action
-     * navigate to the given locstring
+     * Navigate to the given locstring, will change displayed regions if
+     * needed, and wait for assemblies to be initialized
      *
-     * @param locString - e.g. "chr1:1-100"
-     * @param optAssemblyName - (optional) the assembly name to use when navigating to the locstring
+     * @param input - e.g. "chr1:1-100", "chr1:1-100 chr2:1-100", "chr 1 100"
+     * @param optAssemblyName - (optional) the assembly name to use when
+     * navigating to the locstring
+     */
+    navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+    /**
+     * #action
+     * Similar to `navToLocString`, but accepts parsed location objects
+     * instead of strings. Will try to perform `setDisplayedRegions` if
+     * changing regions
      */
-    navToLocString(locString: string, optAssemblyName?: string): Promise<void>;
+    navToLocations(parsedLocStrings: ParsedLocString[], assemblyName?: string): Promise<void>;
     /**
      * #action
      * Navigate to a location based on its refName and optionally start, end,
-     * and assemblyName. Can handle if there are multiple displayedRegions
-     * from same refName. Only navigates to a location if it is entirely
-     * within a displayedRegion. Navigates to the first matching location
-     * encountered.
+     * and assemblyName. Will not try to change displayed regions, use
+     * `navToLocations` instead. Only navigates to a location if it is
+     * entirely within a displayedRegion. Navigates to the first matching
+     * location encountered.
      *
      * Throws an error if navigation was unsuccessful
      *
@@ -476,6 +481,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     navTo(query: NavLocation): void;
     /**
      * #action
+     * Navigate to a location based on its refName and optionally start, end,
+     * and assemblyName. Will not try to change displayed regions, use
+     * navToLocations instead. Only navigates to a location if it is entirely
+     * within a displayedRegion. Navigates to the first matching location
+     * encountered.
+     *
+     * Throws an error if navigation was unsuccessful
+     *
+     * @param locations - proposed location to navigate to
      */
     navToMultiple(locations: NavLocation[]): void;
 } & {