@jbrowse/plugin-linear-genome-view 2.4.1 → 2.5.0

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function VerticalGuide({ model, coordX }: {

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 declare function ZoomControls({ model }: {
     model: LinearGenomeViewModel;

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 @@
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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';
@@ -95,9 +96,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     coarseTotalBp: number;
     leftOffset: BpOffset | undefined;
     rightOffset: BpOffset | undefined;
-    searchResults: BaseResult[] | undefined;
-    searchQuery: string | undefined;
-    seqDialogDisplayed: boolean;
 } & {
     /**
      * #getter
@@ -136,10 +134,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #getter
      */
     readonly hasDisplayedRegions: boolean;
-    /**
-     * #getter
-     */
-    readonly isSearchDialogDisplayed: boolean;
     /**
      * #getter
      */
@@ -256,17 +250,15 @@ 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 +307,13 @@ 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 +331,8 @@ 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 +388,8 @@ 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;
 } & {
@@ -406,19 +402,18 @@ 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
+     * 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
      */
     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
-     * represent exactly what is on screen
+     * visible genome regions on the screen. they are similar to static blocks, but
+     * static blocks can go offscreen while dynamic blocks represent exactly what
+     * is on screen
      */
     readonly dynamicBlocks: BlockSet;
     /**
@@ -446,8 +441,8 @@ 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}`
@@ -455,18 +450,27 @@ 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
+     * 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 +480,15 @@ 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;
 } & {