@jbrowse/plugin-linear-genome-view 2.4.2 → 2.5.0

package/dist/LinearGenomeView/svgcomponents/SVGTracks.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;

package/dist/LinearGenomeView/util.d.ts

@@ -1,3 +1,4 @@
+import { AssemblyManager, ParsedLocString } from '@jbrowse/core/util';
 /**
  * Given a scale ( bp/px ) and minimum distances (px) between major and minor
  * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
@@ -12,3 +13,31 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
     base: number;
     index: number;
 }[];
+/**
+ * Generate location objects for a set of parsed locstrings, which includes
+ * translating the refNames to assembly-canonical refNames and adding the
+ * 'parentRegion'
+ *
+ * Used by navToLocations and navToLocString
+ */
+export declare function generateLocations(regions: ParsedLocString[] | undefined, assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+    assemblyName: string;
+    parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
+    refName: string;
+    start?: number | undefined;
+    end?: number | undefined;
+    reversed?: boolean | undefined;
+}[]>;
+/**
+ * Parses locString or space separated set of locStrings into location objects
+ * Example inputs:
+ * "chr1"
+ * "chr1:1-100"
+ * "chr1:1..100"
+ * "chr1 chr2"
+ * "chr1:1-100 chr2:1-100"
+ * "chr1 100 200" equivalent to "chr1:1-100"
+ *
+ * Used by navToLocString
+ */
+export declare function parseLocStrings(input: string, assemblyName: string, isValidRefName: (str: string, assemblyName: string) => boolean): ParsedLocString[];

package/dist/LinearGenomeView/util.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeTicks = exports.chooseGridPitch = void 0;
+exports.parseLocStrings = exports.generateLocations = exports.makeTicks = exports.chooseGridPitch = void 0;
+const util_1 = require("@jbrowse/core/util");
 /**
  * Given a scale ( bp/px ) and minimum distances (px) between major and minor
  * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
@@ -64,4 +65,81 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     return ticks;
 }
 exports.makeTicks = makeTicks;
+/**
+ * Generate location objects for a set of parsed locstrings, which includes
+ * translating the refNames to assembly-canonical refNames and adding the
+ * 'parentRegion'
+ *
+ * Used by navToLocations and navToLocString
+ */
+async function generateLocations(regions = [], assemblyManager, assemblyName) {
+    return Promise.all(regions.map(async (region) => {
+        const asmName = region.assemblyName || assemblyName;
+        if (!asmName) {
+            throw new Error('no assembly provided');
+        }
+        const asm = await assemblyManager.waitForAssembly(asmName);
+        const { refName } = region;
+        if (!asm) {
+            throw new Error(`assembly ${asmName} not found`);
+        }
+        const { regions } = asm;
+        if (!regions) {
+            throw new Error(`regions not loaded yet for ${asmName}`);
+        }
+        const canonicalRefName = asm.getCanonicalRefName(region.refName);
+        if (!canonicalRefName) {
+            throw new Error(`Could not find refName ${refName} in ${asm.name}`);
+        }
+        const parentRegion = regions.find(r => r.refName === canonicalRefName);
+        if (!parentRegion) {
+            throw new Error(`Could not find refName ${refName} in ${asmName}`);
+        }
+        return {
+            ...region,
+            assemblyName: asmName,
+            parentRegion,
+        };
+    }));
+}
+exports.generateLocations = generateLocations;
+/**
+ * Parses locString or space separated set of locStrings into location objects
+ * Example inputs:
+ * "chr1"
+ * "chr1:1-100"
+ * "chr1:1..100"
+ * "chr1 chr2"
+ * "chr1:1-100 chr2:1-100"
+ * "chr1 100 200" equivalent to "chr1:1-100"
+ *
+ * Used by navToLocString
+ */
+function parseLocStrings(input, assemblyName, isValidRefName) {
+    const inputs = input
+        .split(/(\s+)/)
+        .map(f => f.trim())
+        .filter(f => !!f);
+    // first try interpreting as a whitespace-separated sequence of
+    // multiple locstrings
+    try {
+        return inputs.map(loc => (0, util_1.parseLocString)(loc, ref => isValidRefName(ref, assemblyName)));
+    }
+    catch (e) {
+        // if this fails, try interpreting as a whitespace-separated refname,
+        // start, end if start and end are integer inputs
+        const [refName, start, end] = inputs;
+        if (`${e}`.match(/Unknown reference sequence/) &&
+            Number.isInteger(+start) &&
+            Number.isInteger(+end)) {
+            return [
+                (0, util_1.parseLocString)(refName + ':' + start + '..' + end, ref => isValidRefName(ref, assemblyName)),
+            ];
+        }
+        else {
+            throw e;
+        }
+    }
+}
+exports.parseLocStrings = parseLocStrings;
 //# sourceMappingURL=util.js.map

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