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

package/esm/LinearGenomeView/model.js.map

@@ -1 +1 @@
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package/esm/LinearGenomeView/svgcomponents/SVGBackground.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 export default function SVGBackground({ width, height, shift, }: {
     width: number;
     height: number;
     shift: number;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts

@@ -1,10 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
-type LGV = LinearGenomeViewModel;
 export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }: {
-    model: LGV;
+    model: LinearGenomeViewModel;
     rulerHeight: number;
     fontSize: number;
     cytobandHeight: number;
-}): JSX.Element;
-export {};
+}): React.JSX.Element | null;

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -20,15 +20,20 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
         minimumBlockWidth: model.minimumBlockWidth,
     });
     const visibleRegions = model.dynamicBlocks.contentBlocks;
+    if (!visibleRegions.length) {
+        return null;
+    }
     overview.setVolatileWidth(width);
     overview.showAllRegions();
     const block = overview.dynamicBlocks.contentBlocks[0];
-    const first = visibleRegions[0];
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const first = visibleRegions.at(0);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const last = visibleRegions.at(-1);
     const firstOverviewPx = overview.bpToPx({
         ...first,
         coord: first.reversed ? first.end : first.start,
     }) || 0;
-    const last = visibleRegions[visibleRegions.length - 1];
     const lastOverviewPx = overview.bpToPx({
         ...last,
         coord: last.reversed ? last.start : last.end,

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js.map

@@ -1 +1 @@
-{"version":3,"file":"SVGHeader.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGHeader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,UAAU,MAAM,oCAAoC,CAAA;AAC3D,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,SAAS;AACT,OAAO,EAAyB,sBAAsB,EAAE,MAAM,IAAI,CAAA;AAClE,OAAO,SAAS,MAAM,yBAAyB,CAAA;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,gCAAgC,CAAA;AACxD,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,WAAW,MAAM,eAAe,CAAA;AAIvC,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,KAAK,EACL,QAAQ,EACR,cAAc,EACd,WAAW,GAMZ;IACC,MAAM,EAAE,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IAExB,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAC;QACjC,gBAAgB,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,CAAC;QAC9D,uBAAuB,EAAE,CAAC;QAC1B,iBAAiB,EAAE,KAAK,CAAC,iBAAiB;KAC3C,CAAC,CAAA;IACF,MAAM,cAAc,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IAExD,QAAQ,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAChC,QAAQ,CAAC,cAAc,EAAE,CAAA;IACzB,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAErD,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,eAAe,GACnB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,KAAK;QACR,KAAK,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK;KAChD,CAAC,IAAI,CAAC,CAAA;IAET,MAAM,IAAI,GAAG,cAAc,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACtD,MAAM,cAAc,GAClB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,IAAI;QACP,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG;KAC7C,CAAC,IAAI,CAAC,CAAA;IACT,MAAM,CAAC,GAAG,CAAC,aAAa,GAAG,cAAc,CAAA;IACzC,OAAO,CACL,2BAAG,EAAE,EAAC,QAAQ;QACZ,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,QAAQ,EACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,YAAY,CACR;QAEN,aAAa,CAAC,CAAC,CAAC,CACf,2BAAG,SAAS,EAAE,eAAe,WAAW,GAAG;YACzC,oBAAC,SAAS,IAAC,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,GAAI;YACnE,8BACE,MAAM,EAAC,KAAK,EACZ,IAAI,EAAC,kBAAkB,EACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,cAAc,GAAG,eAAe,EAAE,GAAG,CAAC,EACtD,MAAM,EAAE,sBAAsB,GAAG,CAAC,EAClC,CAAC,EAAE,eAAe,EAClB,CAAC,EAAE,GAAG,GACN;YACF,2BAAG,SAAS,EAAE,eAAe,sBAAsB,GAAG;gBACpD,oBAAC,OAAO,IAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAK,GAAI,CAC7D,CACF,CACL,CAAC,CAAC,CAAC,IAAI;QAER,2BAAG,SAAS,EAAE,eAAe,QAAQ,GAAG,CAAC,GAAG;YAC1C,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC/C;QACJ,2BAAG,SAAS,EAAE,eAAe,WAAW,GAAG,CAAC,GAAG;YAC7C,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC5C,CACF,CACL,CAAA;AACH,CAAC"}
+{"version":3,"file":"SVGHeader.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGHeader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,UAAU,MAAM,oCAAoC,CAAA;AAC3D,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,SAAS;AACT,OAAO,EAAyB,sBAAsB,EAAE,MAAM,IAAI,CAAA;AAClE,OAAO,SAAS,MAAM,yBAAyB,CAAA;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,gCAAgC,CAAA;AACxD,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,WAAW,MAAM,eAAe,CAAA;AAEvC,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,KAAK,EACL,QAAQ,EACR,cAAc,EACd,WAAW,GAMZ;IACC,MAAM,EAAE,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IAExB,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAC;QACjC,gBAAgB,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,CAAC;QAC9D,uBAAuB,EAAE,CAAC;QAC1B,iBAAiB,EAAE,KAAK,CAAC,iBAAiB;KAC3C,CAAC,CAAA;IACF,MAAM,cAAc,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IACxD,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;QAC1B,OAAO,IAAI,CAAA;KACZ;IAED,QAAQ,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAChC,QAAQ,CAAC,cAAc,EAAE,CAAA;IACzB,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACrD,oEAAoE;IACpE,MAAM,KAAK,GAAG,cAAc,CAAC,EAAE,CAAC,CAAC,CAAE,CAAA;IACnC,oEAAoE;IACpE,MAAM,IAAI,GAAG,cAAc,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;IACnC,MAAM,eAAe,GACnB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,KAAK;QACR,KAAK,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK;KAChD,CAAC,IAAI,CAAC,CAAA;IAET,MAAM,cAAc,GAClB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,IAAI;QACP,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG;KAC7C,CAAC,IAAI,CAAC,CAAA;IACT,MAAM,CAAC,GAAG,CAAC,aAAa,GAAG,cAAc,CAAA;IACzC,OAAO,CACL,2BAAG,EAAE,EAAC,QAAQ;QACZ,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,QAAQ,EACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,YAAY,CACR;QAEN,aAAa,CAAC,CAAC,CAAC,CACf,2BAAG,SAAS,EAAE,eAAe,WAAW,GAAG;YACzC,oBAAC,SAAS,IAAC,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,GAAI;YACnE,8BACE,MAAM,EAAC,KAAK,EACZ,IAAI,EAAC,kBAAkB,EACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,cAAc,GAAG,eAAe,EAAE,GAAG,CAAC,EACtD,MAAM,EAAE,sBAAsB,GAAG,CAAC,EAClC,CAAC,EAAE,eAAe,EAClB,CAAC,EAAE,GAAG,GACN;YACF,2BAAG,SAAS,EAAE,eAAe,sBAAsB,GAAG;gBACpD,oBAAC,OAAO,IAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAK,GAAI,CAC7D,CACF,CACL,CAAC,CAAC,CAAC,IAAI;QAER,2BAAG,SAAS,EAAE,eAAe,QAAQ,GAAG,CAAC,GAAG;YAC1C,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC/C;QACJ,2BAAG,SAAS,EAAE,eAAe,WAAW,GAAG,CAAC,GAAG;YAC7C,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC5C,CACF,CACL,CAAA;AACH,CAAC"}

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -26,7 +26,7 @@ export async function renderToSvg(model, opts) {
     const height = totalHeight(tracks, textHeight, trackLabels) + offset + 100;
     const displayResults = await Promise.all(tracks.map(async (track) => {
         const display = track.displays[0];
-        await when(() => (display.ready !== undefined ? display.ready : true));
+        await when(() => !display.renderProps().notReady);
         return { track, result: await display.renderSvg({ ...opts, theme }) };
     }));
     const trackLabelMaxLen = max(tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize)), 0) + 40;

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map

@@ -1 +1 @@
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package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGRegionSeparators({ model, height, }: {
     height: number;
     model: LGV;
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGRuler.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGRuler({ model, fontSize, }: {
     model: LGV;
     fontSize: number;
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGScalebar.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGScalebar({ model, fontSize, }: {
     model: LGV;
     fontSize: number;
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }: {
     trackName: string;
     trackLabels: string;
     fontSize: number;
     trackLabelOffset: number;
     x: number;
-}): JSX.Element | null;
+}): React.JSX.Element | null;

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

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
@@ -19,5 +19,5 @@ export default function SVGTracks({ displayResults, model, offset, textHeight, f
     fontSize: number;
     trackLabels?: string;
     trackLabelOffset?: number;
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

package/esm/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;
+    end?: number | undefined;
+    reversed?: boolean | undefined;
+    start?: number | undefined;
+    refName: string;
+}[]>;
+/**
+ * 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/esm/LinearGenomeView/util.js

@@ -1,3 +1,4 @@
+import { parseLocString, } 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
@@ -59,4 +60,79 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
     }
     return ticks;
 }
+/**
+ * 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 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 ${asmName}`);
+        }
+        return {
+            ...region,
+            assemblyName: asmName,
+            parentRegion,
+        };
+    }));
+}
+/**
+ * Parses locString or space separated set of locStrings into location objects
+ * Example inputs:
+ * "chr1"
+ * "chr1:1-100"
+ * "chr1:1..100"
+ * "chr1 chr2"
+ * "chr1:1-100 chr2:1-100"
+ * "chr1 100 200" equivalent to "chr1:1-100"
+ *
+ * Used by navToLocString
+ */
+export function parseLocStrings(input, assemblyName, isValidRefName) {
+    const inputs = input
+        .split(/(\s+)/)
+        .map(f => f.trim())
+        .filter(f => !!f);
+    // first try interpreting as a whitespace-separated sequence of
+    // multiple locstrings
+    try {
+        return inputs.map(loc => parseLocString(loc, ref => isValidRefName(ref, assemblyName)));
+    }
+    catch (e) {
+        // if this fails, try interpreting as a whitespace-separated refname,
+        // start, end if start and end are integer inputs
+        const [refName, start, end] = inputs;
+        if (`${e}`.match(/Unknown reference sequence/) &&
+            Number.isInteger(+start) &&
+            Number.isInteger(+end)) {
+            return [
+                parseLocString(refName + ':' + start + '..' + end, ref => isValidRefName(ref, assemblyName)),
+            ];
+        }
+        else {
+            throw e;
+        }
+    }
+}
 //# sourceMappingURL=util.js.map

package/esm/LinearGenomeView/util.js.map

@@ -1 +1 @@
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