@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/d3-hierarchy2/treemap/squarify.js

@@ -0,0 +1,46 @@
+import treemapDice from "./dice.js";
+import treemapSlice from "./slice.js";
+export var phi = (1 + Math.sqrt(5)) / 2;
+export function squarifyRatio(ratio, parent, x0, y0, x1, y1) {
+    var rows = [], nodes = parent.children, row, nodeValue, i0 = 0, i1 = 0, n = nodes.length, dx, dy, value = parent.value, sumValue, minValue, maxValue, newRatio, minRatio, alpha, beta;
+    while (i0 < n) {
+        dx = x1 - x0, dy = y1 - y0;
+        do
+            sumValue = nodes[i1++].value;
+        while (!sumValue && i1 < n);
+        minValue = maxValue = sumValue;
+        alpha = Math.max(dy / dx, dx / dy) / (value * ratio);
+        beta = sumValue * sumValue * alpha;
+        minRatio = Math.max(maxValue / beta, beta / minValue);
+        for (; i1 < n; ++i1) {
+            sumValue += nodeValue = nodes[i1].value;
+            if (nodeValue < minValue)
+                minValue = nodeValue;
+            if (nodeValue > maxValue)
+                maxValue = nodeValue;
+            beta = sumValue * sumValue * alpha;
+            newRatio = Math.max(maxValue / beta, beta / minValue);
+            if (newRatio > minRatio) {
+                sumValue -= nodeValue;
+                break;
+            }
+            minRatio = newRatio;
+        }
+        rows.push(row = { value: sumValue, dice: dx < dy, children: nodes.slice(i0, i1) });
+        if (row.dice)
+            treemapDice(row, x0, y0, x1, value ? y0 += dy * sumValue / value : y1);
+        else
+            treemapSlice(row, x0, y0, value ? x0 += dx * sumValue / value : x1, y1);
+        value -= sumValue, i0 = i1;
+    }
+    return rows;
+}
+export default (function custom(ratio) {
+    function squarify(parent, x0, y0, x1, y1) {
+        squarifyRatio(ratio, parent, x0, y0, x1, y1);
+    }
+    squarify.ratio = function (x) {
+        return custom((x = +x) > 1 ? x : 1);
+    };
+    return squarify;
+})(phi);

package/esm/index.d.ts

@@ -4,4 +4,4 @@ export default class VariantsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { default as VcfFeature } from './VcfFeature';
+export { default as VcfFeature } from './VcfFeature/index.ts';

package/esm/index.js

@@ -1,26 +1,23 @@
 import Plugin from '@jbrowse/core/Plugin';
-import ChordVariantDisplayF from './ChordVariantDisplay';
-import LinearVariantDisplayF from './LinearVariantDisplay';
-import MultiLinearVariantDisplayF from './MultiLinearVariantDisplay';
-import LinearVariantMatrixDisplayF from './MultiLinearVariantMatrixDisplay';
-import LinearVariantMatrixRendererF from './MultiLinearVariantMatrixRenderer';
-import MultiVariantRendererF from './MultiLinearVariantRenderer';
-import SplitVcfTabixAdapterF from './SplitVcfTabixAdapter';
-import StructuralVariantChordRendererF from './StructuralVariantChordRenderer';
-import VariantFeatureWidgetF from './VariantFeatureWidget';
-import { MultiVariantClusterGenotypeMatrix } from './VariantRPC/MultiVariantClusterGenotypeMatrix';
-import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix';
-import { MultiVariantGetSimplifiedFeatures } from './VariantRPC/MultiVariantGetSimplifiedFeatures';
-import { MultiVariantGetSources } from './VariantRPC/MultiVariantGetSources';
-import VariantTrackF from './VariantTrack';
-import VcfAdapterF from './VcfAdapter';
-import VcfTabixAdapterF from './VcfTabixAdapter';
-import ExtensionPointsF from './extensionPoints';
+import ChordVariantDisplayF from "./ChordVariantDisplay/index.js";
+import LinearVariantDisplayF from "./LinearVariantDisplay/index.js";
+import MultiLinearVariantDisplayF from "./MultiLinearVariantDisplay/index.js";
+import LinearVariantMatrixDisplayF from "./MultiLinearVariantMatrixDisplay/index.js";
+import LinearVariantMatrixRendererF from "./MultiLinearVariantMatrixRenderer/index.js";
+import MultiVariantRendererF from "./MultiLinearVariantRenderer/index.js";
+import SplitVcfTabixAdapterF from "./SplitVcfTabixAdapter/index.js";
+import StructuralVariantChordRendererF from "./StructuralVariantChordRenderer/index.js";
+import VariantFeatureWidgetF from "./VariantFeatureWidget/index.js";
+import { MultiVariantClusterGenotypeMatrix } from "./VariantRPC/MultiVariantClusterGenotypeMatrix.js";
+import { MultiVariantGetGenotypeMatrix } from "./VariantRPC/MultiVariantGetGenotypeMatrix.js";
+import { MultiVariantGetSimplifiedFeatures } from "./VariantRPC/MultiVariantGetSimplifiedFeatures.js";
+import { MultiVariantGetSources } from "./VariantRPC/MultiVariantGetSources.js";
+import VariantTrackF from "./VariantTrack/index.js";
+import VcfAdapterF from "./VcfAdapter/index.js";
+import ExtensionPointsF from "./VcfExtensionPoints/index.js";
+import VcfTabixAdapterF from "./VcfTabixAdapter/index.js";
 export default class VariantsPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'VariantsPlugin';
-    }
+    name = 'VariantsPlugin';
     install(pluginManager) {
         VcfAdapterF(pluginManager);
         VcfTabixAdapterF(pluginManager);
@@ -41,4 +38,4 @@ export default class VariantsPlugin extends Plugin {
         pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures(pluginManager));
     }
 }
-export { default as VcfFeature } from './VcfFeature';
+export { default as VcfFeature } from "./VcfFeature/index.js";