npm - @jbrowse/plugin-variants - Versions diffs - 4.0.2 → 4.0.4 - Mend

@jbrowse/plugin-variants 4.0.2 → 4.0.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (31) hide show

package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED Viewed

@@ -58,6 +58,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -114,6 +115,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -167,6 +169,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -258,6 +261,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -314,6 +318,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -367,6 +372,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -447,6 +453,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -503,6 +510,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -556,6 +564,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/LinearVariantDisplay/model.d.ts CHANGED Viewed

@@ -143,6 +143,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -199,6 +200,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -252,6 +254,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -533,6 +536,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -589,6 +593,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -642,6 +647,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -868,6 +874,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -924,6 +931,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -977,6 +985,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1083,7 +1092,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly activeFilters: any;
+    readonly activeFilters: string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1171,6 +1180,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1224,11 +1234,14 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    afterAttach(): void;
 } & {
     readonly featureWidgetType: {
         type: string;

package/esm/MultiLinearVariantDisplay/model.d.ts CHANGED Viewed

@@ -153,6 +153,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -209,6 +210,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -262,6 +264,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -543,6 +546,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -599,6 +603,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -652,6 +657,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -878,6 +884,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -934,6 +941,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -987,6 +995,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1139,36 +1148,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly autoHeight: boolean;
     readonly activeFilters: any;
-    readonly sourcesWithoutLayout: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
-    readonly sources: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
+    readonly sourcesWithoutLayout: import("../shared/types.ts").Source[] | undefined;
+    readonly sources: import("../shared/types.ts").Source[] | undefined;
     readonly root: any;
 } & {
     readonly sourceMap: {
-        [k: string]: {
-            label: string;
-            id: string;
-            baseUri?: string;
-            name: string;
-            color?: string;
-            group?: string;
-            HP?: number;
-        };
+        [k: string]: import("../shared/types.ts").Source;
     } | undefined;
     readonly availableHeight: number;
     readonly nrow: number;

package/esm/MultiLinearVariantMatrixDisplay/model.d.ts CHANGED Viewed

@@ -154,6 +154,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -210,6 +211,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -263,6 +265,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -544,6 +547,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -600,6 +604,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -653,6 +658,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -879,6 +885,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -935,6 +942,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -988,6 +996,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1140,36 +1149,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly autoHeight: boolean;
     readonly activeFilters: any;
-    readonly sourcesWithoutLayout: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
-    readonly sources: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
+    readonly sourcesWithoutLayout: import("../shared/types.ts").Source[] | undefined;
+    readonly sources: import("../shared/types.ts").Source[] | undefined;
     readonly root: any;
 } & {
     readonly sourceMap: {
-        [k: string]: {
-            label: string;
-            id: string;
-            baseUri?: string;
-            name: string;
-            color?: string;
-            group?: string;
-            HP?: number;
-        };
+        [k: string]: import("../shared/types.ts").Source;
     } | undefined;
     readonly availableHeight: number;
     readonly nrow: number;

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js CHANGED Viewed

@@ -17,8 +17,10 @@ function drawPhasedMode(drawCtx, mafs) {
             const samp = feature.get('samples');
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name, HP } = sources[j];
-                const s = samp[name];
+                const source = sources[j];
+                const { name, HP, baseName } = source;
+                const sampleName = baseName ?? name;
+                const s = samp[sampleName];
                 if (s) {
                     const genotype = s.GT?.[0];
                     if (genotype) {
@@ -47,8 +49,10 @@ function drawPhasedMode(drawCtx, mafs) {
             }
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name, HP } = sources[j];
-                const genotype = samp[name];
+                const source = sources[j];
+                const { name, HP, baseName } = source;
+                const sampleName = baseName ?? name;
+                const genotype = samp[sampleName];
                 if (genotype) {
                     arr2.push(genotype);
                     const isPhased = genotype.includes('|');
@@ -82,8 +86,9 @@ function drawAlleleCountMode(drawCtx, mafs) {
             const samp = feature.get('samples');
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name } = sources[j];
-                const s = samp[name];
+                const source = sources[j];
+                const sampleName = source.baseName ?? source.name;
+                const s = samp[sampleName];
                 if (s) {
                     const genotype = s.GT?.[0];
                     if (genotype) {
@@ -105,8 +110,9 @@ function drawAlleleCountMode(drawCtx, mafs) {
             }
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name } = sources[j];
-                const genotype = samp[name];
+                const source = sources[j];
+                const sampleName = source.baseName ?? source.name;
+                const genotype = samp[sampleName];
                 if (genotype) {
                     arr2.push(genotype);
                     const c = getAlleleColor(genotype, mostFrequentAlt, colorCache, splitCache, true);

package/esm/MultiLinearVariantRenderer/makeImageData.js CHANGED Viewed

@@ -22,8 +22,10 @@ function drawPhasedMode(drawCtx, itemData, mafs) {
         }
         for (let j = startRow; j < endRow; j++) {
             const y = j * h - scrollTop;
-            const { name, HP } = sources[j];
-            const genotype = samp[name];
+            const source = sources[j];
+            const { name, HP, baseName } = source;
+            const sampleName = baseName ?? name;
+            const genotype = samp[sampleName];
             if (genotype) {
                 const isPhased = genotype.includes('|');
                 if (isPhased) {

package/esm/VariantRPC/executeClusterGenotypeMatrix.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import type { Source } from '../shared/types.ts';
+import type { SampleInfo, Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Region, StopToken } from '@jbrowse/core/util';
@@ -15,6 +15,8 @@ export declare function executeClusterGenotypeMatrix({ pluginManager, args, }: {
         lengthCutoffFilter: number;
         statusCallback: (arg: string) => void;
         sources: Source[];
+        renderingMode?: string;
+        sampleInfo?: Record<string, SampleInfo>;
     };
 }): Promise<{
     order: number[];

package/esm/VariantRPC/executeClusterGenotypeMatrix.js CHANGED Viewed

@@ -1,10 +1,14 @@
 import { clusterData, toNewick } from '@gmod/hclust';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
+import { getPhasedGenotypeMatrix } from "./getPhasedGenotypeMatrix.js";
 export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
-    const matrix = await getGenotypeMatrix({
-        pluginManager,
-        args,
-    });
+    const { renderingMode, sampleInfo } = args;
+    const matrix = renderingMode === 'phased' && sampleInfo
+        ? await getPhasedGenotypeMatrix({
+            pluginManager,
+            args: { ...args, sampleInfo },
+        })
+        : await getGenotypeMatrix({ pluginManager, args });
     const sampleLabels = Object.keys(matrix);
     const result = await clusterData({
         data: Object.values(matrix),

package/esm/VariantRPC/getPhasedGenotypeMatrix.d.ts ADDED Viewed

@@ -0,0 +1,20 @@
+import type { SampleInfo, Source } from '../shared/types.ts';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+import type { StopToken } from '@jbrowse/core/util/stopToken';
+export declare function getPhasedGenotypeMatrix({ pluginManager, args, }: {
+    pluginManager: PluginManager;
+    args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: StopToken;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sources: Source[];
+        bpPerPx: number;
+        minorAlleleFrequencyFilter: number;
+        lengthCutoffFilter: number;
+        sampleInfo: Record<string, SampleInfo>;
+    };
+}): Promise<Record<string, number[]>>;

package/esm/VariantRPC/getPhasedGenotypeMatrix.js ADDED Viewed

@@ -0,0 +1,50 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom, toArray } from 'rxjs';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
+export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, sampleInfo, } = args;
+    const lastCheck = createStopTokenChecker(stopToken);
+    const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
+    const dataAdapter = adapter.dataAdapter;
+    const rows = {};
+    const splitCache = {};
+    for (const { name } of sources) {
+        const info = sampleInfo[name];
+        const ploidy = info?.maxPloidy ?? 2;
+        for (let hp = 0; hp < ploidy; hp++) {
+            rows[`${name} HP${hp}`] = [];
+        }
+    }
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+        lastCheck,
+        splitCache,
+        features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
+    });
+    for (const { feature } of mafs) {
+        const genotypes = feature.get('genotypes');
+        for (const { name } of sources) {
+            const val = genotypes[name];
+            const info = sampleInfo[name];
+            const ploidy = info?.maxPloidy ?? 2;
+            const isPhased = val.includes('|');
+            if (isPhased) {
+                const alleles = splitCache[val] ?? (splitCache[val] = val.split('|'));
+                for (let hp = 0; hp < ploidy; hp++) {
+                    const allele = alleles[hp];
+                    const value = allele === '.' || allele === undefined ? -1 : +allele;
+                    rows[`${name} HP${hp}`].push(value);
+                }
+            }
+            else {
+                for (let hp = 0; hp < ploidy; hp++) {
+                    rows[`${name} HP${hp}`].push(-1);
+                }
+            }
+        }
+        checkStopToken2(lastCheck);
+    }
+    return rows;
+}

package/esm/shared/MultiVariantBaseModel.d.ts CHANGED Viewed

@@ -155,6 +155,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -211,6 +212,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -264,6 +266,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -545,6 +548,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -601,6 +605,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -654,6 +659,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -880,6 +886,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -936,6 +943,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -989,6 +997,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1141,36 +1150,12 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
 } & {
     readonly autoHeight: boolean;
     readonly activeFilters: any;
-    readonly sourcesWithoutLayout: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
-    readonly sources: {
-        label: string;
-        id: string;
-        baseUri?: string;
-        name: string;
-        color?: string;
-        group?: string;
-        HP?: number;
-    }[] | undefined;
+    readonly sourcesWithoutLayout: Source[] | undefined;
+    readonly sources: Source[] | undefined;
     readonly root: any;
 } & {
     readonly sourceMap: {
-        [k: string]: {
-            label: string;
-            id: string;
-            baseUri?: string;
-            name: string;
-            color?: string;
-            group?: string;
-            HP?: number;
-        };
+        [k: string]: Source;
     } | undefined;
     readonly availableHeight: number;
     readonly nrow: number;

package/esm/shared/MultiVariantBaseModel.js CHANGED Viewed

@@ -122,6 +122,10 @@ export default function MultiVariantBaseModelF(configSchema) {
             self.showTree = arg;
         },
         setPhasedMode(arg) {
+            if (self.renderingMode !== arg) {
+                self.layout = [];
+                self.clusterTree = undefined;
+            }
             self.renderingMode = arg;
         },
         setAutoHeight(auto) {
@@ -157,12 +161,10 @@ export default function MultiVariantBaseModelF(configSchema) {
                 : undefined;
         },
         get sources() {
-            const sourcesWithLayout = self.layout.length
-                ? self.layout
-                : self.sourcesVolatile;
-            return sourcesWithLayout
+            return self.sourcesVolatile
                 ? getSources({
-                    sources: sourcesWithLayout,
+                    sources: self.sourcesVolatile,
+                    layout: self.layout.length ? self.layout : undefined,
                     renderingMode: self.renderingMode,
                     sampleInfo: self.sampleInfo,
                 })
@@ -237,7 +239,7 @@ export default function MultiVariantBaseModelF(configSchema) {
                                 },
                             },
                             {
-                                label: 'Show tree',
+                                label: `Show tree${!self.clusterTree ? ' (run clustering first)' : ''}`,
                                 type: 'checkbox',
                                 checked: self.showTree,
                                 disabled: !self.clusterTree,
@@ -305,9 +307,11 @@ export default function MultiVariantBaseModelF(configSchema) {
                                 },
                             },
                             {
-                                label: `Phased${!self.hasPhased
-                                    ? ' (disabled, no phased variants found)'
-                                    : ''}`,
+                                label: `Phased${self.hasPhased
+                                    ? ''
+                                    : !self.featuresVolatile
+                                        ? ' (checking for phased variants...)'
+                                        : ' (disabled, no phased variants found)'}`,
                                 helpText: 'Phased mode splits each sample into multiple rows representing each haplotype, and the phasing of the variants is used to color the variant in the individual haplotype rows. For example, a diploid sample SAMPLE1 will generate two rows SAMPLE1-HP0 and SAMPLE1 HP1 and a variant 1|0 will draw a box in the top row but not the bottom row',
                                 disabled: !self.hasPhased,
                                 checked: self.renderingMode === 'phased',

package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.js CHANGED Viewed

@@ -7,16 +7,18 @@ import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { Button, DialogActions, DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
+import { expandSourcesToHaplotypes } from "../../getSources.js";
 const ClusterDialogAuto = observer(function ClusterDialogAuto({ model, children, handleClose, }) {
     const [progress, setProgress] = useState('');
     const [loading, setLoading] = useState(false);
     const [error, setError] = useState();
     const [stopToken, setStopToken] = useState();
     const { rpcManager } = getSession(model);
-    const { sourcesWithoutLayout, minorAlleleFrequencyFilter, lengthCutoffFilter, adapterConfig, } = model;
-    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs("div", { children: [loading ? (_jsxs("div", { style: { padding: 50 }, children: [_jsx("span", { children: progress || 'Loading...' }), _jsx(Button, { onClick: () => {
+    const { sourcesVolatile, minorAlleleFrequencyFilter, lengthCutoffFilter, adapterConfig, renderingMode, sampleInfo, } = model;
+    const isHaplotypeClustering = renderingMode === 'phased';
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, isHaplotypeClustering ? (_jsx("div", { style: { marginTop: 8, fontStyle: 'italic' }, children: "Note: Clustering by individual haplotypes (phased mode)" })) : null, _jsxs("div", { children: [loading ? (_jsxs("div", { style: { padding: 50 }, children: [_jsx("span", { children: progress || 'Loading...' }), _jsx(Button, { onClick: () => {
                                             stopStopToken(stopToken);
-                                        }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", disabled: loading || !model.sourcesWithoutLayout, onClick: async () => {
+                                        }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", disabled: loading || !sourcesVolatile, onClick: async () => {
                             try {
                                 setError(undefined);
                                 setProgress('Initializing');
@@ -25,23 +27,34 @@ const ClusterDialogAuto = observer(function ClusterDialogAuto({ model, children,
                                 if (!view.initialized) {
                                     return;
                                 }
-                                if (sourcesWithoutLayout) {
+                                if (sourcesVolatile) {
                                     const sessionId = getRpcSessionId(model);
                                     const stopToken = createStopToken();
                                     setStopToken(stopToken);
                                     const ret = (await rpcManager.call(sessionId, 'MultiVariantClusterGenotypeMatrix', {
                                         regions: view.dynamicBlocks.contentBlocks,
-                                        sources: sourcesWithoutLayout,
+                                        sources: sourcesVolatile,
                                         minorAlleleFrequencyFilter,
                                         lengthCutoffFilter,
                                         sessionId,
                                         adapterConfig,
                                         stopToken,
+                                        renderingMode,
+                                        sampleInfo,
                                         statusCallback: (arg) => {
                                             setProgress(arg);
                                         },
                                     }));
-                                    model.setLayout(ret.order.map(idx => sourcesWithoutLayout[idx]), false);
+                                    if (isHaplotypeClustering && sampleInfo) {
+                                        const expandedSources = expandSourcesToHaplotypes({
+                                            sources: sourcesVolatile,
+                                            sampleInfo,
+                                        });
+                                        model.setLayout(ret.order.map(idx => expandedSources[idx]), false);
+                                    }
+                                    else {
+                                        model.setLayout(ret.order.map(idx => sourcesVolatile[idx]), false);
+                                    }
                                     model.setClusterTree(ret.tree);
                                 }
                                 handleClose();

package/esm/shared/components/MultiVariantClusterDialog/types.d.ts CHANGED Viewed

@@ -1,10 +1,13 @@
-import type { Source } from '../../types.ts';
+import type { SampleInfo, Source } from '../../types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface ReducedModel {
     sourcesWithoutLayout?: Source[];
+    sourcesVolatile?: Source[];
     minorAlleleFrequencyFilter?: number;
     lengthCutoffFilter: number;
     adapterConfig: AnyConfigurationModel;
+    renderingMode: string;
+    sampleInfo?: Record<string, SampleInfo>;
     setClusterTree: (arg?: string) => void;
     setLayout: (arg: Source[], clearTree?: boolean) => void;
     clearLayout: () => void;

package/esm/shared/components/MultiVariantColorLegend.js CHANGED Viewed

@@ -10,10 +10,10 @@ const LegendItem = function ({ source, idx, rowHeight, }) {
     return color ? (_jsx(RectBg, { y: idx * rowHeight, x: 0, width: colorBoxWidth + 0.5, height: rowHeight + 0.5, color: color })) : null;
 };
 const LegendItemText = function ({ source, idx, rowHeight, textFillProps, }) {
-    const { color, name, label } = source;
+    const { color, name } = source;
     const svgFontSize = Math.min(rowHeight, 12);
     const colorBoxWidth = 15;
-    return (_jsx("text", { y: idx * rowHeight + svgFontSize, x: color ? colorBoxWidth + 2 : 0, fontSize: svgFontSize, ...textFillProps, children: label || name }));
+    return (_jsx("text", { y: (idx + 0.5) * rowHeight, x: color ? colorBoxWidth + 2 : 0, fontSize: svgFontSize, dominantBaseline: "central", ...textFillProps, children: name }));
 };
 const MultiVariantColorLegend = observer(function MultiVariantColorLegend({ model, labelWidth, }) {
     const { canDisplayLabels, rowHeight, sources } = model;
@@ -22,8 +22,8 @@ const MultiVariantColorLegend = observer(function MultiVariantColorLegend({ mode
     const hasColors = useMemo(() => sources?.some(s => s.color) ?? false, [sources]);
     const legendWidth = labelWidth + (hasColors ? colorBoxWidth + 5 : 0);
     const textFillProps = useMemo(() => getFillProps(theme.palette.text.primary), [theme.palette.text.primary]);
-    return sources ? (_jsxs(_Fragment, { children: [canDisplayLabels ? (_jsx(RectBg, { y: 0, x: 0, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => (_jsx(LegendItem, { source: source, idx: idx, rowHeight: rowHeight }, `${source.label}-${idx}`))), canDisplayLabels
-                ? sources.map((source, idx) => (_jsx(LegendItemText, { source: source, idx: idx, rowHeight: rowHeight, textFillProps: textFillProps }, `${source.label}-text-${idx}`)))
+    return sources ? (_jsxs(_Fragment, { children: [canDisplayLabels ? (_jsx(RectBg, { y: 0, x: 0, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => (_jsx(LegendItem, { source: source, idx: idx, rowHeight: rowHeight }, `${source.name}-${idx}`))), canDisplayLabels
+                ? sources.map((source, idx) => (_jsx(LegendItemText, { source: source, idx: idx, rowHeight: rowHeight, textFillProps: textFillProps }, `${source.name}-text-${idx}`)))
                 : null] })) : null;
 });
 export default MultiVariantColorLegend;

package/esm/shared/components/MultiVariantLegendBar.js CHANGED Viewed

@@ -15,7 +15,7 @@ const MultiVariantLegendBar = observer(function MultiVariantLegendBar(props) {
         let maxWidth = 0;
         for (const s of sources) {
             const width = canDisplayLabels
-                ? measureText(s.label, svgFontSize) + 10
+                ? measureText(s.name, svgFontSize) + 10
                 : 20;
             if (width > maxWidth) {
                 maxWidth = width;

package/esm/shared/components/MultiVariantTooltip.d.ts CHANGED Viewed

@@ -1,6 +1,7 @@
 declare const MultiVariantTooltip: import("react").NamedExoticComponent<{
     source: {
         color?: string;
+        name?: string;
         [key: string]: unknown;
     };
     x: number;

package/esm/shared/components/MultiVariantTooltip.js CHANGED Viewed

@@ -28,9 +28,9 @@ const useStyles = makeStyles()(theme => ({
         marginRight: 4,
     },
 }));
-const EXCLUDE_KEYS = new Set(['color', 'HP', 'name', 'id']);
+const EXCLUDE_KEYS = new Set(['color', 'HP', 'name', 'baseName', 'id']);
 const MultiVariantTooltip = memo(function MultiVariantTooltip({ source, x, y, }) {
     const { classes } = useStyles();
-    return (_jsx(Portal, { children: _jsxs("div", { className: classes.tooltip, style: { transform: `translate(${x + 10}px, ${y + 10}px)` }, children: [source.color ? (_jsx("div", { className: classes.colorBox, style: { backgroundColor: source.color } })) : null, Object.entries(source).map(([key, value]) => !EXCLUDE_KEYS.has(key) && value !== undefined ? (_jsxs("div", { className: classes.row, children: [key, ": ", String(value)] }, key)) : null)] }) }));
+    return (_jsx(Portal, { children: _jsxs("div", { className: classes.tooltip, style: { transform: `translate(${x + 10}px, ${y + 10}px)` }, children: [source.color ? (_jsx("div", { className: classes.colorBox, style: { backgroundColor: source.color } })) : null, source.name ? _jsx("div", { className: classes.row, children: source.name }) : null, Object.entries(source).map(([key, value]) => !EXCLUDE_KEYS.has(key) && value !== undefined ? (_jsxs("div", { className: classes.row, children: [key, ": ", String(value)] }, key)) : null)] }) }));
 });
 export default MultiVariantTooltip;

package/esm/shared/components/RectBg.js CHANGED Viewed

@@ -3,6 +3,6 @@ import { getFillProps } from '@jbrowse/core/util';
 import { alpha, useTheme } from '@mui/material';
 const RectBg = ({ x, y, width, height, color, }) => {
     const theme = useTheme();
-    return (_jsx("rect", { pointerEvents: "auto", x: x, y: y, width: width, height: height, ...getFillProps(color || alpha(theme.palette.background.paper, 0.3)) }));
+    return (_jsx("rect", { pointerEvents: "auto", x: x, y: y, width: width, height: height, ...getFillProps(color || alpha(theme.palette.background.paper, 0.8)) }));
 };
 export default RectBg;

package/esm/shared/components/SourcesDataGrid.js CHANGED Viewed

@@ -14,12 +14,12 @@ const useStyles = makeStyles()({
 });
 export default function SourcesDataGrid({ rows, onChange, setSelected, }) {
     const { classes } = useStyles();
-    const { id: _id, name: _name, label: _label, color: _color, baseUri: _baseUri, HP: _HP, ...rest } = rows[0];
+    const { name: _name, color: _color, baseUri: _baseUri, baseName: _baseName, HP: _HP, ...rest } = rows[0];
     const [currSort, setCurrSort] = useState({
         idx: 0,
         field: null,
     });
-    return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
+    return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, getRowId: row => row.name, onRowSelectionModelChange: arg => {
                 setSelected([...arg.ids]);
             }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
                 {
@@ -37,9 +37,9 @@ export default function SourcesDataGrid({ rows, onChange, setSelected, }) {
                     },
                 },
                 {
-                    field: 'label',
+                    field: 'name',
                     headerName: 'Name',
-                    width: measureGridWidth(rows.map(r => r.label)),
+                    width: measureGridWidth(rows.map(r => r.name)),
                 },
                 ...Object.keys(rest).map(val => ({
                     field: val,

package/esm/shared/components/TreeSidebar.js CHANGED Viewed

@@ -4,6 +4,7 @@ import { ResizeHandle } from '@jbrowse/core/ui';
 import { getContainingView } from '@jbrowse/core/util';
 import Flatbush from '@jbrowse/core/util/flatbush';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { alpha } from '@mui/material';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
@@ -18,6 +19,12 @@ const useStyles = makeStyles()(theme => ({
             background: theme.palette.divider,
         },
     },
+    treeBackground: {
+        position: 'absolute',
+        top: 0,
+        left: 0,
+        background: alpha(theme.palette.background.paper, 0.8),
+    },
 }));
 function getDescendantNames(node) {
     if (!node.children?.length) {
@@ -90,7 +97,10 @@ const TreeSidebar = observer(function TreeSidebar({ model, }) {
                     left: 0,
                     height: 0,
                     zIndex: 100,
-                }, children: [_jsx("canvas", { ref: treeCanvasRef, width: treeAreaWidth * 2, height: height * 2, style: {
+                }, children: [_jsx("div", { className: classes.treeBackground, style: {
+                            width: treeAreaWidth,
+                            height,
+                        } }), _jsx("canvas", { ref: treeCanvasRef, width: treeAreaWidth * 2, height: height * 2, style: {
                             width: treeAreaWidth,
                             height,
                             position: 'absolute',

package/esm/shared/getMultiVariantFeaturesAutorun.d.ts CHANGED Viewed

@@ -9,6 +9,7 @@ export declare function getMultiVariantFeaturesAutorun(self: {
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
     featureDensityStatsReadyAndRegionNotTooLarge: boolean;
+    isMinimized: boolean;
     adapterProps: () => Record<string, unknown>;
     setError: (error: unknown) => void;
     setFeatures: (f: Feature[]) => void;

package/esm/shared/getMultiVariantFeaturesAutorun.js CHANGED Viewed

@@ -7,6 +7,9 @@ import { autorun } from 'mobx';
 export function getMultiVariantFeaturesAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
+            if (!isAlive(self) || self.isMinimized) {
+                return;
+            }
             const view = getContainingView(self);
             if (!view.initialized ||
                 !self.featureDensityStatsReadyAndRegionNotTooLarge) {

package/esm/shared/getMultiVariantSourcesAutorun.d.ts CHANGED Viewed

@@ -4,6 +4,7 @@ import type { StopToken } from '@jbrowse/core/util/stopToken';
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
+    isMinimized: boolean;
     adapterProps: () => Record<string, unknown>;
     setSourcesLoading: (aborter: StopToken) => void;
     setError: (error: unknown) => void;

package/esm/shared/getMultiVariantSourcesAutorun.js CHANGED Viewed

@@ -7,6 +7,9 @@ import { autorun } from 'mobx';
 export function getMultiVariantSourcesAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
+            if (!isAlive(self) || self.isMinimized) {
+                return;
+            }
             const view = getContainingView(self);
             if (!view.initialized) {
                 return;

package/esm/shared/getSources.d.ts CHANGED Viewed

@@ -1,15 +1,11 @@
 import type { SampleInfo, Source } from './types.ts';
+export declare function expandSourcesToHaplotypes({ sources, sampleInfo, }: {
+    sources: Source[];
+    sampleInfo: Record<string, SampleInfo>;
+}): Source[];
 export declare function getSources({ sources, layout, renderingMode, sampleInfo, }: {
     sources: Source[];
     layout?: Source[];
     renderingMode: string;
     sampleInfo?: Record<string, SampleInfo>;
-}): {
-    label: string;
-    id: string;
-    baseUri?: string;
-    name: string;
-    color?: string;
-    group?: string;
-    HP?: number;
-}[];
+}): Source[];

package/esm/shared/getSources.js CHANGED Viewed

@@ -1,31 +1,36 @@
+function makeHaplotypeSources(source, ploidy) {
+    const results = [];
+    for (let i = 0; i < ploidy; i++) {
+        const name = `${source.name} HP${i}`;
+        results.push({ ...source, name, baseName: source.name, HP: i });
+    }
+    return results;
+}
+export function expandSourcesToHaplotypes({ sources, sampleInfo, }) {
+    return sources.flatMap(source => {
+        const ploidy = sampleInfo[source.name]?.maxPloidy ?? 2;
+        return makeHaplotypeSources(source, ploidy);
+    });
+}
 export function getSources({ sources, layout = sources, renderingMode, sampleInfo, }) {
-    const rows = [];
     const sourceMap = Object.fromEntries(sources.map(s => [s.name, s]));
-    for (const row of layout) {
+    return layout.flatMap(row => {
+        const sampleName = row.baseName ?? row.name;
+        const baseSource = sourceMap[sampleName];
+        if (!baseSource) {
+            return [];
+        }
+        const merged = { ...baseSource, ...row };
         if (renderingMode === 'phased') {
-            const info = sampleInfo?.[row.name];
-            if (info?.isPhased) {
-                const ploidy = info.maxPloidy;
-                for (let i = 0; i < ploidy; i++) {
-                    const id = `${row.name} HP${i}`;
-                    rows.push({
-                        ...sourceMap[row.name],
-                        ...row,
-                        label: id,
-                        HP: i,
-                        id: id,
-                    });
-                }
+            if (row.HP !== undefined) {
+                return [{ ...merged, baseName: sampleName }];
             }
+            const ploidy = sampleInfo?.[row.name]?.maxPloidy;
+            if (ploidy) {
+                return makeHaplotypeSources(merged, ploidy);
+            }
+            return [];
         }
-        else {
-            rows.push({
-                ...sourceMap[row.name],
-                ...row,
-                label: row.name,
-                id: row.name,
-            });
-        }
-    }
-    return rows;
+        return [merged];
+    });
 }

package/esm/shared/treeDrawingAutorun.d.ts CHANGED Viewed

@@ -11,6 +11,7 @@ interface TreeDrawingModel {
     totalHeight: number;
     hoveredTreeNode?: HoveredTreeNode;
     sources?: Source[];
+    isMinimized: boolean;
 }
 export declare function setupTreeDrawingAutorun(self: TreeDrawingModel): void;
 export {};

package/esm/shared/treeDrawingAutorun.js CHANGED Viewed

@@ -1,8 +1,11 @@
 import { getContainingView } from '@jbrowse/core/util';
-import { addDisposer } from '@jbrowse/mobx-state-tree';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 export function setupTreeDrawingAutorun(self) {
     addDisposer(self, autorun(function treeDrawAutorun() {
+        if (!isAlive(self) || self.isMinimized) {
+            return;
+        }
         const { treeCanvas, hierarchy, treeAreaWidth, height, scrollTop, totalHeight: _totalHeight, } = self;
         if (!treeCanvas || !hierarchy) {
             return;
@@ -34,6 +37,9 @@ export function setupTreeDrawingAutorun(self) {
         name: 'TreeDraw',
     }));
     addDisposer(self, autorun(function treeHoverAutorun() {
+        if (!isAlive(self) || self.isMinimized) {
+            return;
+        }
         const { mouseoverCanvas, hierarchy, rowHeight, hoveredTreeNode, height, scrollTop, sources, totalHeight, } = self;
         if (!mouseoverCanvas) {
             return;

package/esm/shared/types.d.ts CHANGED Viewed

@@ -3,11 +3,10 @@ import type { Feature } from '@jbrowse/core/util';
 export interface Source {
     baseUri?: string;
     name: string;
-    label?: string;
+    baseName?: string;
     color?: string;
     group?: string;
     HP?: number;
-    id?: string;
     [key: string]: unknown;
 }
 export interface SampleInfo {

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "4.0.2",
+  "version": "4.0.4",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -27,20 +27,20 @@
     "@jbrowse/mobx-state-tree": "^5.5.0",
     "@mui/icons-material": "^7.3.6",
     "@mui/material": "^7.3.6",
-    "@mui/x-charts-vendor": "^8.23.0",
-    "@mui/x-data-grid": "^8.23.0",
+    "@mui/x-charts-vendor": "^8.25.0",
+    "@mui/x-data-grid": "^8.25.0",
+    "@types/file-saver-es": "^2.0.3",
     "copy-to-clipboard": "^3.3.3",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
-    "@types/file-saver-es": "^2.0.3",
     "file-saver-es": "^2.0.5",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/plugin-circular-view": "^4.0.2",
-    "@jbrowse/sv-core": "^4.0.2",
-    "@jbrowse/core": "^4.0.2",
-    "@jbrowse/plugin-linear-genome-view": "^4.0.2"
+    "@jbrowse/plugin-circular-view": "^4.0.4",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.4",
+    "@jbrowse/sv-core": "^4.0.4",
+    "@jbrowse/core": "^4.0.4"
   },
   "peerDependencies": {
     "react": ">=18.0.0"