jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/LinearMafDisplay/stateModel.js

@@ -1,16 +1,23 @@
 import { lazy } from 'react';
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
-import { getEnv, getSession, max, measureText } from '@jbrowse/core/util';
+import { getContainingTrack, getContainingView, getEnv, getSession, max, measureText, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { addDisposer, isAlive, types } from '@jbrowse/mobx-state-tree';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
 import deepEqual from 'fast-deep-equal';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive, types } from 'mobx-state-tree';
-import { maxLength, setBrLength } from './util';
+import { computeNodeDescendantNames, maxLength, setBrLength } from './util';
 import { normalize } from '../util';
+const defaultRowHeight = 15;
+const defaultRowProportion = 0.8;
+const defaultShowAllLetters = false;
+const defaultMismatchRendering = true;
+const defaultShowBranchLen = false;
+const defaultTreeAreaWidth = 80;
+const defaultShowAsUpperCase = true;
+const defaultShowSidebar = true;
 const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog/SetRowHeightDialog'));
-const InsertionSequenceDialog = lazy(() => import('./components/InsertionSequenceDialog/InsertionSequenceDialog'));
 /**
  * #stateModel LinearMafDisplay
  * extends LinearBasicDisplay
@@ -31,35 +38,35 @@ export default function stateModelFactory(configSchema, pluginManager) {
         /**
          * #property
          */
-        rowHeight: 15,
+        rowHeight: defaultRowHeight,
         /**
          * #property
          */
-        rowProportion: 0.8,
+        rowProportion: defaultRowProportion,
         /**
          * #property
          */
-        showAllLetters: false,
+        showAllLetters: defaultShowAllLetters,
         /**
          * #property
          */
-        mismatchRendering: true,
+        mismatchRendering: defaultMismatchRendering,
         /**
          * #property
          */
-        showBranchLen: false,
+        showBranchLen: defaultShowBranchLen,
         /**
          * #property
          */
-        treeAreaWidth: 80,
+        treeAreaWidth: defaultTreeAreaWidth,
         /**
          * #property
          */
-        showAsUpperCase: true,
+        showAsUpperCase: defaultShowAsUpperCase,
         /**
          * #property
          */
-        showSidebar: true,
+        showSidebar: defaultShowSidebar,
     }))
         .volatile(() => ({
         /**
@@ -121,7 +128,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
         /**
          * #action
          */
-        setSamples({ samples, tree }) {
+        setSamples({ samples, tree, }) {
             if (!deepEqual(samples, self.volatileSamples)) {
                 self.volatileSamples = samples;
             }
@@ -158,14 +165,25 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * #action
          */
         showInsertionSequenceDialog(insertionData) {
-            getSession(self).queueDialog(handleClose => [
-                InsertionSequenceDialog,
-                {
-                    model: self,
-                    onClose: handleClose,
-                    insertionData,
+            const { sequence, sampleLabel, chr, pos } = insertionData;
+            const session = getSession(self);
+            const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                featureData: {
+                    uniqueId: `insertion-${chr}-${pos}-${sampleLabel}`,
+                    type: 'insertion',
+                    refName: chr,
+                    start: pos,
+                    end: pos + 1,
+                    sample: sampleLabel,
+                    insertionLength: sequence.length,
+                    sequence: self.showAsUpperCase
+                        ? sequence.toUpperCase()
+                        : sequence.toLowerCase(),
                 },
-            ]);
+                view: getContainingView(self),
+                track: getContainingTrack(self),
+            });
+            session.showWidget(featureWidget);
         },
     }))
         .views(self => ({
@@ -194,8 +212,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
         get root() {
             return self.volatileTree
                 ? hierarchy(self.volatileTree, d => d.children)
-                    // todo: investigate whether needed, typescript says children always true
-                    .sum(d => (d.children ? 0 : 1))
+                    .sum(d => (d.children?.length ? 0 : 1))
                     .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
                 : undefined;
         },
@@ -219,7 +236,8 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 for (const node of r.descendants()) {
                     node.x = node.x + self.rowHeight / 2;
                 }
-                setBrLength(r, (r.data.length = 0), width / maxLength(r));
+                r.data.length = 0;
+                setBrLength(r, 0, width / maxLength(r));
                 return r;
             }
             else {
@@ -267,24 +285,10 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * Precomputed map from hierarchy node to its descendant leaf names
          */
         get nodeDescendantNames() {
-            const map = new Map();
-            function computeDescendants(node) {
-                if (!node.children || node.children.length === 0) {
-                    const names = [node.data.name];
-                    map.set(node, names);
-                    return names;
-                }
-                const names = [];
-                for (const child of node.children) {
-                    names.push(...computeDescendants(child));
-                }
-                map.set(node, names);
-                return names;
-            }
             if (this.hierarchy) {
-                computeDescendants(this.hierarchy);
+                return computeNodeDescendantNames(this.hierarchy);
             }
-            return map;
+            return new Map();
         },
         /**
          * #getter
@@ -314,7 +318,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 const s = superRenderProps();
                 return {
                     ...s,
-                    notReady: (!self.volatileSamples && !self.volatileTree) || super.notReady,
+                    notReady: (!self.volatileSamples && !self.volatileTree) || s.notReady,
                     config: rendererConfig,
                     samples,
                     rowHeight,
@@ -399,6 +403,28 @@ export default function stateModelFactory(configSchema, pluginManager) {
         };
     })
         .views(self => ({
+        /**
+         * #getter
+         * Get highlight regions from connected MSA views
+         */
+        get msaHighlights() {
+            const session = getSession(self);
+            const view = getContainingView(self);
+            const highlights = [];
+            // Find MSA views that are connected to our parent view
+            for (const v of session.views) {
+                if (v.type === 'MsaView' &&
+                    v.connectedViewId === view.id) {
+                    const msaView = v;
+                    if (msaView.connectedHighlights) {
+                        for (const h of msaView.connectedHighlights) {
+                            highlights.push(h);
+                        }
+                    }
+                }
+            }
+            return highlights;
+        },
         /**
          * #getter
          */
@@ -438,7 +464,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
                         adapterConfig: self.adapterConfig,
                         statusCallback: (message) => {
                             if (isAlive(self)) {
-                                self.setMessage(message);
+                                self.setStatusMessage(message);
                             }
                         },
                     })));
@@ -462,6 +488,24 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 return renderSvg(self, opts, superRenderSvg);
             },
         };
+    })
+        .postProcessSnapshot(snap => {
+        const { rowHeight, rowProportion, showAllLetters, mismatchRendering, showBranchLen, treeAreaWidth, showAsUpperCase, showSidebar, ...rest } = snap;
+        return {
+            ...rest,
+            ...(rowHeight !== defaultRowHeight ? { rowHeight } : {}),
+            ...(rowProportion !== defaultRowProportion ? { rowProportion } : {}),
+            ...(showAllLetters !== defaultShowAllLetters ? { showAllLetters } : {}),
+            ...(mismatchRendering !== defaultMismatchRendering
+                ? { mismatchRendering }
+                : {}),
+            ...(showBranchLen !== defaultShowBranchLen ? { showBranchLen } : {}),
+            ...(treeAreaWidth !== defaultTreeAreaWidth ? { treeAreaWidth } : {}),
+            ...(showAsUpperCase !== defaultShowAsUpperCase
+                ? { showAsUpperCase }
+                : {}),
+            ...(showSidebar !== defaultShowSidebar ? { showSidebar } : {}),
+        };
     });
 }
 //# sourceMappingURL=stateModel.js.map

package/dist/LinearMafDisplay/stateModel.js.map

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package/dist/LinearMafDisplay/types.d.ts

@@ -1,14 +1,14 @@
 export interface NodeWithIds {
     id: string;
     name: string;
-    children: NodeWithIds[];
+    children?: NodeWithIds[];
     length?: number;
     noTree?: boolean;
 }
 export interface NodeWithIdsAndLength {
     id: string;
     name: string;
-    children: NodeWithIdsAndLength[];
+    children?: NodeWithIdsAndLength[];
     noTree?: boolean;
     length: number;
 }

package/dist/LinearMafDisplay/util.d.ts

@@ -6,6 +6,8 @@ export interface HoveredInfo {
     pos: number;
     base: string;
     chr: string;
+    isInsertion?: boolean;
+    isLargeInsertion?: boolean;
     [key: string]: unknown;
 }
 export interface GenomicPosition {
@@ -23,3 +25,6 @@ export interface GenomicPosition {
 export declare function generateTooltipContent(hoveredInfo: HoveredInfo | undefined, p1: GenomicPosition | undefined, p2: GenomicPosition): string;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
+export declare function computeNodeDescendantNames<T extends {
+    name: string;
+}>(root: HierarchyNode<T>): Map<HierarchyNode<T>, string[]>;

package/dist/LinearMafDisplay/util.js

@@ -35,12 +35,33 @@ export function maxLength(d) {
 }
 // basically same as setRadius from https://observablehq.com/@d3/tree-of-life
 export function setBrLength(d, y0, k) {
+    const newY0 = y0 + Math.max(d.data.length || 0, 0);
     // @ts-expect-error
-    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    d.len = newY0 * k;
     if (d.children) {
-        d.children.forEach(d => {
-            setBrLength(d, y0, k);
-        });
+        for (const child of d.children) {
+            setBrLength(child, newY0, k);
+        }
+    }
+}
+export function computeNodeDescendantNames(root) {
+    const map = new Map();
+    function visit(node) {
+        if (!node.children || node.children.length === 0) {
+            const names = [node.data.name];
+            map.set(node, names);
+            return names;
+        }
+        const names = [];
+        for (const child of node.children) {
+            for (const name of visit(child)) {
+                names.push(name);
+            }
+        }
+        map.set(node, names);
+        return names;
     }
+    visit(root);
+    return map;
 }
 //# sourceMappingURL=util.js.map

package/dist/LinearMafDisplay/util.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -24,9 +24,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
+        samples: Sample[];
         canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
@@ -35,10 +35,10 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
-        imageData: any;
+        samples: Sample[];
+        imageData: ImageBitmap;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -46,11 +46,47 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         samples: Sample[];
+        html: string;
+        reactElement?: React.ReactElement;
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
-        reactElement: React.ReactElement;
-        html?: string;
+        samples: Sample[];
+        canvasRecordedData: Record<string, unknown>;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
+        samples: Sample[];
+        imageData: ImageBitmap;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
+        samples: Sample[];
+        html: string;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
     }>;
 }
 export {};

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -6,7 +6,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         const { start, end } = region;
         const bpExpansion = 1;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            // xref https://github.com/mobxjs/@jbrowse/mobx-state-tree/issues/1524 for Omit
             ...region,
             start: Math.floor(Math.max(start - bpExpansion, 0)),
             end: Math.ceil(end + bpExpansion),

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAc/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,+EAA+E;YAC/E,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,GAAG,GAAG,CAAA;QAC/C,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;QACpD,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,qBAAqB,EAAE,cAAc,EAAE,GAAG,EAAE,CACzE,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,CAAC,EAAE;YACvD,OAAO,aAAa,CAAC;gBACnB,GAAG;gBACH,UAAU,EAAE;oBACV,GAAG,WAAW;oBACd,QAAQ;iBACT;aACF,CAAC,CAAA;QACJ,CAAC,CAAC,CACH,CAAA;QACD,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC;YACjC,GAAG,WAAW;YACd,GAAG,GAAG;YACN,KAAK;YACL,MAAM;SACP,CAAC,CAAA;QACF,OAAO;YACL,GAAG,OAAO;YACV,GAAG,GAAG;YACN,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,KAAK;YACL,MAAM;YACN,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}

package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts

@@ -1,12 +1,21 @@
 import React from 'react';
-import { Sample } from '../../LinearMafDisplay/types';
-import { RenderedBase } from '../rendering';
-type SerializedRBush = any;
+import type { Sample } from '../../LinearMafDisplay/types';
+import type { RenderedBase } from '../rendering';
+interface DisplayModel {
+    setHoveredInfo?: (info: Record<string, unknown> | undefined) => void;
+    setHighlightedRowNames?: (names: string[] | undefined) => void;
+    showInsertionSequenceDialog?: (data: {
+        sequence: string;
+        sampleLabel: string;
+        chr: string;
+        pos: number;
+    }) => void;
+}
 declare const LinearMafRendering: (props: {
     width: number;
     height: number;
-    displayModel: any;
-    flatbush: SerializedRBush;
+    displayModel: DisplayModel;
+    flatbush: ArrayBuffer;
     items: RenderedBase[];
     samples: Sample[];
 }) => React.JSX.Element;

package/dist/LinearMafRenderer/components/LinearMafRendering.js

@@ -6,33 +6,35 @@ const LinearMafRendering = observer(function (props) {
     const { items, displayModel, height, samples, flatbush } = props;
     const ref = useRef(null);
     const flatbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
-    const [isOverLargeInsertion, setIsOverLargeInsertion] = useState(false);
+    const [isOverInsertion, setIsOverInsertion] = useState(false);
     const getFeatureUnderMouse = useCallback((eventClientX, eventClientY) => {
         let offsetX = 0;
         let offsetY = 0;
         if (ref.current) {
-            const r = ref.current.getBoundingClientRect();
-            offsetX = eventClientX - r.left;
-            offsetY = eventClientY - r.top;
+            const rect = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - rect.left;
+            offsetY = eventClientY - rect.top;
         }
-        const x = flatbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
-        if (x.length) {
-            const elt = x.find(idx => items[idx]?.isInsertion);
-            const r = elt !== undefined ? items[elt] : items[x[0]];
-            const s = samples[r.sampleId];
-            return {
-                ...r,
-                sampleId: s?.id ?? 'unknown',
-                sampleLabel: s?.label || s?.id || 'unknown',
-            };
+        const hits = flatbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
+        if (hits.length === 0) {
+            return undefined;
         }
-        else {
+        const insertionHit = hits.find(idx => items[idx]?.isInsertion);
+        const hitIdx = insertionHit ?? hits[0];
+        const item = hitIdx !== undefined ? items[hitIdx] : undefined;
+        if (!item) {
             return undefined;
         }
+        const sample = samples[item.rowIndex];
+        return {
+            ...item,
+            sampleId: sample?.id ?? 'unknown',
+            sampleLabel: sample?.label || sample?.id || 'unknown',
+        };
     }, [flatbush2, items, samples]);
     return (React.createElement("div", { ref: ref, onClick: e => {
             const feature = getFeatureUnderMouse(e.clientX, e.clientY);
-            if (feature?.isLargeInsertion) {
+            if (feature?.isInsertion) {
                 displayModel.showInsertionSequenceDialog?.({
                     sequence: feature.base,
                     sampleLabel: feature.sampleLabel,
@@ -44,16 +46,16 @@ const LinearMafRendering = observer(function (props) {
             const feature = getFeatureUnderMouse(e.clientX, e.clientY);
             displayModel.setHoveredInfo?.(feature);
             displayModel.setHighlightedRowNames?.(feature?.sampleId ? [feature.sampleId] : undefined);
-            setIsOverLargeInsertion(!!feature?.isLargeInsertion);
+            setIsOverInsertion(!!feature?.isInsertion);
         }, onMouseLeave: () => {
             displayModel.setHoveredInfo?.(undefined);
             displayModel.setHighlightedRowNames?.(undefined);
-            setIsOverLargeInsertion(false);
+            setIsOverInsertion(false);
         }, style: {
             overflow: 'visible',
             position: 'relative',
             height,
-            cursor: isOverLargeInsertion ? 'pointer' : 'default',
+            cursor: isOverInsertion ? 'pointer' : 'default',
         } },
         React.createElement(PrerenderedCanvas, { ...props, style: {
                 position: 'absolute',

package/dist/LinearMafRenderer/components/LinearMafRendering.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/configSchema.d.ts

@@ -1,7 +1,2 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    baseColor: {
-        type: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/LinearMafRenderer/configSchema.js

@@ -3,12 +3,7 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * #config LinearMafRenderer
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = ConfigurationSchema('LinearMafRenderer', {
-    baseColor: {
-        type: 'color',
-        defaultValue: 'lightgrey',
-    },
-}, {
+const configSchema = ConfigurationSchema('LinearMafRenderer', {}, {
     /**
      * #baseConfiguration
      */

package/dist/LinearMafRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB,EAAE,EACF;IACE;;OAEG;IACH,eAAe,EAAE,IAAI;CACtB,CACF,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/LinearMafRenderer/rendering/insertions.d.ts

@@ -1,2 +1,2 @@
 import type { RenderingContext } from './types';
-export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: number, alignmentStart: number, chr: string): void;
+export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, rowIndex: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/insertions.js

@@ -2,7 +2,7 @@ import { measureText } from '@jbrowse/core/util';
 import { fillRect } from '../util';
 import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { CHAR_SIZE_WIDTH, HIGH_BP_PER_PX_THRESHOLD, HIGH_ZOOM_THRESHOLD, INSERTION_BORDER_HEIGHT, INSERTION_BORDER_WIDTH, INSERTION_LINE_WIDTH, INSERTION_PADDING, LARGE_INSERTION_THRESHOLD, MIN_ROW_HEIGHT_FOR_BORDERS, } from './types';
-export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, alignmentStart, chr) {
+export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, rowIndex, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, rowHeight, charHeight } = context;
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
         let insertionSequence = '';
@@ -68,7 +68,7 @@ export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerP
                     pos: genomicOffset + alignmentStart,
                     chr,
                     base: insertionSequence,
-                    sampleId,
+                    rowIndex,
                     isInsertion: true,
                     isLargeInsertion,
                 });