@genome-spy/core 0.53.1 → 0.55.0

package/dist/src/data/transforms/aggregate.js

@@ -1,32 +1,65 @@
 import { group as d3group } from "d3-array";
-import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
+import { BEHAVIOR_CLONES } from "../flowNode.js";
 import { field } from "../../utils/field.js";
 import iterateNestedMaps from "../../utils/iterateNestedMaps.js";
+import Transform from "./transform.js";
+import AGGREGATE_OPS from "./aggregateOps.js";
 
-/**
- * A minimal aggregate transform that just counts grouped (by a single field) data items.
- * Work in progress.
- *
- * Eventually this will implement the most of Vega's aggregate transform:
- * https://vega.github.io/vega/docs/transforms/aggregate/
- */
-export default class AggregateTransform extends FlowNode {
+export default class AggregateTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
 
     /**
      * @param {import("../../spec/transform.js").AggregateParams} params
+     *
+     * @typedef {import("../flowNode.js").Datum} Datum
      */
     constructor(params) {
-        super();
+        super(params);
         this.params = params;
 
         /** @type {any[]} */
         this.buffer = [];
+
+        /**
+         * @type {((arr: Datum[]) => number)[]}
+         */
+        this.ops = [];
+        /**
+         * @type {string[]}
+         */
+        this.as = [];
+
+        if (params.fields) {
+            if (params.fields.length != params.ops.length) {
+                throw new Error("Fields and ops must have the same length!");
+            }
+
+            if (params.as && params.as.length != params.ops.length) {
+                throw new Error(
+                    'If "as" is defined, "fields" and "as" must have the same length!'
+                );
+            }
+
+            params.fields.forEach((fieldName, i) => {
+                const accessor = field(fieldName);
+                const op = AGGREGATE_OPS[params.ops[i]];
+                this.ops.push((arr) => op(arr, accessor));
+                this.as.push(
+                    params.as
+                        ? params.as[i]
+                        : `${params.ops[i]}_${params.fields[i]}`
+                );
+            });
+        } else {
+            this.ops.push((arr) => AGGREGATE_OPS.count(arr));
+            this.as.push("count");
+        }
     }
 
     reset() {
+        super.reset();
         this.buffer = [];
     }
 
@@ -41,26 +74,36 @@ export default class AggregateTransform extends FlowNode {
     complete() {
         const params = this.params;
 
-        const groupby = params.groupby;
+        const groupby = params?.groupby;
+
+        if (groupby?.length > 0) {
+            const groupFieldAccessors = groupby.map((f) => field(f));
 
-        const groupFieldAccessors = groupby.map((f) => field(f));
+            // There's something strange in d3-array's typings
+            const groups = /** @type {Map<any, any>} */ /** @type {any} */ (
+                d3group(this.buffer, ...groupFieldAccessors)
+            );
 
-        // TODO: Fix case where no group fields are specified
+            for (const [group, data] of iterateNestedMaps(groups)) {
+                /** @type {any} */
+                const datum = {};
 
-        // There's something strange in d3-array's typings
-        const groups = /** @type {Map<any, any>} */ /** @type {any} */ (
-            d3group(this.buffer, ...groupFieldAccessors)
-        );
+                for (let i = 0; i < groupby.length; i++) {
+                    datum[groupby[i]] = group[i];
+                }
 
-        for (const [group, data] of iterateNestedMaps(groups)) {
-            /** @type {any} */
-            const datum = {
-                count: data.length,
-            };
+                this.ops.forEach((op, i) => {
+                    datum[this.as[i]] = op(data);
+                });
 
-            for (let i = 0; i < groupby.length; i++) {
-                datum[groupby[i]] = group[i];
+                this._propagate(datum);
             }
+        } else {
+            /** @type {Datum} */
+            const datum = {};
+            this.ops.forEach((op, i) => {
+                datum[this.as[i]] = op(this.buffer);
+            });
 
             this._propagate(datum);
         }

package/dist/src/data/transforms/aggregate.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=aggregate.test.d.ts.map

package/dist/src/data/transforms/aggregate.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"aggregate.test.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.test.js"],"names":[],"mappings":""}

package/dist/src/data/transforms/aggregate.test.js

@@ -0,0 +1,134 @@
+import { describe, expect, test } from "vitest";
+import { processData } from "../flowTestUtils.js";
+import AggregateTransform from "./aggregate.js";
+
+/**
+ * @param {import("../../spec/transform.js").AggregateParams} params
+ * @param {any[]} data
+ */
+function transform(params, data) {
+    return processData(new AggregateTransform(params), data);
+}
+
+describe("Aggregate transform", () => {
+    test("Default to count when no data fields or group-by fields are specified", () => {
+        const input = [
+            { name: "alpha", data: 123 },
+            { name: "beta", data: 456 },
+            { name: "beta", data: 789 },
+        ];
+
+        expect(transform({ type: "aggregate" }, input)).toEqual([{ count: 3 }]);
+    });
+
+    test("Default to count when no data fields fields are specified", () => {
+        const input = [
+            { name: "alpha", data: 123 },
+            { name: "beta", data: 456 },
+            { name: "beta", data: 789 },
+        ];
+
+        expect(
+            transform({ type: "aggregate", groupby: ["name"] }, input)
+        ).toEqual([
+            { name: "alpha", count: 1 },
+            { name: "beta", count: 2 },
+        ]);
+    });
+
+    test("Compute count, sum, min, max, and mean for groups. Use default output field names.", () => {
+        const input = [
+            { name: "alpha", data: 123 },
+            { name: "beta", data: 456 },
+            { name: "beta", data: 789 },
+        ];
+
+        expect(
+            transform(
+                {
+                    type: "aggregate",
+                    groupby: ["name"],
+                    fields: ["data", "data", "data", "data", "data"],
+                    ops: ["count", "sum", "min", "max", "mean"],
+                },
+                input
+            )
+        ).toEqual([
+            {
+                name: "alpha",
+                count_data: 1,
+                sum_data: 123,
+                min_data: 123,
+                max_data: 123,
+                mean_data: 123,
+            },
+            {
+                name: "beta",
+                count_data: 2,
+                sum_data: 1245,
+                min_data: 456,
+                max_data: 789,
+                mean_data: 622.5,
+            },
+        ]);
+    });
+
+    test("Allow custom output field names", () => {
+        const input = [
+            { name: "alpha", data: 123 },
+            { name: "beta", data: 456 },
+            { name: "beta", data: 789 },
+        ];
+
+        expect(
+            transform(
+                {
+                    type: "aggregate",
+                    fields: ["data", "data", "data", "data", "data"],
+                    ops: ["count", "sum", "min", "max", "mean"],
+                    as: ["count", "total", "min", "max", "average"],
+                },
+                input
+            )
+        ).toEqual([
+            {
+                count: 3,
+                total: 1368,
+                min: 123,
+                max: 789,
+                average: 456,
+            },
+        ]);
+    });
+
+    test("Throw if the length of fields and ops does not match", () => {
+        const input = [{ name: "beta", data: 789 }];
+
+        expect(() =>
+            transform(
+                {
+                    type: "aggregate",
+                    fields: ["data", "data", "data", "data"],
+                    ops: ["count", "sum", "min", "max", "mean"],
+                },
+                input
+            )
+        ).toThrow();
+    });
+
+    test("Throw if the length of fields and as does not match", () => {
+        const input = [{ name: "beta", data: 789 }];
+
+        expect(() =>
+            transform(
+                {
+                    type: "aggregate",
+                    fields: ["data"],
+                    ops: ["count"],
+                    as: ["count", "total"],
+                },
+                input
+            )
+        ).toThrow();
+    });
+});

package/dist/src/data/transforms/aggregateOps.d.ts

@@ -0,0 +1,6 @@
+export default AGGREGATE_OPS;
+/**
+ * @type {Record<import("../../spec/transform.js").AggregateOp, (arr: any[], accessor?: (datum: any) => number) => number>}
+ */
+declare const AGGREGATE_OPS: Record<import("../../spec/transform.js").AggregateOp, (arr: any[], accessor?: (datum: any) => number) => number>;
+//# sourceMappingURL=aggregateOps.d.ts.map

package/dist/src/data/transforms/aggregateOps.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAEA;;GAEG;AACH,6BAFU,OAAO,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAWxH"}

package/dist/src/data/transforms/aggregateOps.js

@@ -0,0 +1,17 @@
+import { count, max, mean, median, min, sum, variance } from "d3-array";
+
+/**
+ * @type {Record<import("../../spec/transform.js").AggregateOp, (arr: any[], accessor?: (datum: any) => number) => number>}
+ */
+const AGGREGATE_OPS = {
+    count: (arr) => arr.length,
+    valid: count,
+    sum,
+    min,
+    max,
+    mean,
+    median,
+    variance,
+};
+
+export default AGGREGATE_OPS;

package/dist/src/data/transforms/clone.d.ts

@@ -1,7 +1,7 @@
 /**
  * Clones the data objects that pass through.
  */
-export default class CloneTransform extends FlowNode {
+export default class CloneTransform extends Transform {
     constructor();
     /**
      * Signals that a new batch of data will be propagated.
@@ -11,5 +11,5 @@ export default class CloneTransform extends FlowNode {
     beginBatch: (flowBatch?: import("../../types/flowBatch.js").FlowBatch) => void;
     #private;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=clone.d.ts.map

package/dist/src/data/transforms/clone.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAWI,cAmCC;IAXG;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAOtD;;CAER;qBApDsD,gBAAgB"}
+{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAKA;;GAEG;AACH;IAWI,cAmCC;IAXG;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAOtD;;CAER;sBApDqB,gBAAgB"}

package/dist/src/data/transforms/clone.js

@@ -1,11 +1,12 @@
 import { shallowArrayEquals } from "../../utils/arrayUtils.js";
 import createCloner, { getAllProperties } from "../../utils/cloner.js";
-import FlowNode, { BEHAVIOR_CLONES, isFileBatch } from "../flowNode.js";
+import { BEHAVIOR_CLONES, isFileBatch } from "../flowNode.js";
+import Transform from "./transform.js";
 
 /**
  * Clones the data objects that pass through.
  */
-export default class CloneTransform extends FlowNode {
+export default class CloneTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
@@ -17,7 +18,7 @@ export default class CloneTransform extends FlowNode {
     #clone = (datum) => datum;
 
     constructor() {
-        super();
+        super({ type: "clone" });
 
         /** @param {import("../flowNode.js").Datum} datum */
         const setupCloner = (datum) => {

package/dist/src/data/transforms/coverage.d.ts

@@ -7,7 +7,7 @@
  * way to implement it is a separate transform that bins the coverage
  * segments and calculates weighted averages.
  */
-export default class CoverageTransform extends FlowNode {
+export default class CoverageTransform extends Transform {
     /**
      * @typedef {import("../flowNode.js").Datum} Datum
      */
@@ -36,6 +36,6 @@ export default class CoverageTransform extends FlowNode {
      */
     ends: FlatQueue<number>;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 import FlatQueue from "flatqueue";
 //# sourceMappingURL=coverage.d.ts.map

package/dist/src/data/transforms/coverage.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":";AAKA;;;;;;;GAOG;AACH;IAKI;;OAEG;IAEH;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,sBADoB,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,uBADoB,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAED,sEACsE,MAAM,oCAgBvE;IAEL;;;;OAIG;IACH,MAFU,UAAU,MAAM,CAAC,CAEA;CA0IlC;qBA7MyC,gBAAgB;sBAHpC,WAAW"}
+{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":";AAMA;;;;;;;GAOG;AACH;IAKI;;OAEG;IAEH;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,sBADoB,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,uBADoB,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAED,sEACsE,MAAM,oCAgBvE;IAEL;;;;OAIG;IACH,MAFU,UAAU,MAAM,CAAC,CAEA;CA0IlC;sBA7MqB,gBAAgB;sBAJhB,WAAW"}

package/dist/src/data/transforms/coverage.js

@@ -1,7 +1,8 @@
 import FlatQueue from "flatqueue";
 
 import { field } from "../../utils/field.js";
-import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
+import { BEHAVIOR_CLONES } from "../flowNode.js";
+import Transform from "./transform.js";
 
 /**
  * Computes coverage for sorted segments
@@ -11,7 +12,7 @@ import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
  * way to implement it is a separate transform that bins the coverage
  * segments and calculates weighted averages.
  */
-export default class CoverageTransform extends FlowNode {
+export default class CoverageTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
@@ -24,7 +25,7 @@ export default class CoverageTransform extends FlowNode {
      * @param {import("../../spec/transform.js").CoverageParams} params
      */
     constructor(params) {
-        super();
+        super(params);
         this.params = params;
 
         this.startAccessor = field(params.start);

package/dist/src/data/transforms/filter.d.ts

@@ -8,7 +8,7 @@ export function isExprFilterParams(params: import("../../spec/transform.js").Fil
  * @returns {params is import("../../spec/transform.js").SelectionFilterParams}
  */
 export function isSelectionFilterParams(params: import("../../spec/transform.js").FilterParams): params is import("../../spec/transform.js").SelectionFilterParams;
-export default class FilterTransform extends FlowNode {
+export default class FilterTransform extends Transform {
     /**
      *
      * @param {import("../../spec/transform.js").FilterParams} params
@@ -19,5 +19,5 @@ export default class FilterTransform extends FlowNode {
     /** @type {import("../../view/paramMediator.js").ExprRefFunction} */
     predicate: import("../../view/paramMediator.js").ExprRefFunction;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=filter.d.ts.map

package/dist/src/data/transforms/filter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AA8CA;;;GAGG;AACH,2CAHW,OAAO,yBAAyB,EAAE,YAAY,gEAKxD;AAED;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,YAAY,qEAKxD;AAzDD;IACI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,YAAY,yBAC9C,OAAO,gBAAgB,EAAE,qBAAqB,EASxD;IAJG,uDAAoB;IAEpB,oEAAoE;IACpE,WADW,OAAO,6BAA6B,EAAE,eAAe,CACtC;CA6BjC;qBA3CoB,gBAAgB"}
+{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AA8CA;;;GAGG;AACH,2CAHW,OAAO,yBAAyB,EAAE,YAAY,gEAKxD;AAED;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,YAAY,qEAKxD;AAzDD;IACI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,YAAY,yBAC9C,OAAO,gBAAgB,EAAE,qBAAqB,EASxD;IAJG,uDAAoB;IAEpB,oEAAoE;IACpE,WADW,OAAO,6BAA6B,EAAE,eAAe,CACtC;CA6BjC;sBA3CqB,gBAAgB"}

package/dist/src/data/transforms/filter.js

@@ -1,14 +1,14 @@
 import { makeSelectionTestExpression } from "../../selection/selection.js";
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 
-export default class FilterTransform extends FlowNode {
+export default class FilterTransform extends Transform {
     /**
      *
      * @param {import("../../spec/transform.js").FilterParams} params
      * @param {import("../flowNode.js").ParamMediatorProvider} paramMediatorProvider
      */
     constructor(params, paramMediatorProvider) {
-        super(paramMediatorProvider);
+        super(params, paramMediatorProvider);
 
         this.params = params;
 

package/dist/src/data/transforms/filterScoredLabels.d.ts

@@ -1,4 +1,4 @@
-export default class FilterScoredLabelsTransform extends FlowNode {
+export default class FilterScoredLabelsTransform extends Transform {
     /**
      *
      * @param {import("../../spec/transform.js").FilterScoredLabelsParams} params
@@ -24,6 +24,6 @@ export default class FilterScoredLabelsTransform extends FlowNode {
     _filterAndPropagate(): void;
     groups: Map<any, any>;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 import ReservationMap from "../../utils/reservationMap.js";
 //# sourceMappingURL=filterScoredLabels.d.ts.map

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAMA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,qBADoB,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,IAAI,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BAyCC;IAKG,sBAAuB;CAU9B;qBAjI2C,gBAAgB;2BAEjC,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,qBADoB,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,IAAI,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BAyCC;IAKG,sBAAuB;CAU9B;sBA9HqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -1,10 +1,11 @@
 import { bisector } from "d3-array";
-import FlowNode, { BEHAVIOR_COLLECTS } from "../flowNode.js";
+import { BEHAVIOR_COLLECTS } from "../flowNode.js";
 import { topKSlice } from "../../utils/topK.js";
 import ReservationMap from "../../utils/reservationMap.js";
 import { field } from "../../utils/field.js";
+import Transform from "./transform.js";
 
-export default class FilterScoredLabelsTransform extends FlowNode {
+export default class FilterScoredLabelsTransform extends Transform {
     get behavior() {
         return BEHAVIOR_COLLECTS;
     }
@@ -15,7 +16,7 @@ export default class FilterScoredLabelsTransform extends FlowNode {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params, view) {
-        super();
+        super(params);
 
         this.params = params;
 

package/dist/src/data/transforms/flatten.d.ts

@@ -1,10 +1,11 @@
-export default class FlattenTransform extends FlowNode {
+export default class FlattenTransform extends Transform {
     /**
      * @param {import("../../spec/transform.js").FlattenParams} params
      */
     constructor(params: import("../../spec/transform.js").FlattenParams);
+    params: import("../../spec/transform.js").FlattenParams;
     /** @param {any[]} datum */
     handle: (datum: any[]) => void;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=flatten.d.ts.map

package/dist/src/data/transforms/flatten.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flatten.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flatten.js"],"names":[],"mappings":"AAIA;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,aAAa,EAwDzD;IAvCO,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAwBhB;CAgBZ;qBAjEyC,gBAAgB"}
+{"version":3,"file":"flatten.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flatten.js"],"names":[],"mappings":"AAKA;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,aAAa,EA0DzD;IArDG,wDAAoB;IAchB,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAwBhB;CAgBZ;sBAnEqB,gBAAgB"}

package/dist/src/data/transforms/flatten.js

@@ -1,8 +1,9 @@
 import { asArray } from "../../utils/arrayUtils.js";
 import { field } from "../../utils/field.js";
-import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
+import { BEHAVIOR_CLONES } from "../flowNode.js";
+import Transform from "./transform.js";
 
-export default class FlattenTransform extends FlowNode {
+export default class FlattenTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
@@ -11,7 +12,9 @@ export default class FlattenTransform extends FlowNode {
      * @param {import("../../spec/transform.js").FlattenParams} params
      */
     constructor(params) {
-        super();
+        super(params);
+
+        this.params = params;
 
         const indexField = params.index;
 

package/dist/src/data/transforms/flattenCompressedExons.d.ts

@@ -3,7 +3,7 @@
  * coordinate of the gene body and a comma-delimited string of alternating
  * intron and exon lengths. A new datum is created for each exon.
  */
-export default class FlattenCompressedExonsTransform extends FlowNode {
+export default class FlattenCompressedExonsTransform extends Transform {
     /**
      *
      * @param {import("../../spec/transform.js").FlattenCompressedExonsParams} params
@@ -15,5 +15,5 @@ export default class FlattenCompressedExonsTransform extends FlowNode {
      */
     handle: (datum: any) => void;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=flattenCompressedExons.d.ts.map

package/dist/src/data/transforms/flattenCompressedExons.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flattenCompressedExons.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenCompressedExons.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,4BAA4B,EAmCxE;IA1BG;;;OAGG;IACH,gBAFW,GAAG,UAuBb;CAER;qBAlDyC,gBAAgB"}
+{"version":3,"file":"flattenCompressedExons.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenCompressedExons.js"],"names":[],"mappings":"AAKA;;;;GAIG;AACH;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,4BAA4B,EAmCxE;IA1BG;;;OAGG;IACH,gBAFW,GAAG,UAuBb;CAER;sBAlDqB,gBAAgB"}

package/dist/src/data/transforms/flattenCompressedExons.js

@@ -1,13 +1,14 @@
 import { field } from "../../utils/field.js";
 import numberExtractor from "../../utils/numberExtractor.js";
-import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
+import { BEHAVIOR_CLONES } from "../flowNode.js";
+import Transform from "./transform.js";
 
 /**
  * Flattens "run-length encoded" exons. The transforms inputs the start
  * coordinate of the gene body and a comma-delimited string of alternating
  * intron and exon lengths. A new datum is created for each exon.
  */
-export default class FlattenCompressedExonsTransform extends FlowNode {
+export default class FlattenCompressedExonsTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
@@ -17,7 +18,7 @@ export default class FlattenCompressedExonsTransform extends FlowNode {
      * @param {import("../../spec/transform.js").FlattenCompressedExonsParams} params
      */
     constructor(params) {
-        super();
+        super(params);
 
         const exonsAccessor = field(params.exons ?? "exons");
         const startAccessor = field(params.start ?? "start");

package/dist/src/data/transforms/flattenDelimited.d.ts

@@ -1,4 +1,4 @@
-export default class FlattenDelimitedTransform extends FlowNode {
+export default class FlattenDelimitedTransform extends Transform {
     /**
      * @param {import("../../spec/transform.js").FlattenDelimitedParams} params
      */
@@ -6,5 +6,5 @@ export default class FlattenDelimitedTransform extends FlowNode {
     /** @param {any[]} datum */
     handle: (datum: any[]) => void;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=flattenDelimited.d.ts.map

package/dist/src/data/transforms/flattenDelimited.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flattenDelimited.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenDelimited.js"],"names":[],"mappings":"AAIA;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,sBAAsB,EAuClE;IAnBG,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAkBhB;CAER;qBAhDyC,gBAAgB"}
+{"version":3,"file":"flattenDelimited.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenDelimited.js"],"names":[],"mappings":"AAKA;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,sBAAsB,EAuClE;IAnBG,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAkBhB;CAER;sBAhDqB,gBAAgB"}

package/dist/src/data/transforms/flattenDelimited.js

@@ -1,8 +1,9 @@
 import { asArray } from "../../utils/arrayUtils.js";
 import { field } from "../../utils/field.js";
-import FlowNode, { BEHAVIOR_CLONES } from "../flowNode.js";
+import { BEHAVIOR_CLONES } from "../flowNode.js";
+import Transform from "./transform.js";
 
-export default class FlattenDelimitedTransform extends FlowNode {
+export default class FlattenDelimitedTransform extends Transform {
     get behavior() {
         return BEHAVIOR_CLONES;
     }
@@ -11,7 +12,7 @@ export default class FlattenDelimitedTransform extends FlowNode {
      * @param {import("../../spec/transform.js").FlattenDelimitedParams} params
      */
     constructor(params) {
-        super();
+        super(params);
 
         // TODO: Validate config. string elements, etc...
 

package/dist/src/data/transforms/flattenSequence.d.ts

@@ -1,11 +1,12 @@
-export default class FlattenSequenceTransform extends FlowNode {
+export default class FlattenSequenceTransform extends Transform {
     /**
      *
      * @param {import("../../spec/transform.js").FlattenSequenceParams} params
      */
     constructor(params: import("../../spec/transform.js").FlattenSequenceParams);
+    params: import("../../spec/transform.js").FlattenSequenceParams;
     /** @param {any[]} datum */
     handle: (datum: any[]) => void;
 }
-import FlowNode from "../flowNode.js";
+import Transform from "./transform.js";
 //# sourceMappingURL=flattenSequence.d.ts.map

package/dist/src/data/transforms/flattenSequence.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flattenSequence.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenSequence.js"],"names":[],"mappings":"AAGA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,qBAAqB,EAuBjE;IAfG,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAchB;CAER;qBAjCyC,gBAAgB"}
+{"version":3,"file":"flattenSequence.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/flattenSequence.js"],"names":[],"mappings":"AAIA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,qBAAqB,EAyBjE;IApBG,gEAAoB;IAKpB,2BAA2B;IAC3B,gBADY,GAAG,EAAE,UAchB;CAER;sBAnCqB,gBAAgB"}