nmr-processing 9.4.1 → 9.4.2-pre.1684301205

package/src/xyz/xyzAutoSignalsPicking.ts

@@ -0,0 +1,309 @@
+import { v4 as generateID } from '@lukeed/uuid';
+import * as convolution from 'ml-matrix-convolution';
+import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
+import type { Peak2D } from 'ml-matrix-peaks-finder';
+import simpleClustering from 'ml-simple-clustering';
+
+import { addMissingIDs } from '../peaks/util/addMissingIDs';
+import { determineRealTop } from '../peaks/util/determineRealTop';
+import { getKernel } from '../peaks/util/getKernel';
+import type { GetKernelOptions } from '../peaks/util/getKernel';
+import * as PeakOptimizer from '../peaks/util/peakOptimizer';
+import { MakeMandatory } from '../utilities/MakeMandatory';
+
+import { Data2D } from './Data2D';
+import type { NMRSignal2D } from './NMRSignal2D';
+import { padData } from './util/padData';
+
+const smallFilter = [
+  [0, 0, 1, 2, 2, 2, 1, 0, 0],
+  [0, 1, 4, 7, 7, 7, 4, 1, 0],
+  [1, 4, 5, 3, 0, 3, 5, 4, 1],
+  [2, 7, 3, -12, -23, -12, 3, 7, 2],
+  [2, 7, 0, -23, -40, -23, 0, 7, 2],
+  [2, 7, 3, -12, -23, -12, 3, 7, 2],
+  [1, 4, 5, 3, 0, 3, 5, 4, 1],
+  [0, 1, 3, 7, 7, 7, 3, 1, 0],
+  [0, 0, 1, 2, 2, 2, 1, 0, 0],
+];
+
+export interface XYZAutoSignalsPickingOptions {
+  /**
+   * max number of points in any dimension to pad the input data, this is needed to avoid lost peaks when the input matrix is too small.
+   * @default 14
+   */
+  sizeToPad?: number;
+  /**
+   * If it's true, try to find the real maximum for each bidimensional peak.
+   * @default true
+   */
+  realTopDetection?: boolean;
+  /**
+   * positive value filter small peaks by intensity
+   * @default 0.5
+   */
+  thresholdFactor?: number;
+  /**
+   * specify the nuclei of each dimension
+   * @default ['1H','1H']
+   */
+  nuclei?: string[];
+  /**
+   * specify the frequency for each dimension.
+   */
+  observedFrequencies: number[] | Float64Array;
+  /**
+   * If it's true, it try to ajust the shift and add missing cross peaks, useful only for homonuclear data.
+   * @default false
+   */
+  enhanceSymmetry?: boolean;
+  /**
+   * If it's true, peaks with less than a specific percentage (maxPercentCutOff) of the maximum intensity will be removed.
+   * @default true;
+   */
+  clean?: boolean;
+  /**
+   * percentage of maximum intensity as cutoff for small peaks.
+   * @default 0.03
+   */
+  maxPercentCutOff?: number;
+  /**
+   * Specify the minimum distance in Hz for each dimension to join peaks in a signal.
+   * @default [24,24]
+   */
+  tolerances?: number[];
+  /**
+   * If it is true, the convolution will be forced by FFT
+   * @default true
+   */
+  convolutionByFFT?: boolean;
+  /**
+   * kernel options to calculate a laplacianOfGaussian kernel with a specify size.
+   */
+  kernel?: GetKernelOptions;
+}
+
+export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
+  NMRSignal2D<T>,
+  'id'
+>;
+
+export function xyzAutoSignalsPicking(
+  spectraData: Data2D,
+  options: XYZAutoSignalsPickingOptions,
+) {
+  let {
+    sizeToPad = 14,
+    realTopDetection = true,
+    thresholdFactor = 0.5,
+    nuclei = ['1H', '1H'],
+    observedFrequencies,
+    enhanceSymmetry = false,
+    clean = true,
+    maxPercentCutOff = 0.03,
+    tolerances = [24, 24],
+    convolutionByFFT = true,
+    kernel: kernelOptions,
+  } = options;
+
+  if (
+    !Array.isArray(observedFrequencies) &&
+    !ArrayBuffer.isView(observedFrequencies)
+  ) {
+    throw new Error('observedFrequencies is mandatory');
+  }
+
+  thresholdFactor = thresholdFactor === 0 ? 1 : Math.abs(thresholdFactor);
+
+  let nbPoints = spectraData.z[0].length;
+  let nbSubSpectra = spectraData.z.length;
+
+  if (nbSubSpectra < sizeToPad) {
+    spectraData = padData(spectraData, { width: sizeToPad });
+    nbPoints = spectraData.z[0].length;
+    nbSubSpectra = spectraData.z.length;
+  }
+
+  let absoluteData = new Float64Array(nbPoints * nbSubSpectra);
+  let originalData = new Float64Array(nbPoints * nbSubSpectra);
+
+  for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra; iSubSpectra++) {
+    let spectrum = spectraData.z[iSubSpectra];
+    for (let iCol = 0; iCol < nbPoints; iCol++) {
+      let index = iSubSpectra * nbPoints + iCol;
+      absoluteData[index] = Math.abs(spectrum[iCol]);
+      originalData[index] = spectrum[iCol]; //@todo pensar si se puede evitar originalData
+    }
+  }
+
+  const kernel = kernelOptions ? getKernel(kernelOptions) : smallFilter;
+
+  let convolutedSpectrum = convolutionByFFT
+    ? convolution.fft(absoluteData, kernel, {
+        rows: nbSubSpectra,
+        cols: nbPoints,
+      })
+    : convolution.direct(absoluteData, kernel, {
+        rows: nbSubSpectra,
+        cols: nbPoints,
+      });
+
+  let peaksMC1 = matrixPeakFinders.findPeaks2DRegion(absoluteData, {
+    originalData,
+    filteredData: convolutedSpectrum,
+    rows: nbSubSpectra,
+    cols: nbPoints,
+    nStdDev: thresholdFactor,
+  });
+
+  if (clean) {
+    // Remove peaks with less than x% of the intensity of the highest peak
+    peaksMC1 = PeakOptimizer.clean(peaksMC1, maxPercentCutOff);
+  }
+
+  let signals = createSignals2D(addMissingIDs(peaksMC1), {
+    nRows: nbSubSpectra,
+    nCols: nbPoints,
+    minX: spectraData.minX,
+    maxX: spectraData.maxX,
+    minY: spectraData.minY,
+    maxY: spectraData.maxY,
+    absoluteData,
+    originalData,
+    tolerances,
+    nuclei,
+    observedFrequencies,
+    realTopDetection,
+  });
+
+  if (enhanceSymmetry) {
+    signals = PeakOptimizer.enhanceSymmetry(signals);
+  }
+
+  return signals;
+}
+
+/**
+ * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
+ * of many 2D-peaks, and it has some additional information related to the NMR spectrum.
+ * @private
+ */
+
+export interface CreateSignals2DOptions {
+  nCols: number;
+  nRows: number;
+  absoluteData: number[] | Float64Array;
+  originalData: number[] | Float64Array;
+  observedFrequencies: number[] | Float64Array;
+  tolerances: number[];
+  nuclei: string[];
+  realTopDetection: boolean;
+  minY: number;
+  maxY: number;
+  minX: number;
+  maxX: number;
+}
+
+function createSignals2D<T extends Peak2D>(
+  peaks: T[],
+  options: CreateSignals2DOptions,
+) {
+  let {
+    nCols,
+    nRows,
+    absoluteData,
+    originalData,
+    observedFrequencies,
+    tolerances,
+    nuclei,
+    realTopDetection,
+    minY,
+    maxY,
+    minX,
+    maxX,
+  } = options;
+
+  let [nucleusX, nucleusY] = nuclei;
+  let [toleranceX, toleranceY] = tolerances;
+  let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
+
+  let dy = (maxY - minY) / (nRows - 1);
+  let dx = (maxX - minX) / (nCols - 1);
+
+  if (realTopDetection) {
+    peaks = determineRealTop(peaks, {
+      nCols,
+      absoluteData,
+      originalData,
+      minX,
+      maxX,
+      minY,
+      maxY,
+    });
+  }
+
+  for (let i = peaks.length - 1; i >= 0; i--) {
+    let { x, y } = peaks[i];
+    peaks[i].x = minX + dx * x;
+    peaks[i].y = minY + dy * y;
+    peaks[i].minX = minX + dx * peaks[i].minX;
+    peaks[i].minY = minY + dy * peaks[i].minY;
+    peaks[i].maxX = minX + dx * peaks[i].maxX;
+    peaks[i].maxY = minY + dy * peaks[i].maxY;
+
+    // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
+  }
+  // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
+  // array like form
+  let connectivity = [];
+  for (let i = 0; i < peaks.length; i++) {
+    for (let j = i; j < peaks.length; j++) {
+      if (
+        Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
+        Math.abs(peaks[i].y - peaks[j].y) * observeFrequencyY < toleranceY
+      ) {
+        // 24*24Hz We cannot distinguish peaks with less than 20 Hz of separation
+        connectivity.push(1);
+      } else {
+        connectivity.push(0);
+      }
+    }
+  }
+  let clusters = simpleClustering(connectivity);
+
+  let signals: NMRSignal2DWithID<T>[] = [];
+  if (clusters) {
+    for (const cluster of clusters) {
+      let signal: any = {
+        id: generateID(),
+        x: {
+          delta: 0,
+          nucleus: nucleusX,
+          resolution: dx,
+        },
+        y: {
+          delta: 0,
+          nucleus: nucleusY,
+          resolution: dy,
+        },
+      };
+      let peaks2D: T[] = [];
+      let sumZ = 0;
+
+      for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
+        if (cluster[jPeak] === 1) {
+          peaks2D.push(peaks[jPeak]);
+          signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
+          signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
+          sumZ += peaks[jPeak].z;
+        }
+      }
+
+      signal.x.delta /= sumZ;
+      signal.y.delta /= sumZ;
+      signal.peaks = peaks2D;
+      signals.push(signal as NMRSignal2DWithID<T>);
+    }
+  }
+  return signals;
+}

package/src/xyz/xyzAutoZonesPicking.ts

@@ -1,33 +1,10 @@
-import { v4 as generateID } from '@lukeed/uuid';
-import { Matrix } from 'ml-matrix';
-import * as convolution from 'ml-matrix-convolution';
-import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
-import type { Peak2D } from 'ml-matrix-peaks-finder';
-import simpleClustering from 'ml-simple-clustering';
-
-import { addMissingIDs } from '../peaks/util/addMissingIDs';
-import { determineRealTop } from '../peaks/util/determineRealTop';
-import { getKernel } from '../peaks/util/getKernel';
+import { xyzAutoSignalsPicking } from '..';
 import type { GetKernelOptions } from '../peaks/util/getKernel';
-import * as PeakOptimizer from '../peaks/util/peakOptimizer';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 
-import type { NMRSignal2D } from './NMRSignal2D';
 import { NMRZone } from './NMRZone';
 import { formatZones } from './util/formatZone';
 
-const smallFilter = [
-  [0, 0, 1, 2, 2, 2, 1, 0, 0],
-  [0, 1, 4, 7, 7, 7, 4, 1, 0],
-  [1, 4, 5, 3, 0, 3, 5, 4, 1],
-  [2, 7, 3, -12, -23, -12, 3, 7, 2],
-  [2, 7, 0, -23, -40, -23, 0, 7, 2],
-  [2, 7, 3, -12, -23, -12, 3, 7, 2],
-  [1, 4, 5, 3, 0, 3, 5, 4, 1],
-  [0, 1, 3, 7, 7, 7, 3, 1, 0],
-  [0, 0, 1, 2, 2, 2, 1, 0, 0],
-];
-
 export interface Data2D {
   z: number[][] | Float64Array[];
   minX: number;
@@ -91,263 +68,12 @@ export interface XYZAutoZonesPickingOptions {
    */
   kernel?: GetKernelOptions;
 }
-
-export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
-  NMRSignal2D<T>,
-  'id'
->;
 export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
 
 export function xyzAutoZonesPicking(
   spectraData: Data2D,
   options: XYZAutoZonesPickingOptions,
 ): NMRZoneWithID[] {
-  let {
-    sizeToPad = 14,
-    realTopDetection = true,
-    thresholdFactor = 0.5,
-    nuclei = ['1H', '1H'],
-    observedFrequencies,
-    enhanceSymmetry = false,
-    clean = true,
-    maxPercentCutOff = 0.03,
-    tolerances = [24, 24],
-    convolutionByFFT = true,
-    kernel: kernelOptions,
-  } = options;
-
-  if (
-    !Array.isArray(observedFrequencies) &&
-    !ArrayBuffer.isView(observedFrequencies)
-  ) {
-    throw new Error('observedFrequencies is mandatory');
-  }
-
-  thresholdFactor = thresholdFactor === 0 ? 1 : Math.abs(thresholdFactor);
-
-  let nbPoints = spectraData.z[0].length;
-  let nbSubSpectra = spectraData.z.length;
-
-  if (nbSubSpectra < sizeToPad) {
-    spectraData = padData(spectraData, { width: sizeToPad });
-    nbPoints = spectraData.z[0].length;
-    nbSubSpectra = spectraData.z.length;
-  }
-
-  let absoluteData = new Float64Array(nbPoints * nbSubSpectra);
-  let originalData = new Float64Array(nbPoints * nbSubSpectra);
-
-  for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra; iSubSpectra++) {
-    let spectrum = spectraData.z[iSubSpectra];
-    for (let iCol = 0; iCol < nbPoints; iCol++) {
-      let index = iSubSpectra * nbPoints + iCol;
-      absoluteData[index] = Math.abs(spectrum[iCol]);
-      originalData[index] = spectrum[iCol]; //@todo pensar si se puede evitar originalData
-    }
-  }
-
-  const kernel = kernelOptions ? getKernel(kernelOptions) : smallFilter;
-
-  let convolutedSpectrum = convolutionByFFT
-    ? convolution.fft(absoluteData, kernel, {
-        rows: nbSubSpectra,
-        cols: nbPoints,
-      })
-    : convolution.direct(absoluteData, kernel, {
-        rows: nbSubSpectra,
-        cols: nbPoints,
-      });
-
-  let peaksMC1 = matrixPeakFinders.findPeaks2DRegion(absoluteData, {
-    originalData,
-    filteredData: convolutedSpectrum,
-    rows: nbSubSpectra,
-    cols: nbPoints,
-    nStdDev: thresholdFactor,
-  });
-
-  if (clean) {
-    // Remove peaks with less than x% of the intensity of the highest peak
-    peaksMC1 = PeakOptimizer.clean(peaksMC1, maxPercentCutOff);
-  }
-
-  let signals = createSignals2D(addMissingIDs(peaksMC1), {
-    nRows: nbSubSpectra,
-    nCols: nbPoints,
-    minX: spectraData.minX,
-    maxX: spectraData.maxX,
-    minY: spectraData.minY,
-    maxY: spectraData.maxY,
-    absoluteData,
-    originalData,
-    tolerances,
-    nuclei,
-    observedFrequencies,
-    realTopDetection,
-  });
-
-  if (enhanceSymmetry) {
-    signals = PeakOptimizer.enhanceSymmetry(signals);
-  }
-
+  const signals = xyzAutoSignalsPicking(spectraData, options);
   return formatZones(signals);
 }
-
-/**
- * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
- * of many 2D-peaks, and it has some additional information related to the NMR spectrum.
- * @private
- */
-
-export interface CreateSignals2DOptions {
-  nCols: number;
-  nRows: number;
-  absoluteData: number[] | Float64Array;
-  originalData: number[] | Float64Array;
-  observedFrequencies: number[] | Float64Array;
-  tolerances: number[];
-  nuclei: string[];
-  realTopDetection: boolean;
-  minY: number;
-  maxY: number;
-  minX: number;
-  maxX: number;
-}
-
-function createSignals2D<T extends Peak2D>(
-  peaks: T[],
-  options: CreateSignals2DOptions,
-) {
-  let {
-    nCols,
-    nRows,
-    absoluteData,
-    originalData,
-    observedFrequencies,
-    tolerances,
-    nuclei,
-    realTopDetection,
-    minY,
-    maxY,
-    minX,
-    maxX,
-  } = options;
-
-  let [nucleusX, nucleusY] = nuclei;
-  let [toleranceX, toleranceY] = tolerances;
-  let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
-
-  let dy = (maxY - minY) / (nRows - 1);
-  let dx = (maxX - minX) / (nCols - 1);
-
-  if (realTopDetection) {
-    peaks = determineRealTop(peaks, {
-      nCols,
-      absoluteData,
-      originalData,
-      minX,
-      maxX,
-      minY,
-      maxY,
-    });
-  }
-
-  for (let i = peaks.length - 1; i >= 0; i--) {
-    let { x, y } = peaks[i];
-    peaks[i].x = minX + dx * x;
-    peaks[i].y = minY + dy * y;
-    peaks[i].minX = minX + dx * peaks[i].minX;
-    peaks[i].minY = minY + dy * peaks[i].minY;
-    peaks[i].maxX = minX + dx * peaks[i].maxX;
-    peaks[i].maxY = minY + dy * peaks[i].maxY;
-
-    // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
-  }
-  // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
-  // array like form
-  let connectivity = [];
-  for (let i = 0; i < peaks.length; i++) {
-    for (let j = i; j < peaks.length; j++) {
-      if (
-        Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
-        Math.abs(peaks[i].y - peaks[j].y) * observeFrequencyY < toleranceY
-      ) {
-        // 24*24Hz We cannot distinguish peaks with less than 20 Hz of separation
-        connectivity.push(1);
-      } else {
-        connectivity.push(0);
-      }
-    }
-  }
-  let clusters = simpleClustering(connectivity);
-
-  let signals: NMRSignal2DWithID<T>[] = [];
-  if (clusters) {
-    for (const cluster of clusters) {
-      let signal: any = {
-        id: generateID(),
-        x: {
-          delta: 0,
-          nucleus: nucleusX,
-          resolution: dx,
-        },
-        y: {
-          delta: 0,
-          nucleus: nucleusY,
-          resolution: dy,
-        },
-      };
-      let peaks2D: T[] = [];
-      let sumZ = 0;
-
-      for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
-        if (cluster[jPeak] === 1) {
-          peaks2D.push(peaks[jPeak]);
-          signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
-          signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
-          sumZ += peaks[jPeak].z;
-        }
-      }
-
-      signal.x.delta /= sumZ;
-      signal.y.delta /= sumZ;
-      signal.peaks = peaks2D;
-      signals.push(signal as NMRSignal2DWithID<T>);
-    }
-  }
-  return signals;
-}
-
-function padData(spectraData: Data2D, options: { width: number }) {
-  let { minX, maxX, minY, maxY } = spectraData;
-
-  const width = options.width;
-
-  let nbPoints = spectraData.z[0].length;
-  let nbSubSpectra = spectraData.z.length;
-
-  let yInterval = (maxY - minY) / (nbSubSpectra - 1);
-  let xInterval = (maxX - minX) / (nbPoints - 1);
-
-  let yDiff = width - nbSubSpectra;
-  let xDiff = Math.max(width - nbPoints, 0);
-  if (xDiff % 2) xDiff++;
-  if (yDiff % 2) yDiff++;
-
-  let xOffset = xDiff / 2;
-  let yOffset = yDiff / 2;
-  let newMatrix = Matrix.zeros(nbSubSpectra + yDiff, nbPoints + xDiff);
-  for (let i = 0; i < nbSubSpectra; i++) {
-    for (let j = 0; j < nbPoints; j++) {
-      newMatrix.set(i + yOffset, j + xOffset, spectraData.z[i][j]);
-    }
-  }
-
-  return {
-    z: newMatrix.to2DArray(),
-    minX: minX - xOffset * xInterval,
-    maxX: maxX + xOffset * xInterval,
-    minY: minY - yOffset * yInterval,
-    maxY: maxY + yOffset * yInterval,
-  };
-}

package/lib/utilities/joinPatterns.d.ts

@@ -1 +0,0 @@
-export declare function joinPatterns(patterns: string[]): string;

package/lib/utilities/joinPatterns.js.map

@@ -1 +0,0 @@
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package/lib/utilities/splitPatterns.js.map

@@ -1 +0,0 @@
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package/lib-esm/utilities/joinPatterns.js.map

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package/lib-esm/utilities/splitPatterns.js.map

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