io.github.msdk.featdet.targeteddetection.BuildingChromatogram.java Source code

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Here is the source code for io.github.msdk.featdet.targeteddetection.BuildingChromatogram.java

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/* 
 * (C) Copyright 2015-2016 by MSDK Development Team
 *
 * This software is dual-licensed under either
 *
 * (a) the terms of the GNU Lesser General Public License version 2.1
 * as published by the Free Software Foundation
 *
 * or (per the licensee's choosing)
 *
 * (b) the terms of the Eclipse Public License v1.0 as published by
 * the Eclipse Foundation.
 */

package io.github.msdk.featdet.targeteddetection;

import javax.annotation.Nonnull;

import com.google.common.collect.Range;

import io.github.msdk.datamodel.rawdata.ChromatographyInfo;

class BuildingChromatogram {

    // Initial variables
    private int size = 0;
    private ChromatographyInfo[] rtValues = new ChromatographyInfo[100];
    private double[] mzValues = new double[100];
    private float[] intensityValues = new float[100];

    void addDataPoint(@Nonnull ChromatographyInfo rt, @Nonnull Double mz, @Nonnull Float intensity) {

        // Make sure we have enough space to add a new data point
        if (size == mzValues.length) {
            allocate(size * 2);
        }

        // Add data point
        rtValues[size] = rt;
        mzValues[size] = mz;
        intensityValues[size] = intensity;
        size++;
    }

    ChromatographyInfo[] getRtValues() {
        return rtValues;
    }

    double[] getMzValues() {
        return mzValues;
    }

    float[] getIntensityValues() {
        return intensityValues;
    }

    /**
     * <p>
     * cropChromatogram.
     * </p>
     *
     * @param rtRange
     *            a {@link com.google.common.collect.Range} object.
     * @param intensityTolerance
     *            a {@link java.lang.Double} object.
     * @param noiseLevel
     *            a {@link java.lang.Double} object.
     */
    public void cropChromatogram(Range<Double> rtRange, Double intensityTolerance, Double noiseLevel) {

        // Find peak apex (= most intense data point which fulfill the criteria)
        Integer apexDataPoint = null;
        for (int i = 0; i < size; i++) {
            Float currentIntensity = intensityValues[i];
            Double currentRt = (double) rtValues[i].getRetentionTime();

            // Verify data point
            if ((apexDataPoint == null || currentIntensity > intensityValues[apexDataPoint])
                    && rtRange.contains(currentRt) && currentIntensity > noiseLevel) {
                apexDataPoint = i;
            }
        }

        if (apexDataPoint != null) {
            Integer startIndex = apexDataPoint, endIndex = apexDataPoint;

            // Find start data point
            for (int i = apexDataPoint - 1; i >= 0; i--) {

                // Verify the intensity is within the intensity tolerance
                if (intensityValues[i] > intensityValues[i + 1] * (1 + intensityTolerance)
                        || intensityValues[i + 1] == 0) {
                    break;
                }
                startIndex = i;
            }

            // Find end data point
            for (int i = apexDataPoint + 1; i < size; i++) {

                // Verify the intensity is within the intensity tolerance
                if (intensityValues[i] > intensityValues[i - 1] * (1 + intensityTolerance)
                        || intensityValues[i - 1] == 0) {
                    break;
                }
                endIndex = i;
            }

            // Shift the peakPoints
            int peakPoints = endIndex - startIndex + 1;
            System.arraycopy(rtValues, startIndex, rtValues, 0, peakPoints);
            System.arraycopy(mzValues, startIndex, mzValues, 0, peakPoints);
            System.arraycopy(intensityValues, startIndex, intensityValues, 0, peakPoints);
            size = peakPoints;

        }

    }

    /**
     * <p>
     * allocate.
     * </p>
     *
     * @param newSize
     *            a {@link java.lang.Integer} object.
     */
    public void allocate(int newSize) {

        if (mzValues.length >= newSize)
            return;

        ChromatographyInfo[] rtValuesNew = new ChromatographyInfo[newSize];
        double[] mzValuesNew = new double[newSize];
        float[] intensityValuesNew = new float[newSize];

        if (size > 0) {
            System.arraycopy(rtValues, 0, rtValuesNew, 0, size);
            System.arraycopy(mzValues, 0, mzValuesNew, 0, size);
            System.arraycopy(intensityValues, 0, intensityValuesNew, 0, size);
        }

        rtValues = rtValuesNew;
        mzValues = mzValuesNew;
        intensityValues = intensityValuesNew;
    }

    /**
     * <p>
     * Getter for the field <code>size</code>.
     * </p>
     *
     * @return a {@link java.lang.Integer} object.
     */
    public int getSize() {
        return size;
    }
}