io.github.msdk.datamodel.impl.SimpleChromatogram.java Source code

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Here is the source code for io.github.msdk.datamodel.impl.SimpleChromatogram.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.datamodel.impl;

import java.util.LinkedList;
import java.util.List;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import com.google.common.base.Preconditions;
import com.google.common.collect.Range;

import io.github.msdk.datamodel.chromatograms.Chromatogram;
import io.github.msdk.datamodel.chromatograms.ChromatogramType;
import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.ionannotations.IonAnnotation;
import io.github.msdk.datamodel.rawdata.ChromatographyInfo;
import io.github.msdk.datamodel.rawdata.IsolationInfo;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.msdk.datamodel.rawdata.SeparationType;

/**
 * Simple implementation of the Chromatogram interface.
 */
class SimpleChromatogram implements Chromatogram {

    private @Nonnull DataPointStore dataPointStore;
    private @Nullable RawDataFile dataFile;
    private @Nonnull Integer chromatogramNumber, numOfDataPoints;
    private @Nonnull ChromatogramType chromatogramType;
    private @Nullable Double mz;
    private @Nonnull SeparationType separationType;
    private Object dataStoreRtId = null, dataStoreIntensityId = null, dataStoreMzId = null;
    private @Nullable IonAnnotation ionAnnotation;
    private Range<ChromatographyInfo> rtRange;

    private final @Nonnull List<IsolationInfo> isolations = new LinkedList<>();

    /**
     * <p>
     * Constructor for SimpleChromatogram.
     * </p>
     *
     * @param dataPointStore
     *            a {@link io.github.msdk.datamodel.datastore.DataPointStore}
     *            object.
     * @param chromatogramNumber
     *            a {@link java.lang.Integer} object.
     * @param chromatogramType
     *            a
     *            {@link io.github.msdk.datamodel.chromatograms.ChromatogramType}
     *            object.
     * @param separationType
     *            a {@link io.github.msdk.datamodel.rawdata.SeparationType}
     *            object.
     */
    public SimpleChromatogram(@Nonnull DataPointStore dataPointStore, @Nonnull Integer chromatogramNumber,
            @Nonnull ChromatogramType chromatogramType, @Nonnull SeparationType separationType) {
        Preconditions.checkNotNull(chromatogramNumber);
        this.dataPointStore = dataPointStore;
        this.chromatogramNumber = chromatogramNumber;
        this.chromatogramType = chromatogramType;
        this.separationType = separationType;
        this.numOfDataPoints = 0;
    }

    /** {@inheritDoc} */
    @Override
    @Nullable
    public RawDataFile getRawDataFile() {
        return dataFile;
    }

    /** {@inheritDoc} */
    @Override
    public void setRawDataFile(@Nonnull RawDataFile newRawDataFile) {
        this.dataFile = newRawDataFile;
    }

    /** {@inheritDoc} */
    @Override
    @Nonnull
    public Integer getChromatogramNumber() {
        return chromatogramNumber;
    }

    /** {@inheritDoc} */
    @Override
    public void setChromatogramNumber(@Nonnull Integer chromatogramNumber) {
        this.chromatogramNumber = chromatogramNumber;
    }

    /** {@inheritDoc} */
    @Override
    @Nonnull
    public ChromatogramType getChromatogramType() {
        return chromatogramType;
    }

    /** {@inheritDoc} */
    @Override
    public void setChromatogramType(@Nonnull ChromatogramType newChromatogramType) {
        this.chromatogramType = newChromatogramType;
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull Integer getNumberOfDataPoints() {
        return numOfDataPoints;
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull ChromatographyInfo[] getRetentionTimes() {
        return getRetentionTimes(null);
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull ChromatographyInfo[] getRetentionTimes(@Nullable ChromatographyInfo[] array) {
        if ((array == null) || (array.length < numOfDataPoints))
            array = new ChromatographyInfo[numOfDataPoints];
        dataPointStore.loadData(dataStoreRtId, array);
        return array;
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull double[] getMzValues() {
        return getMzValues(null);
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull double[] getMzValues(@Nullable double array[]) {
        if ((array == null) || (array.length < numOfDataPoints))
            array = new double[numOfDataPoints];
        dataPointStore.loadData(dataStoreMzId, array);
        return array;
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull float[] getIntensityValues() {
        return getIntensityValues(null);
    }

    /** {@inheritDoc} */
    @Override
    public @Nonnull float[] getIntensityValues(@Nullable float array[]) {
        if ((array == null) || (array.length < numOfDataPoints))
            array = new float[numOfDataPoints];
        dataPointStore.loadData(dataStoreIntensityId, array);
        return array;
    }

    /** {@inheritDoc} */
    @Override
    public synchronized void setDataPoints(@Nonnull ChromatographyInfo rtValues[], @Nullable double mzValues[],
            @Nonnull float intensityValues[], @Nonnull Integer size) {

        if (dataStoreRtId != null)
            dataPointStore.removeData(dataStoreRtId);
        if (dataStoreMzId != null)
            dataPointStore.removeData(dataStoreMzId);
        if (dataStoreIntensityId != null)
            dataPointStore.removeData(dataStoreIntensityId);

        dataStoreRtId = dataPointStore.storeData(rtValues, size);
        if (mzValues != null)
            dataStoreMzId = dataPointStore.storeData(mzValues, size);
        else
            dataStoreMzId = null;
        dataStoreIntensityId = dataPointStore.storeData(intensityValues, size);
        this.numOfDataPoints = size;

        if (size > 0)
            this.rtRange = Range.closed(rtValues[0], rtValues[size - 1]);
        else
            this.rtRange = null;
    }

    /** {@inheritDoc} */
    @Override
    @Nonnull
    public List<IsolationInfo> getIsolations() {
        return isolations;
    }

    /** {@inheritDoc} */
    @Override
    @Nonnull
    public SeparationType getSeparationType() {
        return separationType;
    }

    /** {@inheritDoc} */
    @Override
    public void setSeparationType(@Nonnull SeparationType separationType) {
        this.separationType = separationType;
    }

    /** {@inheritDoc} */
    @Override
    @Nullable
    public Double getMz() {
        return mz;
    }

    /** {@inheritDoc} */
    @Override
    public void setMz(@Nullable Double newMz) {
        this.mz = newMz;
    }

    /** {@inheritDoc} */
    @Override
    public void setIonAnnotation(@Nonnull IonAnnotation ionAnnotation) {
        this.ionAnnotation = ionAnnotation;
    }

    /** {@inheritDoc} */
    @Override
    public IonAnnotation getIonAnnotation() {
        return ionAnnotation;
    }

    /** {@inheritDoc} */
    @Override
    @Nullable
    public Range<ChromatographyInfo> getRtRange() {
        return rtRange;
    }

}