net.sf.mzmine.datamodel.impl.MZmineToMSDKMsScan.java Source code

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Here is the source code for net.sf.mzmine.datamodel.impl.MZmineToMSDKMsScan.java

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/*
 * Copyright 2006-2015 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package net.sf.mzmine.datamodel.impl;

import java.util.ArrayList;
import java.util.List;

import com.google.common.collect.Range;

import io.github.msdk.datamodel.ActivationInfo;
import io.github.msdk.datamodel.IsolationInfo;
import io.github.msdk.datamodel.MsScan;
import io.github.msdk.datamodel.MsSpectrumType;
import io.github.msdk.datamodel.PolarityType;
import io.github.msdk.datamodel.RawDataFile;
import io.github.msdk.datamodel.SimpleIsolationInfo;
import io.github.msdk.util.tolerances.MzTolerance;
import net.sf.mzmine.datamodel.DataPoint;
import net.sf.mzmine.datamodel.Scan;

/**
 * Simple implementation of the Scan interface.
 */
public class MZmineToMSDKMsScan implements MsScan {

    private final Scan mzmineScan;
    private final List<IsolationInfo> isolations = new ArrayList<>();

    /**
     * Clone constructor
     */
    public MZmineToMSDKMsScan(Scan mzmineScan) {
        this.mzmineScan = mzmineScan;
        if (mzmineScan.getPrecursorMZ() != 0) {
            Range<Double> isolationMzRange = Range.singleton(mzmineScan.getPrecursorMZ());
            double precursorMz = mzmineScan.getPrecursorMZ();
            int precursorCharge = mzmineScan.getPrecursorCharge();
            ActivationInfo activationInfo = null;
            isolations.add(
                    new SimpleIsolationInfo(isolationMzRange, 0f, precursorMz, precursorCharge, activationInfo));
        }
    }

    @Override
    public MsSpectrumType getSpectrumType() {
        return MsSpectrumType.valueOf(mzmineScan.getSpectrumType().name());
    }

    @Override
    public Integer getNumberOfDataPoints() {
        return mzmineScan.getNumberOfDataPoints();
    }

    @Override
    public double[] getMzValues(double[] array) {
        if (array == null || array.length < mzmineScan.getNumberOfDataPoints())
            array = new double[mzmineScan.getNumberOfDataPoints()];
        DataPoint dp[] = mzmineScan.getDataPoints();
        for (int i = 0; i < mzmineScan.getNumberOfDataPoints(); i++) {
            array[i] = dp[i].getMZ();
        }
        return array;
    }

    @Override
    public float[] getIntensityValues(float[] array) {
        if (array == null || array.length < mzmineScan.getNumberOfDataPoints())
            array = new float[mzmineScan.getNumberOfDataPoints()];
        DataPoint dp[] = mzmineScan.getDataPoints();
        for (int i = 0; i < mzmineScan.getNumberOfDataPoints(); i++) {
            array[i] = (float) dp[i].getIntensity();
        }
        return array;
    }

    @Override
    public Float getTIC() {
        return (float) mzmineScan.getTIC();
    }

    @Override
    public Range<Double> getMzRange() {
        return mzmineScan.getDataPointMZRange();
    }

    @Override
    public MzTolerance getMzTolerance() {
        return null;
    }

    @Override
    public RawDataFile getRawDataFile() {
        return null;
    }

    @Override
    public Integer getScanNumber() {
        return mzmineScan.getScanNumber();
    }

    @Override
    public String getScanDefinition() {
        return mzmineScan.getScanDefinition();
    }

    @Override
    public String getMsFunction() {
        return "ms";
    }

    @Override
    public Integer getMsLevel() {
        return mzmineScan.getMSLevel();
    }

    @Override
    public Float getRetentionTime() {
        return (float) (mzmineScan.getRetentionTime() * 60d);
    }

    @Override
    public Range<Double> getScanningRange() {
        return mzmineScan.getScanningMZRange();
    }

    @Override
    public ActivationInfo getSourceInducedFragmentation() {
        return null;
    }

    @Override
    public List<IsolationInfo> getIsolations() {
        return isolations;
    }

    @Override
    public PolarityType getPolarity() {
        return PolarityType.valueOf(mzmineScan.getPolarity().name());
    }

    public Scan getMzmineScan() {
        return mzmineScan;
    }

}