net.sf.mzmine.util.RawDataFileUtils.java Source code

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Here is the source code for net.sf.mzmine.util.RawDataFileUtils.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.util;

import javax.annotation.Nonnull;

import net.sf.mzmine.datamodel.RawDataFile;
import net.sf.mzmine.datamodel.Scan;

import com.google.common.collect.Range;

/**
 * Raw data file related utilities
 */
public class RawDataFileUtils {

    public static @Nonnull Range<Double> findTotalRTRange(RawDataFile dataFiles[], int msLevel) {
        Range<Double> rtRange = null;
        for (RawDataFile file : dataFiles) {
            Range<Double> dfRange = file.getDataRTRange(msLevel);
            if (dfRange == null)
                continue;
            if (rtRange == null)
                rtRange = dfRange;
            else
                rtRange = rtRange.span(dfRange);
        }
        if (rtRange == null)
            rtRange = Range.singleton(0.0);
        return rtRange;
    }

    public static @Nonnull Range<Double> findTotalMZRange(RawDataFile dataFiles[], int msLevel) {
        Range<Double> mzRange = null;
        for (RawDataFile file : dataFiles) {
            Range<Double> dfRange = file.getDataMZRange(msLevel);
            if (dfRange == null)
                continue;
            if (mzRange == null)
                mzRange = dfRange;
            else
                mzRange = mzRange.span(dfRange);
        }
        if (mzRange == null)
            mzRange = Range.singleton(0.0);
        return mzRange;
    }

    /**
     * Returns true if the given data file has mass lists for all MS1 scans
     * 
     */
    public static boolean hasMassLists(RawDataFile dataFile) {
        for (int scanNum : dataFile.getScanNumbers(1)) {
            Scan scan = dataFile.getScan(scanNum);
            if (scan.getMassLists().length == 0)
                return false;
        }
        return true;
    }

}