/* * Copyright 2006-2018 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; import io.github.msdk.util.RawDataFileUtil; /** * 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; } public static int getClosestScanNumber(RawDataFile dataFile, double rt) { int scanNums[] = dataFile.getScanNumbers(); if (scanNums.length == 0) return -1; int best = 0; double bestRt = dataFile.getScan(scanNums[0]).getRetentionTime(); for (int i = 1; i < scanNums.length; i++) { double thisRt = dataFile.getScan(scanNums[i]).getRetentionTime(); if (Math.abs(bestRt - rt) > Math.abs(thisRt - rt)) { best = i; bestRt = thisRt; } } return scanNums[best]; } }