Java tutorial
/* * 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.modules.masslistmethods.chromatogrambuilder; import java.util.Arrays; import java.util.Iterator; import java.util.LinkedHashSet; import java.util.Set; import com.google.common.collect.Range; import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance; import net.sf.mzmine.util.DataPointSorter; import net.sf.mzmine.util.SortingDirection; import net.sf.mzmine.util.SortingProperty; public class HighestDataPointConnector { private final MZTolerance mzTolerance; private final double minimumTimeSpan, minimumHeight; private final RawDataFile dataFile; private final int allScanNumbers[]; // Mapping of last data point m/z --> chromatogram private Set<Chromatogram> buildingChromatograms; public HighestDataPointConnector(RawDataFile dataFile, int allScanNumbers[], double minimumTimeSpan, double minimumHeight, MZTolerance mzTolerance) { this.mzTolerance = mzTolerance; this.minimumHeight = minimumHeight; this.minimumTimeSpan = minimumTimeSpan; this.dataFile = dataFile; this.allScanNumbers = allScanNumbers; // We use LinkedHashSet to maintain a reproducible ordering. If we use // plain HashSet, the resulting peak list row IDs will have different // order every time the method is invoked. buildingChromatograms = new LinkedHashSet<Chromatogram>(); } public void addScan(int scanNumber, DataPoint mzValues[]) { // Sort m/z peaks by descending intensity Arrays.sort(mzValues, new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending)); // Set of already connected chromatograms in each iteration Set<Chromatogram> connectedChromatograms = new LinkedHashSet<Chromatogram>(); // TODO: these two nested cycles should be optimized for speed for (DataPoint mzPeak : mzValues) { // Search for best chromatogram, which has highest last data point Chromatogram bestChromatogram = null; for (Chromatogram testChrom : buildingChromatograms) { DataPoint lastMzPeak = testChrom.getLastMzPeak(); Range<Double> toleranceRange = mzTolerance.getToleranceRange(lastMzPeak.getMZ()); if (toleranceRange.contains(mzPeak.getMZ())) { if ((bestChromatogram == null) || (testChrom.getLastMzPeak().getIntensity() > bestChromatogram .getLastMzPeak().getIntensity())) { bestChromatogram = testChrom; } } } // If we found best chromatogram, check if it is already connected. // In such case, we may discard this mass and continue. If we // haven't found a chromatogram, we may create a new one. if (bestChromatogram != null) { if (connectedChromatograms.contains(bestChromatogram)) { continue; } } else { bestChromatogram = new Chromatogram(dataFile, allScanNumbers); } // Add this mzPeak to the chromatogram bestChromatogram.addMzPeak(scanNumber, mzPeak); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(bestChromatogram); } // Process those chromatograms which were not connected to any m/z peak for (Chromatogram testChrom : buildingChromatograms) { // Skip those which were connected if (connectedChromatograms.contains(testChrom)) { continue; } // Check if we just finished a long-enough segment if (testChrom.getBuildingSegmentLength() >= minimumTimeSpan) { testChrom.commitBuildingSegment(); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(testChrom); continue; } // Check if we have any committed segments in the chromatogram if (testChrom.getNumberOfCommittedSegments() > 0) { testChrom.removeBuildingSegment(); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(testChrom); continue; } } // All remaining chromatograms in buildingChromatograms are discarded // and buildingChromatograms is replaced with connectedChromatograms buildingChromatograms = connectedChromatograms; } public Chromatogram[] finishChromatograms() { // Iterate through current chromatograms and remove those which do not // contain any committed segment nor long-enough building segment Iterator<Chromatogram> chromIterator = buildingChromatograms.iterator(); while (chromIterator.hasNext()) { Chromatogram chromatogram = chromIterator.next(); if (chromatogram.getBuildingSegmentLength() >= minimumTimeSpan) { chromatogram.commitBuildingSegment(); chromatogram.finishChromatogram(); } else { if (chromatogram.getNumberOfCommittedSegments() == 0) { chromIterator.remove(); continue; } else { chromatogram.removeBuildingSegment(); chromatogram.finishChromatogram(); } } // Remove chromatograms smaller then minimum height if (chromatogram.getHeight() < minimumHeight) chromIterator.remove(); } // All remaining chromatograms are good, so we can return them Chromatogram[] chromatograms = buildingChromatograms.toArray(new Chromatogram[0]); return chromatograms; } }