MSUmpire.DIA.DIAMapClusterUnit.java Source code

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Here is the source code for MSUmpire.DIA.DIAMapClusterUnit.java

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/* 
 * Author: Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 *             Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics, 
 *             University of Michigan, Ann Arbor
 *
 * Copyright 2014 University of Michigan, Ann Arbor, MI
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package MSUmpire.DIA;

import MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2;
import MSUmpire.LCMSPeakStructure.LCMSPeakMS1;
import MSUmpire.PSMDataStructure.PSM;
import MSUmpire.PSMDataStructure.PepIonID;
import MSUmpire.PeakDataStructure.PeakCluster;
import java.util.ArrayList;
import java.util.HashMap;
import org.apache.commons.io.FilenameUtils;
import org.apache.log4j.Logger;

/**
 * Thread unit for assigning MS1 peak cluster and matched MS2 fragment peak for identified peptide ion
 * @author Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 */
public class DIAMapClusterUnit implements Runnable {

    PepIonID pepIonID;
    HashMap<Integer, Integer> ScanClusterMap_Q1;
    HashMap<Integer, Integer> ScanClusterMap_Q2;
    HashMap<Integer, String> ScanClusterMap_Q3;
    String Q1Name;
    String Q2Name;
    String Q3Name;
    LCMSPeakMS1 ms1lcms;
    LCMSPeakDIAMS2 DIAWindow;

    public DIAMapClusterUnit(PepIonID pepIonID, String Q1Name, String Q2Name, String Q3Name,
            HashMap<Integer, Integer> ScanClusterMap_Q1, HashMap<Integer, Integer> ScanClusterMap_Q2,
            HashMap<Integer, String> ScanClusterMap_Q3, LCMSPeakMS1 ms1lcms, LCMSPeakDIAMS2 DIAWindow) {
        this.pepIonID = pepIonID;
        this.ScanClusterMap_Q1 = ScanClusterMap_Q1;
        this.ScanClusterMap_Q2 = ScanClusterMap_Q2;
        this.ScanClusterMap_Q3 = ScanClusterMap_Q3;
        this.Q1Name = Q1Name;
        this.Q2Name = Q2Name;
        this.Q3Name = Q3Name;
        this.ms1lcms = ms1lcms;
        this.DIAWindow = DIAWindow;
    }

    @Override
    public void run() {
        //For each identified PSM
        for (PSM psm : pepIonID.GetPSMList()) {
            int ClusterIndex = -1;
            if (psm.GetRawNameString() == null ? Q1Name == null
                    : psm.GetRawNameString().equals(FilenameUtils.getBaseName(Q1Name))) {
                if (!ScanClusterMap_Q1.containsKey(psm.ScanNo)) {
                    Logger.getRootLogger().error("ScanClusterMapping error");
                    Logger.getRootLogger()
                            .error("ScanClusterMapping " + Q1Name + " doesn't have " + psm.SpecNumber);
                    System.exit(3);
                }
                //Get cluster index fro Q1
                ClusterIndex = ScanClusterMap_Q1.get(psm.ScanNo);
                PeakCluster Cluster = ms1lcms.PeakClusters.get(ClusterIndex - 1);
                Cluster.Identified = true;
                if (!pepIonID.MS1PeakClusters.contains(Cluster)) {
                    pepIonID.MS1PeakClusters.add(Cluster);
                }
            } else if (psm.GetRawNameString() == null ? Q2Name == null
                    : psm.GetRawNameString().equals(FilenameUtils.getBaseName(Q2Name))) {
                if (!ScanClusterMap_Q2.containsKey(psm.ScanNo)) {
                    Logger.getRootLogger().error("ScanClusterMapping error");
                    Logger.getRootLogger()
                            .error("ScanClusterMapping " + Q2Name + " doesn't have " + psm.SpecNumber);
                    System.exit(3);
                }

                //Get cluster index fro Q2
                ClusterIndex = ScanClusterMap_Q2.get(psm.ScanNo);
                PeakCluster Cluster = ms1lcms.PeakClusters.get(ClusterIndex - 1);
                Cluster.Identified = true;
                if (!pepIonID.MS1PeakClusters.contains(Cluster)) {
                    pepIonID.MS1PeakClusters.add(Cluster);
                }
            } else if (psm.GetRawNameString() == null ? Q3Name == null
                    : psm.GetRawNameString().equals(FilenameUtils.getBaseName(Q3Name))) {
                String WindowClusterIndex = ScanClusterMap_Q3.get(psm.ScanNo);
                if (!ScanClusterMap_Q3.containsKey(psm.ScanNo)) {
                    Logger.getRootLogger().error("ScanClusterMapping error");
                    Logger.getRootLogger()
                            .error("ScanClusterMapping " + Q3Name + " doesn't have " + psm.SpecNumber);
                    System.exit(3);
                }
                if (WindowClusterIndex.split(";").length == 2) {
                    String windowname = WindowClusterIndex.split(";")[0];
                    if (windowname.equals(DIAWindow.WindowID)) {
                        //Get cluster index fro Q3
                        ClusterIndex = Integer.parseInt(WindowClusterIndex.split(";")[1]);
                        PeakCluster Cluster = DIAWindow.PeakClusters.get(ClusterIndex - 1);
                        Cluster.Identified = true;
                        pepIonID.MS2UnfragPeakClusters.add(Cluster);
                        ArrayList<PeakCluster> ms1list = ms1lcms.FindPeakClustersByMassRTRange(
                                Cluster.NeutralMass(), Cluster.Charge, Cluster.startRT, Cluster.endRT);
                        for (PeakCluster ms1cluster : ms1list) {
                            ms1cluster.Identified = true;
                            if (!pepIonID.MS1PeakClusters.contains(ms1cluster)) {
                                pepIonID.MS1PeakClusters.add(ms1cluster);
                            }
                        }
                    }
                } else {
                    //Get cluster index fro Q3
                    ClusterIndex = Integer.parseInt(WindowClusterIndex);
                    if (DIAWindow.UnFragIonClu2Cur.containsKey(ClusterIndex)) {
                        PeakCluster Cluster = DIAWindow.PeakClusters.get(ClusterIndex - 1);
                        if (Cluster.Charge == psm.Charge
                                && Math.abs(Cluster.TargetMz() - psm.ObserPrecursorMz()) < 0.01f
                                && Math.abs(Cluster.PeakHeightRT[0] - psm.RetentionTime) < 0.1f) {
                            Cluster.Identified = true;
                            pepIonID.MS2UnfragPeakClusters.add(Cluster);
                        }
                        ArrayList<PeakCluster> ms1list = ms1lcms.FindPeakClustersByMassRTRange(
                                Cluster.NeutralMass(), Cluster.Charge, Cluster.startRT, Cluster.endRT);
                        for (PeakCluster ms1cluster : ms1list) {
                            ms1cluster.Identified = true;
                            if (!pepIonID.MS1PeakClusters.contains(ms1cluster)) {
                                pepIonID.MS1PeakClusters.add(ms1cluster);
                            }
                        }
                    }
                }
            }
        }

        if (pepIonID.MS1PeakClusters.isEmpty() && pepIonID.MS2UnfragPeakClusters.isEmpty()) {
            Logger.getRootLogger().trace("Cannot find feature for identified peptide ion : " + pepIonID.GetKey()
                    + " mz: " + pepIonID.ObservedMz + " in isolation window " + DIAWindow.WindowID);
        }
    }

}