edu.umn.msi.tropix.proteomics.itraqquantitation.impl.ReportSummary.java Source code

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.itraqquantitation.impl;

import java.util.LinkedHashMap;
import java.util.List;

import org.testng.collections.Lists;

import com.google.common.collect.LinkedHashMultimap;
import com.google.common.collect.Maps;
import com.google.common.collect.Multimap;

import edu.umn.msi.tropix.proteomics.itraqquantitation.QuantitationOptions.GroupType;
import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.ReportEntry.CanSplitModifications;
import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.ReportEntry.SequenceWithModifications;

class ReportSummary {
    private final LinkedHashMap<String, GroupSummary> groupSummariesByLabel;
    private final LinkedHashMap<String, ProteinInformation> groupLabelProtein;
    private final int numGroups;
    private final GroupType groupType;

    public int getNumGroups() {
        return numGroups;
    }

    public Iterable<String> getGroups() {
        return groupSummariesByLabel.keySet();
    }

    public GroupType getGroupType() {
        return groupType;
    }

    public GroupSummary getGroupSummary(final String groupLabel) {
        return groupSummariesByLabel.get(groupLabel);
    }

    public ProteinInformation getProteinInformationForPeptideGroup(final String groupLabel) {
        return groupLabelProtein.get(groupLabel);
    }

    public ReportSummary(final Iterable<ITraqMatch> iTraqMatchs, final Iterable<ITraqLabel> labels,
            GroupType groupType) {
        final Multimap<String, ITraqMatch> groupMap = LinkedHashMultimap.create();
        groupLabelProtein = Maps.newLinkedHashMap();

        for (final ITraqMatch iTraqMatch : iTraqMatchs) {
            final ProteinInformation proteinInformation = iTraqMatch.getProteinInformation();
            List<String> groupLabels = Lists.newArrayList();
            if (groupType == GroupType.PROTEIN) {
                groupLabels.add(proteinInformation.getProteinAccession());
            } else if (groupType == GroupType.PEPTIDE) {
                groupLabels.add(iTraqMatch.getPeptideSequence());
            } else if (groupType == GroupType.PEPTIDE_WITH_MODIFICATIONS) {
                groupLabels.add(iTraqMatch.getModifiedPeptideSequence().toString());
            } else if (groupType == GroupType.PEPTIDE_WITH_UNIQUE_MODIFICATION) {
                SequenceWithModifications seqWithMods = iTraqMatch.getModifiedPeptideSequence();
                if (!(seqWithMods instanceof CanSplitModifications)) {
                    throw new IllegalArgumentException(
                            "Attempt to split modifications when operation unavailable for data source.");
                }
                final CanSplitModifications splittableSeqWithMods = (CanSplitModifications) seqWithMods;
                for (SequenceWithModifications seqWithOneMod : splittableSeqWithMods.splitupModifications()) {
                    groupLabels.add(seqWithOneMod.toString());
                }
            } else {
                throw new IllegalArgumentException("Unknown group type " + groupType);
            }
            for (final String groupLabel : groupLabels) {
                groupMap.put(groupLabel, iTraqMatch);
                if (!groupLabelProtein.containsKey(groupLabel)) {
                    groupLabelProtein.put(groupLabel, proteinInformation);
                }
            }
        }

        int numGroups = 0;
        groupSummariesByLabel = Maps.newLinkedHashMap();
        for (final String groupLabel : groupMap.keySet()) {
            final Iterable<ITraqMatch> groupDataEntries = groupMap.get(groupLabel);
            groupSummariesByLabel.put(groupLabel, new GroupSummary(groupDataEntries, labels));
            numGroups++;
        }

        this.numGroups = numGroups;
        this.groupType = groupType;
    }

}