MZmineProject.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 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 3 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 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.project;

import java.io.File;
import java.util.ArrayList;
import java.util.List;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import com.google.common.collect.ImmutableList;

import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.datamodel.featuretables.Sample;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.mzmine.project.auditlog.AuditLogEntry;

/**
 * Simple implementation of the MZmineProject interface.
 */
public class MZmineProject {

  private @Nullable File projectFile;

  private final List<RawDataFile> rawDataFiles = new ArrayList<>();
  private final List<FeatureTable> featureTables = new ArrayList<>();
  private final List<AuditLogEntry> auditLog = new ArrayList<>();

  @Nullable
  public File getProjectFile() {
    return projectFile;
  }

  public void setProjectFile(@Nullable File projectFile) {
    this.projectFile = projectFile;
  }

  @Nonnull
  public List<Sample> getSamples() {
    final ArrayList<Sample> allSamples = new ArrayList<>();
    synchronized (featureTables) {
      for (FeatureTable peakList : featureTables) {
        for (Sample s : peakList.getSamples()) {
          if (!allSamples.contains(s))
            allSamples.add(s);
        }
      }
    }
    return ImmutableList.copyOf(allSamples);
  }

  public void addFile(final RawDataFile rawDataFile) {
    synchronized (rawDataFiles) {
      rawDataFiles.add(rawDataFile);
    }
  }

  public void removeFile(final RawDataFile rawDataFile) {
    synchronized (rawDataFiles) {
      rawDataFiles.remove(rawDataFile);
    }
  }

  public @Nonnull List<RawDataFile> getRawDataFiles() {
    synchronized (rawDataFiles) {
      return ImmutableList.copyOf(rawDataFiles);
    }
  }

  public void addFeatureTable(final FeatureTable featureTable) {
    synchronized (featureTables) {
      featureTables.add(featureTable);
    }
  }

  public void removeFeatureTable(final FeatureTable featureTable) {
    synchronized (featureTables) {
      featureTables.remove(featureTable);
    }
  }

  public @Nonnull List<FeatureTable> getFeatureTables() {
    synchronized (featureTables) {
      return ImmutableList.copyOf(featureTables);
    }
  }

  public void logProcessingStep(final AuditLogEntry auditLog) {
    synchronized (auditLog) {
      if (auditLog != null)
        this.auditLog.add(auditLog);
    }
  }

  public @Nonnull List<AuditLogEntry> getAuditLog() {
    synchronized (auditLog) {
      return ImmutableList.copyOf(auditLog);
    }
  }

}