net.sf.bioutils.proteomics.sample.SampleBean Maven / Gradle / Ivy

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Lightweight framework for handling biological and bioinformatical data related to proteomics.
There is a newer version: 3.1.6
package net.sf.bioutils.proteomics.sample;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.locks.ReadWriteLock;
import java.util.concurrent.locks.ReentrantReadWriteLock;

import net.sf.bioutils.proteomics.User;
import net.sf.bioutils.proteomics.peak.Peak;
import net.sf.kerner.utils.collections.UtilCollection;
import net.sf.kerner.utils.collections.map.MapList;

public class SampleBean implements SampleModifiable {

    protected final ReadWriteLock lock = new ReentrantReadWriteLock();

    private MapList properties = new MapList();

    private String name;

    private String nameBase;

    private User user;

    private List peaks = new ArrayList();

    public SampleBean() {
        this(null, null, null, null, null);
    }

    public SampleBean(final Sample template) {
        this(template.getName(), template.getUser(), template.getNameBase(), template.getPeaks(),
                template.getProperties());
    }

    public SampleBean(final Sample template, final String newName) {
        this(newName, template.getUser(), template.getNameBase(), template.getPeaks(), template
                .getProperties());
    }

    public SampleBean(final Sample template, final String newName, final boolean empty) {
        this(newName, template.getUser(), template.getNameBase(), null, template.getProperties());
        if (!empty) {
            setPeaks(template.getPeaks());
        }
    }

    public SampleBean(final String name) {
        this(name, null, null, null, null);
    }

    public SampleBean(final String name, final Collection peaks) {
        this(name, null, null, peaks, null);
    }

    public SampleBean(final String name, final User user, final String baseName) {
        this(name, user, baseName, null, null);
    }

    public SampleBean(final String name, final User user, final String baseName,
            final Collection peaks, final MapList properties) {
        if (properties != null)
            this.properties.putAll(properties);
        this.name = name;
        nameBase = baseName;
        this.user = user;
        if (UtilCollection.notNullNotEmpty(peaks))
            this.peaks = new ArrayList(peaks);
    }

    @Override
    public void addPeak(final Peak peak) {
        synchronized (this) {
            peaks.add(peak);
            peak.setSample(this);
        }
    }

    @Override
    public void addPeaks(final Collection peaks) {
        this.peaks.addAll(peaks);
        for (final Peak p : peaks) {
            p.setSample(this);
        }
    }

    @Override
    public SampleBean clone() {
        return clone(getName());
    }

    @Override
    public SampleBean clone(final String newName) {
        final SampleBean result = new SampleBean(newName, getUser(), getNameBase(), null,
                getProperties());
        for (final Peak p : getPeaks()) {
            // if (p instanceof PeakAnnotatable && !((PeakAnnotatable)
            // p).getAnnotation().isEmpty()) {
            // final int i = 0;
            // }
            result.addPeak(p.clone());
        }
        return result;
    }

    /**
     * Clones this {@code SampleBean} without peaks.
     *
     * @return a clone of this {@code SampleBean}, that contains no peaks
     */
    @Override
    public SampleBean cloneWOPeaks(final String newName) {
        final SampleBean result = new SampleBean(newName, getUser(), getNameBase(), null,
                getProperties());
        return result;
    }

    @Override
    public boolean equals(final Object obj) {
        return new EqualatorSample().areEqual(this, obj);
    }

    @Override
    public ReadWriteLock getLock() {
        return lock;
    }

    @Override
    public String getName() {
        return name;
    }

    @Override
    public String getNameBase() {
        if (nameBase == null)
            return getName();
        return nameBase;
    }

    @Override
    public List getPeaks() {
        return peaks;
    }

    @Override
    public MapList getProperties() {
        return properties;
    }

    @Override
    public int getSize() {
        return peaks.size();
    }

    @Override
    public User getUser() {
        return user;
    }

    @Override
    public int hashCode() {
        return new HashCalculatorSample().calculateHash(this);
    }

    @Override
    public void removePeak(final Peak peak) {
        peaks.remove(peak);

    }

    @Override
    public void removePeaks(final Collection peaks) {
        this.peaks.removeAll(peaks);

    }

    @Override
    public void setName(final String name) {
        this.name = name;
    }

    @Override
    public void setNameBase(final String nameBase) {
        this.nameBase = nameBase;
    }

    @Override
    public void setPeaks(final List peaks) {
        synchronized (this) {
            for (final Peak p : peaks) {
                addPeak(p);
            }
        }
    }

    @Override
    public void setProperties(final MapList properties) {
        this.properties = properties;
    }

    @Override
    public void setUser(final User user) {
        this.user = user;
    }

    @Override
    public String toString() {
        return getName() + ", " + getSize();
    }

}