ExonDTO.java

package org.molgenis.mutation.dto;

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

public class ExonDTO implements Comparable<ExonDTO>, Serializable
{
	/* The serial version UID of this class. Needed for serialization. */
	private static final long serialVersionUID = 419557906940623900L;
	private Integer id;
	private String name;
	private Boolean isIntron;
	private Integer length;
	private Integer cdnaStart;
	private Integer cdnaEnd;
	private Integer gdnaStart;
	private Integer gdnaEnd;
	private List<Integer> domainId;
	private List<String> domainName;
	private String orientation;
	private Integer numFullAminoAcids;
	private Integer numPartAminoAcids;
	private Integer numGlyXYRepeats;
	private Boolean multiple3Nucl;
	private String nuclSequenceFlankLeft;
	private String nuclSequenceFlankRight;
	private String nuclSequence;
	private String aaSequence;

	public ExonDTO()
	{
		this.init();
	}

	private void init()
	{
		this.id = 0;
		this.name = "";
		this.isIntron = false;
		this.length = 0;
		this.cdnaStart = 0;
		this.cdnaEnd = 0;
		this.gdnaStart = 0;
		this.gdnaEnd = 0;
		this.domainId = new ArrayList<Integer>();
		this.domainName = new ArrayList<String>();
		this.orientation = "F";
		this.numFullAminoAcids = 0;
		this.numPartAminoAcids = 0;
		this.numGlyXYRepeats = 0;
		this.multiple3Nucl = false;
		this.nuclSequenceFlankLeft = "";
		this.nuclSequenceFlankRight = "";
		this.nuclSequence = "";
		this.aaSequence = "";
	}

	public Integer getId()
	{
		return id;
	}

	public void setId(Integer id)
	{
		this.id = id;
	}

	public String getName()
	{
		return name;
	}

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

	public Boolean getIsIntron()
	{
		return isIntron;
	}

	public void setIsIntron(Boolean isIntron)
	{
		this.isIntron = isIntron;
	}

	public Integer getLength()
	{
		return length;
	}

	public void setLength(Integer length)
	{
		this.length = length;
	}

	public Integer getCdnaStart()
	{
		return cdnaStart;
	}

	public void setCdnaStart(Integer cdnaStart)
	{
		this.cdnaStart = cdnaStart;
	}

	public Integer getCdnaEnd()
	{
		return cdnaEnd;
	}

	public void setCdnaEnd(Integer cdnaEnd)
	{
		this.cdnaEnd = cdnaEnd;
	}

	public Integer getGdnaStart()
	{
		return gdnaStart;
	}

	public void setGdnaStart(Integer gdnaStart)
	{
		this.gdnaStart = gdnaStart;
	}

	public Integer getGdnaEnd()
	{
		return gdnaEnd;
	}

	public void setGdnaEnd(Integer gdnaEnd)
	{
		this.gdnaEnd = gdnaEnd;
	}

	public List<Integer> getDomainId()
	{
		return domainId;
	}

	public void setDomainId(List<Integer> domainId)
	{
		this.domainId = domainId;
	}

	public List<String> getDomainName()
	{
		return domainName;
	}

	public void setDomainName(List<String> domainName)
	{
		this.domainName = domainName;
	}

	public String getOrientation()
	{
		return orientation;
	}

	public void setOrientation(String orientation)
	{
		this.orientation = orientation;
	}

	public Integer getNumFullAminoAcids()
	{
		return numFullAminoAcids;
	}

	public void setNumFullAminoAcids(Integer numFullAminoAcids)
	{
		this.numFullAminoAcids = numFullAminoAcids;
	}

	public Integer getNumPartAminoAcids()
	{
		return numPartAminoAcids;
	}

	public void setNumPartAminoAcids(Integer numPartAminoAcids)
	{
		this.numPartAminoAcids = numPartAminoAcids;
	}

	public Integer getNumGlyXYRepeats()
	{
		return numGlyXYRepeats;
	}

	public void setNumGlyXYRepeats(Integer numGlyXYRepeats)
	{
		this.numGlyXYRepeats = numGlyXYRepeats;
	}

	public Boolean getMultiple3Nucl()
	{
		return multiple3Nucl;
	}

	public void setMultiple3Nucl(Boolean multiple3Nucl)
	{
		this.multiple3Nucl = multiple3Nucl;
	}

	public String getNuclSequenceFlankLeft()
	{
		return nuclSequenceFlankLeft;
	}

	public void setNuclSequenceFlankLeft(String nuclSequenceFlankLeft)
	{
		this.nuclSequenceFlankLeft = nuclSequenceFlankLeft;
	}

	public String getNuclSequenceFlankRight()
	{
		return nuclSequenceFlankRight;
	}

	public void setNuclSequenceFlankRight(String nuclSequenceFlankRight)
	{
		this.nuclSequenceFlankRight = nuclSequenceFlankRight;
	}

	public String getNuclSequence()
	{
		return nuclSequence;
	}

	public void setNuclSequence(String nuclSequence)
	{
		this.nuclSequence = nuclSequence;
	}

	public String getAaSequence()
	{
		return aaSequence;
	}

	public void setAaSequence(String aaSequence)
	{
		this.aaSequence = aaSequence;
	}

	@Override
	public int compareTo(ExonDTO exonDTO)
	{
		if ("F".equals(this.orientation))
		{
			return this.getGdnaStart().compareTo(exonDTO.getGdnaStart());
		}
		else
		{
			return -1 * this.getGdnaEnd().compareTo(exonDTO.getGdnaEnd());
		}
	}
}