EDIT

/**

 *

 */

package eu.etaxonomy.cdm.model.molecular;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.Lob;

import javax.persistence.ManyToOne;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.annotations.Type;

import org.hibernate.envers.Audited;

import eu.etaxonomy.cdm.model.common.VersionableEntity;

/**

 * @author a.mueller

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "SingleReadAlignment", propOrder = {

	"consensusAlignment",

	"singleRead",

	"shifts",

	"editedSequence",

	"reverseComplement",

	"firstSeqPosition",

	"leftCutPosition",

	"rightCutPosition"

})

@XmlRootElement(name = "SingleReadAlignment")

@Entity

@Audited

public class SingleReadAlignment extends VersionableEntity {

	private static final long serialVersionUID = 6141518347067279304L;

	/** @see #getDnaMarker() */

	@XmlElement(name = "ConsensusAlignment")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

	//for now we do not cascade but expect the user to save the sequence manually

	private Sequence consensusAlignment;

	/** @see #getDnaMarker() */

	@XmlElement(name = "SingleRead")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

	@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

	private SingleRead singleRead;

	//TODO XML mapping / user type

	@Type(type="shiftUserType")

    private Shift[] shifts = new Shift[0];

	private Integer firstSeqPosition;

	private Integer leftCutPosition;

	private Integer rightCutPosition;

	@XmlElement(name = "EditedSequence")

    @Lob

    private String editedSequence;

	@XmlElement(name = "ReverseComplement")

    private boolean reverseComplement;

	public static class Shift implements Cloneable{

		public int position;

		public int shift;

		public Shift(){};

		public Shift(int position, int steps) {

			this.position = position;

			this.shift = steps;

		}

		@Override

		public String toString(){

			return String.valueOf(position) + "," + String.valueOf(shift);

		}

		@Override

		protected Object clone() throws CloneNotSupportedException {

			return super.clone();

		}

	}

//****************** FACTORY *******************/

	public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead){

		return new SingleReadAlignment(consensusSequence, singleRead, null, null);

	}

	public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead,

			Shift[] shifts, String editedSequence){

		return new SingleReadAlignment(consensusSequence, singleRead, shifts, editedSequence);

	}

// ***************** CONSTRUCTOR *************************/

	protected SingleReadAlignment(){};

	private SingleReadAlignment(Sequence consensusAlignment, SingleRead singleRead,

			Shift[] shifts, String editedSequence){

		setConsensusAlignment(consensusAlignment);

		setSingleRead(singleRead);

		this.shifts = shifts;

		this.editedSequence = editedSequence;

	}

// ****************** GETTER / SETTER ***********************/

	//consensus sequence

	public Sequence getConsensusSequence() {

		return consensusAlignment;

	}

	public void setConsensusAlignment(Sequence consensusAlignment) {

		if (this.consensusAlignment != null && this.consensusAlignment.getSingleReadAlignments().contains(this)){

			this.consensusAlignment.removeSingleReadAlignment(this);

		}

		this.consensusAlignment = consensusAlignment;

		if (consensusAlignment != null && ! consensusAlignment.getSingleReadAlignments().contains(this)){

			consensusAlignment.addSingleReadAlignment(this);

		}

	}

	public SingleRead getSingleRead() {

		return singleRead;

	}

	public void setSingleRead(SingleRead singleRead) {

//		if (this.singleRead != null xxx){

//			this.singleRead.removeSingleReadAlignment(this);

//		}

		this.singleRead = singleRead;

//		if (singleRead != null && singleRead.getSingleReadAlignments().contains(this)){

//			singleRead.addSingleReadAlignment(this);

//		}

	}

	//shifts

	public Shift[] getShifts() {

		return shifts == null ? new Shift[0] : shifts;

	}

	public void setShifts(Shift[] shifts) {

		this.shifts = shifts;

		if (shifts == null){

			shifts = new Shift[0];

		}

	}

	//edited sequence

	public String getEditedSequence() {

		return editedSequence;

	}

	public void setEditedSequence(String editedSequence) {

		this.editedSequence = editedSequence;

	}

	public boolean isReverseComplement() {

		return reverseComplement;

	}

	public void setReverseComplement(boolean reverseComplement) {

		this.reverseComplement = reverseComplement;

	}

// ******************* CLONE *********************/

	@Override

	public Object clone() throws CloneNotSupportedException {

		SingleReadAlignment result = (SingleReadAlignment)super.clone();

		//deep copy shifts

		Shift[] oldShifts = this.getShifts();

		int shiftLength = oldShifts.length;

		Shift[] newShift = new Shift[shiftLength];

		for (int i = 0; i< shiftLength; i++){

			Shift oldShift = oldShifts[i];

			newShift[0] = (Shift)oldShift.clone();

		}

		//all other objects can be reused

		return result;

	}

    /**

     * Returns the position in the {@link Sequence sequence}

     * this {@link SingleReadAlignment single read align} is attached to

     * where the output of the visible part of the pherogram starts.

     * @return a valid index in the sequence carrying this data area

     * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/dataarea/implementations/pherogram/PherogramArea.html#getFirstSeqPos

     *

     */

    public Integer getFirstSeqPosition() {

        return firstSeqPosition;

    }

    /**

     * @see #getFirstSeqPosition()

     */

    public void setFirstSeqPosition(Integer firstSeqPosition) {

        this.firstSeqPosition = firstSeqPosition;

    }

    /**

     * Returns the first base call index of the pherogram which has not been cut off.

     * @return a base call index > 0

     * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getLeftCutPosition

     */

    public Integer getLeftCutPosition() {

        return leftCutPosition;

    }

    /**

     * @param see {@link #getLeftCutPosition()}

     */

    public void setLeftCutPosition(Integer leftCutPosition) {

        this.leftCutPosition = leftCutPosition;

    }

    /**

     * Returns the first base call index of the pherogram that has been cut off (so that the length of the visible

     * area of the pherogram can be calculated as getRightCutPosition()

     * @return a base call inde

     * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getRightCutPosition

     */

    public Integer getRightCutPosition() {

        return rightCutPosition;

    }

    /**

     * @param see {@link #getRightCutPosition()}

     */

    public void setRightCutPosition(Integer rightCutPosition) {

        this.rightCutPosition = rightCutPosition;

    }

}