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The protein structure modules of BioJava.
There is a newer version: 7.2.2
/*
 *                    PDB web development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 *
 * Created on May 24, 2009
 * Created by Andreas Prlic
 *
 */

package org.biojava.nbio.structure.align.pairwise;

import java.io.*;

/** A class to track the alignment results in a flat file
 *
 * @author andreas
 *
 */
public class AlignmentResult implements Serializable
{

	/**
	 *
	 */
	private static final long serialVersionUID = -4132105905712445473L;
	AlternativeAlignment[] alignments;
	String pdb1;
	String pdb2;

	String chain1;
	String chain2;

	int length1;
	int length2;

	long calculationTime;
	long ioTime;

	@Override
public String toString(){
		StringBuffer buf = new StringBuffer();
		buf.append(pdb1);
		buf.append("_");
		buf.append(chain1);
		buf.append(" vs. ");
		buf.append(pdb2);
		buf.append("_");
		buf.append(chain2);
		buf.append(" : ");
		buf.append(" l1: ");
		buf.append(length1);
		buf.append(" l2: ");
		buf.append(length2);
		buf.append(" ");
		if ( alignments != null)
			if ( alignments.length > 0) {
				AlternativeAlignment a = alignments[0];
				buf.append(a.toString());
				int eqr = a.getEqr();
				buf.append(" %res1: ");
				buf.append(Math.round((eqr/(float)length2)*100));
				buf.append(" %res2: ");
				buf.append(Math.round((eqr/(float)length1)*100));
				buf.append(" ");

			}
		buf.append(" ioTime: ");
		buf.append(ioTime);
		buf.append(" compTime: ");
		buf.append(calculationTime);
		return buf.toString();

	}

	public AlternativeAlignment[] getAlignments()
	{
		return alignments;
	}

	/** we only keep the first alternative...
	 *
	 * @param alignments
	 */
	public void setAlignments(AlternativeAlignment[] alignments)
	{
		if ( alignments.length > 0){
			this.alignments = new AlternativeAlignment[1];
			this.alignments[0]=alignments[0];
		}

	}
	public String getPdb1()
	{
		return pdb1;
	}
	public void setPdb1(String pdb1)
	{
		this.pdb1 = pdb1;
	}
	public String getPdb2()
	{
		return pdb2;
	}
	public void setPdb2(String pdb2)
	{
		this.pdb2 = pdb2;
	}
	public String getChain1()
	{
		return chain1;
	}
	public void setChain1(String chain1)
	{
		this.chain1 = chain1;
	}
	public String getChain2()
	{
		return chain2;
	}
	public void setChain2(String chain2)
	{
		this.chain2 = chain2;
	}
	public int getLength1()
	{
		return length1;
	}
	public void setLength1(int length1)
	{
		this.length1 = length1;
	}
	public int getLength2()
	{
		return length2;
	}
	public void setLength2(int length2)
	{
		this.length2 = length2;
	}


	public long getCalculationTime()
	{
		return calculationTime;
	}
	public void setCalculationTime(long calculationTime)
	{
		this.calculationTime = calculationTime;
	}
	public long getIoTime()
	{
		return ioTime;
	}
	public void setIoTime(long ioTime)
	{
		this.ioTime = ioTime;
	}
	public void serialize (File output)
	throws FileNotFoundException, IOException{
		// save alignment result:

		FileOutputStream outStream = new FileOutputStream(output);
		ObjectOutputStream objStream = new ObjectOutputStream(outStream);
		objStream.writeObject(this);
		objStream.close();

	}

	public static AlignmentResult deserialize(File output)
	throws FileNotFoundException, IOException, ClassNotFoundException{
		FileInputStream fin = new FileInputStream(output);
		ObjectInputStream objIn = new ObjectInputStream(fin);
		AlignmentResult result = (AlignmentResult) objIn.readObject();
		objIn.close();
		return result;
	}


}