org.biojava.bio.structure.align.pairwise
Class AlignmentResult

java.lang.Object
  org.biojava.bio.structure.align.pairwise.AlignmentResult

All Implemented Interfaces:

java.io.Serializable

public class AlignmentResult
extends java.lang.Object
implements java.io.Serializable

A class to track the alignment results in a flat file

Author:

andreas

See Also:

Serialized Form

Constructor Summary

AlignmentResult()

Method Summary

static AlignmentResult	deserialize(java.io.File output)
AlternativeAlignment[]	getAlignments()
long	getCalculationTime()
java.lang.String	getChain1()
java.lang.String	getChain2()
long	getIoTime()
int	getLength1()
int	getLength2()
java.lang.String	getPdb1()
java.lang.String	getPdb2()
void	serialize(java.io.File output)
void	setAlignments(AlternativeAlignment[] alignments) we only keep the first alternative...
void	setCalculationTime(long calculationTime)
void	setChain1(java.lang.String chain1)
void	setChain2(java.lang.String chain2)
void	setIoTime(long ioTime)
void	setLength1(int length1)
void	setLength2(int length2)
void	setPdb1(java.lang.String pdb1)
void	setPdb2(java.lang.String pdb2)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AlignmentResult

public AlignmentResult()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAlignments

public AlternativeAlignment[] getAlignments()

setAlignments

public void setAlignments(AlternativeAlignment[] alignments)

we only keep the first alternative...

Parameters:

alignments -

getPdb1

public java.lang.String getPdb1()

setPdb1

public void setPdb1(java.lang.String pdb1)

getPdb2

public java.lang.String getPdb2()

setPdb2

public void setPdb2(java.lang.String pdb2)

getChain1

public java.lang.String getChain1()

setChain1

public void setChain1(java.lang.String chain1)

getChain2

public java.lang.String getChain2()

setChain2

public void setChain2(java.lang.String chain2)

getLength1

public int getLength1()

setLength1

public void setLength1(int length1)

getLength2

public int getLength2()

setLength2

public void setLength2(int length2)

getCalculationTime

public long getCalculationTime()

setCalculationTime

public void setCalculationTime(long calculationTime)

getIoTime

public long getIoTime()

setIoTime

public void setIoTime(long ioTime)

serialize

public void serialize(java.io.File output)
               throws java.io.FileNotFoundException,
                      java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

deserialize

public static AlignmentResult deserialize(java.io.File output)
                                   throws java.io.FileNotFoundException,
                                          java.io.IOException,
                                          java.lang.ClassNotFoundException

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException