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

java.lang.Object
  extended by org.biojava.bio.structure.align.pairwise.AlignmentResult
All Implemented Interfaces:
Serializable

public class AlignmentResult
extends Object
implements 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(File output)
           
 AlternativeAlignment[] getAlignments()
           
 long getCalculationTime()
           
 String getChain1()
           
 String getChain2()
           
 long getIoTime()
           
 int getLength1()
           
 int getLength2()
           
 String getPdb1()
           
 String getPdb2()
           
 void serialize(File output)
           
 void setAlignments(AlternativeAlignment[] alignments)
          we only keep the first alternative...
 void setCalculationTime(long calculationTime)
           
 void setChain1(String chain1)
           
 void setChain2(String chain2)
           
 void setIoTime(long ioTime)
           
 void setLength1(int length1)
           
 void setLength2(int length2)
           
 void setPdb1(String pdb1)
           
 void setPdb2(String pdb2)
           
 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 String toString()
Overrides:
toString in class Object

getAlignments

public AlternativeAlignment[] getAlignments()

setAlignments

public void setAlignments(AlternativeAlignment[] alignments)
we only keep the first alternative...

Parameters:
alignments -

getPdb1

public String getPdb1()

setPdb1

public void setPdb1(String pdb1)

getPdb2

public String getPdb2()

setPdb2

public void setPdb2(String pdb2)

getChain1

public String getChain1()

setChain1

public void setChain1(String chain1)

getChain2

public String getChain2()

setChain2

public void setChain2(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(File output)
               throws FileNotFoundException,
                      IOException
Throws:
FileNotFoundException
IOException

deserialize

public static AlignmentResult deserialize(File output)
                                   throws FileNotFoundException,
                                          IOException,
                                          ClassNotFoundException
Throws:
FileNotFoundException
IOException
ClassNotFoundException