AlignmentResult (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.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

Constructors
Constructor and Description

AlignmentResult()

Constructors
Constructor and Description
`AlignmentResult()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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

Class AlignmentResult

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AlignmentResult

Method Detail

toString

getAlignments

setAlignments

getPdb1

setPdb1

getPdb2

setPdb2

getChain1

setChain1

getChain2

setChain2

getLength1

setLength1

getLength2

setLength2

getCalculationTime

setCalculationTime

getIoTime

setIoTime

serialize

deserialize