NeedlemanWunschOverlap (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.align.NeedlemanWunschOverlap

```
public class NeedlemanWunschOverlap
extends java.lang.Object
```
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)

Author:

pcingola

Constructor Summary

Constructors
Constructor Description

NeedlemanWunschOverlap(java.lang.String a, java.lang.String b)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`align()`
`java.lang.String`	`calcAlignment()`
`int`	`calcAlignmentScore()`	Calculate score matrix
`int`	`getAligmentScore()`
`java.lang.String`	`getAlignment()`
`void`	`setDeletion(int deletion)`
`void`	`setMatch(int match)`
`void`	`setMissMatch(int missMatch)`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

NeedlemanWunschOverlap

public NeedlemanWunschOverlap(java.lang.String a,
                              java.lang.String b)

Method Detail

align
```
public java.lang.String align()
```

calcAlignment

public java.lang.String calcAlignment()

calcAlignmentScore
```
public int calcAlignmentScore()
```
Calculate score matrix

getAligmentScore
```
public int getAligmentScore()
```

getAlignment

public java.lang.String getAlignment()

setDeletion

public void setDeletion(int deletion)

setMatch
```
public void setMatch(int match)
```

setMissMatch

public void setMissMatch(int missMatch)

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object