java.lang.Object
- org.biojava.bio.alignment.AlignmentAlgorithm
- - org.biojava.bio.alignment.NeedlemanWunsch

```
public class NeedlemanWunsch
extends AlignmentAlgorithm
```
Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence. This class is able to perform such global sequence comparisons efficiently by dynamic programming. If inserts and deletes are equally expensive and as expensive as the extension of a gap, the alignment method of this class does not use affine gap penalties. Otherwise it does. Those costs need four times as much memory, which has significant effects on the run time, if the computer needs to swap.

Since:

1.5

Author:

Andreas Dräger, Gero Greiner, Mark Schreiber

Field Summary

Fields
Modifier and Type	Field	Description
`protected int[][]`	`CostMatrix`	A matrix with the size length(sequence1) times length(sequence2)
`protected SubstitutionMatrix`	`subMatrix`	A matrix with the size length(alphabet) times length(alphabet)

Constructor Summary

Constructors
Constructor	Description
`NeedlemanWunsch(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix subMat)`	Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`short`	`getDelete()`	Returns the current expenses of a single delete operation.
`int`	`getEditDistance()`	This gives the edit distance according to the given parameters of this certain object.
`short`	`getGapExt()`	Returns the current expenses of any extension of a gap operation.
`short`	`getInsert()`	Returns the current expenses of a single insert operation.
`short`	`getMatch()`	Returns the current expenses of a single match operation.
`short`	`getReplace()`	Returns the current expenses of a single replace operation.
`protected static int`	`min(int x, int y, int z)`	This just computes the minimum of three integer values.
`AlignmentPair`	`pairwiseAlignment(SymbolList query, SymbolList subject)`	Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
`static String`	`printCostMatrix(int[][] CostMatrix, char[] queryChar, char[] targetChar)`	Prints a String representation of the CostMatrix for the given Alignment on the screen.
`void`	`setDelete(short del)`	Sets the penalty for a delete operation to the specified value.
`void`	`setGapExt(short ge)`	Sets the penalty for an extension of any gap (insert or delete) to the specified value.
`void`	`setInsert(short ins)`	Sets the penalty for an insert operation to the specified value.
`void`	`setMatch(short ma)`	Sets the penalty for a match operation to the specified value.
`void`	`setReplace(short rep)`	Sets the penalty for a replace operation to the specified value.
`void`	`setSubstitutionMatrix(SubstitutionMatrix matrix)`	Sets the substitution matrix to be used to the specified one.

Methods inherited from class org.biojava.bio.alignment.AlignmentAlgorithm
alignAll

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

- Field Detail
  - CostMatrix
```
protected int[][] CostMatrix
```
    A matrix with the size length(sequence1) times length(sequence2)
  - subMatrix
```
protected SubstitutionMatrix subMatrix
```
    A matrix with the size length(alphabet) times length(alphabet)
- Constructor Detail
  - NeedlemanWunsch
```
public NeedlemanWunsch(short match,
                       short replace,
                       short insert,
                       short delete,
                       short gapExtend,
                       SubstitutionMatrix subMat)
```
    Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
    
    Parameters:
    
    match - This gives the costs for a match operation. It is only used, if there is no entry for a certain match of two symbols in the substitution matrix (default value).
    
    replace - This is like the match parameter just the default, if there is no entry in the substitution matrix object.
    
    insert - The costs of a single insert operation.
    
    delete - The expenses of a single delete operation.
    
    gapExtend - The expenses of an extension of a existing gap (that is a previous insert or delete. If the costs for insert and delete are equal and also equal to gapExtend, no affine gap penalties will be used, which saves a significant amount of memory.
    
    subMat - The substitution matrix object which gives the costs for matches and replaces.
- Method Detail
  - min
```
protected static int min(int x,
                         int y,
                         int z)
```
    This just computes the minimum of three integer values.
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
    
    Gives the minimum of three integers
  - printCostMatrix
```
public static String printCostMatrix(int[][] CostMatrix,
                                     char[] queryChar,
                                     char[] targetChar)
```
    Prints a String representation of the CostMatrix for the given Alignment on the screen. This can be used to get a better understanding of the algorithm. There is no other purpose. This method also works for all extensions of this class with all kinds of matrices.
    
    Parameters:
    
    CostMatrix - The matrix that contains all expenses for swapping symbols.
    
    queryChar - a character representation of the query sequence ( mySequence.seqString().toCharArray()).
    
    targetChar - a character representation of the target sequence.
    
    Returns:
    
    a String representation of the matrix.
  - getDelete
```
public short getDelete()
```
    Returns the current expenses of a single delete operation.
    
    Returns:
    
    delete
  - getEditDistance
```
public int getEditDistance()
```
    This gives the edit distance according to the given parameters of this certain object. It returns just the last element of the internal cost matrix (left side down). So if you extend this class, you can just do the following: int myDistanceValue = foo; this.CostMatrix = new int[1][1]; this.CostMatrix[0][0] = myDistanceValue;
    
    Returns:
    
    returns the edit_distance computed with the given parameters.
  - getGapExt
```
public short getGapExt()
```
    Returns the current expenses of any extension of a gap operation.
    
    Returns:
    
    gapExt
  - getInsert
```
public short getInsert()
```
    Returns the current expenses of a single insert operation.
    
    Returns:
    
    insert
  - getMatch
```
public short getMatch()
```
    Returns the current expenses of a single match operation.
    
    Returns:
    
    match
  - getReplace
```
public short getReplace()
```
    Returns the current expenses of a single replace operation.
    
    Returns:
    
    replace
  - pairwiseAlignment
```
public AlignmentPair pairwiseAlignment(SymbolList query,
                                       SymbolList subject)
                                throws BioException
```
    Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
    
    Specified by:
    
    pairwiseAlignment in class AlignmentAlgorithm
    
    Returns:
    
    score of the alignment or the distance.
    
    Throws:
    
    BioException
    
    See Also:
    
    AlignmentAlgorithm.pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)
  - setDelete
```
public void setDelete(short del)
```
    Sets the penalty for a delete operation to the specified value.
    
    Parameters:
    
    del - costs for a single deletion operation
  - setGapExt
```
public void setGapExt(short ge)
```
    Sets the penalty for an extension of any gap (insert or delete) to the specified value.
    
    Parameters:
    
    ge - costs for any gap extension
  - setInsert
```
public void setInsert(short ins)
```
    Sets the penalty for an insert operation to the specified value.
    
    Parameters:
    
    ins - costs for a single insert operation
  - setMatch
```
public void setMatch(short ma)
```
    Sets the penalty for a match operation to the specified value.
    
    Parameters:
    
    ma - costs for a single match operation
  - setReplace
```
public void setReplace(short rep)
```
    Sets the penalty for a replace operation to the specified value.
    
    Parameters:
    
    rep - costs for a single replace operation
  - setSubstitutionMatrix
```
public void setSubstitutionMatrix(SubstitutionMatrix matrix)
```
    Sets the substitution matrix to be used to the specified one. Afterwards it is only possible to align sequences of the alphabet of this substitution matrix.
    
    Parameters:
    
    matrix - an instance of a substitution matrix.

Class NeedlemanWunsch

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.biojava.bio.alignment.AlignmentAlgorithm

Methods inherited from class java.lang.Object

Field Detail

CostMatrix

subMatrix

Constructor Detail

NeedlemanWunsch

Method Detail

min

printCostMatrix

getDelete

getEditDistance

getGapExt

getInsert

getMatch

getReplace

pairwiseAlignment

setDelete

setGapExt

setInsert

setMatch

setReplace

setSubstitutionMatrix