Package org.biojava.bio.alignment
Class NeedlemanWunsch
- java.lang.Object
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- org.biojava.bio.alignment.SequenceAlignment
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- org.biojava.bio.alignment.NeedlemanWunsch
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- Direct Known Subclasses:
SmithWaterman
public class NeedlemanWunsch extends SequenceAlignment
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
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
alignment
The result of a successful alignment as a simple String.protected int[][]
CostMatrix
A matrix with the size length(sequence1) times length(sequence2)protected Alignment
pairalign
The result of a successful alignmentprotected SubstitutionMatrix
subMatrix
A matrix with the size length(alphabet) times length(alphabet)
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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.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<Alignment>
alignAll(SequenceIterator source, SequenceDB subjectDB)
Alignment
getAlignment(SymbolList query, SymbolList target)
This method is good if one wants to reuse the alignment calculated by this class in another BioJava class.java.lang.String
getAlignmentString()
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.int
pairwiseAlignment(SymbolList query, SymbolList subject)
Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.static void
printAlignment(java.lang.String align)
prints the alignment String on the screen (standard output).static java.lang.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.SequenceAlignment
formatOutput
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Field Detail
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CostMatrix
protected int[][] CostMatrix
A matrix with the size length(sequence1) times length(sequence2)
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subMatrix
protected SubstitutionMatrix subMatrix
A matrix with the size length(alphabet) times length(alphabet)
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pairalign
protected Alignment pairalign
The result of a successful alignment
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alignment
protected java.lang.String alignment
The result of a successful alignment as a simple String.
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Constructor Detail
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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.
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Method Detail
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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.
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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
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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
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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
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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
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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
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getInsert
public short getInsert()
Returns the current expenses of a single insert operation.- Returns:
- insert
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getDelete
public short getDelete()
Returns the current expenses of a single delete operation.- Returns:
- delete
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getGapExt
public short getGapExt()
Returns the current expenses of any extension of a gap operation.- Returns:
- gapExt
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getMatch
public short getMatch()
Returns the current expenses of a single match operation.- Returns:
- match
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getReplace
public short getReplace()
Returns the current expenses of a single replace operation.- Returns:
- replace
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printCostMatrix
public static java.lang.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.
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printAlignment
public static void printAlignment(java.lang.String align)
prints the alignment String on the screen (standard output).- Parameters:
align
- The parameter is typically given by thegetAlignmentString()
method.
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getAlignment
public Alignment getAlignment(SymbolList query, SymbolList target) throws java.lang.Exception
This method is good if one wants to reuse the alignment calculated by this class in another BioJava class. It just performspairwiseAlignment
and returns anAlignment
instance containing the two aligned sequences.- Specified by:
getAlignment
in classSequenceAlignment
- Returns:
- Alignment object containing the two gapped sequences constructed from query and target.
- Throws:
java.lang.Exception
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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.
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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
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getAlignmentString
public java.lang.String getAlignmentString() throws BioException
- Specified by:
getAlignmentString
in classSequenceAlignment
- Returns:
- a string representation of the alignment
- Throws:
BioException
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alignAll
public java.util.List<Alignment> alignAll(SequenceIterator source, SequenceDB subjectDB) throws java.util.NoSuchElementException, BioException
- Specified by:
alignAll
in classSequenceAlignment
- Parameters:
source
- a SequenceIterator containing a set of sequences to be aligned withsubjectDB
- the SequenceDB containing another set of sequences.- Returns:
- a list containing the results of all single alignments performed by this method.
- Throws:
java.util.NoSuchElementException
BioException
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pairwiseAlignment
public int pairwiseAlignment(SymbolList query, SymbolList subject) throws BioRuntimeException
Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.- Specified by:
pairwiseAlignment
in classSequenceAlignment
- Returns:
- score of the alignment or the distance.
- Throws:
BioRuntimeException
- See Also:
SequenceAlignment.pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)
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