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java.lang.Objectorg.biojava.bio.alignment.SequenceAlignment
org.biojava.bio.alignment.NeedlemanWunsch
public class NeedlemanWunsch
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.
Field Summary | |
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protected 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 alignment |
protected SubstitutionMatrix |
subMatrix
A matrix with the size length(alphabet) times length(alphabet) |
Constructor Summary | |
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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 | |
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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. |
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(String align)
prints the alignment String on the screen (standard output). |
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.SequenceAlignment |
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formatOutput |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected int[][] CostMatrix
protected SubstitutionMatrix subMatrix
protected Alignment pairalign
protected String alignment
Constructor Detail |
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public NeedlemanWunsch(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix subMat)
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 |
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public void setSubstitutionMatrix(SubstitutionMatrix matrix)
matrix
- an instance of a substitution matrix.public void setInsert(short ins)
ins
- costs for a single insert operationpublic void setDelete(short del)
del
- costs for a single deletion operationpublic void setGapExt(short ge)
ge
- costs for any gap extensionpublic void setMatch(short ma)
ma
- costs for a single match operationpublic void setReplace(short rep)
rep
- costs for a single replace operationpublic short getInsert()
public short getDelete()
public short getGapExt()
public short getMatch()
public short getReplace()
public static String printCostMatrix(int[][] CostMatrix, char[] queryChar, char[] targetChar)
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.
public static void printAlignment(String align)
align
- The parameter is typically given by the
getAlignmentString()
method.public Alignment getAlignment(SymbolList query, SymbolList target) throws Exception
pairwiseAlignment
and
returns an Alignment
instance containing the two aligned
sequences.
getAlignment
in class SequenceAlignment
Exception
public int getEditDistance()
int myDistanceValue = foo; this.CostMatrix = new int[1][1]; this.CostMatrix[0][0] = myDistanceValue;
protected static int min(int x, int y, int z)
x
- y
- z
-
public String getAlignmentString() throws BioException
getAlignmentString
in class SequenceAlignment
BioException
public List<Alignment> alignAll(SequenceIterator source, SequenceDB subjectDB) throws NoSuchElementException, BioException
alignAll
in class SequenceAlignment
source
- a SequenceIterator containing a set of sequences to be aligned
withsubjectDB
- the SequenceDB containing another set of sequences.
NoSuchElementException
BioException
public int pairwiseAlignment(SymbolList query, SymbolList subject) throws BioRuntimeException
pairwiseAlignment
in class SequenceAlignment
BioRuntimeException
SequenceAlignment.pairwiseAlignment(org.biojava.bio.symbol.SymbolList,
org.biojava.bio.symbol.SymbolList)
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