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java.lang.Object blinAlignment.PairwiseAlignment
public class PairwiseAlignment
Constructor Summary | |
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PairwiseAlignment(double match,
double replace,
double insert,
double delete,
double 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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PairwiseAlignment(org.biojava.bio.symbol.FiniteAlphabet alpha,
double match,
double replace,
double insert,
double delete,
double gapExtend)
Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm. |
Method Summary | |
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void |
align(org.biojava.bio.seq.Sequence source,
org.biojava.bio.seq.Sequence target)
Computes the alignment of source and target. |
org.biojava.bio.symbol.Alignment |
getAlignment()
Returns the current alignment |
java.lang.String |
getAlignmentString()
Gives a human readable representation of the alignment. |
double |
getDelete()
Returns the current expenses of a single delete operation. |
double |
getEditDistance()
Returns the score of the current alignment. |
double |
getGapExt()
Returns the current expenses of any extension of a gap operation. |
double |
getInsert()
Returns the current expenses of a single insert operation. |
double |
getMatch()
Returns the current expenses of a single match operation. |
double |
getReplace()
Returns the current expenses of a single replace operation. |
org.biojava.bio.seq.Sequence |
getSource()
Returns the current source sequence of the alignment. |
org.biojava.bio.seq.Sequence |
getTarget()
Returns the current target sequence of the alignment. |
java.lang.String |
printCostMatrix()
Prints a String representation of the current CostMatrix. |
void |
setDelete(double del)
Sets the penalty for a delete operation to the specified value. |
void |
setGapExt(double ge)
Sets the penalty for an extension of any gap (insert or delete) to the specified value. |
void |
setInsert(double ins)
Sets the penalty for an insert operation to the specified value. |
void |
setMatch(double ma)
Sets the penalty for a match operation to the specified value. |
void |
setReplace(double 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 java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PairwiseAlignment(double match, double replace, double insert, double delete, double 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.public PairwiseAlignment(org.biojava.bio.symbol.FiniteAlphabet alpha, double match, double replace, double insert, double delete, double gapExtend)
alpha
- The alphabet of sequencesmatch
- This gives the costs for any match operationreplace
- This gives the costs for any replace operationinsert
- The costs of a single insert operation.delete
- The expenses of a single delete operationgapExtend
- 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 memoryMethod Detail |
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public void setSubstitutionMatrix(SubstitutionMatrix matrix)
matrix
- an instance of a substitution matrix.public void setInsert(double ins)
ins
- costs for a single insert operationpublic void setDelete(double del)
del
- costs for a single deletion operationpublic void setGapExt(double ge)
ge
- costs for any gap extensionpublic void setMatch(double ma)
ma
- costs for a single match operationpublic void setReplace(double rep)
rep
- costs for a single replace operationpublic double getInsert()
public double getDelete()
public double getGapExt()
public double getMatch()
public double getReplace()
public org.biojava.bio.seq.Sequence getSource()
public org.biojava.bio.seq.Sequence getTarget()
public java.lang.String printCostMatrix()
public void align(org.biojava.bio.seq.Sequence source, org.biojava.bio.seq.Sequence target)
source
- The source sequence to be alignedtarget
- The target onepublic org.biojava.bio.symbol.Alignment getAlignment()
public double getEditDistance()
public java.lang.String getAlignmentString() throws org.biojava.bio.BioException
org.biojava.bio.BioException
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