AffineCosts

java.lang.Object
- de.jstacs.algorithms.alignment.cost.AffineCosts

All Implemented Interfaces:

Costs, Storable
```
public class AffineCosts
extends Object
implements Costs
```
This class implements affine gap costs, i.e., the costs for starting a new gap are given by start, and the costs for elongating a gap by one position are given by elong. In this implementation, we may differentiate between the costs of opening an insert gap, i.e., a gap in the first string, and a delete gap, i.e., a gap in the second string.

Author:

Jan Grau, Jens Keilwagen

Constructor Summary

Constructors
Constructor and Description
`AffineCosts(double start, Costs c)` This constructor creates a new instance of cost using affine gap costs.
`AffineCosts(double startInsert, double startDelete, Costs c)` This constructor creates a new instance of cost using affine gap costs.
`AffineCosts(StringBuffer xml)` Restores `AffineCosts` object from its XML representation.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`getCostFor(Sequence s1, Sequence s2, int i, int j)` Returns the costs for the alignment of `s1(i)` and `s2(j)`.
`double`	`getDeleteCosts()` Returns the costs for a delete gap, i.e., a gap in the second string.
`double`	`getDeleteCostsFor(int length)` Returns the costs for a delete gap of length `length`.
`double`	`getElongateDeleteCosts()` Returns the costs for elongating a delete gap by one position.
`double`	`getElongateInsertCosts()` Returns the costs for elongating an insert gap by one position.
`double`	`getGapCostsFor(int length)` Returns the costs for a gap of length `length`.
`double`	`getInsertCosts()` Returns the costs for an insert gap, i.e., a gap in the first string.
`double`	`getInsertCostsFor(int length)` Returns the costs for an insert gap of length `length`.
`Costs`	`getInternalCosts()` Returns the internal costs (supplied as `c` to `AffineCosts(double, Costs)`) used for matches and mismatches.
`StringBuffer`	`toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

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

- Constructor Detail
  - AffineCosts
```
public AffineCosts(double start,
                   Costs c)
```
    This constructor creates a new instance of cost using affine gap costs. The costs for match, mismatch and gap elongation are defined by c, while the costs for a start of a gap are given by start.
    
    Parameters:
    
    start - the costs for starting a gap
    
    c - the cost for match, mismatch and gap elongation
  - AffineCosts
```
public AffineCosts(double startInsert,
                   double startDelete,
                   Costs c)
```
    This constructor creates a new instance of cost using affine gap costs. The costs for match, mismatch and gap elongation are defined by c, while the costs for a start of a gap are given by startInsert and startDelete, respectively.
    
    Parameters:
    
    startInsert - the costs for starting an insert gap
    
    startDelete - the costs for starting a delete gap
    
    c - the cost for match, mismatch and gap elongation
  - AffineCosts
```
public AffineCosts(StringBuffer xml)
            throws NonParsableException
```
    Restores AffineCosts object from its XML representation.
    
    Parameters:
    
    xml - the XML representation
    
    Throws:
    
    NonParsableException - if the XML could not be parsed
- Method Detail
  - toXML
```
public StringBuffer toXML()
```
    Description copied from interface: Storable
    
    This method returns an XML representation as StringBuffer of an instance of the implementing class.
    
    Specified by:
    
    toXML in interface Storable
    
    Returns:
    
    the XML representation
  - getInternalCosts
```
public Costs getInternalCosts()
```
    Returns the internal costs (supplied as c to AffineCosts(double, Costs)) used for matches and mismatches.
    
    Returns:
    
    the internal costs
  - getElongateInsertCosts
```
public double getElongateInsertCosts()
```
    Returns the costs for elongating an insert gap by one position.
    
    Returns:
    
    the corresponding costs
  - getElongateDeleteCosts
```
public double getElongateDeleteCosts()
```
    Returns the costs for elongating a delete gap by one position.
    
    Returns:
    
    the corresponding costs
  - getInsertCostsFor
```
public double getInsertCostsFor(int length)
```
    Returns the costs for an insert gap of length length.
    
    Parameters:
    
    length - the length of the gap
    
    Returns:
    
    the corresponding costs
  - getDeleteCostsFor
```
public double getDeleteCostsFor(int length)
```
    Returns the costs for a delete gap of length length.
    
    Parameters:
    
    length - the length of the gap
    
    Returns:
    
    the corresponding costs
  - getGapCostsFor
```
public double getGapCostsFor(int length)
```
    Returns the costs for a gap of length length.
    
    Parameters:
    
    length - the length of the gap
    
    Returns:
    
    the corresponding costs
  - getCostFor
```
public double getCostFor(Sequence s1,
                         Sequence s2,
                         int i,
                         int j)
```
    Description copied from interface: Costs
    
    Returns the costs for the alignment of s1(i) and s2(j).
    
    Specified by:
    
    getCostFor in interface Costs
    
    Parameters:
    
    s1 - the first sequence
    
    s2 - the second sequence
    
    i - the index in the first sequence
    
    j - the index in the second sequence
    
    Returns:
    
    the costs
    
    See Also:
    
    Sequence.discreteVal(int)
  - getInsertCosts
```
public double getInsertCosts()
```
    Description copied from interface: Costs
    
    Returns the costs for an insert gap, i.e., a gap in the first string.
    
    Specified by:
    
    getInsertCosts in interface Costs
    
    Returns:
    
    the costs for an insert gap
  - getDeleteCosts
```
public double getDeleteCosts()
```
    Description copied from interface: Costs
    
    Returns the costs for a delete gap, i.e., a gap in the second string.
    
    Specified by:
    
    getDeleteCosts in interface Costs
    
    Returns:
    
    the costs for a delete gap

Class AffineCosts

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AffineCosts

AffineCosts

AffineCosts

Method Detail

toXML

getInternalCosts

getElongateInsertCosts

getElongateDeleteCosts

getInsertCostsFor

getDeleteCostsFor

getGapCostsFor

getCostFor

getInsertCosts

getDeleteCosts