SimpleSubstitutionMatrix

java.lang.Object
- org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix<C>

Type Parameters:

C - each element of the matrix corresponds to a pair of Compounds of type C

All Implemented Interfaces:

java.io.Serializable, SubstitutionMatrix<C>
```
public class SimpleSubstitutionMatrix<C extends Compound>
extends java.lang.Object
implements SubstitutionMatrix<C>, java.io.Serializable
```
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

Author:

Mark Chapman, Daniel Cameron, Paolo Pavan

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, java.io.File fileInput)` Creates a substitution matrix by reading in a file.
`SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, java.io.Reader input, java.lang.String name)` Creates a substitution matrix by parsing some input.
`SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short replace)` Creates an identity substitution matrix from match and replace values.
`SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, java.lang.String matrixInput, java.lang.String name)` Creates a substitution matrix by parsing a String.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static SubstitutionMatrix<AminoAcidCompound>`	`getBlosum62()`
`java.util.Map<C,java.lang.Short>`	`getColumn(C column)`
`CompoundSet<C>`	`getCompoundSet()` Returns the `CompoundSet` on which the matrix is defined.
`java.lang.String`	`getDescription()` Returns the description of this matrix.
`short[][]`	`getMatrix()` Returns entire matrix.
`java.lang.String`	`getMatrixAsString()` Returns this matrix as a formatted String with `Compound` labels along the axes.
`short`	`getMaxValue()` Returns the maximum value in this matrix.
`short`	`getMinValue()` Returns the minimum value in this matrix.
`java.lang.String`	`getName()` Returns the name (short description) of this matrix.
`java.util.Map<C,java.lang.Short>`	`getRow(C row)`
`short`	`getValue(C from, C to)` Returns value in matrix for conversion from first `Compound` to the second.
`SubstitutionMatrix<C>`	`normalizeMatrix(short scale)` Rescales the matrix so that to `SubstitutionMatrix.getMaxValue()` - `SubstitutionMatrix.getMinValue()` = scale.
`void`	`setDescription(java.lang.String description)` Sets the description of this matrix.
`void`	`setName(java.lang.String name)` Sets the name (short description) of this matrix.
`java.lang.String`	`toString()` Returns in a format similar to the standard NCBI files.

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

- Constructor Detail
  - SimpleSubstitutionMatrix
```
public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
                                java.io.File fileInput)
                         throws java.io.FileNotFoundException
```
    Creates a substitution matrix by reading in a file.
    
    Parameters:
    
    compoundSet - the CompoundSet on which the matrix is defined
    
    fileInput - file parsed for a substitution matrix
    
    Throws:
    
    java.io.FileNotFoundException - if fileInput parameter cannot be read
  - SimpleSubstitutionMatrix
```
public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
                                java.io.Reader input,
                                java.lang.String name)
```
    Creates a substitution matrix by parsing some input.
    
    Parameters:
    
    compoundSet - the CompoundSet on which the matrix is defined
    
    input - input parsed for a substitution matrix
    
    name - the name (short description) of this matrix
  - SimpleSubstitutionMatrix
```
public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
                                java.lang.String matrixInput,
                                java.lang.String name)
```
    Creates a substitution matrix by parsing a String.
    
    Parameters:
    
    compoundSet - the CompoundSet on which the matrix is defined
    
    matrixInput - String parsed for a substitution matrix
    
    name - the name (short description) of this matrix
  - SimpleSubstitutionMatrix
```
public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
                                short match,
                                short replace)
```
    Creates an identity substitution matrix from match and replace values.
    
    Parameters:
    
    compoundSet - the CompoundSet on which the matrix is defined
    
    match - matrix value used for equivalent Compounds
    
    replace - matrix value used for differing Compounds
- Method Detail
  - getBlosum62
```
public static SubstitutionMatrix<AminoAcidCompound> getBlosum62()
```
  - getCompoundSet
```
public CompoundSet<C> getCompoundSet()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns the CompoundSet on which the matrix is defined.
    
    Specified by:
    
    getCompoundSet in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    the CompoundSet on which the matrix is defined
  - getDescription
```
public java.lang.String getDescription()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns the description of this matrix.
    
    Specified by:
    
    getDescription in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    description
  - getMatrix
```
public short[][] getMatrix()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns entire matrix.
    
    Specified by:
    
    getMatrix in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    matrix
  - getMatrixAsString
```
public java.lang.String getMatrixAsString()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns this matrix as a formatted String with Compound labels along the axes.
    
    Specified by:
    
    getMatrixAsString in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    this matrix as a formatted String
  - getMaxValue
```
public short getMaxValue()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns the maximum value in this matrix.
    
    Specified by:
    
    getMaxValue in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    the maximum value in this matrix
  - getMinValue
```
public short getMinValue()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns the minimum value in this matrix.
    
    Specified by:
    
    getMinValue in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    the minimum value in this matrix
  - getName
```
public java.lang.String getName()
```
    Description copied from interface: SubstitutionMatrix
    
    Returns the name (short description) of this matrix.
    
    Specified by:
    
    getName in interface SubstitutionMatrix<C extends Compound>
    
    Returns:
    
    name
  - getValue
```
public short getValue(C from,
                      C to)
```
    Description copied from interface: SubstitutionMatrix
    
    Returns value in matrix for conversion from first Compound to the second. If an argument does not belong to the CompoundSet, this could either throw an IllegalArgumentException or it could return SubstitutionMatrix.getMinValue().
    
    Specified by:
    
    getValue in interface SubstitutionMatrix<C extends Compound>
    
    Parameters:
    
    from - original Compound
    
    to - replacement Compound
    
    Returns:
    
    value in matrix for conversion from first Compound to the second
  - normalizeMatrix
```
public SubstitutionMatrix<C> normalizeMatrix(short scale)
```
    Description copied from interface: SubstitutionMatrix
    
    Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
    
    Specified by:
    
    normalizeMatrix in interface SubstitutionMatrix<C extends Compound>
    
    Parameters:
    
    scale - new normalization scale of this matrix
  - setDescription
```
public void setDescription(java.lang.String description)
```
    Description copied from interface: SubstitutionMatrix
    
    Sets the description of this matrix.
    
    Specified by:
    
    setDescription in interface SubstitutionMatrix<C extends Compound>
    
    Parameters:
    
    description - new description
  - setName
```
public void setName(java.lang.String name)
```
    Description copied from interface: SubstitutionMatrix
    
    Sets the name (short description) of this matrix.
    
    Specified by:
    
    setName in interface SubstitutionMatrix<C extends Compound>
    
    Parameters:
    
    name - new name
  - toString
```
public java.lang.String toString()
```
    Returns in a format similar to the standard NCBI files.
    
    Overrides:
    
    toString in class java.lang.Object
  - getRow
```
public java.util.Map<C,java.lang.Short> getRow(C row)
```
    Specified by:
    
    getRow in interface SubstitutionMatrix<C extends Compound>
  - getColumn
```
public java.util.Map<C,java.lang.Short> getColumn(C column)
```
    Specified by:
    
    getColumn in interface SubstitutionMatrix<C extends Compound>

Class SimpleSubstitutionMatrix<C extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

Method Detail

getBlosum62

getCompoundSet

getDescription

getMatrix

getMatrixAsString

getMaxValue

getMinValue

getName

getValue

normalizeMatrix

setDescription

setName

toString

getRow

getColumn