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:: Serializable, SubstitutionMatrix<C>

public class SimpleSubstitutionMatrix<C extends Compound> extends Object implements SubstitutionMatrix<C>, 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

Description

SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short replace)

Creates an identity substitution matrix from match and replace values.

SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, File fileInput)

Creates a substitution matrix by reading in a file.

SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Reader input, String name)

Creates a substitution matrix by parsing some input.

SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, String matrixInput, String name)

Creates a substitution matrix by parsing a String.
Method Summary

Modifier and Type

Method

Description

static SubstitutionMatrix<AminoAcidCompound>

getBlosum62()

Map<C,Short>

getColumn(C column)

CompoundSet<C>

getCompoundSet()

Returns the CompoundSet on which the matrix is defined.

String

getDescription()

Returns the description of this matrix.

short[][]

getMatrix()

Returns entire matrix.

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.

String

getName()

Returns the name (short description) of this matrix.

Map<C,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(String description)

Sets the description of this matrix.

void

setName(String name)

Sets the name (short description) of this matrix.

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 Details
- SimpleSubstitutionMatrix
  
  public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, File fileInput) throws 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:
  
  FileNotFoundException - if fileInput parameter cannot be read
- SimpleSubstitutionMatrix
  
  public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Reader input, 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, String matrixInput, 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 Details
- 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 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 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 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(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(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 String toString()
  
  Returns in a format similar to the standard NCBI files.
  
  Overrides:
  
  toString in class Object
- getRow
  
  public Map<C,Short> getRow(C row)
  
  Specified by:
  
  getRow in interface SubstitutionMatrix<C extends Compound>
- getColumn
  
  public Map<C,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 Details

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

SimpleSubstitutionMatrix

Method Details

getBlosum62

getCompoundSet

getDescription

getMatrix

getMatrixAsString

getMaxValue

getMinValue

getName

getValue

normalizeMatrix

setDescription

setName

toString

getRow

getColumn