org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

All Implemented Interfaces:: SubstitutionMatrix<AminoAcidCompound>

public class ScaledSubstitutionMatrix extends Object implements SubstitutionMatrix<AminoAcidCompound>

The biojava-alignment module represents substitution matrices with short values. This is for performance reasons. Some substitution matrices, however, are provided as float values with up to 2 decimal places.

In order to be able to use them in the alignment module these are scaled in order to be able to represent as short values. The method getScale() provides access to the scaling factor.

Author:: Andreas Prlic

Constructor Summary

Constructors

Constructor

Description

ScaledSubstitutionMatrix()
Method Summary

Modifier and Type

Method

Description

List<AminoAcidCompound>

getCols()

Map<AminoAcidCompound,Short>

getColumn(AminoAcidCompound column)

static String

getComment()

CompoundSet<AminoAcidCompound>

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

getMax()

short

getMaxValue()

Returns the maximum value in this matrix.

short

getMin()

short

getMinValue()

Returns the minimum value in this matrix.

String

getName()

Returns the name (short description) of this matrix.

Map<AminoAcidCompound,Short>

getRow(AminoAcidCompound row)

List<AminoAcidCompound>

getRows()

int

getScale()

short

getValue(AminoAcidCompound from, AminoAcidCompound to)

Returns value in matrix for conversion from first Compound to the second.

SubstitutionMatrix<AminoAcidCompound>

normalizeMatrix(short scale)

Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.

void

setCols(List<AminoAcidCompound> cols)

void

setDescription(String description)

Sets the description of this matrix.

void

setMatrix(short[][] matrix)

void

setMax(short max)

void

setMin(short min)

void

setName(String name)

Sets the name (short description) of this matrix.

void

setRows(List<AminoAcidCompound> rows)

void

setScale(int scale)

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
- ScaledSubstitutionMatrix
  
  public ScaledSubstitutionMatrix()
Method Details
- getScale
  
  public int getScale()
- setScale
  
  public void setScale(int scale)
- getDescription
  
  public String getDescription()
  
  Description copied from interface: SubstitutionMatrix
  
  Returns the description of this matrix.
  
  Specified by:
  
  getDescription in interface SubstitutionMatrix<AminoAcidCompound>
  
  Returns:
  
  description
- setDescription
  
  public void setDescription(String description)
  
  Description copied from interface: SubstitutionMatrix
  
  Sets the description of this matrix.
  
  Specified by:
  
  setDescription in interface SubstitutionMatrix<AminoAcidCompound>
  
  Parameters:
  
  description - new description
- getName
  
  public String getName()
  
  Description copied from interface: SubstitutionMatrix
  
  Returns the name (short description) of this matrix.
  
  Specified by:
  
  getName in interface SubstitutionMatrix<AminoAcidCompound>
  
  Returns:
  
  name
- 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<AminoAcidCompound>
  
  Parameters:
  
  name - new name
- getMatrix
  
  public short[][] getMatrix()
  
  Description copied from interface: SubstitutionMatrix
  
  Returns entire matrix.
  
  Specified by:
  
  getMatrix in interface SubstitutionMatrix<AminoAcidCompound>
  
  Returns:
  
  matrix
- setMatrix
  
  public void setMatrix(short[][] matrix)
- getMax
  
  public short getMax()
- setMax
  
  public void setMax(short max)
- getMin
  
  public short getMin()
- setMin
  
  public void setMin(short min)
- getRows
  
  public List<AminoAcidCompound> getRows()
- setRows
  
  public void setRows(List<AminoAcidCompound> rows)
- getCols
  
  public List<AminoAcidCompound> getCols()
- setCols
  
  public void setCols(List<AminoAcidCompound> cols)
- getComment
  
  public static String getComment()
- toString
  
  public String toString()
  
  Returns in a format similar to the standard NCBI files.
  
  Overrides:
  
  toString in class Object
- getCompoundSet
  
  public CompoundSet<AminoAcidCompound> getCompoundSet()
  
  Description copied from interface: SubstitutionMatrix
  
  Returns the CompoundSet on which the matrix is defined.
  
  Specified by:
  
  getCompoundSet in interface SubstitutionMatrix<AminoAcidCompound>
  
  Returns:
  
  the CompoundSet on which the matrix is defined
- 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<AminoAcidCompound>
  
  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<AminoAcidCompound>
  
  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<AminoAcidCompound>
  
  Returns:
  
  the minimum value in this matrix
- getValue
  
  public short getValue(AminoAcidCompound from, AminoAcidCompound 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<AminoAcidCompound>
  
  Parameters:
  
  from - original Compound
  
  to - replacement Compound
  
  Returns:
  
  value in matrix for conversion from first Compound to the second
- normalizeMatrix
  
  public SubstitutionMatrix<AminoAcidCompound> 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<AminoAcidCompound>
  
  Parameters:
  
  scale - new normalization scale of this matrix
- getRow
  
  public Map<AminoAcidCompound,Short> getRow(AminoAcidCompound row)
  
  Specified by:
  
  getRow in interface SubstitutionMatrix<AminoAcidCompound>
- getColumn
  
  public Map<AminoAcidCompound,Short> getColumn(AminoAcidCompound column)
  
  Specified by:
  
  getColumn in interface SubstitutionMatrix<AminoAcidCompound>

Class ScaledSubstitutionMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ScaledSubstitutionMatrix

Method Details

getScale

setScale

getDescription

setDescription

getName

setName

getMatrix

setMatrix

getMax

setMax

getMin

setMin

getRows

setRows

getCols

setCols

getComment

toString

getCompoundSet

getMatrixAsString

getMaxValue

getMinValue

getValue

normalizeMatrix

getRow

getColumn