Package org.biojava.nbio.core.alignment.template

Interface SubstitutionMatrix<C extends Compound>

Type Parameters:
C - each element of the matrix corresponds to a pair of Compounds of type C
All Known Implementing Classes:
ScaledSubstitutionMatrix, SimpleSubstitutionMatrix
public interface SubstitutionMatrix<C extends Compound>
Defines 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, Paolo Pavan

  • Method Details

    • getCompoundSet

      CompoundSet<C> getCompoundSet()
      Returns the CompoundSet on which the matrix is defined.
      Returns:
      the CompoundSet on which the matrix is defined

    • getDescription

      String getDescription()
      Returns the description of this matrix.
      Returns:
      description

    • getMatrix

      short[][] getMatrix()
      Returns entire matrix.
      Returns:
      matrix

    • getMatrixAsString

      String getMatrixAsString()
      Returns this matrix as a formatted String with Compound labels along the axes.
      Returns:
      this matrix as a formatted String

    • getMaxValue

      short getMaxValue()
      Returns the maximum value in this matrix.
      Returns:
      the maximum value in this matrix

    • getMinValue

      short getMinValue()
      Returns the minimum value in this matrix.
      Returns:
      the minimum value in this matrix

    • getName

      String getName()
      Returns the name (short description) of this matrix.
      Returns:
      name

    • getValue

      short getValue(C from, C to)
      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 getMinValue().
      Parameters:
      from - original Compound
      to - replacement Compound
      Returns:
      value in matrix for conversion from first Compound to the second
      Throws:
      IllegalArgumentException - possibly, if an argument does not belong to the CompoundSet

    • normalizeMatrix

      SubstitutionMatrix<C> normalizeMatrix(short scale)
      Rescales the matrix so that to getMaxValue() - getMinValue() = scale.
      Parameters:
      scale - new normalization scale of this matrix
      Throws:
      IllegalArgumentException - if scale < 1

    • setDescription

      void setDescription(String description)
      Sets the description of this matrix.
      Parameters:
      description - new description

    • setName

      void setName(String name)
      Sets the name (short description) of this matrix.
      Parameters:
      name - new name

    • getRow

      Map<C,Short> getRow(C row)

    • getColumn

      Map<C,Short> getColumn(C column)