Method Detail

• getCompoundSet

  CompoundSet<C> getCompoundSet()

  Returns the CompoundSet on which the matrix is defined.

  Returns:

  the CompoundSet on which the matrix is defined

• getDescription

  java.lang.String getDescription()

  Returns the description of this matrix.

  Returns:

  description

• getMatrix

  short[][] getMatrix()

  Returns entire matrix.

  Returns:

  matrix

• getMatrixAsString

  java.lang.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

  java.lang.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:

  java.lang.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:

  java.lang.IllegalArgumentException - if scale < 1

• setDescription

  void setDescription(java.lang.String description)

  Sets the description of this matrix.

  Parameters:

  description - new description

• setName

  void setName(java.lang.String name)

  Sets the name (short description) of this matrix.

  Parameters:

  name - new name

• getRow

  java.util.Map<C,java.lang.Short> getRow(C row)

• getColumn

  java.util.Map<C,java.lang.Short> getColumn(C column)