java.lang.Object
de.uni_trier.wi2.procake.similarity.nest.sequence.utils.impl.ScoringMatrixImpl
All Implemented Interfaces:
ScoringMatrix

public class ScoringMatrixImpl extends Object implements ScoringMatrix
  • Constructor Details

  • Method Details

    • initialize

      public void initialize()
      Description copied from interface: ScoringMatrix
      Initialize the first row and first column to value zero.
      Specified by:
      initialize in interface ScoringMatrix
    • set

      public void set(int queryIdx, int caseIdx, int stepToSource, double value)
      Description copied from interface: ScoringMatrix
      Set a cell of the matrix to a given value and also provide the direction to the source cell.
      Specified by:
      set in interface ScoringMatrix
      Parameters:
      queryIdx - Index of the query task to set.
      caseIdx - Index of the case task to set.
      stepToSource - Either DIAGONAL, VERTICAL or HORIZONTAL.
      value - The value to set this cell to.
    • set

      public void set(int queryIdx, int caseIdx, MatrixPath.MatrixCellPair sourceCell, double value)
      Description copied from interface: ScoringMatrix
      Set a cell of the matrix to a given value and also provide a reference to the source cell.
      Specified by:
      set in interface ScoringMatrix
      Parameters:
      queryIdx - Index of the query task to set.
      caseIdx - Index of the case task to set.
      sourceCell - The source cell.
      value - The value to set this cell to.
    • set

      public void set(MatrixPath.MatrixCellPair pair)
      Description copied from interface: ScoringMatrix
      Set a cell of the matrix to the given pair.
      Specified by:
      set in interface ScoringMatrix
      Parameters:
      pair - The new cell entry containing also the indices.
    • get

      public double get(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Get the value of a cell.
      Specified by:
      get in interface ScoringMatrix
      Parameters:
      queryIdx - The query task index.
      caseIdx - The case task index.
      Returns:
      The value at the given position.
    • get

      public double get(MatrixPath.MatrixCellPair pair)
      Description copied from interface: ScoringMatrix
      Get the value of a cell.
      Specified by:
      get in interface ScoringMatrix
      Parameters:
      pair - Specifies the cell's position in the matrix.
      Returns:
      The value at the given position.
    • getPair

      public MatrixPath.MatrixCellPair getPair(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Get the NESTTaskPair object at the specified position.
      Specified by:
      getPair in interface ScoringMatrix
      Returns:
    • getSourceOf

      public MatrixPath.MatrixCellPair getSourceOf(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Get the source of a cell.
      Specified by:
      getSourceOf in interface ScoringMatrix
      Parameters:
      queryIdx - The query task index of the cell.
      caseIdx - The case task index of the dell.
      Returns:
      A pair representing the source cell.
    • getSourceStepOf

      public int getSourceStepOf(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Get the source step of a cell.
      Specified by:
      getSourceStepOf in interface ScoringMatrix
      Parameters:
      queryIdx - The query task index of the cell.
      caseIdx - The case task index of the dell.
      Returns:
      Either DIAGONAL, VERTICAL or HORIZONTAL.
    • getHighestScore

      public double getHighestScore()
      Description copied from interface: ScoringMatrix
      Get the highest score in the last row of the matrix.
      Specified by:
      getHighestScore in interface ScoringMatrix
      Returns:
      The score.
    • getStartCell

      public MatrixPath.MatrixCellPair getStartCell(boolean onlyLastRow)
      Description copied from interface: ScoringMatrix
      Get the start cell of the alignment path. Always returns the cell with the highest value in the last row of the matrix.
      Specified by:
      getStartCell in interface ScoringMatrix
      Parameters:
      onlyLastRow - Depicts whether only to search in last row of matrix.
      Returns:
      A pair representing the start cell.
    • backtrackFrom

      public MatrixPath backtrackFrom(MatrixPath.MatrixCellPair cell)
      Description copied from interface: ScoringMatrix
      Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).
      Specified by:
      backtrackFrom in interface ScoringMatrix
      Parameters:
      cell - The cell to start the backtrack from.
      Returns:
      The found path.
    • backtrackFrom

      public MatrixPath backtrackFrom(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).
      Specified by:
      backtrackFrom in interface ScoringMatrix
      Parameters:
      queryIdx - The query task index of the starting cell.
      caseIdx - The case task index of the starting cell.
      Returns:
      The found path.
    • isInBounds

      public boolean isInBounds(int queryIdx, int caseIdx)
      Description copied from interface: ScoringMatrix
      Whether or not the indices are in bounds.
      Specified by:
      isInBounds in interface ScoringMatrix
      Returns:
      True, if the indices are in bounds.
    • toString

      public String toString()
      Overrides:
      toString in class Object