Package de.uni_trier.wi2.procake.similarity.nest.sequence.utils

Interface ScoringMatrix

All Known Implementing Classes:
ScoringMatrixImpl
public interface ScoringMatrix
Representation of the scoring matrix of an dp algorithm.

  • Field Details

  • Method Details

    • initialize

      void initialize()
      Initialize the first row and first column to value zero.

    • set

      void set(int queryIdx, int caseIdx, int stepToSource, double value)
      Set a cell of the matrix to a given value and also provide the direction to the source cell.
      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

      void set(int queryIdx, int caseIdx, MatrixPath.MatrixCellPair source, double value)
      Set a cell of the matrix to a given value and also provide a reference to the source cell.
      Parameters:
      queryIdx - Index of the query task to set.
      caseIdx - Index of the case task to set.
      source - The source cell.
      value - The value to set this cell to.

    • set

      void set(MatrixPath.MatrixCellPair pair)
      Set a cell of the matrix to the given pair.
      Parameters:
      pair - The new cell entry containing also the indices.

    • get

      double get(int queryIdx, int caseIdx)
      Get the value of a cell.
      Parameters:
      queryIdx - The query task index.
      caseIdx - The case task index.
      Returns:
      The value at the given position.

    • get

      double get(MatrixPath.MatrixCellPair pair)
      Get the value of a cell.
      Parameters:
      pair - Specifies the cell's position in the matrix.
      Returns:
      The value at the given position.

    • getPair

      MatrixPath.MatrixCellPair getPair(int queryIdx, int caseIdx)
      Get the NESTTaskPair object at the specified position.
      Parameters:
      queryIdx -
      caseIdx -
      Returns:

    • getSourceOf

      MatrixPath.MatrixCellPair getSourceOf(int queryIdx, int caseIdx)
      Get the source of a cell.
      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

      int getSourceStepOf(int queryIdx, int caseIdx)
      Get the source step of a cell.
      Parameters:
      queryIdx - The query task index of the cell.
      caseIdx - The case task index of the dell.
      Returns:
      Either DIAGONAL, VERTICAL or HORIZONTAL.

    • getHighestScore

      double getHighestScore()
      Get the highest score in the last row of the matrix.
      Returns:
      The score.

    • getStartCell

      MatrixPath.MatrixCellPair getStartCell(boolean onlyLastRow)
      Get the start cell of the alignment path. Always returns the cell with the highest value in the last row of the matrix.
      Parameters:
      onlyLastRow - Depicts whether only to search in last row of matrix.
      Returns:
      A pair representing the start cell.

    • backtrackFrom

      MatrixPath backtrackFrom(MatrixPath.MatrixCellPair cell)
      Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).
      Parameters:
      cell - The cell to start the backtrack from.
      Returns:
      The found path.

    • backtrackFrom

      MatrixPath backtrackFrom(int queryIdx, int caseIdx)
      Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).
      Parameters:
      queryIdx - The query task index of the starting cell.
      caseIdx - The case task index of the starting cell.
      Returns:
      The found path.

    • isInBounds

      boolean isInBounds(int queryIdx, int caseIdx)
      Whether or not the indices are in bounds.
      Parameters:
      queryIdx -
      caseIdx -
      Returns:
      True, if the indices are in bounds.