Class DistanceMatrixFilter

java.lang.Object
ffx.potential.parsers.DistanceMatrixFilter

public class DistanceMatrixFilter extends Object
The DistanceMatrixFilter class parses a Distance Matrix (*.DST) files.
Since:
1.0
Author:
Michael J. Schnieders
  • Constructor Details

    • DistanceMatrixFilter

      public DistanceMatrixFilter()
      No public constructor for DistanceMatrixFilter.
  • Method Details

    • getRestartRow

      public int getRestartRow()
      Get the number of rows read in.
      Returns:
      The number of rows read in.
    • getRestartColumn

      public int getRestartColumn()
      Get the number of columns in the last row that was read in.
      Returns:
      The number of columns in the last row that was read in.
    • readDistanceMatrix

      public RunningStatistics readDistanceMatrix(String filename, List<double[]> distanceList)
      Read in the distance matrix from a file. This method is used from the Clustering code, where the size of the distance matrix is unknown, and the full N^2 matrix is needed.
      Parameters:
      filename - The filename to read from.
      distanceList - The distance matrix (if null, only the last row is returned).
      Returns:
      Statistics for the parsed values.
    • readDistanceMatrix

      public RunningStatistics readDistanceMatrix(String filename, int expectedRows, int expectedColumns)
      Read in the distance matrix from a file.
      Parameters:
      filename - The filename to read from.
      expectedRows - The number of rows to expect.
      expectedColumns - The number of columns to expect.
      Returns:
      Statistics for the parsed values.
    • toDistanceMatrixString

      public static String toDistanceMatrixString(List<double[]> distanceMatrix)
      Convert a distance matrix to a String.
      Parameters:
      distanceMatrix - The distance matrix.
      Returns:
      Return a String representation (or null if the distanceMatrix is null).
    • toDistanceMatrixString

      public static String toDistanceMatrixString(double[][] distanceMatrix)
      Convert a distance matrix to a String.
      Parameters:
      distanceMatrix - The distance matrix.
      Returns:
      Return a String representation (or null if the distanceMatrix is null).
    • writeDistanceMatrix

      public static boolean writeDistanceMatrix(String filename, List<double[]> distanceMatrix)
      Write the distance matrix to a file.
      Parameters:
      filename - The filename to write to.
      distanceMatrix - a list containing rows of the distance matrix.
      Returns:
      a boolean.
    • writeDistanceMatrixRow

      public static boolean writeDistanceMatrixRow(String filename, double[] distanceMatrixRow, int firstColumn)
      Write the distance matrix to a file.
      Parameters:
      filename - The filename to write to.
      distanceMatrixRow - A row of the distance matrix.
      firstColumn - The first column of the distance matrix row to write.
      Returns:
      a boolean.