Package ffx.potential.parsers

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 Summary

Constructors

Constructor	Description
DistanceMatrixFilter()	No public constructor for DistanceMatrixFilter.

Method Summary

Modifier and Type	Method	Description
int	getRestartColumn()	Get the number of columns in the last row that was read in.
int	getRestartRow()	Get the number of rows read in.
RunningStatistics	readDistanceMatrix(String filename, int expectedRows, int expectedColumns)	Read in the distance matrix from a file.
RunningStatistics	readDistanceMatrix(String filename, List<double[]> distanceList)	Read in the distance matrix from a file.
static String	toDistanceMatrixString(double[][] distanceMatrix)	Convert a distance matrix to a String.
static String	toDistanceMatrixString(List<double[]> distanceMatrix)	Convert a distance matrix to a String.
static boolean	writeDistanceMatrix(String filename, List<double[]> distanceMatrix)	Write the distance matrix to a file.
static boolean	writeDistanceMatrixRow(String filename, double[] distanceMatrixRow, int firstColumn)	Write the distance matrix to a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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.