de.jstacs.utils

Class PFMComparator

java.lang.Object

de.jstacs.utils.PFMComparator

public class PFMComparator
extends Object

This class implements a number of methods for the comparison of position frequency matrices (PFMs) as described in the Amadeus paper

Author:

Jens Keilwagen

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PFMComparator.NormalizedEuclideanDistance This class implements the normalized Euclidean distance.
static class	PFMComparator.OneMinusPearsonCorrelationCoefficient This class implements the Pearson correlation coefficient.
static class	PFMComparator.PFMDistance This interface declares a method for comparing different PFMs.
static class	PFMComparator.SymmetricKullbackLeiblerDivergence This class implements the symmetric Kullback-Leibler-divergence.
static class	PFMComparator.UniformBorderWrapper Wraps a given PFMComparator.PFMDistance and pads the considered PFMs with uniformly distributed positions.

Constructor Summary

Constructors

Constructor and Description
PFMComparator()

Method Summary

Methods

Modifier and Type	Method and Description
static ComparableElement<String,Double>[]	find(ComplementableDiscreteAlphabet abc, double[][] pfm, ArrayList<AbstractMap.SimpleEntry<String,double[][]>> knownPFMs, PFMComparator.PFMDistance distance, int minOverlap, int allowMiniShift, boolean pValues, double threshold) This methods finds for a user specified PFM pfm similar PFMs in a list of known PFMs.
static String	getConsensus(AlphabetContainer con, double[][] pfm) This method extracts the The method does not use any degenerated IUPAC code.
static double[]	getCounts(DataSet... data) This method counts the occurrences of symbols in the given data sets.
static double[][]	getPFM(DataSet data) This method creates a PFM from a DataSet of Sequences.
static double[][]	getPFM(DataSet data, double[] weights) This method creates a PFM from a DataSet of Sequences.
static double[][]	getPFM(DataSet data, int start, int end) Returns a position frequency matrix (PFM, rows=positions, columns=symbols) for the given subset of DataSet.
static double[][]	getPWM(DataSet data, int start, int end) Returns a position weight matrix (PWM, rows=positions, columns=symbols, containing probabilities) for the given subset of DataSet.
static double[][]	getReverseComplement(ComplementableDiscreteAlphabet abc, double[][] pfm) This method returns the PFM that is the reverse complement of the given PFM.
static String	matrixToString(double[][] matrix) Returns a string representation of the matrix, where each row of the matrix is printed on one line and columns are separated by tabstops.
static void	normalize(double[] counts) This method enables the user to normalize a array containing counts.
static AbstractMap.SimpleEntry<String,double[][]>	readPFMFromUniprobe(String annotPrefix, File file) Reads a PFM from the UniProbe format.
static ArrayList<AbstractMap.SimpleEntry<String,double[][]>>	readPFMsFromEMBL(String fileName, int max) This method reads a number of PFMs from a file and return them in an ArrayList together with some annotation.
static ArrayList<AbstractMap.SimpleEntry<String,double[][]>>	readPFMsFromJasparFastA(BufferedReader r) Reads a list of PFMs from the Jaspar format
static ArrayList<AbstractMap.SimpleEntry<String,double[][]>>	readPFMsFromJasparFastA(String filename) This method reads a number of PFMs from a file in the Jaspar FastA-like format and returns them in an ArrayList together with some annotation.
static ArrayList<AbstractMap.SimpleEntry<String,double[][]>>	readPFMsFromTransfac(String fileName, int max) Reads a set of PFM from the Transfac format
static ArrayList<AbstractMap.SimpleEntry<String,double[][]>>	readPFMsFromUniprobe(String startdir) This method reads a number of PFMs from a directory as downloaded from the Uniprobe data base and returns them in an ArrayList together with some annotation.

Methods inherited from class java.lang.Object

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

Constructor Detail

PFMComparator

public PFMComparator()

Method Detail

matrixToString

public static String matrixToString(double[][] matrix)

Returns a string representation of the matrix, where each row of the matrix is printed on one line and columns are separated by tabstops.

Parameters:

matrix - the matrix

Returns:

the string representation

getConsensus

public static String getConsensus(AlphabetContainer con,
                  double[][] pfm)

This method extracts the The method does not use any degenerated IUPAC code.

Parameters:

con - the AlphabetContainer that was used to create the PFM

pfm - the position frequency matrix (or also possible the position weight matrix)

Returns:

the consensus which is the string with most probable symbol at each position

getCounts

public static double[] getCounts(DataSet... data)

This method counts the occurrences of symbols in the given data sets. This method can therefore be used to create a background distribution.

Parameters:

data - the data sets

Returns:

an array containing the counts

normalize

public static void normalize(double[] counts)

This method enables the user to normalize a array containing counts. After using this method the array contain probabilities.

Parameters:

counts - the array of counts

getPFM

public static double[][] getPFM(DataSet data)

This method creates a PFM from a DataSet of Sequences.

Parameters:

data - the DataSet

Returns:

the PFM

getPFM

public static double[][] getPFM(DataSet data,
                int start,
                int end)

Returns a position frequency matrix (PFM, rows=positions, columns=symbols) for the given subset of DataSet.

Parameters:

data - the data set

start - the first sequence to consider

end - the first sequence not not consider

Returns:

the PFM

getPWM

public static double[][] getPWM(DataSet data,
                int start,
                int end)

Returns a position weight matrix (PWM, rows=positions, columns=symbols, containing probabilities) for the given subset of DataSet.

Parameters:

data - the data set

start - the first sequence to consider

end - the first sequence not not consider

Returns:

the PWM

getPFM

public static double[][] getPFM(DataSet data,
                double[] weights)

This method creates a PFM from a DataSet of Sequences.

Parameters:

data - the DataSet

weights - the weights on the sequences in data

Returns:

the PFM

getReverseComplement

public static double[][] getReverseComplement(ComplementableDiscreteAlphabet abc,
                              double[][] pfm)

This method returns the PFM that is the reverse complement of the given PFM.

Parameters:

abc - the ComplementableDiscreteAlphabet that is used to create the reverse complement

pfm - the absolute frequencies for each position and symbol;

Returns:

the PFM that is the reverse complement of the given PFM

readPFMsFromUniprobe

public static ArrayList<AbstractMap.SimpleEntry<String,double[][]>> readPFMsFromUniprobe(String startdir)
                                                                                  throws IOException

This method reads a number of PFMs from a directory as downloaded from the Uniprobe data base and returns them in an ArrayList together with some annotation.

Parameters:

startdir - the directory containing the PFMs in Uniprobe format

Returns:

an ArrayList containing AbstractMap.SimpleEntrys with annotation and PFM

Throws:

IOException - if something went wrong while reading a file

readPFMFromUniprobe

public static AbstractMap.SimpleEntry<String,double[][]> readPFMFromUniprobe(String annotPrefix,
                                                             File file)
                                                                      throws IOException

Reads a PFM from the UniProbe format.

Parameters:

annotPrefix - a prefix on the PFM's annotation

file - the File to read

Returns:

the PFM and annotation

Throws:

IOException

readPFMsFromJasparFastA

public static ArrayList<AbstractMap.SimpleEntry<String,double[][]>> readPFMsFromJasparFastA(String filename)
                                                                                     throws IOException

This method reads a number of PFMs from a file in the Jaspar FastA-like format and returns them in an ArrayList together with some annotation.

Parameters:

filename - the path to the file containing the Jaspar PFMs

Returns:

an ArrayList containing AbstractMap.SimpleEntrys with annotation and PFM

Throws:

IOException - if something went wrong while reading the file

readPFMsFromJasparFastA

public static ArrayList<AbstractMap.SimpleEntry<String,double[][]>> readPFMsFromJasparFastA(BufferedReader r)
                                                                                     throws IOException

Reads a list of PFMs from the Jaspar format

Parameters:

r - the BufferedReader on the Jaspar file

Returns:

the PFMs

Throws:

IOException - if the contents of r could not be read

readPFMsFromEMBL

public static ArrayList<AbstractMap.SimpleEntry<String,double[][]>> readPFMsFromEMBL(String fileName,
                                                                     int max)
                                                                              throws IOException

This method reads a number of PFMs from a file and return them in an ArrayList together with some annotation.

Parameters:

fileName - the name of the file containing the PFMs in EMBL format

max - the maximal number of PFMs that should be read

Returns:

an ArrayList containing AbstractMap.SimpleEntrys with annotation and PFM

Throws:

IOException - if something went wrong while reading the file

readPFMsFromTransfac

public static ArrayList<AbstractMap.SimpleEntry<String,double[][]>> readPFMsFromTransfac(String fileName,
                                                                         int max)
                                                                                  throws IOException

Reads a set of PFM from the Transfac format

Parameters:

fileName - the Transfac file

max - the maximum number of PFMs to read

Returns:

the PFMs

Throws:

IOException - if the file could not be read

find

public static ComparableElement<String,Double>[] find(ComplementableDiscreteAlphabet abc,
                                      double[][] pfm,
                                      ArrayList<AbstractMap.SimpleEntry<String,double[][]>> knownPFMs,
                                      PFMComparator.PFMDistance distance,
                                      int minOverlap,
                                      int allowMiniShift,
                                      boolean pValues,
                                      double threshold)

This methods finds for a user specified PFM pfm similar PFMs in a list of known PFMs.

Parameters:

abc - the alphabet of this PFM

pfm - the PFM to be compare to the known PFMs

knownPFMs - a ArrayList of known PFMs

distance - a distance measure to assess the similarity of the PFMs

minOverlap - the minimal number of consecutive positions in an alignment

allowMiniShift - the minimal number of allowed shifts (even if the minimal overlap is bigger)

pValues - compute p-values for matrix similarity

threshold - only hits with a distance below this threshold will be reported

Returns:

an array of similar PFMs and their annotations

See Also:

readPFMsFromEMBL(String, int)