de.uni_leipzig.bf.eval
Class DataReader

java.lang.Object
  de.uni_leipzig.bf.eval.DataReader

public class DataReader
extends java.lang.Object

Author:

an

Field Summary

(package private) java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.String>>	cluster2protMap
(package private) java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.String>>	complex2protMap
(package private) java.util.HashMap<java.lang.String,java.lang.Integer>	complexIds
(package private) java.util.TreeSet<java.lang.String>	complexList
(package private) double[][]	contingencyMatrix
(package private) double[][]	separationMatrix

Constructor Summary

DataReader(double[][] _contingencyMatrix, java.util.HashMap<java.lang.String,java.lang.Integer> _complexIds)
Creates a new instance of DataReader

DataReader(java.lang.String complexes, java.lang.String clusters)

Method Summary

void	buildContingencyTable(java.lang.String complexes, java.lang.String clusters) public double computeComplexwiseSeparation() { } /** Compute contingency table from cluster2protMap and complex2protMap
static void	cleanGraph(java.lang.String input, java.lang.String complexes, java.lang.String output) Cleans graph from unclassified proteins
static double	complexWiseSensitivity(java.util.HashMap<java.lang.String,java.util.TreeSet<java.lang.String>> complexes, java.util.ArrayList<java.util.TreeSet<java.lang.String>> clusters) Computes complex-wise sensitivity of a clustering
double	computeAccuracy() Accuracy is the geometric mean of PPV and sensitivity
double	computeComplexwiseSperation()
double	computePPV() Compute PPV of a clustering
double	computePPVDebug() Compute PPV (and print debug informations) of a clustering
double	computeSensitivity() Compute sensitivity of a clustering
double	computeSensitivityDebug() Compute sensitivity (and print debug informations) of a clustering
void	computeSeparationByColumn() Computes separation by column
void	computeSeparationMatrix() Computes separation by row
double[]	computeSeparations()
void	initClusterIds(java.lang.String file) Read results of BorderFlow and write them in cluster2protMap
void	initComplexIds(java.lang.String file)
static int	intersection(java.util.TreeSet<java.lang.String> a, java.util.TreeSet<java.lang.String> b) Computes the intersection of two TreeSet
static void	main(java.lang.String[] args)
static java.util.HashMap<java.lang.String,java.util.TreeSet<java.lang.String>>	readComplexes(java.lang.String file)
static void	runtest()
java.util.TreeSet<java.lang.String>	string2treeSet(java.lang.String s) Transforms strings of the form [X(, Y)*] to TreeSet

Methods inherited from class java.lang.Object

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

Field Detail

cluster2protMap

java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.String>> cluster2protMap

complex2protMap

java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.String>> complex2protMap

complexIds

java.util.HashMap<java.lang.String,java.lang.Integer> complexIds

complexList

java.util.TreeSet<java.lang.String> complexList

contingencyMatrix

double[][] contingencyMatrix

separationMatrix

double[][] separationMatrix

Constructor Detail

DataReader

public DataReader(double[][] _contingencyMatrix,
                  java.util.HashMap<java.lang.String,java.lang.Integer> _complexIds)

Creates a new instance of DataReader

DataReader

public DataReader(java.lang.String complexes,
                  java.lang.String clusters)

Method Detail

buildContingencyTable

public void buildContingencyTable(java.lang.String complexes,
                                  java.lang.String clusters)

public double computeComplexwiseSeparation() { } /** Compute contingency table from cluster2protMap and complex2protMap

cleanGraph

public static void cleanGraph(java.lang.String input,
                              java.lang.String complexes,
                              java.lang.String output)

Cleans graph from unclassified proteins

complexWiseSensitivity

public static double complexWiseSensitivity(java.util.HashMap<java.lang.String,java.util.TreeSet<java.lang.String>> complexes,
                                            java.util.ArrayList<java.util.TreeSet<java.lang.String>> clusters)

Computes complex-wise sensitivity of a clustering

computeAccuracy

public double computeAccuracy()

Accuracy is the geometric mean of PPV and sensitivity

computeComplexwiseSperation

public double computeComplexwiseSperation()

computePPV

public double computePPV()

Compute PPV of a clustering

computePPVDebug

public double computePPVDebug()

Compute PPV (and print debug informations) of a clustering

computeSensitivity

public double computeSensitivity()

Compute sensitivity of a clustering

computeSensitivityDebug

public double computeSensitivityDebug()

Compute sensitivity (and print debug informations) of a clustering

computeSeparationByColumn

public void computeSeparationByColumn()

Computes separation by column

computeSeparationMatrix

public void computeSeparationMatrix()

Computes separation by row

computeSeparations

public double[] computeSeparations()

initClusterIds

public void initClusterIds(java.lang.String file)

Read results of BorderFlow and write them in cluster2protMap

initComplexIds

public void initComplexIds(java.lang.String file)

intersection

public static int intersection(java.util.TreeSet<java.lang.String> a,
                               java.util.TreeSet<java.lang.String> b)

Computes the intersection of two TreeSet

main

public static void main(java.lang.String[] args)

readComplexes

public static java.util.HashMap<java.lang.String,java.util.TreeSet<java.lang.String>> readComplexes(java.lang.String file)

runtest

public static void runtest()

string2treeSet

public java.util.TreeSet<java.lang.String> string2treeSet(java.lang.String s)

Transforms strings of the form [X(, Y)*] to TreeSet