merge upstream/master

13 files changed, 0 insertions, 875 deletions

diff --git a/gi/posterior-regularisation/prjava/src/util/Array.java b/gi/posterior-regularisation/prjava/src/util/Array.java
deleted file mode 100644
index cc4725af..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Array.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package util;
-
-import java.util.Arrays;
-
-public class Array {
-
-	
-	
-	public  static void sortDescending(double[] ds){
-		for (int i = 0; i < ds.length; i++) ds[i] = -ds[i];
-		Arrays.sort(ds);
-		for (int i = 0; i < ds.length; i++) ds[i] = -ds[i];
-	}
-	
-	/** 
-	 * Return a new reversed array
-	 * @param array
-	 * @return
-	 */
-	public static int[] reverseIntArray(int[] array){
-		int[] reversed = new int[array.length];
-		for (int i = 0; i < reversed.length; i++) {
-			reversed[i] = array[reversed.length-1-i];
-		}
-		return reversed;
-	}
-	
-	public static String[] sumArray(String[] in, int from){
-		String[] res = new String[in.length-from];
-		for (int i = from; i < in.length; i++) {
-			res[i-from] = in[i];
-		}
-		return res;
-	}
-	
-	public static void main(String[] args) {
-		int[] i = {1,2,3,4};
-		util.Printing.printIntArray(i, null, "original");
-		util.Printing.printIntArray(reverseIntArray(i), null, "reversed");
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/ArrayMath.java b/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
deleted file mode 100644
index 398a13a2..00000000
--- a/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
+++ /dev/null
@@ -1,186 +0,0 @@
-package util;
-
-import java.util.Arrays;
-
-public class ArrayMath {
-
-	public static double dotProduct(double[] v1, double[] v2) {
-		assert(v1.length == v2.length);
-		double result = 0;
-		for(int i = 0; i < v1.length; i++)
-			result += v1[i]*v2[i];
-		return result;
-	}
-
-	public static double twoNormSquared(double[] v) {
-		double result = 0;
-		for(double d : v)
-			result += d*d;
-		return result;
-	}
-
-	public static boolean containsInvalid(double[] v) {
-		for(int i = 0; i < v.length; i++)
-			if(Double.isNaN(v[i]) || Double.isInfinite(v[i]))
-				return true;
-		return false;
-	}
-
-
-	
-	public static double safeAdd(double[] toAdd) {
-		// Make sure there are no positive infinities
-		double sum = 0;
-		for(int i = 0; i < toAdd.length; i++) {
-			assert(!(Double.isInfinite(toAdd[i]) && toAdd[i] > 0));
-			assert(!Double.isNaN(toAdd[i]));
-			sum += toAdd[i];
-		}
-		
-		return sum;
-	}
-
-	/* Methods for filling integer and double arrays (of up to four dimensions) with the given value. */
-	
-	public static void set(int[][][][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[][][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[] array, int value) {
-		Arrays.fill(array, value);
-	}
-	
-	
-	public static void set(double[][][][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[][][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[] array, double value) {
-		Arrays.fill(array, value);
-	}
-
-	public static void setEqual(double[][][][] dest, double[][][][] source){
-		for (int i = 0; i < source.length; i++) {
-			setEqual(dest[i],source[i]);
-		}
-	}
-
-	
-	public static void setEqual(double[][][] dest, double[][][] source){
-		for (int i = 0; i < source.length; i++) {
-			set(dest[i],source[i]);
-		}
-	}
-
-	
-	public static void set(double[][] dest, double[][] source){
-		for (int i = 0; i < source.length; i++) {
-			setEqual(dest[i],source[i]);
-		}
-	}
-
-	public static void setEqual(double[] dest, double[] source){
-		System.arraycopy(source, 0, dest, 0, source.length);
-	}
-
-	public static void plusEquals(double[][][][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[][][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			array[i] += val;
-		}
-	}
-
-	
-	public static double sum(double[] array) {
-		double res = 0;
-		for (int i = 0; i < array.length; i++) res += array[i];
-		return res;
-	}
-
-
-	
-	public static  double[][] deepclone(double[][] in){
-		double[][] res = new double[in.length][];
-		for (int i = 0; i < res.length; i++) {
-			res[i] = in[i].clone();
-		}
-		return res;
-	}
-
-	
-	public static  double[][][] deepclone(double[][][] in){
-		double[][][] res = new double[in.length][][];
-		for (int i = 0; i < res.length; i++) {
-			res[i] = deepclone(in[i]);
-		}
-		return res;
-	}
-
-	public static double cosine(double[] a,
-			double[] b) {
-		return (dotProduct(a, b)+1e-5)/(Math.sqrt(dotProduct(a, a)+1e-5)*Math.sqrt(dotProduct(b, b)+1e-5));
-	}
-
-	public static double max(double[] ds) {
-		double max = Double.NEGATIVE_INFINITY;
-		for(double d:ds) max = Math.max(d,max);
-		return max;
-	}
-
-	public static void exponentiate(double[] a) {
-		for (int i = 0; i < a.length; i++) {
-			a[i] = Math.exp(a[i]);
-		}
-	}
-
-	public static int sum(int[] array) {
-		int res = 0;
-		for (int i = 0; i < array.length; i++) res += array[i];
-		return res;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java b/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java
deleted file mode 100644
index 1ff1ae4a..00000000
--- a/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package util;
-
-public interface DifferentiableObjective {
-
-	public double getValue();
-
-	public void getGradient(double[] gradient);
-
-	public void getParameters(double[] params);
-
-	public void setParameters(double[] newParameters);
-
-	public int getNumParameters();
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java b/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java
deleted file mode 100644
index ff1478ad..00000000
--- a/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package util;
-
-public class DigammaFunction {
-	public static double expDigamma(double number){
-		if(number==0)return number;
-		return Math.exp(digamma(number));
-	}
-	
-	public static double digamma(double number){
-		if(number > 7){
-			return digammApprox(number-0.5);
-		}else{
-			return digamma(number+1) - 1.0/number;
-		}
-	}
-	
-	private static double digammApprox(double value){
-		return Math.log(value) + 0.04167*Math.pow(value, -2) - 0.00729*Math.pow(value, -4) 
-		+  0.00384*Math.pow(value, -6) - 0.00413*Math.pow(value, -8);
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/FileSystem.java b/gi/posterior-regularisation/prjava/src/util/FileSystem.java
deleted file mode 100644
index d7812e40..00000000
--- a/gi/posterior-regularisation/prjava/src/util/FileSystem.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package util;
-
-import java.io.File;
-
-public class FileSystem {
-	public static boolean createDir(String directory) {
-
-		File dir = new File(directory);
-		if (!dir.isDirectory()) {
-			boolean success = dir.mkdirs();
-			if (!success) {
-				System.out.println("Unable to create directory " + directory);
-				return false;
-			}
-			System.out.println("Created directory " + directory);
-		} else {
-			System.out.println("Reusing directory " + directory);
-		}
-		return true;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/InputOutput.java b/gi/posterior-regularisation/prjava/src/util/InputOutput.java
deleted file mode 100644
index da7f71bf..00000000
--- a/gi/posterior-regularisation/prjava/src/util/InputOutput.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package util;
-
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.io.UnsupportedEncodingException;
-import java.util.Properties;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
-
-public class InputOutput {
-
-	/**
-	 * Opens a file either compress with gzip or not compressed.
-	 */
-	public static BufferedReader openReader(String fileName) throws UnsupportedEncodingException, FileNotFoundException, IOException{
-		System.out.println("Reading: " + fileName);
-		BufferedReader reader;
-		fileName = fileName.trim();
-		if(fileName.endsWith("gz")){
-			reader = new BufferedReader(
-			new InputStreamReader(new GZIPInputStream(new FileInputStream(fileName)),"UTF8"));
-		}else{
-			reader = new BufferedReader(new InputStreamReader(
-					new FileInputStream(fileName), "UTF8"));
-		}
-		
-		return reader;
-	}
-	
-	
-	public static PrintStream openWriter(String fileName) 
-	throws UnsupportedEncodingException, FileNotFoundException, IOException{
-		System.out.println("Writting to file: " + fileName);
-		PrintStream writter;
-		fileName = fileName.trim();
-		if(fileName.endsWith("gz")){
-			writter = new PrintStream(new GZIPOutputStream(new FileOutputStream(fileName)),
-					true, "UTF-8");
-
-		}else{
-			writter = new PrintStream(new FileOutputStream(fileName),
-					true, "UTF-8");
-
-		}
-		
-		return writter;
-	}
-	
-	public static Properties readPropertiesFile(String fileName) {
-		Properties properties = new Properties();
-		try {
-			properties.load(new FileInputStream(fileName));
-		} catch (IOException e) {
-			e.printStackTrace();
-			throw new AssertionError("Wrong properties file " + fileName);
-		}
-		System.out.println(properties.toString());
-		
-		return properties;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/LogSummer.java b/gi/posterior-regularisation/prjava/src/util/LogSummer.java
deleted file mode 100644
index 117393b9..00000000
--- a/gi/posterior-regularisation/prjava/src/util/LogSummer.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package util;
-
-import java.lang.Math;
-
-/*
- * Math tool for computing logs of sums, when the terms of the sum are already in log form.
- * (Useful if the terms of the sum are very small numbers.)
- */
-public class LogSummer {
-	
-	private LogSummer() {
-	}
-		
-	/**
-	 * Given log(a) and log(b), computes log(a + b).
-	 * 
-	 * @param  loga log of first sum term
-	 * @param  logb log of second sum term
-	 * @return     log(sum), where sum = a + b
-	 */
-	public static double sum(double loga, double logb) {
-		assert(!Double.isNaN(loga));
-		assert(!Double.isNaN(logb));
-		
-		if(Double.isInfinite(loga))
-			return logb;
-		if(Double.isInfinite(logb))
-			return loga;
-
-		double maxLog;
-		double difference;
-		if(loga > logb) {
-			difference = logb - loga;
-			maxLog = loga;
-		}
-		else {
-			difference = loga - logb;
-			maxLog = logb;
-		}
-
-		return Math.log1p(Math.exp(difference)) + maxLog;
-	}
-
-	/**
-	 * Computes log(exp(array[index]) + b), and
-	 * modifies array[index] to contain this new value.
-	 * 
-	 * @param array array to modify
-	 * @param index index at which to modify
-	 * @param logb  log of the second sum term
-	 */
-	public static void sum(double[] array, int index, double logb) {
-		array[index] = sum(array[index], logb);
-	}
-	
-	/**
-	 * Computes log(a + b + c + ...) from log(a), log(b), log(c), ...
-	 * by recursively splitting the input and delegating to the sum method.
-	 * 
-	 * @param  terms an array containing the log of all the terms for the sum
-	 * @return log(sum), where sum = exp(terms[0]) + exp(terms[1]) + ...
-	 */
-	public static double sumAll(double... terms) {
-		return sumAllHelper(terms, 0, terms.length);
-	}
-	
-	/**
-	 * Computes log(a_0 + a_1 + ...) from a_0 = exp(terms[begin]),
-	 * a_1 = exp(terms[begin + 1]), ..., a_{end - 1 - begin} = exp(terms[end - 1]).
-	 * 
-	 * @param  terms an array containing the log of all the terms for the sum,
-	 *               and possibly some other terms that will not go into the sum
-	 * @return log of the sum of the elements in the [begin, end) region of the terms array
-	 */
-	private static double sumAllHelper(final double[] terms, final int begin, final int end) {
-		int length = end - begin;
-		switch(length) {
-			case 0: return Double.NEGATIVE_INFINITY;
-			case 1: return terms[begin];
-			default:
-				int midIndex = begin + length/2;
-				return sum(sumAllHelper(terms, begin, midIndex), sumAllHelper(terms, midIndex, end));
-		}
-	}
-
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/util/MathUtil.java b/gi/posterior-regularisation/prjava/src/util/MathUtil.java
deleted file mode 100644
index 799b1faf..00000000
--- a/gi/posterior-regularisation/prjava/src/util/MathUtil.java
+++ /dev/null
@@ -1,148 +0,0 @@
-package util;
-
-import java.util.Random;
-
-public class MathUtil {
-	public static final boolean closeToOne(double number){
-		return Math.abs(number-1) < 1.E-10;
-	}
-	
-	public static final boolean closeToZero(double number){
-		return Math.abs(number) < 1.E-5;
-	}
-	
-	/**
-	 * Return a ramdom multinominal distribution.
-	 * 
-	 * @param size
-	 * @return
-	 */
-	public static final double[] randomVector(int size, Random r){
-		double[] random = new double[size];
-		double sum=0;
-		for(int i = 0; i < size; i++){
-			double number = r.nextDouble();
-			random[i] = number;
-			sum+=number;
-		}
-		for(int i = 0; i < size; i++){
-			random[i] = random[i]/sum;
-		}
-		return random;
-	}
-	
-	
-
-	public static double sum(double[] ds) {
-		double res = 0;
-		for (int i = 0; i < ds.length; i++) {
-			res+=ds[i];
-		}
-		return res;
-	}
-
-	public static double max(double[] ds) {
-		double res = Double.NEGATIVE_INFINITY;
-		for (int i = 0; i < ds.length; i++) {
-			res = Math.max(res, ds[i]);
-		}
-		return res;
-	}
-
-	public static double min(double[] ds) {
-		double res = Double.POSITIVE_INFINITY;
-		for (int i = 0; i < ds.length; i++) {
-			res = Math.min(res, ds[i]);
-		}
-		return res;
-	}
-
-	
-	public static double KLDistance(double[] p, double[] q) {
-		int len = p.length;
-		double kl = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					kl += q[j] * Math.log(q[j] / p[j]);
-				}
-
-		}
-		return kl;
-	}
-	
-	public static double L2Distance(double[] p, double[] q) {
-		int len = p.length;
-		double l2 = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					l2 += (q[j] - p[j])*(q[j] - p[j]);
-				}
-
-		}
-		return Math.sqrt(l2);
-	}
-	
-	public static double L1Distance(double[] p, double[] q) {
-		int len = p.length;
-		double l1 = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					l1 += Math.abs(q[j] - p[j]);
-				}
-
-		}
-		return l1;
-	}
-
-	public static double dot(double[] ds, double[] ds2) {
-		double res = 0;
-		for (int i = 0; i < ds2.length; i++) {
-			res+= ds[i]*ds2[i];
-		}
-		return res;
-	}
-	
-	public static double expDigamma(double number){
-		return Math.exp(digamma(number));
-	}
-	
-	public static double digamma(double number){
-		if(number > 7){
-			return digammApprox(number-0.5);
-		}else{
-			return digamma(number+1) - 1.0/number;
-		}
-	}
-	
-	private static double digammApprox(double value){
-		return Math.log(value) + 0.04167*Math.pow(value, -2) - 0.00729*Math.pow(value, -4) 
-		+  0.00384*Math.pow(value, -6) - 0.00413*Math.pow(value, -8);
-	}
-
-	public static double eulerGamma = 0.57721566490152386060651209008240243;
-	// FIXME -- so far just the initialization from Minka's paper "Estimating a Dirichlet distribution". 
-	public static double invDigamma(double y) {
-		if (y>= -2.22) return Math.exp(y)+0.5;
-		return -1.0/(y+eulerGamma);
-	}
-
-	
-	
-	public static void main(String[] args) {
-		for(double i = 0; i < 10 ; i+=0.1){
-			System.out.println(i+"\t"+expDigamma(i)+"\t"+(i-0.5));
-		}
-//		double gammaValue = (expDigamma(3)/expDigamma(10) + expDigamma(3)/expDigamma(10) + expDigamma(4)/expDigamma(10));
-//		double normalValue = 3/10+3/4+10/10;
-//		System.out.println("Gamma " + gammaValue + " normal " + normalValue);
-	}
-
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Matrix.java b/gi/posterior-regularisation/prjava/src/util/Matrix.java
deleted file mode 100644
index 8fb6d911..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Matrix.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package util;
-
-public class Matrix {
-	int x;
-	int y;
-	double[][] values;
-	
-	public Matrix(int x, int y){
-		this.x = x;
-		this.y=y;
-		values = new double[x][y];
-	}
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java b/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java
deleted file mode 100644
index 83a65611..00000000
--- a/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package util;
-
-
-public class MemoryTracker {
-	
-	double initM,finalM;
-	boolean start = false,finish = false;
-	
-	public MemoryTracker(){
-		
-	}
-	
-	public void start(){
-		System.gc();
-	    System.gc();
-	    System.gc();
-	    initM = (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/(1024*1024);  
-	    start = true;
-	}
-	
-	public void finish(){
-		if(!start){
-			throw new RuntimeException("Canot stop before starting");
-		}
-		System.gc();
-	    System.gc();
-	    System.gc();
-	    finalM = (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/(1024*1024);  
-	    finish = true;
-	}
-	
-	public String print(){
-		if(!finish){
-			throw new RuntimeException("Canot print before stopping");
-		}
-		return "Used: " + (finalM - initM) + "MB";
-	}
-	
-	public void clear(){
-		initM = 0;
-		finalM = 0;
-		finish = false;
-		start = false;
-	}
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Pair.java b/gi/posterior-regularisation/prjava/src/util/Pair.java
deleted file mode 100644
index 7b1f108d..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Pair.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package util;
-
-public class Pair<O1, O2> {
-	public O1 _first;
-	public O2 _second;
-
-	public final O1 first() {
-		return _first;
-	}
-
-	public final O2 second() {
-		return _second;
-	}
-
-	public final void setFirst(O1 value){
-		_first = value;
-	}
-	
-	public final void setSecond(O2 value){
-		_second = value;
-	}
-	
-	public Pair(O1 first, O2 second) {
-		_first = first;
-		_second = second;
-	}
-
-	public String toString(){
-		return _first + " " + _second; 
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Printing.java b/gi/posterior-regularisation/prjava/src/util/Printing.java
deleted file mode 100644
index 14fcbe91..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Printing.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package util;
-
-public class Printing {
-	static java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-
-	public static String padWithSpace(String s, int len){
-		StringBuffer sb = new StringBuffer();
-		while(sb.length() +s.length() < len){
-			sb.append(" ");
-		}
-		sb.append(s);
-		return sb.toString();
-	}
-	
-	public static String prettyPrint(double d, String patt, int len) {
-		fmt.applyPattern(patt);
-		String s = fmt.format(d);
-		while (s.length() < len) {
-			s = " " + s;
-		}
-		return s;
-	}
-	
-	public static  String formatTime(long duration) {
-		StringBuilder sb = new StringBuilder();
-		double d = duration / 1000;
-		fmt.applyPattern("00");
-		sb.append(fmt.format((int) (d / (60 * 60))) + ":");
-		d -= ((int) d / (60 * 60)) * 60 * 60;
-		sb.append(fmt.format((int) (d / 60)) + ":");
-		d -= ((int) d / 60) * 60;
-		fmt.applyPattern("00.0");
-		sb.append(fmt.format(d));
-		return sb.toString();
-	}
-	
-	
-	public static String doubleArrayToString(double[] array, String[] labels, String arrayName) {
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		res.append("\n");
-		for (int i = 0; i < array.length; i++) {
-			if (labels == null){
-				res.append(i+"       \t");
-			}else{
-				res.append(labels[i]+     "\t");
-			}
-		}
-		res.append("sum\n");
-		double sum = 0;
-		for (int i = 0; i < array.length; i++) {
-			res.append(prettyPrint(array[i],
-					"0.00000E00", 8) + "\t");
-			sum+=array[i];
-		}
-		res.append(prettyPrint(sum,
-				"0.00000E00", 8)+"\n");
-		return res.toString();
-	}
-	
-	
-	
-	public static void printDoubleArray(double[] array, String labels[], String arrayName) {
-		System.out.println(doubleArrayToString(array, labels,arrayName));
-	}
-	
-	
-	public static String doubleArrayToString(double[][] array, String[] labels1, String[] labels2,
-			String arrayName){
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		res.append("\n\t");
-		//Calculates the column sum to keeps the sums
-		double[] sums = new double[array[0].length+1];
-		//Prints rows headings
-		for (int i = 0; i < array[0].length; i++) {
-			if (labels1 == null){
-				res.append(i+"        \t");
-			}else{
-				res.append(labels1[i]+"        \t");
-			}
-		}
-		res.append("sum\n");
-		double sum = 0;
-		//For each row print heading
-		for (int i = 0; i < array.length; i++) {
-			if (labels2 == null){
-				res.append(i+"\t");
-			}else{
-				res.append(labels2[i]+"\t");
-			}
-			//Print values for that row
-			for (int j = 0; j < array[0].length; j++) {
-				res.append(" " + prettyPrint(array[i][j],
-						"0.00000E00", 8) + "\t");
-				sums[j] += array[i][j]; 
-				sum+=array[i][j]; //Sum all values of that row
-			}
-			//Print row sum
-			res.append(prettyPrint(sum,"0.00000E00", 8)+"\n");
-			sums[array[0].length]+=sum;
-			sum=0;
-		}
-		res.append("sum\t");
-		//Print values for colums sum
-		for (int i = 0; i < array[0].length+1; i++) {
-			res.append(prettyPrint(sums[i],"0.00000E00", 8)+"\t");
-		}
-		res.append("\n");
-		return res.toString();
-	}
-	
-	public static void printDoubleArray(double[][] array, String[] labels1, String[] labels2
-			, String arrayName) {
-		System.out.println(doubleArrayToString(array, labels1,labels2,arrayName));
-	}
-	
-	
-	public static void printIntArray(int[][] array, String[] labels1, String[] labels2, String arrayName,
-			int size1, int size2) {
-		System.out.println(arrayName);
-		for (int i = 0; i < size1; i++) {
-			for (int j = 0; j < size2; j++) {
-				System.out.print(" " + array[i][j] +  " ");
-
-			}
-			System.out.println();
-		}
-		System.out.println();
-	}
-	
-	public static String intArrayToString(int[] array, String[] labels, String arrayName) {
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		for (int i = 0; i < array.length; i++) {
-			res.append(" " + array[i] + " ");
-			
-		}
-		res.append("\n");
-		return res.toString();
-	}
-	
-	public static void printIntArray(int[] array, String[] labels, String arrayName) {
-		System.out.println(intArrayToString(array, labels,arrayName));
-	}
-	
-	public static String toString(double[][] d){
-		StringBuffer sb = new StringBuffer();
-		for (int i = 0; i < d.length; i++) {
-			for (int j = 0; j < d[0].length; j++) {
-				sb.append(prettyPrint(d[i][j], "0.00E0", 10));
-			}
-			sb.append("\n");
-		}
-		return sb.toString();
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Sorters.java b/gi/posterior-regularisation/prjava/src/util/Sorters.java
deleted file mode 100644
index 836444e5..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Sorters.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package util;
-
-import java.util.Comparator;
-
-public class Sorters {
-	public static class sortWordsCounts implements Comparator{
-		
-		/**
-		 * Sorter for a pair of word id, counts. Sort ascending by counts
-		 */
-		public int compare(Object arg0, Object arg1) {
-			Pair<Integer,Integer> p1 = (Pair<Integer,Integer>)arg0;
-			Pair<Integer,Integer> p2 = (Pair<Integer,Integer>)arg1;
-			if(p1.second() > p2.second()){
-				return 1;
-			}else{
-				return -1;
-			}
-		}
-		
-	}
-	
-public static class sortWordsDouble implements Comparator{
-		
-		/**
-		 * Sorter for a pair of word id, counts. Sort by counts
-		 */
-		public int compare(Object arg0, Object arg1) {
-			Pair<Integer,Double> p1 = (Pair<Integer,Double>)arg0;
-			Pair<Integer,Double> p2 = (Pair<Integer,Double>)arg1;
-			if(p1.second() < p2.second()){
-				return 1;
-			}else{
-				return -1;
-			}
-		}
-		
-	}
-}