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Create Utilities.java

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sus11005 committed Sep 28, 2016
1 parent 8156e81 commit ac2d9e915f0b79acd9ca37accbecc56786c90222
Showing with 226 additions and 0 deletions.
  1. +226 −0 COMPRESSION/Utilities.java
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import java.io.*;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Random;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class Utilities {

public static String genomic_sequence = "";
public static List<Integer> position_list = new ArrayList<Integer>();

public static List<Contig> restList;

public static String readSequence(String sequenceFileName) throws IOException {
System.out.println("READING SEQUENCE...");

FileInputStream fileInputStream = new FileInputStream(sequenceFileName);
DataInputStream dataInputStream = new DataInputStream(fileInputStream);
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(dataInputStream));
String line;
StringBuilder sequence = new StringBuilder();

while ((line = bufferedReader.readLine()) != null) {
if (!line.startsWith(">")) {
sequence.append(line);
}
}
return sequence.toString();
}

public static List<String> readContigs(String contigsFileName) throws IOException {
List<String> list = new ArrayList<String>();
FileInputStream fileInputStream = new FileInputStream(contigsFileName);
DataInputStream dataInputStream = new DataInputStream(fileInputStream);
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(dataInputStream));
String line;
while ((line = bufferedReader.readLine()) != null) {
if (!line.contains("contig")) {
list.add(line);
}
}
return list;
}

public static List<Integer> positionsOfPattern(String text, String pattern, double probability) {
List<Integer> positions = new ArrayList<Integer>();
Pattern p = Pattern.compile(pattern);
Matcher m = p.matcher(text);
while (m.find()) {
positions.add(m.start());
/*if (!canNotBeAdded(probability)) {
positions.add(m.start());
} else {
//System.out.println("MISSED...");
}*/
}
return positions;
}

public static int count_occurrences(String text, String pattern) {
Pattern p = Pattern.compile(pattern);
Matcher m = p.matcher(text);
int count = 0;
while (m.find()) {
count++;
}
return count;
}

public static boolean canNotBeAdded(double probability) {

if (probability <= 0.0) {
return false;
}
Random random = new Random();
double randomNumber = random.nextDouble();
return randomNumber <= probability;
}

public static void writeToDisk(String fileName, String text, boolean append) throws IOException {
FileWriter fstream = new FileWriter(fileName, append);
BufferedWriter out = new BufferedWriter(fstream);
out.write(text);
out.close();
}

public static void write(String fileName, String text, boolean append) throws IOException {
FileWriter fileWriter = new FileWriter(fileName, append);
BufferedWriter out = new BufferedWriter(fileWriter);
out.write(text);
out.close();
}

public static List<Double> getFragmentSizeList(String sequence, String pattern, double probability, double elongation) throws IOException {

List<Integer> list = positionsOfPattern(sequence, pattern, probability);
position_list.addAll(list);

if (list.size() <= 1) {

if (list.size() == 1) {
Contig contig = new Contig();
contig.setStartingPosition(list.get(0));
restList.add(contig);
}

return null;
}

List<Double> fragmentSizeList = new ArrayList<Double>();
fragmentSizeList.add((double) (list.get(0) + pattern.length()));
if (elongation > 1) {
Random random = new Random();
for (int i = 1; i < list.size(); i++) {
if (random.nextInt(2) == 1) {
double size = list.get(i) - list.get(i - 1);
double increaseBy = size * ((double) random.nextInt((int) elongation)) / 100;
size = size + increaseBy;
fragmentSizeList.add(size);
} else {
double size = list.get(i) - list.get(i - 1);
double decreaseBy = size * ((double) random.nextInt((int) elongation)) / 100;
size = size - decreaseBy;
fragmentSizeList.add(size);
}
}
} else {
for (int i = 1; i < list.size(); i++) {
double size = list.get(i) - list.get(i - 1);
fragmentSizeList.add(size);
}
}

return fragmentSizeList;
}

public static void createOpMap(String opFileName, List<Double> list) throws IOException {
deleteFile(opFileName);
StringBuilder text = new StringBuilder();
for (int i = 0; i < list.size(); i++) {
text.append(String.valueOf(list.get(i).intValue()) + "\n");
}
writeToDisk(opFileName, text.toString(), false);
}

public static void deleteFile(String fileName) {
File file = new File(fileName);
if (file.exists()) {
file.delete();
}
}

public static List<Double> readOpMap(String fileName) throws IOException {
List<Double> list = new ArrayList<Double>();
FileInputStream fileInputStream = new FileInputStream(fileName);

DataInputStream dataInputStream = new DataInputStream(fileInputStream);
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(dataInputStream));

String strLine;

while ((strLine = bufferedReader.readLine()) != null) {
list.add((double) Integer.parseInt(strLine));
}

dataInputStream.close();
return list;
}

public static int min(int a, int b, int c) {
return (Math.min(Math.min(a, b), c));
}

public static List<String> createContigs(String sequence, int length) throws IOException {

List<String> contigs = new ArrayList<String>();

System.out.println("TARGET SIZE: " + sequence.length());

int parts = sequence.length() / length;
String contig = "";
int start = 0, end = 0;

for (int i = 0; i <= parts; i++) {
if (i == 0) {
end = length;
contig = sequence.substring(start, end);
contigs.add(contig);
} else if (i < parts) {
start = end;
end = start + length;
contig = sequence.substring(start, end);
contigs.add(contig);
} else {
/*start = end;
contig = sequence.substring(start);
contigs.add(contig);*/

start = end;
contig = sequence.substring(start);
contig = contigs.get(contigs.size() - 1) + contig;
contigs.set((contigs.size() - 1), contig);
}
}
return contigs;
}

public static void similarityCheck(String fileOne, String fileTwo) throws IOException {
String s1 = readSequence(fileOne);
List<String> list = readContigs(fileTwo);
String s2 = "";
for (String string : list) {
s2 += string;
}

if (s1.equals(s2)) {
System.out.println("HURRAY! SIMILAR...");
} else {
System.out.println("OH GOD! NOT SIMILAR...");
}

System.out.println(s1.length() + " " + s2.length());
}
}

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