JAVA 多线程解决复杂度较高的算法问题

//再求基于GOTerm的基因相似度算法的时候 使用JAVA多线程开启20个线程

package com.txt;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Vector;
import java.util.concurrent.CopyOnWriteArrayList;
import java.util.regex.*;

public class genesSimilarityF {

public static double genePairSimilarity(String gene1, String gene2,
List<String> allgene, List<String> allgo,List<String> GO,List<String> GOTime) throws IOException {

List<String> term1 = findgenesGo(gene1, allgene, allgo);
List<String> term2 = findgenesGo(gene2, allgene, allgo);
List<String> goterm = findSame(term1, term2);
double result = genesSimilarity(goterm,allgene,allgo,GO,GOTime);
return result;
}

public static List<String> findSame(List<String> term1, List<String> term2) {
List<String> same = new ArrayList<String>();
for (String s1 : term1) {
for (String s2 : term2) {
if (s1.equals(s2) || s1 == s2) {
same.add(s2);
}
}
}
return same;
}

public static List<String> findgenesGo(String gene, List<String> allgene,
List<String> allgo) {
List<String> term1 = new ArrayList<String>();
for (int i = 0; i < allgene.size(); i++) {
String s = allgene.get(i);
if (gene.equals(s) || gene == s) {
term1.add(allgo.get(i));
}
}
return term1;
}

public static int Count(String in, List<String> Go,List<String> GoTime) {
int count = 0;
for (int i =0;i<Go.size();i++) {
if (in.equals(Go.get(i)) || in == Go.get(i)) {
count = Integer.parseInt(GoTime.get(i));
}
}
return count;
}

public static double genesSimilarity(List<String>Go, List<String> allgene,
List<String> allgo,List<String> GO,List<String> GOTime) throws IOException {
if (Go.size() == 0) {
return 0.0;
}

int[] count = new int[Go.size()];
int i = 0;
for (String go : Go) {

count[i++] = Count(go,GO,GOTime);
}

int min = count[0];

for (int j = 1; j < count.length; j++) {
if (count[j] < min) {
4000

min = count[j];
}
}

double result = 0.0;

DecimalFormat df = new DecimalFormat();
df.setMaximumFractionDigits(5);
result = 2.0 / (double) min;
return result;
}

public static String[] cutString(String in) {

return in.split(" ");
}

public static HashSet<String> getAllGenes(String disease) {
String realFile = "GeneSet\\" + disease;
HashSet<String> genes = new HashSet<String>();
try {
BufferedReader br = new BufferedReader(new FileReader(new File(
realFile)));

String line = br.readLine();
while (line != null) {
genes.add(line.trim());
line = br.readLine();
}
} catch (FileNotFoundException e) {

e.printStackTrace();
} catch (IOException e) {

e.printStackTrace();
}
return genes;
}

public static void diseaseSimilarity(String s1, String s2,
HashSet<String> genes1, HashSet<String> genes2,
List<String> ALLGene, List<String> AllGo,List<String> GO,List<String> GOTime) throws IOException {

double simsum = 0.0;
for (String g1 : genes1) {
for (String g2 : genes2) {
simsum += genePairSimilarity(g1, g2, ALLGene, AllGo,GO,GOTime);
}
}
System.out.println("Similarity:"
+ s1
+ ","
+ s2
+ ":"
+ String.format("%1$.6f",
simsum / (genes1.size() * genes2.size())));
try {
FileWriter writer = new FileWriter("D://genesSimilarityFFF1//"+s1+"--"+s2+".txt", true);
writer.write(s1+ " "+ s2+ " "+ String.format("%1$.6f",
simsum / (genes1.size() * genes2.size()))+"\n");
writer.close();
} catch (IOException e) {
e.printStackTrace();
}

}

public static List<String> readAllGene(File f) throws IOException {
List<String> r = new ArrayList<String>();
if (f.isFile() && f.exists()) {
InputStreamReader reader = new InputStreamReader(
new FileInputStream(f));
BufferedReader bufferR = new BufferedReader(reader);
String lineTxt = "";
while ((lineTxt = bufferR.readLine()) != null) {
String[] out = cutString(lineTxt);
String in = out[0];
r.add(in);
}
}
return r;
}

public static List<String> readAllGo(File f) throws IOException {
List<String> r = new ArrayList<String>();
if (f.isFile() && f.exists()) {
InputStreamReader reader = new InputStreamReader(
new FileInputStream(f));
BufferedReader bufferR = new BufferedReader(reader);
// String GoTermId = null;
String lineTxt = "";
while ((lineTxt = bufferR.readLine()) != null) {
String[] out = cutString(lineTxt);
String in = out[1];
r.add(in);
}
}
return r;
}

public static LinkedList<String> Disease1() throws IOException {
LinkedList<String> r = new LinkedList<String>();
File f = new File("GeneSet//HPOName.txt");
if (f.isFile() && f.exists()) {
InputStreamReader reader = new InputStreamReader(
new FileInputStream(f));
BufferedReader bufferR = new BufferedReader(reader);
// String GoTermId = null;
String lineTxt = "";
while ((lineTxt = bufferR.readLine()) != null) {
String[] out = cutString(lineTxt);
String in = out[0];
r.add(in);
}
}
return r;
}

public static LinkedList<String> Disease2() throws IOException {
LinkedList<String> r = new LinkedList<String>();
File f = new File("GeneSet//HPOName.txt");
if (f.isFile() && f.exists()) {
InputStreamReader reader = new InputStreamReader(
new FileInputStream(f));
BufferedReader bufferR = new BufferedReader(reader);
// String GoTermId = null;
String lineTxt = "";
while ((lineTxt = bufferR.readLine()) != null) {
String[] out = cutString(lineTxt);
String in = out[1];
r.add(in);
}
}
return r;
}

public static void main(String[] args) throws Exception{
File file = new File("E:\\开题\\gene_association.goa_human\\FFF.txt");
File file2 = new File("E:\\开题\\gene_association.goa_human\\fgo.txt");
List<String> AllGene = readAllGene(file);
List<String> AllGo = readAllGo(file);
List<String> GO = readAllGene(file2);
List<String> GOTime = readAllGo(file2);
LinkedList<String> disease1 = Disease1();
LinkedList<String> disease2 = Disease2();
// List<String> dis1 = Collections.synchronizedList(disease1);
// List<String> dis2 = Collections.synchronizedList(disease2);
// for (int i = 0; i < disease1.size(); i++) {
// HashSet<String> genes1 = getAllGenes(disease1.get(i) + ".txt");
// HashSet<String> genes2 = getAllGenes(disease2.get(i) + ".txt");
// diseaseSimilarity(disease1.get(i), disease2.get(i), genes1, genes2,
// AllGene, AllGo,GO,GOTime);
// }
// for(int i =0;i<disease2.size();i++)
// System.out.println(i+"###"+disease2.get(i));

for(int i =0;i<20;i++){
new Thread(new MultiThread(disease1,disease2, AllGene, AllGo, GO, GOTime)).start();
}

}
}