文本处理，将交互组数据转化成邻接矩阵

public static void main(String[] args) throws Exception {File file = new File("C:\\Users\\xuchichi\\Desktop\\method3\\123.txt");List<String> gene1 = readGeneName1(file);List<String> gene2 = readGeneName2(file);List<String> weight = readGeneName3(file);HashSet<String> geneId = insertGene(gene1,gene2);//读二元关系List<String> geneID = new ArrayList<String>(geneId);int n = geneID.size();float [][]arr = new float[n][n];for(int i=0;i<n;i++)for(int j=0;j<n;j++)arr[i][j] = 0;//initial(arr,gene1,gene2,weight,geneID);//初始化矩阵//ComputePath_IR_Whole((float) 0.2,arr,n);//迭代更新矩阵并将结果写入文件File file2 = new File("C:\\Users\\xuchichi\\Desktop\\method3\\456.txt");List <String> sim = readFileOne(file2);//读基因相似度readGeneSet(geneID,sim);//for(int i =0;i<n;i++)//System.out.println(geneID.get(i)+" "+i);}private static List<String> readFileOne(File file2) throws IOException{// TODO Auto-generated method stubList<String> r = new ArrayList<String>();if (file2.isFile() && file2.exists()) {InputStreamReader reader = new InputStreamReader(new FileInputStream(file2));BufferedReader bufferR = new BufferedReader(reader);// String GoTermId = null;String lineTxt = "";int count =0;while((lineTxt = bufferR.readLine()) != null){count++;if(count==6){String[] out = cutString(lineTxt);for(String s:out)r.add(s);break;}lineTxt = "";}}return r;}public static void readGeneSet(List<String> geneID,List <String> sim) throws IOException{File file2= new File("C:\\Users\\xuchichi\\Desktop\\method3\\result.txt");FileWriter out = new FileWriter(file2);System.out.println(geneID.size()+" "+sim.size());for(int i =0;i<geneID.size();i++){System.out.println(geneID.get(5)+" "+geneID.get(i)+sim.get(i));out.write(geneID.get(5)+"\t"+geneID.get(i)+"\t"+sim.get(i)+"\n");}}public static void initial(float[][]arr,List<String>gene1,List<String>gene2,List<String>weight,List<String>geneId){for(int i=0;i<gene1.size();i++){String str1 = gene1.get(i);String str2 = gene2.get(i);int x=-1;int y=-1;for(int j=0;j<geneId.size();j++){if(str1.equals(geneId.get(j)))x = j;if(str2.equals(geneId.get(j)))y = j;}arr[x][y] = Float.valueOf(weight.get(i));//System.out.println(i+" "+str1+" "+str2+" "+x+" "+y+" "+arr[x][y]);}}public static List<String> readGeneName1(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[0];r.add(in);}}return r;}public static List<String> readGeneName2(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 List<String> readGeneName3(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[2];r.add(in);}}return r;}public static String[] cutString(String in) {return in.split("");}public static HashSet<String>insertGene(List<String>list1,List<String>list2){HashSet<String> res = new HashSet<String>();for(int i =0;i<list1.size();i++){res.add(list1.get(i));res.add(list2.get(i));}return res;}