I am stuck witch Java project : i am having trouble in this lines 
//obj.generateIndexes(failuSarasas, 2);
HashMap<String, HashMap<String, Integer>> indTwoList = obj.generateIndexes(failuSarasas, 2);
obj.printHashMap(indTwoList);
//obj.generateIndexMatrix(indTwoList, failuSarasas);

 and 

HashMap<String, HashMap<String, Integer>> indexList = new HashMap<String, HashMap<String, Integer>>();
for (int i = 0; i < fileList.length; i++)
		

maybe can somebody help me?

        package modeliavimas2;

        import java.io.*;
        import java.util.*;
 
        import org.apache.commons.io.FileUtils;

        public class mainas
     {
	  public static void main(String[] args) throws IOException
	{
		mainas obj = new mainas();
		File[] failuSarasas = obj.getFileList();

		//obj.generateIndexes(failuSarasas, 2);
		HashMap<String, HashMap<String, Integer>> indTwoList = obj.generateIndexes(failuSarasas, 2);
		obj.printHashMap(indTwoList);
		//obj.generateIndexMatrix(indTwoList, failuSarasas);
		
		Scanner scaner = new Scanner(System.in);
		System.out.println("Iveskite termina arba 1, kad iseit");
		while(true)
		{
			String phrase = scaner.nextLine();
			if(phrase.equals("1"))
			{
				break;
			}
			obj.search(phrase, 2);
			System.out.println("Iveskite termina arba 1, kad iseit");
		}
		 
		scaner.close();
	}
	public File[] getFileList()
	{
		File folder = new File(
				" C:\\Users\\Dell Pc\\Desktop\\inform\\Informacijos modeliavimas\\Informacijos modeliavimas\\ld2\\pages");
		File[] listOfFiles = folder.listFiles();
		return listOfFiles;
	}

	public HashMap<String, HashMap<String, Integer>> generateIndexes(File[] fileList, int phraseLen) throws IOException
	{
		HashMap<String, HashMap<String, Integer>> indexList = new HashMap<String, HashMap<String, Integer>>();
		for (int i = 0; i < fileList.length; i++)
		{
			ArrayList<String> pageWords = new ArrayList<String>();
			HashMap<String, Integer> hashMap = new HashMap<String, Integer>();
			File file = fileList[i];
			if (file.isFile() && file.getName().endsWith(".txt"))
			{
				String content = FileUtils.readFileToString(file, "UTF8");
				for (String a : content.split(" "))
				{
					a = a.toLowerCase();
					a = a.replaceAll("\\W|\\d|\\_", ""); // isvalyt visus
															// neraidinius arba neskaicius
					if (a.length() >= 3 && a.length() <= 15)
					{
						pageWords.add(a); // 
					}
				}
				if(phraseLen <= 1)
				{
					for(String a : pageWords)
					{
						if(!hashMap.containsKey(a))
						{
							hashMap.put(a, 1);
						} else
						{
							hashMap.put(a, hashMap.get(a) + 1);
						}
					}
				}
				else
				{
					for(int j = phraseLen; j < pageWords.size(); j++)
					{
						String a = pageWords.get(j-1) + " "+ pageWords.get(j);
						if(!hashMap.containsKey(a))
						{
							hashMap.put(a, 1);
						}
						else
						{
							hashMap.put(a, hashMap.get(a) + 1);
						}
					}
				}
				indexList.put(file.getName(), hashMap);
			}
		}
		return indexList;
	}

	public void printHashMap(HashMap<String, HashMap<String, Integer>> indexList)
	{
		for (String a : indexList.keySet())
		{
			HashMap<String, Integer> map = indexList.get(a);
			for (String b : map.keySet())
			{
				String key = b.toString();
				String value = map.get(b).toString();
				System.out.println(key + " " + value);
			}
		}

	}

	public void generateIndexMatrix(HashMap<String, HashMap<String, Integer>> indexList, File[] fileList)
			throws FileNotFoundException, UnsupportedEncodingException
	{
		PrintWriter writer = new PrintWriter("debug2.txt", "UTF-8");
		ArrayList<String> termList = new ArrayList<String>();
		for (String a : indexList.keySet())
		{
			HashMap<String, Integer> map = indexList.get(a);
			for (String b : map.keySet())
			{
				if (!termList.contains(b.toString()))
				{
					termList.add(b.toString());
				}
			}
		}
		String[][] matrix = new String[fileList.length+1][termList.size()+1];
		int counter = 1;
		for (String a : termList)
		{
			matrix[0][counter++] = a;
		}
		counter = 1;
		for(File a : fileList)
		{
			matrix[counter++][0] = a.getName();
		}
		for(int i = 0; i < matrix.length; i++)
		{
			for(int j = 0; j < matrix[i].length; j++)
			{
				if(i > 0 && j > 0)
				{
					if(indexList.get(matrix[i][0]).get(matrix[0][j]) != null)
					{
						writer.print(indexList.get(matrix[i][0]).get(matrix[0][j]) + " ");
					}
					else
					{
						writer.print(0+" ");
					}
				}
				else
				{
					writer.print(matrix[i][j]+" ");
				}
			}
			writer.println();
		}
		writer.close();
	}
	public void search(String searchPhrase, int phraseLen) throws IOException
	{
		String[] searchTermsRaw = searchPhrase.split(" ");
		ArrayList<String> searchTermsProc = new ArrayList<String>();
		
		// apdorojam paieskos zodzius
		if(phraseLen <= 1)
		{
			for(String a : searchTermsRaw)
			{
				a = a.toLowerCase();
				a = a.replaceAll("\\W|\\d|\\_", "");
				searchTermsProc.add(a);
			}
		}
		else
		{
			for(int i = 1; i < searchTermsRaw.length; i++)
			{
				searchTermsRaw[i] = searchTermsRaw[i].replaceAll("\\W|\\d|\\_", "");
				String a = searchTermsRaw[i - 1] + " " + searchTermsRaw[i];
				a = a.toLowerCase();
				searchTermsProc.add(a);
			}
		}


		ArrayList<ArrayList<String>> indexMatrix = new ArrayList<ArrayList<String>>();
		ArrayList<String> containingPages = new ArrayList<String>();
		try (BufferedReader br = new BufferedReader(new FileReader("c:\\Users\\ASUSPC\\Documents\\Uni stuff\\Eclipse projects\\modeliavimas2\\debug2.txt"))) // irasyti indexu matricos faila
		{
			String line = br.readLine();
            Boolean firstLine = true;
			while (line != null)
			{
				ArrayList<String> list = new ArrayList<String>();
				if(phraseLen <= 1)
				{
					for(String a : line.split(" "))
					{
						list.add(a);
					}
				}
				else
				{
					String[] a = line.split(" ");
					for(int i = 1; i < a.length; i++)
					{
					    String temp = "";
					    if(firstLine)
                        {
                            if(i+1 < a.length)
                            {
                                temp = a[i] + " " + a[i + 1];
                            }
                            i++;
                        }
						else
                        {
                             temp = a[i];
                        }
						list.add(temp);
					}
				}
				indexMatrix.add(list);
                firstLine = false;
				line = br.readLine();
			}
		}
		for(int i = 1; i < indexMatrix.size(); i++)
		{
			int counter = 0;
			for(String a : searchTermsProc)
			{
				int xpos = indexMatrix.get(0).indexOf(a);
				if(xpos == -1)
				{
					continue;
				}
				if(Integer.parseInt(indexMatrix.get(i).get(xpos)) != 0)
				{
					counter++;
				}
			}
			if(counter == searchTermsProc.size())
			{
				containingPages.add(String.valueOf(i));
			}
			counter = 0;
		}
		System.out.println("Rasti terminai rasti:");
		for(String a: containingPages)
		{
			System.out.println(a);
		}
		if(containingPages.size() == 0)
		{
			System.out.println("Terminas nerastas nei viename dokumente");
		}
	}
}
