package edu.ucsc.genome.qa.lib;
import java.io.*;
import java.util.*;

/**
 *  Genome Library Tools. 
 */
public class QALibrary {

 /**
  *  Checks for existence of file.
  *
  *  @param  filename  The name of the file.
  *
  *  @return  True if filename exists.
  */
  static public boolean checkFile(String filename) {

    try {
      File fin = new File(filename);
      if (fin.exists()) {
        return (true);
      }
      return (false);
    } catch (Exception e) {
      return (false);
    }
  }

 /**
  *  Checks for existence of directory.
  *
  *  @param  dirname  The name of the directory.
  *
  *  @return  True if directory name exists.
  */
  static public boolean checkDir(String dirname) {
  
    try {
      File fin = new File(dirname);
      if (fin.exists() && fin.isDirectory()) {
        return (true);
      }
      return (false);
    } catch (Exception e) {
      return (false);
    }
  }

 /**
  *  Reads a file into an ArrayList.
  *
  *  @param  inputfile  The name of the input file.
  *
  *  @return  List of Strings representing lines in the file.
  */
  static public ArrayList readFile(String inputfile) {

    ArrayList newList = new ArrayList();
    String thisLine;
    BufferedReader br;

    try {
      FileReader fin = new FileReader(inputfile);
      br = new BufferedReader(fin);
      while ((thisLine = br.readLine()) != null) {
        newList.add(thisLine);
      }
      br.close();
      fin.close();
    } catch (Exception e) {
      System.out.println("Exception reading file " + inputfile);
      System.out.println(e.getMessage());
    }
    return (newList);
  }
      
  // read properties
 /**
  *  Reads a property list into a Properties object.
  *
  *  @param  filename  The file containing the properties.
  *
  *  @return  The Properties listed in the file.
  */
  public static Properties readProps(String filename) {
    FileInputStream fin = null;
    Properties proplist = new Properties();
    try {
      fin = new FileInputStream(filename);
      proplist.load(fin);
      fin.close();
    } catch (FileNotFoundException e) {
      System.out.println("Can't find properties file");
      // proplist.put("prop0", "??");
    } catch (IOException e) {
      System.out.println("Error reading properties file");
    }
    return proplist;
  }

 /**
  *  Counts the hnubmer of characters in a file.
  *
  *  @param  filename  The file.
  *
  *  @return  The number of characters in the file.
  */
  static public int numCharsInFile(String filename) {

    FileReader fin;
    BufferedReader br;
    int inputChar;
    int inputlen=0; 

    try {
      fin = new FileReader(filename);
      br = new BufferedReader(fin);
      while (true) {
        inputChar = br.read();
        if (inputChar == -1) break;
        inputlen++;
      }
      br.close();
      fin.close();
    } catch (Exception e) {
      System.out.println("Error counting chars in " + filename);
      System.out.println(e.getMessage());
    }
    return (inputlen);
  }

  /**
   * Select a random sample out of ArrayList, optionally forcing ends to be used.
   */
  public static ArrayList randomSubArray(ArrayList full, Random random,
  	int sampleCount, boolean useEnds) {
    int size = full.size();
    if (size <= sampleCount)
        return full;
    ArrayList samples = new ArrayList();
    if (useEnds) {
        samples.add(full.get(0));
	samples.add(full.get(size-1));
	sampleCount -= 2;
    }
    for (int i=0; i<sampleCount; ++i)
	samples.add(full.get(random.nextInt(size)));
    return samples;
  }


  static public HashSet getSetFromFile(String filename) {

    FileReader fin;
    BufferedReader br;
    String thisline;
    HashSet set;

    set = new HashSet();

    try {
      fin = new FileReader(filename);
      br = new BufferedReader(fin);

      while ((thisline = br.readLine()) != null) {
        set.add(thisline);
      }

      fin.close();
      System.out.println(set.size() + " items found");

    } catch (FileNotFoundException e) { 
      System.out.println("HGLibrary:getSetFromFile:");
      System.out.println("Can't open input file");
    } catch (IOException e) {
      System.out.println("HGLibrary:getSetFromFile:");
      System.out.println("Error reading input file");
    }

    return (set);
  }
}