package cquest.utils;
//------------------------------------------------------------------------
//                           FileAccess.java
//------------------------------------------------------------------------
//
// HISTORY :
//------------------------------------------------------------------------
//|Date    |Author     |Method/Description                               |
//------------------------------------------------------------------------
//------------------------------------------------------------------------
//
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;
/** this class allows to do read/write a file. It is used to save or load a metabolite
or a model. In the first case, the file matches with the metabolite and in the second with
a model. A model is the prior knowledge used by Amares, so it is the GroupManager
@author 	C. Couturier
@version 	%I%, %U%*/
public class FileAccess  {
  //------------------------------------------------------------------------
  //variables
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  //constructor
  //------------------------------------------------------------------------
  /** constructor
  @author 	C. Couturier
  @version 	%I%, %U%*/
  public FileAccess() {
  }
  //------------------------------------------------------------------------
  //methods
  //------------------------------------------------------------------------
  /** this method allows to compress a file
  	@param file to be compressed
   	@param 		extension of the compressed file
    	@return		compressed file
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  private static File compress(File filein, String extension) {
    String s = filein.getName();
    int k = s.lastIndexOf('.');
    String name;
    if (k > 0) {
      name = s.substring(0, k);
    }
    else {
      name = filein.getName();
    }
    File filetemp = new File(filein.getParent(), name + extension);
		//Mrui.logger.info("compress " + filetemp.getName());
    FileInputStream fis = null;
    FileOutputStream fos = null;
    try {
      fis = new FileInputStream(filein);
      fos = new FileOutputStream(filetemp);
      ZipOutputStream zos = new ZipOutputStream(fos);
      ZipEntry ze = new ZipEntry(s);
      zos.putNextEntry(ze);
      final int BUFSIZ = 4096;
      byte inbuf[] = new byte[BUFSIZ];
      int n;
      while ((n = fis.read(inbuf)) != -1)
        zos.write(inbuf, 0, n);
      fis.close();
      fis = null;
      zos.close();
      fos = null;
    }
    catch (IOException e) {
      return (File) null;
    }
    finally {
      try {
        if (fis != null)
          fis.close();
        if (fos != null)
          fos.close();
      }
      catch (IOException e) {
      }
    }
    try {
      filein.delete();
    }
    catch (Exception e) {
			System.out.println(e.getMessage());
      return (File) null;
    }
    return filetemp;
  }
  /** this method uncompresses a file
  @param 		file to uncompress
  @return 	uncompressed file
  @author 	C. Couturier
  @version 	%I%, %U%*/
  private static File uncompress(File filein) {
    String s = filein.getName();
    int k = s.lastIndexOf('.');
    String name = s.substring(0, k);
    File fileout = new File(filein.getParent(), name);
    FileInputStream fis = null;
    FileOutputStream fos = null;
    try {
      fis = new FileInputStream(filein);
      fos = new FileOutputStream(fileout);
      ZipInputStream zis = new ZipInputStream(fis);
      ZipEntry ze = zis.getNextEntry();
      final int BUFSIZ = 4096;
      byte inbuf[] = new byte[BUFSIZ];
      int n;
      while ((n = zis.read(inbuf, 0, BUFSIZ)) != -1)
        fos.write(inbuf, 0, n);
      zis.close();
      fis = null;
      fos.close();
      fos = null;
    }
    catch (IOException e) {
      System.out.println(e.getMessage());
    }
    finally {
      try {
        if (fis != null)
          fis.close();
        if (fos != null)
          fos.close();
      }
      catch (IOException e) {
				System.out.println(e.getMessage());
      }
    }
    return fileout;
  }
  /** to write the Model in file.
  @param 		file in to write
  @param 		group manager
  @return 	void
  @author 	C. Couturier
  @version 	%I%, %U%*/
  /*	public void writeModel(File fmodel, GroupManager gmn)
  	{
  		try{
  			FileOutputStream fileOut = new FileOutputStream(fmodel);
  			ObjectOutputStream dataOut = new ObjectOutputStream(fileOut);
  			dataOut.writeObject((GroupManager)gmn);
  			dataOut.close();
  			fileOut.close();
  		} catch (Exception e){;}
  		File fileout = compress(fmodel, ".mod");
  	}
  
  	/** to read the model useful for Amares
  	@param 		file to read
  	@return 	model (GroupManager)
  	@return 	void
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  /*	public GroupManager readModel(File fmodel)
  	{
  		GroupManager gmn =(GroupManager)null;
  		if (!(checkExtension("mod", fmodel))) return gmn;
  		File f = uncompress(fmodel);
  		try{
  			FileInputStream fileIn = new FileInputStream(f);
  			ObjectInputStream dataIn = new ObjectInputStream(fileIn);
  			gmn = (GroupManager)dataIn.readObject();
  			dataIn.close();
  			fileIn.close();
  		}catch (Exception e) {return (GroupManager)null;}
  		try{
  			f.delete();
  		}catch(Exception e){return gmn;}
  		return gmn;
  	}
  
  	/** to write the prior knowledge in file.
  	@param 		file in to write
  	@param 		prior knowledge
  	@return 	void
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  /*	public void writePK(File fvs, PriorKnowledge pk)
  	{
  		try{
  			FileOutputStream fileOut = new FileOutputStream(fvs);
  			ObjectOutputStream dataOut = new ObjectOutputStream(fileOut);
  			dataOut.writeObject((PriorKnowledge)pk);
  			dataOut.close();
  			fileOut.close();
  		} catch (Exception e){;}
  		File fileout = compress(fvs, ".pk");
  	}
  
  	/** to read the prior knowledge useful for Amares
  	@param 		file to read
  	@return 	prior knowledge
  	@return 	void
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  /*	public PriorKnowledge readPK(File fpk)
  	{
  		PriorKnowledge pk =(PriorKnowledge)null;
  		if (!(checkExtension("pk", fpk))) return pk;
  		File f = uncompress(fpk);
  		try{
  			FileInputStream fileIn = new FileInputStream(f);
  			ObjectInputStream dataIn = new ObjectInputStream(fileIn);
  			pk = (PriorKnowledge)dataIn.readObject();
  			dataIn.close();
  			fileIn.close();
  		}catch (Exception e) {return (PriorKnowledge)null;}
  		try{
  			f.delete();
  		}catch(Exception e){return pk;}
  		return pk;
  	}
  
  	/** write the starting values in file. The starting values are the values used by Amares
  	to initialize the process
  	@param 		file in to write
  	@param 		starting values
  	@return 	void
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  /*	public void writeSV(File fvs, StartingValues sv)
  	{
  		try{
  			FileOutputStream fileOut = new FileOutputStream(fvs);
  			ObjectOutputStream dataOut = new ObjectOutputStream(fileOut);
  			dataOut.writeObject((StartingValues)sv);
  			dataOut.close();
  			fileOut.close();
  		} catch (Exception e){;}
  		File fileout = compress(fvs, ".sv");
  	}
  
  	/** to read the starting values useful for Amares
  	@param 		file to read
  	@return 	starting values [2 (Xcoordinates/Ycoordinates)][2*nbpoints] --> a starting value is
  composed of 2 points (spot of the top of the peak, spot of the half height of the peak)
  	@return 	void
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  /*	public StartingValues readSV(File fvs)
  	{
  		StartingValues sv =(StartingValues)null;
  		if (!(checkExtension("sv", fvs))) return sv;
  		File f = uncompress(fvs);
  		try{
  			FileInputStream fileIn = new FileInputStream(f);
  			ObjectInputStream dataIn = new ObjectInputStream(fileIn);
  			sv = (StartingValues)dataIn.readObject();
  			dataIn.close();
  			fileIn.close();
  		}catch (Exception e) {return (StartingValues)null;}
  		try{
  			f.delete();
  		}catch(Exception e){return sv;}
  		return sv;
  	}
  
  	/** to check out whether <file> has an extension <extension>
  	@param 		extension
  	@param 		file name
  	@author 	C. Couturier
  	@version 	%I%, %U%*/
  private boolean checkExtension(String extension, File file) {
    int i = file.getName().lastIndexOf('.');
    String ext = null;
    if (i > 0 && i < file.getName().length() - 1) {
      ext = file.getName().substring(i + 1).toLowerCase();
    }
    else {
      return false;
    }
    if (ext.equals(extension)) {
      return true;
    }
    return false;
  }
}