/*
Research Project:   Graphical Database for Category Theory
                    J. Bradbury, Dr. R. Rosebrugh, I. Rutherford
                    Mount Allison University 2001
File:               FileProcessing.java
Description:	      This class handles the opening and saving of CAT, CGL,
                    FUN, and FGL files.
*/

//import statements
import java.io.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.lang.System;
import java.io.StringBufferInputStream;
import java.net.*;

public class FileProcessing extends Frame
{
  BufferedReader input;
  BufferedWriter output;
  boolean moreRecords = true;
  boolean badfile = false;
  MainWindow edit;
  String fname = new String();

  public FileProcessing(String filename, MainWindow ed, boolean save, boolean localfile)
  //Constructor
  {
    edit = ed;
    fname = filename;
    //If file is on server...
    if (localfile == false)
    {
      URL fileURL;
      try
      {
        fileURL = new URL(filename);
        try {
        InputStream i = fileURL.openStream();
        input = new BufferedReader(new InputStreamReader(i));
      }
      catch (Exception e) {
        new MessageDialog(this, "Error", "Unable to load file " + filename, true);
        badfile = true;
      }

      }
      catch (MalformedURLException except)
      {
        new MessageDialog(this, "Error", "Unable to open file File unable to Load", true);
        badfile = true;
      }
      //cat.filename = cons.server + cons.catdir + fname;
      //this.setTitle("Graphical Database for Category Theory [" + cat.filename + "]");
      //validate();
      //try
      //{
      //  input = fileURL.openStream();
      //  dataInput = new DataInputStream(input);

    }
    //If file is on local machine....
    else
    {
    try
    {
      if (!save)
        input = new BufferedReader(new InputStreamReader(new FileInputStream(filename)));
    }
    catch(IOException e)
    {
      new MessageDialog(this, "Error", "Unable to open file " + filename, true);
      badfile = true;
    }
    try
    {
      if (save)
      {
        output = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename)));
        edit.cat.filename = filename;
        edit.setTitle("Category Theory Database Tools [" + edit.cat.filename + "]");
        edit.validate();
      }
    }
    catch(IOException e)
    {
      new MessageDialog(this, "Error", "Unable to save file " + filename, true);
      badfile = true;
    }
    }
  }


  boolean readCATFile(Category c)
  //Method reads a category file (*.CAT from a drive on the local computer
  {
  	if (!fname.toLowerCase().endsWith(".cat"))
  	{
  	  new MessageDialog(this, "Error", "Invalid file - please choose a *.CAT file", true);
  	  return false;
  	}

    //Update graphCanvas info from ini file
    edit.graphCanvas_.setFont(edit.ini.getCatFont());
    edit.graphCanvas_.setScale(edit.ini.getCatScale());

    int filelength = 20;
    boolean morelines = true;

    try
    {
      try
      {
        for(int i=0; i < filelength; i++)
        {
          try {
            String currLine = input.readLine();
            if (currLine.charAt(0) == '#')
            {
              String com = currLine.substring(1, currLine.length());
              c.comment = c.comment + com;
              //edit.commentArea.appendText(currLine);
            }
            else
            {
              if(currLine.equals("category"))
              {
                currLine = input.readLine();
                for (int j=0; j < currLine.length(); j++)
                {
                  if ((currLine.charAt(j)  == ' ') || (currLine.charAt(j)  == '\t'))
                  {
                    if (j == 0)
                      currLine = currLine.substring(j+1, currLine.length());
                    else
                      currLine = currLine.substring(0, j) + currLine.substring(j+1, currLine.length());
                  }
                }
                CategoryNode current = edit.catList.head;
                boolean name = false;
                while(current != null)
                {
                  if (current.cat.name.equals(currLine))
                    name = true;
                  current = current.next;
                }
                if (name == false)
                  c.name = currLine;
                else
                {
                  new NameDialog(this, "Error", true, edit, c);
                }
              }
              else if (currLine.equals("objects"))
              {
                String objects = new String();
                while (!currLine.equals("arrows"))
                {
                  currLine = input.readLine();
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("arrows"))
                    objects = objects.concat(currLine);
                }
                parseObjects(objects, c);
				if (badfile) return false;

                //edit.objectArea.appendText("\nOBJECTS = " + objects);
              }
              if (currLine.equals("arrows"))
              {
                String arrows = new String();
                while (!currLine.equals("relations"))
                {
                  currLine = input.readLine();
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("relations"))
                    arrows = arrows.concat(currLine);
                }
                parseArrows(arrows, c);
				if (badfile) return false;
                //edit.objectArea.appendText("\nARROWS = " + arrows);
              }
              if (currLine.equals("relations"))
              {
                String relations = new String();
                boolean relend = false;
                while (relend == false)
                {
                  currLine = input.readLine();
                  //edit.objectArea.appendText("HERE");
                  for (int r = 0; r < currLine.length(); r++)
                  {
                      if (currLine.charAt(r) == '.')
                      {
                        relend = true;
                      }
                  }
                  relations = relations.concat(currLine);
                }
                //edit.error_message("\nRELATIONS = " + relations);
                parseRelations(relations, c);
				if (badfile) return false;
              }
            }
            //edit.objectArea.appendText("\nLINE = " + currLine);
            //edit.displayArea.appendText(input.readLine() + "\n");
          }
          catch(EOFException eof) {
            morelines = false;
          }
        }
        input.close();
      }
      catch (IOException e1) {
//        edit.objectArea.setText("Error: Data File not found!");
      }
    }
    catch (NullPointerException aie)
    {
    }
    if (!c.name.equals(""))
      edit.catList.insertNode(c);
    return true;
  }

  void parseObjects (String obj, Category c)
  //This method parse a string of objects
  {
    int i =0;
    int prev = 0;

    for (i=0; i < obj.length(); i++)
    {
      if (obj.charAt(i)  == ' ')
      {
        prev++;
      }
      else
      {
        if ((obj.charAt(i) == ',') || (obj.charAt(i) == '.'))
        {
          if (prev == 0)
            c.obj[c.numobj] = obj.substring(prev, i);
          else
            c.obj[c.numobj] = obj.substring(prev+1, i);
          c.numobj++;
          prev = i;
        }
      }
    }
  }

  void parseArrows(String arr, Category c)
  //This method parses a string of arrows
  {
    int i =0;
    int prev = 0;
    int colon = 0;
    int tail = 0; int head = 0;

    if (arr.charAt(0) != '.')
    for (i=0; i < arr.length(); i++)
    {
      if (arr.charAt(i)  == ' ')
      {
        prev++;
      }
      else
      {
        if (arr.charAt(i) == ':')
          colon = i;
        if (arr.charAt(i) == '>')
        {
          head = i-1;
          tail = i;
        }
        if ((arr.charAt(i) == ',') || (arr.charAt(i) == '.'))
        {
          if (prev == 0)
            c.arrow[c.numarr] = arr.substring(prev, colon);
          else
            c.arrow[c.numarr] = arr.substring(prev+1, colon);
          String domain = arr.substring(colon+1, head);
          for (int j = 0; j < c.numobj; j++)
          {
            if (c.obj[j].equals(domain))
                c.arr[c.numarr][0] = j;
          }
          String codomain = arr.substring(tail+1, i);
          for (int j = 0; j < c.numobj; j++)
          {
            if (c.obj[j].equals(codomain))
                c.arr[c.numarr][1] = j;
          }
          c.numarr++;
          prev = i;
        }
      }
    }
  }

  void parseRelations(String rel, Category c)
  //This method parses a string of relations
  {
    int i =0;
    int prev = 0;
    int equals = 0;
    String right = new String();
    String left = new String();

    for (i=0; i < rel.length(); i++)
    {
      if ((rel.charAt(i)  == ' ') || (rel.charAt(i)  == '\t'))
      {
        rel = rel.substring(0, i) + rel.substring(i+1, rel.length());
      }
    }
    if (rel.charAt(0) != '.')
    {
      for (i=0; i < rel.length(); i++)
      {
        //if ((rel.charAt(i)  == ' ') || (rel.charAt(i)  == '\t'))
        //{
        //  prev++;
        //}
        //else
        //{
        if (rel.charAt(i) == '=')
          equals = i;
        if ((rel.charAt(i) == ',') || (rel.charAt(i) == '.'))
        {
          //if (c.num_rel == 0)
          //{
            left = rel.substring(prev, equals);
            right = rel.substring(equals+1, i);
          //}
          //else
          //{
          //  left = rel.substring(prev+1, equals);
          //  right = rel.substring(equals+1, i);
          //}
          prev = i+1;
          //edit.relationArea.append("left = " + left);
          //edit.relationArea.append("right = " + right + "\n");
          edit.get_rel(left, right, c);

        }
      //}
      }
    }
  }


  boolean readCGLFile(Category c)
  //Method reads a category file (*.CGL) from a drive on the local computer
  {
  	if (!fname.toLowerCase().endsWith(".cgl"))
  	{
  	  new MessageDialog(this, "Error", "Invalid file - please choose a *.CGL file", true);
  	  return false;
  	}

    //Update graphCanvas info from ini file
    edit.graphCanvas_.setFont(edit.ini.getCatFont());
    edit.graphCanvas_.setScale(edit.ini.getCatScale());

    int filelength = 20;
    boolean morelines = true;

    try
    {
      try
      {
        for(int i=0; i < filelength; i++)
        {
          try {
            String currLine = input.readLine();
            if (currLine.charAt(0) == '#')
            {
              String com = currLine.substring(1, currLine.length());
              c.comment = c.comment + com;
              //edit.commentArea.appendText(currLine);
            }
            else if (currLine.length() != 0)
            {
              if(currLine.equals("category"))
              {
                currLine = input.readLine();
                for (int j=0; j < currLine.length(); j++)
                {
                  if ((currLine.charAt(j)  == ' ') || (currLine.charAt(j)  == '\t'))
                  {
                    if (j == 0)
                      currLine = currLine.substring(j+1, currLine.length());
                    else
                      currLine = currLine.substring(0, j) + currLine.substring(j+1, currLine.length());
                  }
                }
                CategoryNode current = edit.catList.head;
                boolean name = false;
                while(current != null)
                {
                  if (current.cat.name.equals(currLine))
                    name = true;
                  current = current.next;
                }
                if (name == false)
                  c.name = currLine;
                else
                {
                  new NameDialog(this, "Error", true, edit, c);
                }
              }
              else if (currLine.equals("objects"))
              {
                String objects = new String();
                while (!currLine.equals("arrows"))
                {
                  currLine = input.readLine();
                  if (currLine.length() != 0 && currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("arrows") && currLine.length() != 0)
                    objects = objects.concat(currLine);
                }
                parseObjects(objects, c);
				if (badfile) return false;
                //edit.objectArea.appendText("\nOBJECTS = " + objects);
              }
              if (currLine.equals("arrows"))
              {
                String arrows = new String();
                while (!currLine.equals("relations"))
                {
                  currLine = input.readLine();
                  if (currLine.length() != 0 && currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("relations"))
                    arrows = arrows.concat(currLine);
                }
                parseArrows(arrows, c);
				if (badfile) return false;
                //edit.objectArea.appendText("\nARROWS = " + arrows);
              }
              if (currLine.equals("relations"))
              {
                String relations = new String();
                while (!currLine.equals("gml"))
                {
                  currLine = input.readLine();
                  if (currLine.length() != 0 && currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("gml") && currLine.length() != 0)
                    relations = relations.concat(currLine);
                }
                parseRelations(relations, c);
				if (badfile) return false;
              }
              if (currLine.equals("gml"))
              {
                int left = 0;
                int right = 0;
                String gml = new String();
                boolean gmlend = false;
                while (gmlend == false)
                {
                  currLine = input.readLine();
                  //edit.objectArea.appendText("HERE");
                  for (int r = 0; r < currLine.length(); r++)
                  {
                      if (currLine.charAt(r) == '[')
                        left++;
                      if (currLine.charAt(r) == ']')
                        right++;
                      if ((left == right) && (left != 0) && (right != 0))
                        gmlend = true;
                  }
                  gml = gml.concat(currLine);
                }
                //Strore gml in category
                c.gml = gml;
                c.originalGml = gml;
                //Store orginal gml in category
                if (c.gml.equals(""))
                  edit.GraphCategory(edit.graph_, edit.graphCanvas_, c);
                else
                {
                  //Category temp = new Category();
                  //edit.GraphCategory(edit.graph_, edit.graphCanvas_, temp);
                  boolean test = edit.displayCategoryGraph(c.gml);
                  edit.graphCanvas_.update(true);
                  GraphEdit ge = new GraphEdit(edit.graph_, edit.graphCanvas_);
                  c.originalGml = ge.getGMLText();
                  c.gml = c.originalGml;
                }
              }
            }
            //edit.objectArea.appendText("\nLINE = " + currLine);
            //edit.displayArea.appendText(input.readLine() + "\n");
          }
          catch(EOFException eof) {
            morelines = false;
          }
        }
        input.close();
      }
      catch (IOException e1) {
//        edit.objectArea.setText("Error: Data File not found!");
      }
    }
    catch (NullPointerException aie)
    {
    }
    if (!c.name.equals(""))
      edit.catList.insertNode(c);
    return true;
  }

  void saveCATFile()
  //This method saves the text version of a category file (*.CAT)
  {
      try
      {
          try {
            String comments = edit.commentArea.getText();
            /*String comments = "This is a test\nIt should work";
            for (int i=0; i < comments.length(); i++)
            {
              if (comments.charAt(i) == '\n')
              {
                comments = comments.substring(0, i) + "#" + comments.substring(i, comments.length());
              }
            } */
            if (!comments.equals(""))
                output.write("#" + comments + "\n");
            output.write("category\n");
            output.write(edit.categoryChoice.getSelectedItem() + "\n");
            output.write("objects\n");
            output.write(edit.objectArea.getText());
            if (edit.objectArea.getText().length() == 0)
               output.write(".\n");
            output.write("arrows\n");
            output.write(edit.arrowArea.getText());
            if (edit.arrowArea.getText().length() == 0)
               output.write(".\n");
            output.write("relations\n");
            output.write(edit.relationArea.getText());
            if (edit.relationArea.getText().length() == 0)
               output.write(".\n");
          }
          catch(EOFException eof) {
          }
      output.close();
      }
      catch (IOException e1) {
        //edit.displayArea.setText("Error: Data File not found!");
      }
  }

  void saveCGLFile()
  //This method saves the text and graphical versions of a category file (*.CGL)
  {
      try
      {
          try {
            String comments = edit.commentArea.getText();
            /*String comments = "This is a test\nIt should work";
            for (int i=0; i < comments.length(); i++)
            {
              if (comments.charAt(i) == '\n')
              {
                comments = comments.substring(0, i) + "#" + comments.substring(i, comments.length());
              }
            } */
            if (!comments.equals(""))
                output.write("#" + comments + "\n");
            output.write("category\n");
            output.write(edit.categoryChoice.getSelectedItem() + "\n");
            output.write("objects\n");
            output.write(edit.objectArea.getText() + "\n");
            if (edit.objectArea.getText().length() == 0)
               output.write(".\n");
            output.write("arrows\n");
            output.write(edit.arrowArea.getText() + "\n");
            if (edit.arrowArea.getText().length() == 0)
               output.write(".\n");
            output.write("relations\n");
            output.write(edit.relationArea.getText() + "\n");
            if (edit.relationArea.getText().length() == 0)
               output.write(".\n");
            output.write("gml\n");
            output.write(edit.cat.gml);
          }
          catch(EOFException eof) {
          }
      output.close();
      }
      catch (IOException e1) {
        //edit.displayArea.setText("Error: Data File not found!");
      }
  }

  boolean readFUNFile(CatFunctor func, Category A, Category B)
  {
/*
    //Update graphCanvas info from ini file
    edit.functorFromCanvas.setFont(edit.ini.getCatAFont());
    edit.functorFromCanvas.setScale(edit.ini.getCatAScale());
    edit.functorToCanvas.setFont(edit.ini.getCatBFont());
    edit.functorToCanvas.setScale(edit.ini.getCatBScale());
*/
  	if (!fname.toLowerCase().endsWith(".fun"))
  	{
  	  new MessageDialog(this, "Error", "Invalid file - please choose a *.FUN file", true);
  	  return false;
  	}

    //func = new cat_functor();
    //A = new Category();
    //B = new Category();
    readFuncCATFile(A, false);
	if (badfile) return false;
    readFuncCATFile(B, false);
	if (badfile) return false;
    readFunctorFile(func, A, B);
	if (badfile) return false;
    edit.funcDisplayControls.setVisible(true);
    validate();
    //create functor node
    edit.fnode = new FunctorNode(edit);
    edit.fnode.functor_type = 0;
    edit.fnode.A = A;
    edit.fnode.B = B;
    func.filename = fname;
    edit.fnode.f = func;

    edit.f_list.insertNode(edit.fnode, edit.functorArrowArea);
    edit.functorChoice.add(func.name);
    edit.functorChoice.select(func.name);
    try
    {
      input.close();
    }
    catch (IOException e1)
    {
      //edit.objectArea.setText("Error: Data File not found!");
    }
    return true;
  }

  boolean readFGLFile(CatFunctor func, Category A, Category B)
  {
    //Update graphCanvas info from ini file
/*
    edit.functorFromCanvas.setFont(edit.ini.getCatAFont());
    edit.functorFromCanvas.setScale(edit.ini.getCatAScale());
    edit.functorToCanvas.setFont(edit.ini.getCatBFont());
    edit.functorToCanvas.setScale(edit.ini.getCatBScale());
*/
  	if (!fname.toLowerCase().endsWith(".fgl"))
  	{
  	  new MessageDialog(this, "Error", "Invalid file - please choose a *.FGL file", true);
  	  return false;
  	}
    
    readFuncCATFile(A, true);
	if (badfile) return false;
    readFuncCATFile(B, true);
	if (badfile) return false;
    readFunctorFile(func, A, B);
	if (badfile) return false;
    edit.funcDisplayControls.setVisible(true);
    validate();
    edit.textCardLayout.show(edit.textPanel, "Functor Display");
    //create functor node
    edit.fnode = new FunctorNode(edit);
    edit.fnode.functor_type = 0;
    edit.fnode.A = A;
    edit.fnode.B = B;
    func.filename = fname;
    edit.fnode.f = func;
    edit.f_list.insertNode(edit.fnode, edit.functorArrowArea);
    edit.functorChoice.add(func.name);
    edit.functorChoice.select(func.name);
    try
    {
      input.close();
    }
    catch (IOException e1)
    {
      //edit.objectArea.setText("Error: Data File not found!");
    }
    return true;
  }

  void readFuncCATFile(Category c, boolean graphical)
  //Method reads a category file (*.CAT) from a drive on the local computer
  {
    int filelength = 20;
    boolean morelines = true;
    boolean relend = false;
    String gml = new String();
    boolean gmlend = false;

    try
    {
      try
      {
        while (gmlend == false)
        {
          try {
            String currLine = input.readLine();
            if (currLine.length() == 0)
            {
              //edit.functorObjectArea.append("EMPTY LINE\n");
            }
            else if (currLine.charAt(0) == '#')
            {
              String com = currLine.substring(1, currLine.length());
              c.comment = c.comment + com;
              //edit.functorObjectArea.append(currLine);
            }
            else
            {
              if(currLine.equals("category"))
              {
                currLine = input.readLine();
                for (int j=0; j < currLine.length(); j++)
                {
                  if ((currLine.charAt(j)  == ' ') || (currLine.charAt(j)  == '\t'))
                  {
                    if (j == 0)
                      currLine = currLine.substring(1, currLine.length());
                    else
                      currLine = currLine.substring(0, j) + currLine.substring(j+1, currLine.length());
                  }
                }
                CategoryNode current = edit.catList.head;
                boolean name = false;
                while(current != null)
                {
                  if (current.cat.name.equals(currLine))
                    name = true;
                  current = current.next;
                }
                if (name == false)
                {
                  c.name = new String(currLine);
                  //edit.functorObjectArea.append("CAT NAME = " + c.name + "\n");
                }
                //Error message if category name is already in use
                else
                {
                  name = false;
                  c.name = new String(currLine + "diagram");
                }
              }
              else if (currLine.equals("objects"))
              {
                String objects = new String();
                while (!currLine.equals("arrows"))
                {
                  currLine = input.readLine();
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("arrows"))
                    objects = objects.concat(currLine);
                }
                //edit.functorObjectArea.append("OBJECTS = " + objects + "\n");
                parseObjects(objects, c);
				      if (badfile) return;
			        }
              if (currLine.equals("arrows"))
              {
                String arrows = new String();
                while (!currLine.equals("relations"))
                {
                  currLine = input.readLine();
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    c.comment = c.comment + com;
                  }
                  else if (!currLine.equals("relations"))
                    arrows = arrows.concat(currLine);
                }
                parseArrows(arrows, c);
				if (badfile) return;
                //edit.functorObjectArea.append("ARROWS = " + arrows);
              }
              if (currLine.equals("relations"))
              {
                String relations = new String();
                while (relend == false)
                {
                  currLine = input.readLine();
                  //edit.objectArea.appendText("HERE");
                  for (int r = 0; r < currLine.length(); r++)
                  {
                    if (currLine.charAt(r) == '.')
                    {
                      relend = true;
                    }
                  }
                  relations = relations.concat(currLine);
                }
                if (!graphical)
                  gmlend = true;
                //edit.functorObjectArea.append("\nRELATIONS = " + relations);
                parseRelations(relations, c);
				if (badfile) return;
              }
              if (graphical == true)
              {
                if (currLine.equals("gml") && gmlend == false)
                {
                  int left = 0;
                  int right = 0;
                  while (gmlend == false)
                  {
                    currLine = input.readLine();
                    if (currLine == null || currLine.length() == 0)
                      gmlend = true;
                    else
                    {
                      for (int r = 0; r < currLine.length(); r++)
                      {
                        if (currLine.charAt(r) == '[')
                          left++;
                        if (currLine.charAt(r) == ']')
                          right++;
                        if ((left == right) && (left != 0) && (right != 0))
                          gmlend = true;
                      }
                      gml = gml.concat(currLine);
                    }
                  }
                  c.gml = new String(gml);
                  gmlend = true;
                  //if (c.gml.equals(""))
                  //  edit.GraphCategory(edit.graph_, edit.graphCanvas_, c);
                  //else
                  //{
                  //  boolean test = edit.displayCategory(c.gml);
                  //  edit.graphCanvas_.update(true);
                  //}
                }
              }
            }
            //edit.objectArea.appendText("\nLINE = " + currLine);
            //edit.displayArea.appendText(input.readLine() + "\n");
          }
          catch(EOFException eof) {
            morelines = false;
          }
        }

      }
      catch (IOException e1) {
//        edit.objectArea.setText("Error: Data File not found!");
      }
    }
    catch (NullPointerException aie)
    {
    }
// Add the current category to the list, even tho it was opened from a functor file
// option removed
//    if (!c.name.equals(""))
//    {
//      edit.catList.insertNode(c);
//      edit.categoryChoice.add(c.name);
//    }
  }

  void readFunctorFile(CatFunctor f, Category A, Category B)
  //This method reads and parses the functor part of a *.FUN file
  {
    boolean arrowend = false;
    String comment = new String();

    try
    {
      try
      {
        //Repeat until end of arrows is found
        while (arrowend == false)
        {
          try {
            //Read Current Line
            String currLine = input.readLine();
            //If current line is blank do nothing
            if (currLine.length() == 0)
            {
            //  edit.functorObjectArea.append("EMPTY LINE\n");
            }
            //If current line has # it is a comment
            else if (currLine.charAt(0) == '#')
            {
              String com = currLine.substring(1, currLine.length());
              comment = comment + com;
              edit.functorObjectArea.append(currLine);
            }
            //Otherwise current line is part of the functor
            else
            {
              if(currLine.equals("functor"))
              {
                currLine = input.readLine();
                for (int j=0; j < currLine.length(); j++)
                {
                  if ((currLine.charAt(j)  == ' ') || (currLine.charAt(j)  == '\t'))
                  {
                    if (j == 0)
                      currLine = currLine.substring(j+1, currLine.length());
                    else
                      currLine = currLine.substring(0, j) + currLine.substring(j+1, currLine.length());
                  }
                }
                FunctorNode current = edit.f_list.head;
                boolean name = false;
                while(current != null)
                {
                  if (current.f.name.equals(currLine))
                    name = true;
                  current = current.next;
                }
                if (name == false)
                  f.name = currLine;
                else
                {
                  new FuncNameDialog(this, "Error", true, edit, f);
                }
              }
              else if (currLine.equals("objects"))
              {
                String objects = new String();
                while (!currLine.equals("arrows"))
                {
                  currLine = input.readLine();
                  //If current line has # it is a comment
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    comment = comment + com;
                  }
                  else if (!currLine.equals("arrows"))
                    objects = objects.concat(currLine);
                }
                //edit.functorObjectArea.append("OBJECTS = " + objects + "\n");

                //Parse object string into individual objects
                parseFunctorObjects(objects, f, A, B);
                if (badfile) return;
              }
              if (currLine.equals("arrows"))
              {
                String arrows = new String();
                while (arrowend == false)
                {
                  currLine = input.readLine();
                  //If current line has # it is a comment
                  if (currLine.charAt(0) == '#')
                  {
                    String com = currLine.substring(1, currLine.length());
                    comment = comment + com;
                  }
                  for (int r = 0; r < currLine.length(); r++)
                  {
                      if (currLine.charAt(r) == '.')
                      {
                        arrowend = true;
                      }
                  }
                  arrows = arrows.concat(currLine);
                }
                //edit.functorObjectArea.append("ARROWS = " + arrows);
                //Parse arrow string into individual arrows
                parseFunctorArrows(arrows, f, A, B);
				if (badfile) return;
              }
            }
          }
          catch(EOFException eof)
          {
          }
        }
      }
      catch (IOException e1)
      {
      }
    }
    catch (NullPointerException aie)
    {

    }
  }

  void parseFunctorObjects(String objs, CatFunctor func, Category A, Category B)
  //This method parses a string of functor objects
  {
    int i =0;

    //Positions of "(", ")", "=", and "," for parsing purposes
    int prevcomma = -1;
    int bar = 0;
    int arrow = 0;
    int comma = 0;

    //Strings to store current object from and object to
    String objectfrom = new String();
    String objectto = new String();

    //Read until end of string is reached
    //and remove all tabs and spaces
    for (i=0; i < objs.length(); i++)
    {
      if ((objs.charAt(i)  == ' ') || (objs.charAt(i)  == '\t'))
      {
        objs = objs.substring(0, i) + objs.substring(i+1, objs.length());
      }
    }

	if (objs.charAt(0) != '.')
    {
      //Parse string into objects
      for (i=0; i < objs.length(); i++)
      {
        if (objs.charAt(i) == '|')
          bar = i;
        if (objs.charAt(i) == '>')
          arrow = i;

        if ((objs.charAt(i) == ',') || (objs.charAt(i) == '.'))
        {
          comma = i;
          if (bar < prevcomma || comma < arrow)
          {
            new MessageDialog(this, "Error", fname + " is not a valid functor file", true);
            badfile = true;
            return;
          }
          objectfrom = objs.substring(prevcomma+1, bar);
          objectto = objs.substring(arrow+1, comma);
          //check to see that objectfrom and objectto are valid in categories A and B
          if(A.check_obj(objectfrom))
          {
            new MessageDialog(this, "Error", objectfrom + " is not an object of Category " + A.name, true);
          }
          else if (B.check_obj(objectto))
          {
            new MessageDialog(this, "Error", objectto + " is not an object of Category " + B.name, true);
          }
          else
          {
            func.obj[A.object_number(objectfrom)] = B.object_number(objectto);
          }
          prevcomma = comma;
        }
      }
    }
  }

  void parseFunctorArrows(String arrs, CatFunctor func, Category A, Category B)
  //This method parses a string of functor objects
  {
    int i =0;
    int arrnum = 0;
    int pathfrom[] = new int[edit.ini.getMAXWORD()];
    int pathto[] = new int[edit.ini.getMAXWORD()];
    int reduced_path[] = new int[edit.ini.getMAXWORD()];

    //Positions of "(", ")", "=", and "," for parsing purposes
    int prevcomma = -1;
    int closebracket = 0;
    int equals = 0;
    int comma = 0;

    //Strings to store current object from and object to
    String objectfrom = new String();
    String objectto = new String();

    //Read until end of string is reached
    //and remove all tabs and spaces
    for (i=0; i < arrs.length(); i++)
    {
      if ((arrs.charAt(i)  == ' ') || (arrs.charAt(i)  == '\t'))
      {
        arrs = arrs.substring(0, i) + arrs.substring(i+1, arrs.length());
      }
    }
    if (arrs.charAt(0) != '.')
    {
      //Parse string into objects
      for (i=0; i < arrs.length(); i++)
      {
        if (arrs.charAt(i) == '|')
          closebracket = i;
        if (arrs.charAt(i) == '>')
          equals = i;
        if ((arrs.charAt(i) == ',') || (arrs.charAt(i) == '.'))
        {
          comma = i;
          objectfrom = arrs.substring(prevcomma+1, closebracket);
          objectto = arrs.substring(equals+1, comma);
          //edit.functorObjectArea.append("FROM = " + objectfrom + "  TO = " + objectto + "\n");
          //checks to see that the string the user enters
          //contains only arrows that exist in category A
          if ((objectfrom.equals("1")) || (objectto.equals("1")))
          {
            //path = copy_path(path,string_to_path(path_string, cat));
            //func.arr[editsub] = copy_path(func.arr[editsub],path);
          }
          else
          {
            if(!(A.check_string(objectfrom)))
            {
              new MessageDialog(this, "Error", "One or more of the arrows specified do not exist in Category" + A.name, true);
            }
            //checks to see that the string the user enters
            //contains only arrows that exist in category B
            else if(!(B.check_string(objectto)))
            {
              new MessageDialog(this, "Error", "One or more of the arrows specified do not exist in Category" + B.name, true);
            }
            else
            {
              pathto = B.copy_path(B.string_to_path(objectto));
              //checks to see that domains and codomains of each arrow in path match up
              if(!(B.check_path(pathto)))
              {
                new MessageDialog(this, "Error", "Domains and codomains of each arrow in path do not match", true);
              }
              else
              {
                //Checks to see that domain and codomain of path
                //match up with domain and codomain of arrow under the functor
                if((!(edit.check_domain(pathto,arrnum,func,A,B))) || (!(edit.check_codomain(pathto,arrnum,func,A,B))))
                {
                  //viewbox.append("if((!(check_domain(path,editsub,func,A,B))) || (!(check_codomain(path,editsub,func,A,B))))");
                }
                else
                {
                  reduced_path = B.reduce(pathto);
                  //reduced_path = pathto;
                  func.arr[arrnum] = B.copy_path(reduced_path);
                  arrnum++;
                }
              }
            }
          }
          prevcomma = comma;
        }
      //}
      }
    }
  }

  void saveFUNFile(Category A, Category B, CatFunctor f)
  //This method saves the text version of a functor file (*.FUN)
  {
    //Save Category A
    savefuncCATFile(A, false);
    //edit.functorObjectArea.append("Category A " + A.name + " DONE!");

    //Save Category B
    savefuncCATFile(B, false);
    //edit.functorObjectArea.append("Category B " + B.name + " DONE!");

    //Save cat_functor f
    saveFunctorFile(A, B, f);

    //Close *.FUN File
    try
    {
      output.close();
    }
    catch (IOException e1)
    {
      //edit.objectArea.setText("Error: Data File not found!");
    }

  }

  void saveFGLFile(Category A, Category B, CatFunctor f)
  //This method saves the text version of a functor file (*.FUN)
  {
    //Save Category A
    savefuncCATFile(A, true);
    //edit.functorObjectArea.append("Category A " + A.name + " DONE!");

    //Save Category B
    savefuncCATFile(B, true);
    //edit.functorObjectArea.append("Category B " + B.name + " DONE!");

    //Save cat_functor f
    saveFunctorFile(A, B, f);

    //Close *.FGL File
    try
    {
      output.close();
    }
    catch (IOException e1)
    {
      //edit.objectArea.setText("Error: Data File not found!");
    }

  }

  void saveFunctorFile(Category A, Category B,CatFunctor f)
  //This method saves the cat_functor assoicated with the
  //current functor
  {
    int i =0,j;

    try
    {
      try
      {
        //Display functor name
        output.write("\nfunctor\n " + f.name + "\n");

        //Display functor objects
        output.write("objects\n");
        for (i=0;i<A.numobj-1;i++)
        {
          output.write(A.obj[i] + " |--> " + B.obj[f.obj[i]]);
          //output.write(f.name + "(" + A.obj[i] + ") = " + B.obj[f.obj[i]]);
          output.write(", ");
        }
        output.write(A.obj[i] + " |--> " + B.obj[f.obj[i]] + ".\n");
        //output.write(f.name + "(" + A.obj[i] + ") = " + B.obj[f.obj[i]] + ".\n");

        //Display functor arrows
        output.write("arrows\n");
        for (i=0;i<A.numarr-1;i++)
        {
          output.write(A.arrow[i] + " |--> ");
          //output.write(f.name + "(" + A.arrow[i] + ") = ");
          j = 0;
          while (f.arr[i][j] != -1)
          {
            output.write("" + B.arrow[f.arr[i][j]]);
            j++;
          }
          if (j==0)
            output.write("1");
          output.write(", ");
        }
        if (A.numarr != 0)
        {
          output.write(A.arrow[i] + " |--> ");
          //output.write(f.name + "(" + A.arrow[i] + ") = ");
          j = 0;
          while (f.arr[i][j] != -1)
          {
            output.write("" + B.arrow[f.arr[i][j]]);
            j++;
          }
          if (j==0)
            output.write("1");
          output.write(".\n");
        }
        else
          output.write(".\n");
      }
      catch(EOFException eof)
      {
      }
    }
    catch (IOException e1)
    {
      //edit.displayArea.setText("Error: Data File not found!");
    }
  }

  void savefuncCATFile(Category c, boolean graphical)
  //This method saves the text version of a category assoicated with the
  //current functor
  {
      int counter = 0;
      int i,j;

      try
      {
          try {
            String comments = edit.commentArea.getText();
            /*for (int i=0; i < comments.length(); i++)
            {
              if (comments.charAt(i) == '\n')
              {
                comments = comments.substring(0, i) + "#" + comments.substring(i+1, comments.length());
              }
            } */
            if (!comments.equals(""))
                output.write("#" + comments + "\n");
            output.write("category\n");
            output.write(c.name + "\n");
            output.write("objects\n");
            for (i = 0; i < c.numobj; i++)
            {
              if (i < (c.numobj - 1))
                output.write(c.obj[i] + ", ");
              if (i == (c.numobj - 1))
                output.write(c.obj[i] + ".\n");
            }
            output.write("arrows\n");
            for (i = 0; i < c.numarr; i++)
            {
              if (i < (c.numarr - 1))
              {
                output.write(c.arrow[i] + ":");
                output.write(c.obj[c.arr[i][0]] + "->");
                output.write(c.obj[c.arr[i][1]] + ", ");
              }
              if (i == (c.numarr - 1))
              {
                output.write(c.arrow[i] + ":");
                output.write(c.obj[c.arr[i][0]] + "->");
                output.write(c.obj[c.arr[i][1]] +". " );
              }
              counter++;
              if ((counter == 4) || (i == (c.numarr-1)))
              {
                counter = 0;
                output.write("\n");
              }
            }

            output.write("relations\n");
            for (i=0;i<c.num_rel-1;i++)
            {
              j = 0;
              //Display left side of relation
              while (c.rel_set[i].lhs[j] != -1)
              {
                if (j == 0)
                  output.write("" + c.arrow[c.rel_set[i].lhs[j]]);
                else
                  output.write("*" + c.arrow[c.rel_set[i].lhs[j]]);
                j++;
              }
              output.write(" = ");
              j = 0;
              //Display right side of relation
              if (c.rel_set[i].rhs[0] == edit.ini.getIdentityCode())
                output.write("1");
              else
              {
                while (c.rel_set[i].rhs[j] != -1)
                {
                  if (j == 0)
                    output.write("" + c.arrow[c.rel_set[i].rhs[j]]);
                  else
                    output.write("*" + c.arrow[c.rel_set[i].rhs[j]]);
                  j++;
                }
              }
              counter++;
              output.write(", ");
              if (counter == 4)
              {
                counter = 0;
                output.write("\n");
              }
            }
            if (c.num_rel != 0)
            {
              j = 0;
              while (c.rel_set[i].lhs[j] != -1)
              {
                if (j == 0)
                  output.write("" + c.arrow[c.rel_set[i].lhs[j]]);
                else
                  output.write("*" + c.arrow[c.rel_set[i].lhs[j]]);
                j++;
              }
              output.write(" = ");
              j = 0;
              if (c.rel_set[i].rhs[0] == edit.ini.getIdentityCode())
                output.write("1");
              else
              {
                while (c.rel_set[i].rhs[j] != -1)
                {
                  if (j == 0)
                    output.write("" + c.arrow[c.rel_set[i].rhs[j]]);
                  else
                    output.write("*" + c.arrow[c.rel_set[i].rhs[j]]);
                  j++;
                }
              }
              output.write(".\n");
            }
            else
              output.write(".\n");
            if (graphical == true)
            {
              output.write("gml\n");
              output.write(c.gml);
            }
            output.write("\n");
          }
          catch(EOFException eof) {
          }
      }
      catch (IOException e1) {
        //edit.displayArea.setText("Error: Data File not found!");
      }
  }


  public void cleanup()
  //Closes the file when finished
  {
    try {
        input.close();
    }

    catch (IOException e) {
      System.err.println("ERROR during reading of file");
    }
  }
}