Construction of skeleton SBML model using a list of yeast ORF numbers

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

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flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

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//Output
ArrayList speciesIds = new ArrayList();

//Iterate thru reactants, products and modifiers
for(ArrayList al: reactants)
{
  for(String reactant: al)
  {
    if(!speciesIds.contains(reactant))
      speciesIds.add(reactant);
  }
}

for(ArrayList al: products)
{
  for(String product: al)
  {
    if(!speciesIds.contains(product))
      speciesIds.add(product);
  }
}

for(ArrayList al: modifiers)
{
  for(String modifier: al)
  {
    if(!speciesIds.contains(modifier))
      speciesIds.add(modifier);
  }
}

//Final clean up - remove empty strings
speciesIds.remove("");

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List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

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//Output
finalCompIds = new ArrayList();

//Copy items into final list
for(int i = 0; i < compIds.size(); i++)
{
  String compId = compIds.get(i);
  finalCompIds.add(compId);
}

//Copy outside compIds into final list
for(int x = 0; x < outsideCompIds.size(); x++)
{
  String outsideCompId = outsideCompIds.get(x);
  if(!finalCompIds.contains(outsideCompId))
    finalCompIds.add(outsideCompId);
}

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String compMetaId = "metaid_" + compId;

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if(sboTermIn.equals(""))
{
  sboTermOut = "0";
}
else
{
  sboTermOut = sboTermIn;
}

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String speciesMetaId = "metaid_" + speciesId;

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if(sboTermIn.equals(""))
{
  sboTermOut = "0";
}
else
{
  sboTermOut = sboTermIn;
}

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output = new ArrayList();

for(int i = 0 ; i < input.size(); i++)
{
  String item = input.get(i);
  String number = reactantNumber.get(i);
  int x = Integer.parseInt(number);
  al = new ArrayList();

  for(int y = 0; y < x; y++)
  {
    al.add(item);
  }
  output.add(al);
}

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output = new ArrayList();

for(int i = 0 ; i < input.size(); i++)
{
  String item = input.get(i);
  String number = reactantNumber.get(i);
  int x = Integer.parseInt(number);
  al = new ArrayList();

  for(int y = 0; y < x; y++)
  {
    al.add(item);
  }
  output.add(al);
}

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import org.kohsuke.graphviz.Graph;
import org.kohsuke.graphviz.Node;
import org.sbml.libsbml.*;

boolean displayEnzymes = false;

int cloneCount = 1;

Graph graph = new Graph();
graph.id("SBML");
graph.addGlobalGraphAttr("ranksep","0.22");
graph.addGlobalGraphAttr("nodesep","0.05");
graph.addGlobalNodeAttr("fontname","Helvetica");
graph.addGlobalNodeAttr("fontsize","7");
graph.addGlobalNodeAttr("fontcolor","black");
graph.addGlobalNodeAttr("color","lightgoldenrodyellow");
graph.addGlobalNodeAttr("fillcolor","lightgoldenrodyellow");
graph.addGlobalNodeAttr("style","filled");

SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromString(sbml);
Model model = doc.getModel();

//Sort out metabolites
ListOfSpecies specieslist = model.getListOfSpecies();
for(int i = 0; i < specieslist.size(); i++)
{
  Species sp = (Species)specieslist.get(i);
  Node node = new Node();
  String name  = sp.getName();
  //System.out.println(name);
  if(name.equals("ATP")
    || name.equals("ADP") 
    || name.equals("Phosphate")
    || name.equals("H+")
    || name.equals("H2O")
    || name.equals("CO2")
    || name.equals("Nicotinamide adenine dinucleotide - reduced")
    || name.equals("Nicotinamide adenine dinucleotide")
    || name.equals("Nicotinamide adenine dinucleotide phosphate")
    || name.equals("Nicotinamide adenine dinucleotide phosphate - reduced"))
    continue;
    //For enzymes
    if(!name.startsWith("Y"))
      node.id("\"" + name + "\" [fillcolor = \"lightgoldenrodyellow\" shape=\"ellipse\"]");
    else
      if(displayEnzymes)
        node.id("\"" + name + "\" [fillcolor = \"steelblue1\" shape=\"ellipse\"]");
      else
        continue;
  graph.node(node);
}

//Sort out reactions
ListOfReactions reactionslist = model.getListOfReactions();
for(int x = 0; x < reactionslist.size(); x ++)
{
  Reaction r = (Reaction)reactionslist.get(x);
  Node reaction = new Node();
  reaction.id("\"" + r.getId() + "\"");
  reaction.attr("shape", "rectangle");
  reaction.attr("fillcolor", "darkolivegreen3");
  graph.node(reaction);

  ListOfSpeciesReferences reactants = r.getListOfReactants();
  for(int y = 0; y < reactants.size(); y++)
  {
    SpeciesReference sref = (SpeciesReference)reactants.get(y);
    Species sp = model.getSpecies(sref.getSpecies());
    String rname = sp.getName();
    Node n = new Node();
    //Check if node needs cloning
    if(rname.equalsIgnoreCase("ATP") 
      || rname.equals("ADP") 
      || rname.equals("Phosphate") 
      || rname.equals("H+")
      || rname.equals("Nicotinamide adenine dinucleotide - reduced")
      || rname.equals("Nicotinamide adenine dinucleotide")
      || rname.equals("Nicotinamide adenine dinucleotide phosphate - reduced")
      || rname.equals("Nicotinamide adenine dinucleotide phosphate")
      || rname.equals("H2O"))
    {
      continue;
    }
    else
    {
      n.id("\"" + rname + "\"");
    }
  graph.edge(n, reaction);
  }

  ListOfSpeciesReferences products = r.getListOfProducts();
  for(int y = 0; y < products.size(); y++)
  {
    SpeciesReference sref = (SpeciesReference)products.get(y);
    Species sp = model.getSpecies(sref.getSpecies());
    String pname = sp.getName();
    Node n = new Node();
    //Check if node needs cloning
    if(pname.equals("ATP") 
      || pname.equals("ADP") 
      || pname.equals("Phosphate") 
      || pname.equals("H+")
      || pname.equals("Nicotinamide adenine dinucleotide - reduced")
      || pname.equals("Nicotinamide adenine dinucleotide")
      || pname.equals("Nicotinamide adenine dinucleotide phosphate - reduced")
      || pname.equals("Nicotinamide adenine dinucleotide phosphate")
      || pname.equals("H2O"))
    {
      continue;
    }
    else
    {
      n.id("\"" + pname + "\"");
    }
  graph.edge(reaction, n);
  }

  if(displayEnzymes)
  {
    //Add edges from enzyme species modifiers to reactions
    ListOfSpeciesReferences modifiers = r.getListOfModifiers(); 
    for(int y = 0; y < modifiers.size(); y++)
    {
      SimpleSpeciesReference msref = (SimpleSpeciesReference)modifiers.get(y);
      String id = msref.getSpecies();
      //Deal with empty list of modifier references
      if(id.equals(""))
        continue;
      Species species = model.getSpecies(id);
      String mname = species.getName();
      Node n = new Node();
      n.id("\"" + mname + "\"");
      graph.edge(n, reaction);
    }
  }

}

baos = new ByteArrayOutputStream();
graph.writeTo(baos); 

String dot = baos.toString();

Script

import java.io.*;
import java.util.*;

// GraphViz.java - a simple API to call dot from Java programs

/*$Id$*/
/*
 ******************************************************************************
 *                                                                            *
 *              (c) Copyright 2003 Laszlo Szathmary                           *
 *                                                                            *
 * This program is free software; you can redistribute it and/or modify it    *
 * under the terms of the GNU Lesser General Public License as published by   *
 * the Free Software Foundation; either version 2.1 of the License, or        *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful, but        *
 * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY *
 * or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public    *
 * License for more details.                                                  *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program; if not, write to the Free Software Foundation,    *
 * Inc., 675 Mass Ave, Cambridge, MA 02139, USA.                              *
 *                                                                            *
 ******************************************************************************
 */



/**
 * 

 * 
Purpose: GraphViz Java API
 * 

 *
 * 
Description:
 * 
 With this Java class you can simply call dot
 *      from your Java programs
 * 
Example usage:
 * 

 * 
 *    GraphViz gv = new GraphViz();
 *    gv.addln(gv.start_graph());
 *    gv.addln("A -> B;");
 *    gv.addln("A -> C;");
 *    gv.addln(gv.end_graph());
 *    System.out.println(gv.getDotSource());
 *
 *    File out = new File("out.gif");
 *    gv.writeGraphToFile(gv.getGraph(gv.getDotSource()), out);
 * 
 * 
 *
 * 
 *
 * @version v0.1, 2003/12/04 (Decembre)
 * @author  Laszlo Szathmary (szathml@delfin.unideb.hu)
 */
public class GraphViz
{
   /**
    * Where is your dot program located? It will be called externally.
    */
   private static String DOT_LOCATION        = "/usr/bin/dot";

   /**
    * The source of the graph written in dot language.
    */
	private StringBuffer graph = new StringBuffer();

   /**
    * Constructor: creates a new GraphViz object that will contain
    * a graph.
    */
   public GraphViz() {
     //Platform check to determine location of dot
     String platform = System.getProperty("os.name");
     if(platform.equals("Mac OS X"))
       DOT_LOCATION  = "/Applications/Taverna 2.1.app/Contents/MacOS/dot";
     else if (platform.startsWith("Windows"))
       DOT_LOCATION  = "C:/Program Files/Taverna Workbench 2.1.0/bin/win32i386/dot.exe";
   }

   /**
    * Returns the graph's source description in dot language.
    * @return Source of the graph in dot language.
    */
   public String getDotSource() {
      return graph.toString();
   }

   /**
    * Adds a string to the graph's source (without newline).
    */
   public void add(String line) {
      graph.append(line);
   }

   /**
    * Adds a string to the graph's source (with newline).
    */
   public void addln(String line) {
      graph.append(line+"\n");
   }

   /**
    * Adds a newline to the graph's source.
    */
   public void addln() {
      graph.append('\n');
   }

   /**
    * Returns the graph as an image in binary format.
    * @param dot_source Source of the graph to be drawn.
    * @return A byte array containing the image of the graph.
    */
   public byte[] getGraph(String dot_source)
   {
      File dot;
      byte[] img_stream = null;
   
      try {
         dot = writeDotSourceToFile(dot_source);
         if (dot != null)
         {
            img_stream = get_img_stream(dot);
            if (dot.delete() == false) 
               System.err.println("Warning: "+dot.getAbsolutePath()+" could not be deleted!");
            return img_stream;
         }
         return null;
      } catch (java.io.IOException ioe) { return null; }
   }

   /**
    * Writes the graph's image in a file.
    * @param img   A byte array containing the image of the graph.
    * @param file  Name of the file to where we want to write.
    * @return Success: 1, Failure: -1
    */
   public int writeGraphToFile(byte[] img, String file)
   {
      File to = new File(file);
      return writeGraphToFile(img, to);
   }

   /**
    * Writes the graph's image in a file.
    * @param img   A byte array containing the image of the graph.
    * @param to    A File object to where we want to write.
    * @return Success: 1, Failure: -1
    */
   public int writeGraphToFile(byte[] img, File to)
   {
      try {
         FileOutputStream fos = new FileOutputStream(to);
         fos.write(img);
         fos.close();
      } catch (java.io.IOException ioe) { return -1; }
      return 1;
   }

   /**
    * It will call the external dot program, and return the image in
    * binary format.
    * @param dot Source of the graph (in dot language).
    * @return The image of the graph in .gif format.
    */
   public byte[] get_img_stream(File dot)
   {
      File img;
      byte[] img_stream = null;

      try {
         img = File.createTempFile("graph_", ".png");
         String temp = img.getAbsolutePath();

         Runtime rt = Runtime.getRuntime();
         Process p = rt.exec(new String[]{DOT_LOCATION, "-Tpng",  dot.getAbsolutePath(), "-o", img.getAbsolutePath()});
         p.waitFor();

         FileInputStream in = new FileInputStream(img.getAbsolutePath());
         img_stream = new byte[in.available()];
         in.read(img_stream);
         // Close it if we need to
         if( in != null ) in.close();

         if (img.delete() == false) 
            System.err.println("Warning: "+img.getAbsolutePath()+" could not be deleted!");
      }
      catch (java.io.IOException ioe) {
         System.err.println("Error: in I/O processing of tempfile or in calling external command");
         ioe.printStackTrace();
      }
      catch (java.lang.InterruptedException ie) {
         System.err.println("Error: the execution of the external program was interrupted");
         ie.printStackTrace();
      }

      return img_stream;
   }

   /**
    * Writes the source of the graph in a file, and returns the written file
    * as a File object.
    * @param str Source of the graph (in dot language).
    * @return The file (as a File object) that contains the source of the graph.
    */
   public File writeDotSourceToFile(String str) throws java.io.IOException
   {
      File temp;
      try {
         temp = File.createTempFile("graph_", ".dot.tmp");
         FileWriter fout = new FileWriter(temp);
         fout.write(str);
         fout.close();
      }
      catch (Exception e) {
         System.err.println("Error: I/O error while writing the dot source to temp file!");
         return null;
      }
      return temp;
   }

   /**
    * Returns a string that is used to start a graph.
    * @return A string to open a graph.
    */
   public String start_graph() {
      return "digraph G {";
   }

   /**
    * Returns a string that is used to end a graph.
    * @return A string to close a graph.
    */
   public String end_graph() {
      return "}";
   }
}

GraphViz gv = new GraphViz();
byte[] out = gv.getGraph(dot);

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flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);