/*
 * TestDigest2.java
 *
 * Created on July 10, 2001, 1:10 PM
 */

package prot;




import org.biojava.bio.proteomics.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.BioException;
import org.biojava.utils.*;
import java.io.*;
import java.util.*;
import java.text.NumberFormat;

/**
 *
 * @author  mjones
 * @version 
 */
public class TestDigestIO extends Object {

    /** Creates new TestDigest2 */
    public TestDigestIO(String fileName) throws BioException, 
                                                ChangeVetoException, 
                                                IOException {
        //Initiate Digest
        Digest bioJavaDigest = new Digest();
        bioJavaDigest.setMaxMissedCleavages(2);
        
        
       // Protease protease = new Protease();
       // String[] list = Protease.getProteaseList();
       // for(int i=0; i<list.length ;i++)
       //         System.out.println(list[i]);
        
       String proteaseName = Protease.ASP_N;

       bioJavaDigest.setProtese(Protease.getProteaseByName(proteaseName));
        
        //Get the Sequence Iterator
        Alphabet alpha = ProteinTools.getAlphabet();
        SymbolParser protParser = alpha.getParser("token");
        BufferedReader br = new BufferedReader(
                               new FileReader(fileName));

                                        
      SequenceBuilderFactory sFact = new FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY);
      SequenceFormat sFormat = new FastaFormat();
      
      SequenceIterator sourceI = new StreamReader(
        br,
        sFormat,
        protParser,
        sFact
      );
      
      ArrayList list  = new ArrayList();
      while(sourceI.hasNext()) {
         Sequence sourceSeq = sourceI.nextSequence();
         bioJavaDigest.setSequence(sourceSeq);
         bioJavaDigest.addDigestFeatures();
         list.add(sourceSeq);
         printFeatures(sourceSeq.features(), sourceSeq.getName() + " " );
      }
      
      
        
    }
    
    private  static void printFeatures(Iterator i, String prefix)
           {
                NumberFormat nf = NumberFormat.getInstance();

		nf.setMaximumFractionDigits(2);
		nf.setMinimumFractionDigits(2);
		
                MassCalc massCalc = new MassCalc(SymbolPropertyTable.AVG_MASS);
                                
    try{
        massCalc.setSymbolModification('W', 100000.00); 
    }catch(Exception e){}
               for (; i.hasNext(); ) {
                   Feature f = (Feature) i.next();
                   System.out.print(prefix);
                   System.out.print(f.getType());
                   System.out.print(f.getLocation().toString()+ " ");
                   
                   //Use this for static 
                   double mass = MassCalc.getMass(
                                                f.getSymbols(), 
                                                SymbolPropertyTable.AVG_MASS, 
                                                true);
                   System.out.print(nf.format(mass) + " ");
                    
                    //Use this for instances of MassCalc
                   mass = massCalc.getMass(f.getSymbols(),true);
                    
                    System.out.print(" PTM " + nf.format(mass) + " ");
                    
                    
                   System.out.print(" " + f.getSymbols().seqString() + "    " );
                   
                   
                   
                   System.out.println();
                 //  printFeatures(f, pw, prefix + "    ");
                
                
               }
           }

    /**
    * @param args the command line arguments
    */
    public static void main (String args[]) {
        if(args.length < 1){
            System.out.println("Usage: java prot.TestDigest <fastaFile>");
            System.exit(-1);
        }
        try{
           new TestDigestIO(args[0]); 
        }catch (BioException bioe){
            bioe.printStackTrace();
        }catch (IOException ioe){
            ioe.printStackTrace();
        }catch (ChangeVetoException cve){
            cve.printStackTrace();
        }
    }

}