Team:Freiburg software/Code/BioBrick DAS DNA Handler.java

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 /*
    Copyright: synbiowave
     
    License: GPL
     
    Authors: Jörg Wassolesk
     
    Version: 0.1 
    
    DESCRIPTION:
    	This class provides the functions for handling DAS DNA requests.
 */

 package org.synbiowave.biobrick;


 import org.xml.sax.helpers.DefaultHandler;
 import org.xml.sax.Attributes;

 // TODO: Auto-generated Javadoc
 /**
 * a class to parse the XML response of a DAS-DNA request.
 * 
 * @author Jörg
 */
 public class BioBrick_DAS_DNA_Handler extends DefaultHandler {

	/** The sequence. */
	String sequence ;
	
	/** The length. */
	int length ;
	
	/** The dna_flag. */
	boolean dna_flag; 
	
	/**
	 * Instantiates a new bio brick_ da s_ dn a_ handler.
	 */
	public BioBrick_DAS_DNA_Handler() {
		super();
		// TODO Auto-generated constructor stub
		sequence = "" ;
		length = 0;
		dna_flag = false ;
	}

	/* (non-Javadoc)
	 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, 
         * java.lang.String, org.xml.sax.Attributes)
	 */
	public void startElement (String uri, String name, String qName, Attributes atts){

	    if ( qName.equals("DNA")){
		//System.out.println("new element >" + name + "< >" + qName+"<");
		// was : length
		String lenstr 	= atts.getValue("length");
		length = Integer.parseInt(lenstr);
		dna_flag = true ;
	    }
		
	}
	
	/* (non-Javadoc)
	 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
	 */
	public void characters (char ch[], int start, int length){
	    //System.out.print("Characters:    \"");
		if (dna_flag) 
		 for (int i = start; i < start + length; i++) {
		 	switch (ch[i]) {
		 	case '\\':
		 		//System.out.print("\\\\");
		 		break;
		 	case '"':
		 		//System.out.print("\\\"");
		 		break;
		 	case '\n':
		 		//System.out.print("\\n");
		 		break;
		 	case '\r':
		 		//System.out.print("\\r");
		 		break;
		 	case '\t':
		 		//System.out.print("\\t");
		 		break;
		 	case ' ':
		 		break;
		 	default:
		 		sequence = sequence + ch[i];
		 		//System.out.print(ch[i]);
		 break;
		 }
		 }
		 //System.out.print("\"\n");
		 
	}
	
	/**
	 * Gets the _sequence.
	 * 
	 * @return the _sequence
	 */
	public String get_sequence() {
		if ( length != sequence.length()) {		
			System.err.println("Sequence does not match specified length!");
		}
		
		return sequence;
	}	
 }