src/org/biojava/dasobert/das/DAS_DNA_Handler.java

   1 /*
   2  *                    BioJava development code
   3  *
   4  * This code may be freely distributed and modified under the
   5  * terms of the GNU Lesser General Public Licence.  This should
   6  * be distributed with the code.  If you do not have a copy,
   7  * see:
   8  *
   9  *      http://www.gnu.org/copyleft/lesser.html
  10  *
  11  * Copyright for this code is held jointly by the individual
  12  * authors.  These should be listed in @author doc comments.
  13  *
  14  * For more information on the BioJava project and its aims,
  15  * or to join the biojava-l mailing list, visit the home page
  16  * at:
  17  *
  18  *      http://www.biojava.org/
  19  *
  20  * Created on 19.03.2004
  21  * @author Andreas Prlic
  22  *
  23  */
  24 package org.biojava.dasobert.das;
  25
  26
  27 import org.xml.sax.helpers.DefaultHandler;
  28 import org.xml.sax.Attributes;
  29
  30 /**
  31  * a class to parse the XML response of a DAS-DNA request.
  32  * @author andreas
  33  */
  34 public class DAS_DNA_Handler extends DefaultHandler {
  35
  36         String sequence ;
  37         int length ;
  38         boolean dna_flag;
  39         /**
  40          *
  41          */
  42         public DAS_DNA_Handler() {
  43                 super();
  44                 // TODO Auto-generated constructor stub
  45                 sequence = "" ;
  46                 length = 0;
  47                 dna_flag = false ;
  48         }
  49
  50         public void startElement (String uri, String name, String qName, Attributes atts){
  51
  52             if ( qName.equals("DNA")){
  53                 //System.out.println("new element >" + name + "< >" + qName+"<");
  54                 // was : length
  55                 String lenstr   = atts.getValue("length");
  56                 length = Integer.parseInt(lenstr);
  57                 dna_flag = true ;
  58             }
  59
  60         }
  61
  62         public void characters (char ch[], int start, int length){
  63             //System.out.print("Characters:    \"");
  64                 if (dna_flag)
  65                  for (int i = start; i < start + length; i++) {
  66                         switch (ch[i]) {
  67                         case '\\':
  68                                 //System.out.print("\\\\");
  69                                 break;
  70                         case '"':
  71                                 //System.out.print("\\\"");
  72                                 break;
  73                         case '\n':
  74                                 //System.out.print("\\n");
  75                                 break;
  76                         case '\r':
  77                                 //System.out.print("\\r");
  78                                 break;
  79                         case '\t':
  80                                 //System.out.print("\\t");
  81                                 break;
  82                         case ' ':
  83                                 break;
  84                         default:
  85                                 sequence = sequence + ch[i];
  86                                 //System.out.print(ch[i]);
  87                  break;
  88                  }
  89                  }
  90                  //System.out.print("\"\n");
  91
  92         }
  93
  94         public String get_sequence() {
  95                 if ( length != sequence.length()) {
  96                         System.err.println("Sequence does not match specified length!");
  97                 }
  98
  99                 return sequence;
 100         }
 101
 102
 103
 104 }