src/org/biojava/dasobert/das/DAS_Sequence_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 import java.util.logging.*                ;
  30
  31 /**
  32  * a class that parses the XML response of a DAS - sequence command.
  33  * @author Andreas Prlic
  34  *
  35  */
  36 public class DAS_Sequence_Handler extends DefaultHandler {
  37
  38         String sequence ;
  39         int length ;
  40         boolean dna_flag;
  41         /**
  42          *
  43          */
  44         public DAS_Sequence_Handler() {
  45                 super();
  46                 // TODO Auto-generated constructor stub
  47                 sequence = "" ;
  48                 length = 0;
  49                 dna_flag = false ;
  50         }
  51
  52         public void startElement (String uri, String name, String qName, Attributes atts){
  53
  54             if ( qName.equals("SEQUENCE")){
  55                 //System.out.println("new element >" + name + "< >" + qName+"<");
  56                 // was : length
  57                 String lenstr   = atts.getValue("stop");
  58                 length = Integer.parseInt(lenstr);
  59                 dna_flag = true ;
  60             }
  61
  62         }
  63
  64         public void characters (char ch[], int start, int length){
  65             //System.out.print("Characters:    \"");
  66                 if (dna_flag)
  67                  for (int i = start; i < start + length; i++) {
  68                         switch (ch[i]) {
  69                         case '\\':
  70                                 //System.out.print("\\\\");
  71                                 break;
  72                         case '"':
  73                                 //System.out.print("\\\"");
  74                                 break;
  75                         case '\n':
  76                                 //System.out.print("\\n");
  77                                 break;
  78                         case '\r':
  79                                 //System.out.print("\\r");
  80                                 break;
  81                         case '\t':
  82                                 //System.out.print("\\t");
  83                                 break;
  84                         case ' ':
  85                                 break;
  86                         default:
  87                                 sequence = sequence + ch[i];
  88                                 //System.out.print(ch[i]);
  89                  break;
  90                  }
  91                  }
  92                  //System.out.print("\"\n");
  93
  94         }
  95
  96         public String get_sequence() {
  97                 if ( length != sequence.length()) {
  98                     Logger logger  = Logger.getLogger("org.biojava.spice");
  99                     logger.warning("Sequence does not match specified length!");
 100
 101                 }
 102
 103                 return sequence;
 104         }
 105
 106
 107
 108 }