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         StringBuffer sequence ;
  39         int length ;
  40
  41         int maxLength;
  42         String version;
  43
  44         boolean dna_flag;
  45         /**
  46          *
  47          */
  48         public DAS_Sequence_Handler() {
  49                 super();
  50
  51                 sequence = new StringBuffer() ;
  52                 length = 0;
  53                 dna_flag = false ;
  54                 maxLength = -1;
  55                 version = "";
  56         }
  57
  58
  59
  60         /** set a maximum length of sequence that should be loaded
  61          * default: -1. if -1 no length restriction is being supplied
  62          * @return the maximum length or -1 if no restriction
  63          */
  64         public int getMaxLength() {
  65                 return maxLength;
  66         }
  67
  68
  69
  70         /** set a maximum length of sequence that should be loaded
  71          * default: -1. if -1 no length restriction is being supplied
  72          * @param maxLength the maximum length or -1 if unrestricted
  73          */
  74         public void setMaxLength(int maxLength) {
  75                 this.maxLength = maxLength;
  76         }
  77
  78
  79
  80
  81         public void startElement (String uri, String name, String qName, Attributes atts){
  82
  83                 if ( qName.equals("SEQUENCE")){
  84                         version = atts.getValue("version");
  85                         String lenstr   = atts.getValue("stop");
  86                         length = Integer.parseInt(lenstr);
  87                         dna_flag = true ;
  88                 }
  89
  90         }
  91
  92         public void characters (char ch[], int start, int length){
  93
  94                 if (maxLength > 0)
  95                         if ( sequence.length() > maxLength)
  96                                 return;
  97
  98                 if (dna_flag)
  99                         for (int i = start; i < start + length; i++) {
 100
 101                                 // all sorts of characters can be found in "seqeunces" ... ignore them...
 102                                 switch (ch[i]) {
 103                                 case '\\':
 104                                         //System.out.print("\\\\");
 105                                         break;
 106                                 case '"':
 107                                         //System.out.print("\\\"");
 108                                         break;
 109                                 case '\n':
 110                                         //System.out.print("\\n");
 111                                         break;
 112                                 case '\r':
 113                                         //System.out.print("\\r");
 114                                         break;
 115                                 case '\t':
 116                                         //System.out.print("\\t");
 117                                         break;
 118                                 case ' ':
 119                                         break;
 120                                 default:
 121                                         sequence = sequence.append(ch[i]);
 122
 123                                 break;
 124                                 }
 125                         }
 126
 127         }
 128
 129         public String get_sequence() {
 130
 131                 if ( maxLength < 0) {
 132                         if ( length != sequence.length()) {
 133                                 Logger logger  = Logger.getLogger("org.biojava.spice");
 134                                 logger.warning("Sequence does not match specified length!");
 135                         }
 136                 }
 137
 138                 return sequence.toString();
 139         }
 140
 141         public String getVersion() {
 142                 return version;
 143         }
 144
 145 }