Not used in Jalview

[jalview.git] / src / org / biojava / dasobert / das / DAS_Sequence_Handler.java

diff --git a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
deleted file mode 100755 (executable)
index 0d39e15..0000000
--- a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- *                    BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence.  This should
- * be distributed with the code.  If you do not have a copy,
- * see:
- *
- *      http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors.  These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- *      http://www.biojava.org/
- *
- * Created on 19.03.2004
- * @author Andreas Prlic
- *
- */
-package org.biojava.dasobert.das;
-
-
-import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes            ;
-import java.util.logging.*                ;
-
-/**
- * a class that parses the XML response of a DAS - sequence command.
- * @author Andreas Prlic
- *
- */
-public class DAS_Sequence_Handler extends DefaultHandler {
-
-       String sequence ;
-       int length ;
-       boolean dna_flag; 
-       /**
-        * 
-        */
-       public DAS_Sequence_Handler() {
-               super();
-               // TODO Auto-generated constructor stub
-               sequence = "" ;
-               length = 0;
-               dna_flag = false ;
-       }
-
-       public void startElement (String uri, String name, String qName, Attributes atts){
-
-           if ( qName.equals("SEQUENCE")){
-               //System.out.println("new element >" + name + "< >" + qName+"<");
-               // was : length
-               String lenstr   = atts.getValue("stop");
-               length = Integer.parseInt(lenstr);
-               dna_flag = true ;
-           }
-               
-       }
-       
-       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");
-                
-       }
-       
-       public String get_sequence() {
-               if ( length != sequence.length()) {     
-                   Logger logger  = Logger.getLogger("org.biojava.spice");
-                   logger.warning("Sequence does not match specified length!");
-                       
-               }
-               
-               return sequence;
-       }
-               
-       
-       
-}