Das client files

[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
new file mode 100755 (executable)
index 0000000..0d39e15
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+++ b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
@@ -0,0 +1,108 @@
+/*
+ *                    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;
+       }
+               
+       
+       
+}