X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Forg%2Fbiojava%2Fdasobert%2Fdas%2FDAS_Sequence_Handler.java;h=fe5be8b19e5cffb5159d3970c891321260d20155;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0d39e15614235897c7c05396cc59d91731837bbf;hpb=ac8acb905e84708b759ae1e87eaf6691d9376d57;p=jalview.git

diff --git a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
index 0d39e15..fe5be8b 100755
--- a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
@@ -23,86 +23,139 @@
  */
 package org.biojava.dasobert.das;
 
-
 import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes            ;
-import java.util.logging.*                ;
+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;
-	}
-		
-	
-	
+public class DAS_Sequence_Handler extends DefaultHandler
+{
+
+  StringBuffer sequence;
+
+  int length;
+
+  int maxLength;
+
+  String version;
+
+  boolean dna_flag;
+
+  /**
+   * 
+   */
+  public DAS_Sequence_Handler()
+  {
+    super();
+
+    sequence = new StringBuffer();
+    length = 0;
+    dna_flag = false;
+    maxLength = -1;
+    version = "";
+  }
+
+  /**
+   * set a maximum length of sequence that should be loaded default: -1. if -1
+   * no length restriction is being supplied
+   * 
+   * @return the maximum length or -1 if no restriction
+   */
+  public int getMaxLength()
+  {
+    return maxLength;
+  }
+
+  /**
+   * set a maximum length of sequence that should be loaded default: -1. if -1
+   * no length restriction is being supplied
+   * 
+   * @param maxLength
+   *                the maximum length or -1 if unrestricted
+   */
+  public void setMaxLength(int maxLength)
+  {
+    this.maxLength = maxLength;
+  }
+
+  public void startElement(String uri, String name, String qName,
+          Attributes atts)
+  {
+
+    if (qName.equals("SEQUENCE"))
+    {
+      version = atts.getValue("version");
+      String lenstr = atts.getValue("stop");
+      length = Integer.parseInt(lenstr);
+      dna_flag = true;
+    }
+
+  }
+
+  public void characters(char ch[], int start, int length)
+  {
+
+    if (maxLength > 0)
+      if (sequence.length() > maxLength)
+        return;
+
+    if (dna_flag)
+      for (int i = start; i < start + length; i++)
+      {
+
+        // all sorts of characters can be found in "seqeunces" ... ignore
+        // them...
+        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.append(ch[i]);
+
+          break;
+        }
+      }
+
+  }
+
+  public String get_sequence()
+  {
+
+    if (maxLength < 0)
+    {
+      if (length != sequence.length())
+      {
+        Logger logger = Logger.getLogger("org.biojava.spice");
+        logger.warning("Sequence does not match specified length!");
+      }
+    }
+
+    return sequence.toString();
+  }
+
+  public String getVersion()
+  {
+    return version;
+  }
+
 }