removed all dasobert code and begun to replace with Jdas calls.

[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 fe5be8b..0000000
--- a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
+++ /dev/null
@@ -1,161 +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
-{
-
-  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;
-  }
-
-}