(JAL-1016) noted position where race condition occurs

[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
index 0d39e15..fe5be8b 100755 (executable)
--- 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;
+  }
+
 }