X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAlignmentSequence.java;h=58c866f23a9aba35c41da600cdc72f4cd8c1f458;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=6e611a34f24cb2d919caf88b78da41f30cd28508;hpb=a06295cc0912455e0bc53b26cb4e0134e6759d0f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/AlignmentSequence.java b/src/uk/ac/vamsas/objects/core/AlignmentSequence.java
index 6e611a3..58c866f 100644
--- a/src/uk/ac/vamsas/objects/core/AlignmentSequence.java
+++ b/src/uk/ac/vamsas/objects/core/AlignmentSequence.java
@@ -1,385 +1,548 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:AlignmentSequence.java 264 2006-12-14 17:42:54Z JimP $
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package uk.ac.vamsas.objects.core;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
 
 /**
  * Class AlignmentSequence.
  * 
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ *          $
  */
-public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType 
-implements java.io.Serializable
-{
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Primary Key for vamsas object
-     *  referencing 
-     */
-    private java.lang.String _id;
-
-    /**
-     * Dataset Sequence from which
-     *  this alignment sequence is taken from
-     *  
-     */
-    private java.lang.Object _refid;
-
-    /**
-     * Field _alignmentSequenceAnnotationList
-     */
-    private java.util.Vector _alignmentSequenceAnnotationList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlignmentSequence() 
-     {
-        super();
-        _alignmentSequenceAnnotationList = new Vector();
-    } //-- uk.ac.vamsas.objects.core.AlignmentSequence()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param vAlignmentSequenceAnnotation
-     */
-    public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
-    } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 
-
-    /**
-     * Method addAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignmentSequenceAnnotation
-     */
-    public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
-    } //-- void addAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 
-
-    /**
-     * Method enumerateAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
-    {
-        return _alignmentSequenceAnnotationList.elements();
-    } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation() 
-
-    /**
-     * Note: hashCode() has not been overriden
-     * 
-     * @param obj
-     * @return boolean
-     */
-    public boolean equals(java.lang.Object obj)
-    {
-        if ( this == obj )
-            return true;
-        
-        if (super.equals(obj)==false)
-            return false;
-        
-        if (obj instanceof AlignmentSequence) {
-        
-            AlignmentSequence temp = (AlignmentSequence)obj;
-            if (this._id != null) {
-                if (temp._id == null) return false;
-                else if (!(this._id.equals(temp._id))) 
-                    return false;
+public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
+    implements java.io.Serializable {
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Primary Key for vamsas object referencing
+   */
+  private java.lang.String _id;
+
+  /**
+   * Dataset Sequence from which this alignment sequence is taken from
+   * 
+   */
+  private java.lang.Object _refid;
+
+  /**
+   * Field _alignmentSequenceAnnotationList.
+   */
+  private java.util.Vector _alignmentSequenceAnnotationList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlignmentSequence() {
+    super();
+    this._alignmentSequenceAnnotationList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlignmentSequenceAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlignmentSequenceAnnotation(
+      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+      throws java.lang.IndexOutOfBoundsException {
+    this._alignmentSequenceAnnotationList
+        .addElement(vAlignmentSequenceAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignmentSequenceAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlignmentSequenceAnnotation(
+      final int index,
+      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+      throws java.lang.IndexOutOfBoundsException {
+    this._alignmentSequenceAnnotationList.add(index,
+        vAlignmentSequenceAnnotation);
+  }
+
+  /**
+   * Method enumerateAlignmentSequenceAnnotation.
+   * 
+   * @return an Enumeration over all
+   *         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
+   */
+  public java.util.Enumeration enumerateAlignmentSequenceAnnotation() {
+    return this._alignmentSequenceAnnotationList.elements();
+  }
+
+  /**
+   * Overrides the java.lang.Object.equals method.
+   * 
+   * @param obj
+   * @return true if the objects are equal.
+   */
+  public boolean equals(final java.lang.Object obj) {
+    if (this == obj)
+      return true;
+
+    if (super.equals(obj) == false)
+      return false;
+
+    if (obj instanceof AlignmentSequence) {
+
+      AlignmentSequence temp = (AlignmentSequence) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._id != null) {
+        if (temp._id == null)
+          return false;
+        if (this._id != temp._id) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
             }
-            else if (temp._id != null)
-                return false;
-            if (this._refid != null) {
-                if (temp._refid == null) return false;
-                else if (!(this._refid.equals(temp._refid))) 
-                    return false;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
             }
-            else if (temp._refid != null)
-                return false;
-            if (this._alignmentSequenceAnnotationList != null) {
-                if (temp._alignmentSequenceAnnotationList == null) return false;
-                else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList))) 
-                    return false;
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._id.equals(temp._id)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+              return false;
             }
-            else if (temp._alignmentSequenceAnnotationList != null)
-                return false;
-            return true;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+          }
         }
+      } else if (temp._id != null)
         return false;
-    } //-- boolean equals(java.lang.Object) 
-
-    /**
-     * Method getAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @return AlignmentSequenceAnnotation
-     */
-    public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
-            throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
-        }
-        
-        return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int) 
-
-    /**
-     * Method getAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @return AlignmentSequenceAnnotation
-     */
-    public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
-    {
-        int size = _alignmentSequenceAnnotationList.size();
-        uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() 
-
-    /**
-     * Method getAlignmentSequenceAnnotationCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAlignmentSequenceAnnotationCount()
-    {
-        return _alignmentSequenceAnnotationList.size();
-    } //-- int getAlignmentSequenceAnnotationCount() 
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     *  referencing 
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'refid'. The field 'refid' has
-     * the following description: Dataset Sequence from which
-     *  this alignment sequence is taken from
-     *  
-     * 
-     * @return Object
-     * @return the value of field 'refid'.
-     */
-    public java.lang.Object getRefid()
-    {
-        return this._refid;
-    } //-- java.lang.Object getRefid() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+      if (this._refid != null) {
+        if (temp._refid == null)
+          return false;
+        if (this._refid != temp._refid) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refid);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refid);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+            }
+            ;
             return false;
+          }
+          if (!thcycle) {
+            if (!this._refid.equals(temp._refid)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+          }
         }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @return AlignmentSequenceAnnotation
-     */
-    public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
-    {
-        java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
-        _alignmentSequenceAnnotationList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
-    } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int) 
-
-    /**
-     * Method removeAllAlignmentSequenceAnnotation
-     * 
-     */
-    public void removeAllAlignmentSequenceAnnotation()
-    {
-        _alignmentSequenceAnnotationList.removeAllElements();
-    } //-- void removeAllAlignmentSequenceAnnotation() 
-
-    /**
-     * Method setAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignmentSequenceAnnotation
-     */
-    public void setAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
-            throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
-        }
-        _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
-    } //-- void setAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 
-
-    /**
-     * Method setAlignmentSequenceAnnotation
-     * 
-     * 
-     * 
-     * @param alignmentSequenceAnnotationArray
-     */
-    public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
-    {
-        //-- copy array
-        _alignmentSequenceAnnotationList.removeAllElements();
-        for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
-            _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+      } else if (temp._refid != null)
+        return false;
+      if (this._alignmentSequenceAnnotationList != null) {
+        if (temp._alignmentSequenceAnnotationList == null)
+          return false;
+        if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._alignmentSequenceAnnotationList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._alignmentSequenceAnnotationList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._alignmentSequenceAnnotationList
+                .equals(temp._alignmentSequenceAnnotationList)) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+              return false;
+            }
+            org.castor.util.CycleBreaker
+                .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+            org.castor.util.CycleBreaker
+                .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+          }
         }
-    } //-- void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     *  referencing 
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'refid'. The field 'refid' has the
-     * following description: Dataset Sequence from which
-     *  this alignment sequence is taken from
-     *  
-     * 
-     * @param refid the value of field 'refid'.
-     */
-    public void setRefid(java.lang.Object refid)
-    {
-        this._refid = refid;
-    } //-- void setRefid(java.lang.Object) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return SequenceType
-     */
-    public static uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (uk.ac.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
-    } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
+      } else if (temp._alignmentSequenceAnnotationList != null)
+        return false;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Method getAlignmentSequenceAnnotation.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the
+   *         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation at the given
+   *         index
+   */
+  public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
+      final int index) throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+      throw new IndexOutOfBoundsException(
+          "getAlignmentSequenceAnnotation: Index value '" + index
+              + "' not in range [0.."
+              + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList
+        .get(index);
+  }
+
+  /**
+   * Method getAlignmentSequenceAnnotation.Returns the contents of the
+   * collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() {
+    uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
+    return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList
+        .toArray(array);
+  }
+
+  /**
+   * Method getAlignmentSequenceAnnotationAsReference.Returns a reference to
+   * '_alignmentSequenceAnnotationList'. No type checking is performed on any
+   * modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getAlignmentSequenceAnnotationAsReference() {
+    return this._alignmentSequenceAnnotationList;
+  }
+
+  /**
+   * Method getAlignmentSequenceAnnotationCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlignmentSequenceAnnotationCount() {
+    return this._alignmentSequenceAnnotationList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Primary Key for vamsas object referencing
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId() {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'refid'. The field 'refid' has the following
+   * description: Dataset Sequence from which this alignment sequence is taken
+   * from
+   * 
+   * 
+   * @return the value of field 'Refid'.
+   */
+  public java.lang.Object getRefid() {
+    return this._refid;
+  }
+
+  /**
+   * Overrides the java.lang.Object.hashCode method.
+   * <p>
+   * The following steps came from <b>Effective Java Programming Language
+   * Guide</b> by Joshua Bloch, Chapter 3
+   * 
+   * @return a hash code value for the object.
+   */
+  public int hashCode() {
+    int result = super.hashCode();
+
+    long tmp;
+    if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+      result = 37 * result + _id.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+    }
+    if (_refid != null && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
+      result = 37 * result + _refid.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
+    }
+    if (_alignmentSequenceAnnotationList != null
+        && !org.castor.util.CycleBreaker
+            .startingToCycle(_alignmentSequenceAnnotationList)) {
+      result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
+      org.castor.util.CycleBreaker
+          .releaseCycleHandle(_alignmentSequenceAnnotationList);
+    }
+
+    return result;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid() {
+    try {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex) {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlignmentSequenceAnnotation.
+   * 
+   * @param vAlignmentSequenceAnnotation
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlignmentSequenceAnnotation(
+      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
+    boolean removed = _alignmentSequenceAnnotationList
+        .remove(vAlignmentSequenceAnnotation);
+    return removed;
+  }
+
+  /**
+   * Method removeAlignmentSequenceAnnotationAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(
+      final int index) {
+    java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index);
+    return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
+  }
+
+  /**
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  public void removeAllAlignmentSequenceAnnotation() {
+    this._alignmentSequenceAnnotationList.clear();
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignmentSequenceAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAlignmentSequenceAnnotation(
+      final int index,
+      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+      throw new IndexOutOfBoundsException(
+          "setAlignmentSequenceAnnotation: Index value '" + index
+              + "' not in range [0.."
+              + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
+    }
+
+    this._alignmentSequenceAnnotationList.set(index,
+        vAlignmentSequenceAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlignmentSequenceAnnotationArray
+   */
+  public void setAlignmentSequenceAnnotation(
+      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
+    // -- copy array
+    _alignmentSequenceAnnotationList.clear();
+
+    for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) {
+      this._alignmentSequenceAnnotationList
+          .add(vAlignmentSequenceAnnotationArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_alignmentSequenceAnnotationList' by copying the given
+   * Vector. All elements will be checked for type safety.
+   * 
+   * @param vAlignmentSequenceAnnotationList
+   *          the Vector to copy.
+   */
+  public void setAlignmentSequenceAnnotation(
+      final java.util.Vector vAlignmentSequenceAnnotationList) {
+    // copy vector
+    this._alignmentSequenceAnnotationList.clear();
+
+    this._alignmentSequenceAnnotationList
+        .addAll(vAlignmentSequenceAnnotationList);
+  }
+
+  /**
+   * Sets the value of '_alignmentSequenceAnnotationList' by setting it to the
+   * given Vector. No type checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param alignmentSequenceAnnotationVector
+   *          the Vector to set.
+   */
+  public void setAlignmentSequenceAnnotationAsReference(
+      final java.util.Vector alignmentSequenceAnnotationVector) {
+    this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector;
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * Primary Key for vamsas object referencing
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id) {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'refid'. The field 'refid' has the following
+   * description: Dataset Sequence from which this alignment sequence is taken
+   * from
+   * 
+   * 
+   * @param refid
+   *          the value of field 'refid'.
+   */
+  public void setRefid(final java.lang.Object refid) {
+    this._refid = refid;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp
+   */
+  public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
+      final java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(
+        uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }