X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FRangeType.java;h=b2573e95601c9f8213c3758ffeee66f054d0bb56;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=3e1f6da181a70c54000388f6da10b310b1166a94;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/RangeType.java b/src/uk/ac/vamsas/objects/core/RangeType.java
index 3e1f6da..b2573e9 100644
--- a/src/uk/ac/vamsas/objects/core/RangeType.java
+++ b/src/uk/ac/vamsas/objects/core/RangeType.java
@@ -1,601 +1,600 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * 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;
 
 /**
- * Specify an ordered set of positions and/or regions on the
- * principle
- *  dimension of some associated vamsas object Keeping to jaxb-1.0
- * specification for the moment - this choice should
- *  become a substitution group when we use jaxb-2.0 capable
- * bindings
- *  
+ * Specify an ordered set of positions and/or regions on the principle dimension
+ * of some associated vamsas object Keeping to jaxb-1.0 specification for the
+ * moment - this choice should become a substitution group when we use jaxb-2.0
+ * capable bindings
+ * 
  * 
  * @version $Revision$ $Date$
  */
-public abstract class RangeType extends uk.ac.vamsas.client.Vobject 
-implements java.io.Serializable
-{
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Internal choice value storage
-     */
-    private java.lang.Object _choiceValue;
-
-    /**
-     * a position within the associated object's coordinate system
-     *  
-     */
-    private java.util.Vector _posList;
-
-    /**
-     * a region from start to end, with flag for inclusivity of
-     *  terminii 
-     */
-    private java.util.Vector _segList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public RangeType() {
-        super();
-        this._posList = new java.util.Vector();
-        this._segList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPos
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPos(
-            final uk.ac.vamsas.objects.core.Pos vPos)
-    throws java.lang.IndexOutOfBoundsException {
-        this._posList.addElement(vPos);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPos
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPos(
-            final int index,
-            final uk.ac.vamsas.objects.core.Pos vPos)
-    throws java.lang.IndexOutOfBoundsException {
-        this._posList.add(index, vPos);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSeg
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeg(
-            final uk.ac.vamsas.objects.core.Seg vSeg)
-    throws java.lang.IndexOutOfBoundsException {
-        this._segList.addElement(vSeg);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeg
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeg(
-            final int index,
-            final uk.ac.vamsas.objects.core.Seg vSeg)
-    throws java.lang.IndexOutOfBoundsException {
-        this._segList.add(index, vSeg);
-    }
-
-    /**
-     * Method enumeratePos.
-     * 
-     * @return an Enumeration over all
-     * uk.ac.vamsas.objects.core.Pos elements
-     */
-    public java.util.Enumeration enumeratePos(
-    ) {
-        return this._posList.elements();
-    }
-
-    /**
-     * Method enumerateSeg.
-     * 
-     * @return an Enumeration over all
-     * uk.ac.vamsas.objects.core.Seg elements
-     */
-    public java.util.Enumeration enumerateSeg(
-    ) {
-        return this._segList.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)
+public abstract class RangeType extends uk.ac.vamsas.client.Vobject implements
+    java.io.Serializable {
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Internal choice value storage
+   */
+  private java.lang.Object _choiceValue;
+
+  /**
+   * a position within the associated object's coordinate system
+   * 
+   */
+  private java.util.Vector _posList;
+
+  /**
+   * a region from start to end, with flag for inclusivity of terminii
+   */
+  private java.util.Vector _segList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public RangeType() {
+    super();
+    this._posList = new java.util.Vector();
+    this._segList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPos
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPos(final uk.ac.vamsas.objects.core.Pos vPos)
+      throws java.lang.IndexOutOfBoundsException {
+    this._posList.addElement(vPos);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPos
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPos(final int index, final uk.ac.vamsas.objects.core.Pos vPos)
+      throws java.lang.IndexOutOfBoundsException {
+    this._posList.add(index, vPos);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSeg
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeg(final uk.ac.vamsas.objects.core.Seg vSeg)
+      throws java.lang.IndexOutOfBoundsException {
+    this._segList.addElement(vSeg);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeg
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeg(final int index, final uk.ac.vamsas.objects.core.Seg vSeg)
+      throws java.lang.IndexOutOfBoundsException {
+    this._segList.add(index, vSeg);
+  }
+
+  /**
+   * Method enumeratePos.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Pos elements
+   */
+  public java.util.Enumeration enumeratePos() {
+    return this._posList.elements();
+  }
+
+  /**
+   * Method enumerateSeg.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Seg elements
+   */
+  public java.util.Enumeration enumerateSeg() {
+    return this._segList.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 RangeType) {
+
+      RangeType temp = (RangeType) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._choiceValue != null) {
+        if (temp._choiceValue == null)
+          return false;
+        if (this._choiceValue != temp._choiceValue) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._choiceValue);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._choiceValue);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._choiceValue);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._choiceValue);
+            }
+            ;
             return false;
-        
-        if (obj instanceof RangeType) {
-        
-            RangeType temp = (RangeType)obj;
-            boolean thcycle;
-            boolean tmcycle;
-            if (this._choiceValue != null) {
-                if (temp._choiceValue == null) return false;
-                if (this._choiceValue != temp._choiceValue) {
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._choiceValue);
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._choiceValue);
-                    if (thcycle!=tmcycle) {
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue); };
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); };
-                        return false;
-                    }
-                    if (!thcycle) {
-                        if (!this._choiceValue.equals(temp._choiceValue)) {
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);
-                            return false;
-                        }
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);
-                    }
-                }
-            } else if (temp._choiceValue != null)
-                return false;
-            if (this._posList != null) {
-                if (temp._posList == null) return false;
-                if (this._posList != temp._posList) {
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._posList);
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._posList);
-                    if (thcycle!=tmcycle) {
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._posList); };
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList); };
-                        return false;
-                    }
-                    if (!thcycle) {
-                        if (!this._posList.equals(temp._posList)) {
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._posList);
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList);
-                            return false;
-                        }
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._posList);
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList);
-                    }
-                }
-            } else if (temp._posList != null)
-                return false;
-            if (this._segList != null) {
-                if (temp._segList == null) return false;
-                if (this._segList != temp._segList) {
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._segList);
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._segList);
-                    if (thcycle!=tmcycle) {
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._segList); };
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList); };
-                        return false;
-                    }
-                    if (!thcycle) {
-                        if (!this._segList.equals(temp._segList)) {
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._segList);
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList);
-                            return false;
-                        }
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._segList);
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList);
-                    }
-                }
-            } else if (temp._segList != null)
-                return false;
-            return true;
+          }
+          if (!thcycle) {
+            if (!this._choiceValue.equals(temp._choiceValue)) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._choiceValue);
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._choiceValue);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);
+          }
         }
+      } else if (temp._choiceValue != null)
         return false;
-    }
-
-    /**
-     * Returns the value of field 'choiceValue'. The field
-     * 'choiceValue' has the following description: Internal choice
-     * value storage
-     * 
-     * @return the value of field 'ChoiceValue'.
-     */
-    public java.lang.Object getChoiceValue(
-    ) {
-        return this._choiceValue;
-    }
-
-    /**
-     * Method getPos.
-     * 
-     * @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.Pos at
-     * the given index
-     */
-    public uk.ac.vamsas.objects.core.Pos getPos(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._posList.size()) {
-            throw new IndexOutOfBoundsException("getPos: Index value '" + index + "' not in range [0.." + (this._posList.size() - 1) + "]");
-        }
-        
-        return (uk.ac.vamsas.objects.core.Pos) _posList.get(index);
-    }
-
-    /**
-     * Method getPos.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.Pos[] getPos(
-    ) {
-        uk.ac.vamsas.objects.core.Pos[] array = new uk.ac.vamsas.objects.core.Pos[0];
-        return (uk.ac.vamsas.objects.core.Pos[]) this._posList.toArray(array);
-    }
-
-    /**
-     * Method getPosAsReference.Returns a reference to '_posList'.
-     * No type checking is performed on any modifications to the
-     * Vector.
-     * 
-     * @return a reference to the Vector backing this class
-     */
-    public java.util.Vector getPosAsReference(
-    ) {
-        return this._posList;
-    }
-
-    /**
-     * Method getPosCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPosCount(
-    ) {
-        return this._posList.size();
-    }
-
-    /**
-     * Method getSeg.
-     * 
-     * @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.Seg at
-     * the given index
-     */
-    public uk.ac.vamsas.objects.core.Seg getSeg(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._segList.size()) {
-            throw new IndexOutOfBoundsException("getSeg: Index value '" + index + "' not in range [0.." + (this._segList.size() - 1) + "]");
-        }
-        
-        return (uk.ac.vamsas.objects.core.Seg) _segList.get(index);
-    }
-
-    /**
-     * Method getSeg.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.Seg[] getSeg(
-    ) {
-        uk.ac.vamsas.objects.core.Seg[] array = new uk.ac.vamsas.objects.core.Seg[0];
-        return (uk.ac.vamsas.objects.core.Seg[]) this._segList.toArray(array);
-    }
-
-    /**
-     * Method getSegAsReference.Returns a reference to '_segList'.
-     * No type checking is performed on any modifications to the
-     * Vector.
-     * 
-     * @return a reference to the Vector backing this class
-     */
-    public java.util.Vector getSegAsReference(
-    ) {
-        return this._segList;
-    }
-
-    /**
-     * Method getSegCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSegCount(
-    ) {
-        return this._segList.size();
-    }
-
-    /**
-     * 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 (_choiceValue != null
-            && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) {
-           result = 37 * result + _choiceValue.hashCode();
-           org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue);
-        }
-        if (_posList != null
-            && !org.castor.util.CycleBreaker.startingToCycle(_posList)) {
-           result = 37 * result + _posList.hashCode();
-           org.castor.util.CycleBreaker.releaseCycleHandle(_posList);
-        }
-        if (_segList != null
-            && !org.castor.util.CycleBreaker.startingToCycle(_segList)) {
-           result = 37 * result + _segList.hashCode();
-           org.castor.util.CycleBreaker.releaseCycleHandle(_segList);
-        }
-        
-        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) {
+      if (this._posList != null) {
+        if (temp._posList == null)
+          return false;
+        if (this._posList != temp._posList) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._posList);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._posList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._posList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList);
+            }
+            ;
             return false;
+          }
+          if (!thcycle) {
+            if (!this._posList.equals(temp._posList)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._posList);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._posList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList);
+          }
         }
-        return true;
-    }
-
-    /**
-     */
-    public void removeAllPos(
-    ) {
-        this._posList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSeg(
-    ) {
-        this._segList.clear();
-    }
-
-    /**
-     * Method removePos.
-     * 
-     * @param vPos
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePos(
-            final uk.ac.vamsas.objects.core.Pos vPos) {
-        boolean removed = _posList.remove(vPos);
-        return removed;
-    }
-
-    /**
-     * Method removePosAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public uk.ac.vamsas.objects.core.Pos removePosAt(
-            final int index) {
-        java.lang.Object obj = this._posList.remove(index);
-        return (uk.ac.vamsas.objects.core.Pos) obj;
-    }
-
-    /**
-     * Method removeSeg.
-     * 
-     * @param vSeg
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSeg(
-            final uk.ac.vamsas.objects.core.Seg vSeg) {
-        boolean removed = _segList.remove(vSeg);
-        return removed;
-    }
-
-    /**
-     * Method removeSegAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public uk.ac.vamsas.objects.core.Seg removeSegAt(
-            final int index) {
-        java.lang.Object obj = this._segList.remove(index);
-        return (uk.ac.vamsas.objects.core.Seg) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPos
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPos(
-            final int index,
-            final uk.ac.vamsas.objects.core.Pos vPos)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._posList.size()) {
-            throw new IndexOutOfBoundsException("setPos: Index value '" + index + "' not in range [0.." + (this._posList.size() - 1) + "]");
-        }
-        
-        this._posList.set(index, vPos);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPosArray
-     */
-    public void setPos(
-            final uk.ac.vamsas.objects.core.Pos[] vPosArray) {
-        //-- copy array
-        _posList.clear();
-        
-        for (int i = 0; i < vPosArray.length; i++) {
-                this._posList.add(vPosArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of '_posList' by copying the given Vector.
-     * All elements will be checked for type safety.
-     * 
-     * @param vPosList the Vector to copy.
-     */
-    public void setPos(
-            final java.util.Vector vPosList) {
-        // copy vector
-        this._posList.clear();
-        
-        this._posList.addAll(vPosList);
-    }
-
-    /**
-     * Sets the value of '_posList' by setting it to the given
-     * Vector. No type checking is performed.
-     * @deprecated
-     * 
-     * @param posVector the Vector to set.
-     */
-    public void setPosAsReference(
-            final java.util.Vector posVector) {
-        this._posList = posVector;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeg
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSeg(
-            final int index,
-            final uk.ac.vamsas.objects.core.Seg vSeg)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._segList.size()) {
-            throw new IndexOutOfBoundsException("setSeg: Index value '" + index + "' not in range [0.." + (this._segList.size() - 1) + "]");
-        }
-        
-        this._segList.set(index, vSeg);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSegArray
-     */
-    public void setSeg(
-            final uk.ac.vamsas.objects.core.Seg[] vSegArray) {
-        //-- copy array
-        _segList.clear();
-        
-        for (int i = 0; i < vSegArray.length; i++) {
-                this._segList.add(vSegArray[i]);
+      } else if (temp._posList != null)
+        return false;
+      if (this._segList != null) {
+        if (temp._segList == null)
+          return false;
+        if (this._segList != temp._segList) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._segList);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._segList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._segList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._segList.equals(temp._segList)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._segList);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._segList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList);
+          }
         }
-    }
-
-    /**
-     * Sets the value of '_segList' by copying the given Vector.
-     * All elements will be checked for type safety.
-     * 
-     * @param vSegList the Vector to copy.
-     */
-    public void setSeg(
-            final java.util.Vector vSegList) {
-        // copy vector
-        this._segList.clear();
-        
-        this._segList.addAll(vSegList);
-    }
-
-    /**
-     * Sets the value of '_segList' by setting it to the given
-     * Vector. No type checking is performed.
-     * @deprecated
-     * 
-     * @param segVector the Vector to set.
-     */
-    public void setSegAsReference(
-            final java.util.Vector segVector) {
-        this._segList = segVector;
-    }
-
-    /**
-     * 
-     * 
-     * @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);
-    }
+      } else if (temp._segList != null)
+        return false;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+   * following description: Internal choice value storage
+   * 
+   * @return the value of field 'ChoiceValue'.
+   */
+  public java.lang.Object getChoiceValue() {
+    return this._choiceValue;
+  }
+
+  /**
+   * Method getPos.
+   * 
+   * @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.Pos at the given index
+   */
+  public uk.ac.vamsas.objects.core.Pos getPos(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._posList.size()) {
+      throw new IndexOutOfBoundsException("getPos: Index value '" + index
+          + "' not in range [0.." + (this._posList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Pos) _posList.get(index);
+  }
+
+  /**
+   * Method getPos.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.Pos[] getPos() {
+    uk.ac.vamsas.objects.core.Pos[] array = new uk.ac.vamsas.objects.core.Pos[0];
+    return (uk.ac.vamsas.objects.core.Pos[]) this._posList.toArray(array);
+  }
+
+  /**
+   * Method getPosAsReference.Returns a reference to '_posList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getPosAsReference() {
+    return this._posList;
+  }
+
+  /**
+   * Method getPosCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPosCount() {
+    return this._posList.size();
+  }
+
+  /**
+   * Method getSeg.
+   * 
+   * @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.Seg at the given index
+   */
+  public uk.ac.vamsas.objects.core.Seg getSeg(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._segList.size()) {
+      throw new IndexOutOfBoundsException("getSeg: Index value '" + index
+          + "' not in range [0.." + (this._segList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Seg) _segList.get(index);
+  }
+
+  /**
+   * Method getSeg.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.Seg[] getSeg() {
+    uk.ac.vamsas.objects.core.Seg[] array = new uk.ac.vamsas.objects.core.Seg[0];
+    return (uk.ac.vamsas.objects.core.Seg[]) this._segList.toArray(array);
+  }
+
+  /**
+   * Method getSegAsReference.Returns a reference to '_segList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getSegAsReference() {
+    return this._segList;
+  }
+
+  /**
+   * Method getSegCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSegCount() {
+    return this._segList.size();
+  }
+
+  /**
+   * 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 (_choiceValue != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) {
+      result = 37 * result + _choiceValue.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue);
+    }
+    if (_posList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_posList)) {
+      result = 37 * result + _posList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_posList);
+    }
+    if (_segList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_segList)) {
+      result = 37 * result + _segList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_segList);
+    }
+
+    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;
+  }
+
+  /**
+     */
+  public void removeAllPos() {
+    this._posList.clear();
+  }
+
+  /**
+     */
+  public void removeAllSeg() {
+    this._segList.clear();
+  }
+
+  /**
+   * Method removePos.
+   * 
+   * @param vPos
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePos(final uk.ac.vamsas.objects.core.Pos vPos) {
+    boolean removed = _posList.remove(vPos);
+    return removed;
+  }
+
+  /**
+   * Method removePosAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Pos removePosAt(final int index) {
+    java.lang.Object obj = this._posList.remove(index);
+    return (uk.ac.vamsas.objects.core.Pos) obj;
+  }
+
+  /**
+   * Method removeSeg.
+   * 
+   * @param vSeg
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSeg(final uk.ac.vamsas.objects.core.Seg vSeg) {
+    boolean removed = _segList.remove(vSeg);
+    return removed;
+  }
+
+  /**
+   * Method removeSegAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Seg removeSegAt(final int index) {
+    java.lang.Object obj = this._segList.remove(index);
+    return (uk.ac.vamsas.objects.core.Seg) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPos
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPos(final int index, final uk.ac.vamsas.objects.core.Pos vPos)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._posList.size()) {
+      throw new IndexOutOfBoundsException("setPos: Index value '" + index
+          + "' not in range [0.." + (this._posList.size() - 1) + "]");
+    }
+
+    this._posList.set(index, vPos);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPosArray
+   */
+  public void setPos(final uk.ac.vamsas.objects.core.Pos[] vPosArray) {
+    // -- copy array
+    _posList.clear();
+
+    for (int i = 0; i < vPosArray.length; i++) {
+      this._posList.add(vPosArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_posList' by copying the given Vector. All elements will
+   * be checked for type safety.
+   * 
+   * @param vPosList
+   *          the Vector to copy.
+   */
+  public void setPos(final java.util.Vector vPosList) {
+    // copy vector
+    this._posList.clear();
+
+    this._posList.addAll(vPosList);
+  }
+
+  /**
+   * Sets the value of '_posList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param posVector
+   *          the Vector to set.
+   */
+  public void setPosAsReference(final java.util.Vector posVector) {
+    this._posList = posVector;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeg
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSeg(final int index, final uk.ac.vamsas.objects.core.Seg vSeg)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._segList.size()) {
+      throw new IndexOutOfBoundsException("setSeg: Index value '" + index
+          + "' not in range [0.." + (this._segList.size() - 1) + "]");
+    }
+
+    this._segList.set(index, vSeg);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSegArray
+   */
+  public void setSeg(final uk.ac.vamsas.objects.core.Seg[] vSegArray) {
+    // -- copy array
+    _segList.clear();
+
+    for (int i = 0; i < vSegArray.length; i++) {
+      this._segList.add(vSegArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_segList' by copying the given Vector. All elements will
+   * be checked for type safety.
+   * 
+   * @param vSegList
+   *          the Vector to copy.
+   */
+  public void setSeg(final java.util.Vector vSegList) {
+    // copy vector
+    this._segList.clear();
+
+    this._segList.addAll(vSegList);
+  }
+
+  /**
+   * Sets the value of '_segList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param segVector
+   *          the Vector to set.
+   */
+  public void setSegAsReference(final java.util.Vector segVector) {
+    this._segList = segVector;
+  }
+
+  /**
+   * 
+   * 
+   * @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);
+  }
 
 }