/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Annotation for a rangeSpec - values can be attached for the\r
private java.lang.String _id;\r
\r
/**\r
- * Field _modifiable\r
+ * Field _modifiable.\r
*/\r
private java.lang.String _modifiable;\r
\r
private java.util.Vector _scoreList;\r
\r
/**\r
- * Field _linkList\r
+ * Field _linkList.\r
*/\r
private java.util.Vector _linkList;\r
\r
//- Constructors -/\r
//----------------/\r
\r
- public RangeAnnotation() \r
- {\r
+ public RangeAnnotation() {\r
super();\r
setGroup("");\r
- _annotationElementList = new Vector();\r
- _scoreList = new Vector();\r
- _linkList = new Vector();\r
- _propertyList = new Vector();\r
- } //-- uk.ac.vamsas.objects.core.RangeAnnotation()\r
+ this._annotationElementList = new java.util.Vector();\r
+ this._scoreList = new java.util.Vector();\r
+ this._linkList = new java.util.Vector();\r
+ this._propertyList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addAnnotationElement\r
- * \r
* \r
* \r
* @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method addAnnotationElement\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addAnnotationElement(int index, uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, uk.ac.vamsas.objects.core.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.add(index, vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method addLink\r
- * \r
* \r
* \r
* @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addLink(uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.addElement(vLink);\r
- } //-- void addLink(uk.ac.vamsas.objects.core.Link) \r
+ public void addLink(\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._linkList.addElement(vLink);\r
+ }\r
\r
/**\r
- * Method addLink\r
- * \r
* \r
* \r
* @param index\r
* @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addLink(int index, uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.insertElementAt(vLink, index);\r
- } //-- void addLink(int, uk.ac.vamsas.objects.core.Link) \r
+ public void addLink(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._linkList.add(index, vLink);\r
+ }\r
\r
/**\r
- * Method addProperty\r
- * \r
* \r
* \r
* @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.addElement(vProperty);\r
- } //-- void addProperty(uk.ac.vamsas.objects.core.Property) \r
+ public void addProperty(\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.addElement(vProperty);\r
+ }\r
\r
/**\r
- * Method addProperty\r
- * \r
* \r
* \r
* @param index\r
* @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.insertElementAt(vProperty, index);\r
- } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property) \r
+ public void addProperty(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.add(index, vProperty);\r
+ }\r
\r
/**\r
- * Method addScore\r
- * \r
* \r
* \r
* @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addScore(uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.addElement(vScore);\r
- } //-- void addScore(uk.ac.vamsas.objects.core.Score) \r
+ public void addScore(\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._scoreList.addElement(vScore);\r
+ }\r
\r
/**\r
- * Method addScore\r
- * \r
* \r
* \r
* @param index\r
* @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addScore(int index, uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.insertElementAt(vScore, index);\r
- } //-- void addScore(int, uk.ac.vamsas.objects.core.Score) \r
+ public void addScore(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._scoreList.add(index, vScore);\r
+ }\r
\r
/**\r
- * Method enumerateAnnotationElement\r
- * \r
- * \r
+ * Method enumerateAnnotationElement.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * uk.ac.vamsas.objects.core.AnnotationElement elements\r
*/\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
+ public java.util.Enumeration enumerateAnnotationElement(\r
+ ) {\r
+ return this._annotationElementList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateLink\r
+ * Method enumerateLink.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * uk.ac.vamsas.objects.core.Link elements\r
*/\r
- public java.util.Enumeration enumerateLink()\r
- {\r
- return _linkList.elements();\r
- } //-- java.util.Enumeration enumerateLink() \r
+ public java.util.Enumeration enumerateLink(\r
+ ) {\r
+ return this._linkList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateProperty\r
- * \r
+ * Method enumerateProperty.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * uk.ac.vamsas.objects.core.Property elements\r
*/\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return _propertyList.elements();\r
- } //-- java.util.Enumeration enumerateProperty() \r
+ public java.util.Enumeration enumerateProperty(\r
+ ) {\r
+ return this._propertyList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateScore\r
- * \r
+ * Method enumerateScore.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * uk.ac.vamsas.objects.core.Score elements\r
*/\r
- public java.util.Enumeration enumerateScore()\r
- {\r
- return _scoreList.elements();\r
- } //-- java.util.Enumeration enumerateScore() \r
+ public java.util.Enumeration enumerateScore(\r
+ ) {\r
+ return this._scoreList.elements();\r
+ }\r
\r
/**\r
- * Note: hashCode() has not been overriden\r
+ * Overrides the java.lang.Object.equals method.\r
* \r
* @param obj\r
- * @return boolean\r
+ * @return true if the objects are equal.\r
*/\r
- public boolean equals(java.lang.Object obj)\r
- {\r
+ public boolean equals(\r
+ final java.lang.Object obj) {\r
if ( this == obj )\r
return true;\r
\r
return true;\r
}\r
return false;\r
- } //-- boolean equals(java.lang.Object) \r
+ }\r
\r
/**\r
- * Method getAnnotationElement\r
- * \r
- * \r
+ * Method getAnnotationElement.\r
* \r
* @param index\r
- * @return AnnotationElement\r
- */\r
- public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * uk.ac.vamsas.objects.core.AnnotationElement at the given inde\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
}\r
\r
- return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(int) \r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotationElement\r
- * \r
- * \r
+ * Method getAnnotationElement.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
* \r
- * @return AnnotationElement\r
+ * @return this collection as an Array\r
*/\r
- public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- uk.ac.vamsas.objects.core.AnnotationElement[] mArray = new uk.ac.vamsas.objects.core.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement() \r
+ public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement(\r
+ ) {\r
+ uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0];\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getAnnotationElementCount\r
- * \r
+ * Method getAnnotationElementAsReference.Returns a reference\r
+ * to '_annotationElementList'. No type checking is performed\r
+ * on any modifications to the Vector.\r
* \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getAnnotationElementAsReference(\r
+ ) {\r
+ return this._annotationElementList;\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
+ public int getAnnotationElementCount(\r
+ ) {\r
+ return this._annotationElementList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'description'. The field\r
* description of the annotation\r
* \r
* \r
- * @return String\r
- * @return the value of field 'description'.\r
+ * @return the value of field 'Description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription(\r
+ ) {\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ }\r
\r
/**\r
* Returns the value of field 'group'. The field 'group' has\r
* non-empty group name are grouped\r
* together \r
* \r
- * @return String\r
- * @return the value of field 'group'.\r
+ * @return the value of field 'Group'.\r
*/\r
- public java.lang.String getGroup()\r
- {\r
+ public java.lang.String getGroup(\r
+ ) {\r
return this._group;\r
- } //-- java.lang.String getGroup() \r
+ }\r
\r
/**\r
* Returns the value of field 'id'. The field 'id' has the\r
* referencing\r
* \r
* \r
- * @return String\r
- * @return the value of field 'id'.\r
+ * @return the value of field 'Id'.\r
*/\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId(\r
+ ) {\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ }\r
\r
/**\r
* Returns the value of field 'label'. The field 'label' has\r
* place.\r
* \r
* \r
- * @return String\r
- * @return the value of field 'label'.\r
+ * @return the value of field 'Label'.\r
*/\r
- public java.lang.String getLabel()\r
- {\r
+ public java.lang.String getLabel(\r
+ ) {\r
return this._label;\r
- } //-- java.lang.String getLabel() \r
+ }\r
\r
/**\r
- * Method getLink\r
- * \r
- * \r
+ * Method getLink.\r
* \r
* @param index\r
- * @return Link\r
- */\r
- public uk.ac.vamsas.objects.core.Link getLink(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Link at\r
+ * the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link getLink(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("getLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
}\r
\r
- return (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.Link getLink(int) \r
+ return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);\r
+ }\r
\r
/**\r
- * Method getLink\r
- * \r
+ * Method getLink.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * @return Link\r
+ * @return this collection as an Array\r
*/\r
- public uk.ac.vamsas.objects.core.Link[] getLink()\r
- {\r
- int size = _linkList.size();\r
- uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.Link[] getLink() \r
+ public uk.ac.vamsas.objects.core.Link[] getLink(\r
+ ) {\r
+ uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];\r
+ return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getLinkCount\r
- * \r
+ * Method getLinkAsReference.Returns a reference to\r
+ * '_linkList'. No type checking is performed on any\r
+ * modifications to the Vector.\r
* \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getLinkAsReference(\r
+ ) {\r
+ return this._linkList;\r
+ }\r
+\r
+ /**\r
+ * Method getLinkCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getLinkCount()\r
- {\r
- return _linkList.size();\r
- } //-- int getLinkCount() \r
+ public int getLinkCount(\r
+ ) {\r
+ return this._linkList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'modifiable'.\r
* \r
- * @return String\r
- * @return the value of field 'modifiable'.\r
+ * @return the value of field 'Modifiable'.\r
*/\r
- public java.lang.String getModifiable()\r
- {\r
+ public java.lang.String getModifiable(\r
+ ) {\r
return this._modifiable;\r
- } //-- java.lang.String getModifiable() \r
+ }\r
\r
/**\r
- * Method getProperty\r
- * \r
- * \r
+ * Method getProperty.\r
* \r
* @param index\r
- * @return Property\r
- */\r
- public uk.ac.vamsas.objects.core.Property getProperty(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Property\r
+ * at the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property getProperty(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
}\r
\r
- return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.Property getProperty(int) \r
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);\r
+ }\r
\r
/**\r
- * Method getProperty\r
- * \r
- * \r
+ * Method getProperty.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * @return Property\r
+ * @return this collection as an Array\r
*/\r
- public uk.ac.vamsas.objects.core.Property[] getProperty()\r
- {\r
- int size = _propertyList.size();\r
- uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.Property[] getProperty() \r
+ public uk.ac.vamsas.objects.core.Property[] getProperty(\r
+ ) {\r
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];\r
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getPropertyCount\r
- * \r
+ * Method getPropertyAsReference.Returns a reference to\r
+ * '_propertyList'. No type checking is performed on any\r
+ * modifications to the Vector.\r
* \r
- * \r
- * @return int\r
+ * @return a reference to the Vector backing this class\r
*/\r
- public int getPropertyCount()\r
- {\r
- return _propertyList.size();\r
- } //-- int getPropertyCount() \r
+ public java.util.Vector getPropertyAsReference(\r
+ ) {\r
+ return this._propertyList;\r
+ }\r
\r
/**\r
- * Method getScore\r
- * \r
+ * Method getPropertyCount.\r
* \r
+ * @return the size of this collection\r
+ */\r
+ public int getPropertyCount(\r
+ ) {\r
+ return this._propertyList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getScore.\r
* \r
* @param index\r
- * @return Score\r
- */\r
- public uk.ac.vamsas.objects.core.Score getScore(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Score at\r
+ * the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score getScore(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("getScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
}\r
\r
- return (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- } //-- uk.ac.vamsas.objects.core.Score getScore(int) \r
+ return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index);\r
+ }\r
\r
/**\r
- * Method getScore\r
+ * Method getScore.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
- * \r
- * \r
- * @return Score\r
+ * @return this collection as an Array\r
*/\r
- public uk.ac.vamsas.objects.core.Score[] getScore()\r
- {\r
- int size = _scoreList.size();\r
- uk.ac.vamsas.objects.core.Score[] mArray = new uk.ac.vamsas.objects.core.Score[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- uk.ac.vamsas.objects.core.Score[] getScore() \r
+ public uk.ac.vamsas.objects.core.Score[] getScore(\r
+ ) {\r
+ uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0];\r
+ return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getScoreCount\r
- * \r
+ * Method getScoreAsReference.Returns a reference to\r
+ * '_scoreList'. No type checking is performed on any\r
+ * modifications to the Vector.\r
* \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getScoreAsReference(\r
+ ) {\r
+ return this._scoreList;\r
+ }\r
+\r
+ /**\r
+ * Method getScoreCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getScoreCount()\r
- {\r
- return _scoreList.size();\r
- } //-- int getScoreCount() \r
+ public int getScoreCount(\r
+ ) {\r
+ return this._scoreList.size();\r
+ }\r
\r
/**\r
* Returns the value of field 'status'. The field 'status' has\r
* quality to an\r
* annotation. \r
* \r
- * @return String\r
- * @return the value of field 'status'.\r
+ * @return the value of field 'Status'.\r
*/\r
- public java.lang.String getStatus()\r
- {\r
+ public java.lang.String getStatus(\r
+ ) {\r
return this._status;\r
- } //-- java.lang.String getStatus() \r
+ }\r
\r
/**\r
* Returns the value of field 'type'. The field 'type' has the\r
* and\r
* considered distinct from someotherDB:CHAIN \r
* \r
- * @return String\r
- * @return the value of field 'type'.\r
+ * @return the value of field 'Type'.\r
*/\r
- public java.lang.String getType()\r
- {\r
+ public java.lang.String getType(\r
+ ) {\r
return this._type;\r
- } //-- java.lang.String getType() \r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
+ * Overrides the java.lang.Object.hashCode method.\r
+ * <p>\r
+ * The following steps came from <b>Effective Java Programming\r
+ * Language Guide</b> by Joshua Bloch, Chapter 3\r
* \r
+ * @return a hash code value for the object.\r
+ */\r
+ public int hashCode(\r
+ ) {\r
+ int result = super.hashCode();\r
+ \r
+ long tmp;\r
+ if (_id != null) {\r
+ result = 37 * result + _id.hashCode();\r
+ }\r
+ if (_modifiable != null) {\r
+ result = 37 * result + _modifiable.hashCode();\r
+ }\r
+ if (_group != null) {\r
+ result = 37 * result + _group.hashCode();\r
+ }\r
+ if (_type != null) {\r
+ result = 37 * result + _type.hashCode();\r
+ }\r
+ if (_label != null) {\r
+ result = 37 * result + _label.hashCode();\r
+ }\r
+ if (_description != null) {\r
+ result = 37 * result + _description.hashCode();\r
+ }\r
+ if (_status != null) {\r
+ result = 37 * result + _status.hashCode();\r
+ }\r
+ if (_annotationElementList != null) {\r
+ result = 37 * result + _annotationElementList.hashCode();\r
+ }\r
+ if (_scoreList != null) {\r
+ result = 37 * result + _scoreList.hashCode();\r
+ }\r
+ if (_linkList != null) {\r
+ result = 37 * result + _linkList.hashCode();\r
+ }\r
+ if (_propertyList != null) {\r
+ result = 37 * result + _propertyList.hashCode();\r
+ }\r
+ \r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\r
- * \r
* \r
* \r
* @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllAnnotationElement\r
- * \r
*/\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
+ public void removeAllAnnotationElement(\r
+ ) {\r
+ this._annotationElementList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllLink\r
- * \r
*/\r
- public void removeAllLink()\r
- {\r
- _linkList.removeAllElements();\r
- } //-- void removeAllLink() \r
+ public void removeAllLink(\r
+ ) {\r
+ this._linkList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllProperty\r
- * \r
*/\r
- public void removeAllProperty()\r
- {\r
- _propertyList.removeAllElements();\r
- } //-- void removeAllProperty() \r
+ public void removeAllProperty(\r
+ ) {\r
+ this._propertyList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllScore\r
- * \r
*/\r
- public void removeAllScore()\r
- {\r
- _scoreList.removeAllElements();\r
- } //-- void removeAllScore() \r
+ public void removeAllScore(\r
+ ) {\r
+ this._scoreList.clear();\r
+ }\r
\r
/**\r
- * Method removeAnnotationElement\r
- * \r
+ * Method removeAnnotationElement.\r
* \r
+ * @param vAnnotationElement\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) {\r
+ boolean removed = _annotationElementList.remove(vAnnotationElement);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElementAt.\r
* \r
* @param index\r
- * @return AnnotationElement\r
+ * @return the element removed from the collection\r
*/\r
- public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
+ public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
return (uk.ac.vamsas.objects.core.AnnotationElement) obj;\r
- } //-- uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) \r
+ }\r
\r
/**\r
- * Method removeLink\r
- * \r
+ * Method removeLink.\r
* \r
+ * @param vLink\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeLink(\r
+ final uk.ac.vamsas.objects.core.Link vLink) {\r
+ boolean removed = _linkList.remove(vLink);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeLinkAt.\r
* \r
* @param index\r
- * @return Link\r
+ * @return the element removed from the collection\r
*/\r
- public uk.ac.vamsas.objects.core.Link removeLink(int index)\r
- {\r
- java.lang.Object obj = _linkList.elementAt(index);\r
- _linkList.removeElementAt(index);\r
+ public uk.ac.vamsas.objects.core.Link removeLinkAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._linkList.remove(index);\r
return (uk.ac.vamsas.objects.core.Link) obj;\r
- } //-- uk.ac.vamsas.objects.core.Link removeLink(int) \r
+ }\r
\r
/**\r
- * Method removeProperty\r
- * \r
+ * Method removeProperty.\r
* \r
+ * @param vProperty\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeProperty(\r
+ final uk.ac.vamsas.objects.core.Property vProperty) {\r
+ boolean removed = _propertyList.remove(vProperty);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePropertyAt.\r
* \r
* @param index\r
- * @return Property\r
+ * @return the element removed from the collection\r
*/\r
- public uk.ac.vamsas.objects.core.Property removeProperty(int index)\r
- {\r
- java.lang.Object obj = _propertyList.elementAt(index);\r
- _propertyList.removeElementAt(index);\r
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._propertyList.remove(index);\r
return (uk.ac.vamsas.objects.core.Property) obj;\r
- } //-- uk.ac.vamsas.objects.core.Property removeProperty(int) \r
+ }\r
\r
/**\r
- * Method removeScore\r
- * \r
+ * Method removeScore.\r
* \r
+ * @param vScore\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeScore(\r
+ final uk.ac.vamsas.objects.core.Score vScore) {\r
+ boolean removed = _scoreList.remove(vScore);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeScoreAt.\r
* \r
* @param index\r
- * @return Score\r
+ * @return the element removed from the collection\r
*/\r
- public uk.ac.vamsas.objects.core.Score removeScore(int index)\r
- {\r
- java.lang.Object obj = _scoreList.elementAt(index);\r
- _scoreList.removeElementAt(index);\r
+ public uk.ac.vamsas.objects.core.Score removeScoreAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._scoreList.remove(index);\r
return (uk.ac.vamsas.objects.core.Score) obj;\r
- } //-- uk.ac.vamsas.objects.core.Score removeScore(int) \r
+ }\r
\r
/**\r
- * Method setAnnotationElement\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotationElement(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
}\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, uk.ac.vamsas.objects.core.AnnotationElement) \r
+ \r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method setAnnotationElement\r
- * \r
* \r
* \r
- * @param annotationElementArray\r
+ * @param vAnnotationElementArray\r
*/\r
- public void setAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement[] annotationElementArray)\r
- {\r
+ public void setAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) {\r
//-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
+ _annotationElementList.clear();\r
+ \r
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
}\r
- } //-- void setAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement) \r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by copying the\r
+ * given Vector. All elements will be checked for type safety.\r
+ * \r
+ * @param vAnnotationElementList the Vector to copy.\r
+ */\r
+ public void setAnnotationElement(\r
+ final java.util.Vector vAnnotationElementList) {\r
+ // copy vector\r
+ this._annotationElementList.clear();\r
+ \r
+ this._annotationElementList.addAll(vAnnotationElementList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by setting it to\r
+ * the given Vector. No type checking is performed.\r
+ * @deprecated\r
+ * \r
+ * @param annotationElementVector the Vector to set.\r
+ */\r
+ public void setAnnotationElementAsReference(\r
+ final java.util.Vector annotationElementVector) {\r
+ this._annotationElementList = annotationElementVector;\r
+ }\r
\r
/**\r
* Sets the value of field 'description'. The field\r
* \r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'group'. The field 'group' has the\r
* \r
* @param group the value of field 'group'.\r
*/\r
- public void setGroup(java.lang.String group)\r
- {\r
+ public void setGroup(\r
+ final java.lang.String group) {\r
this._group = group;\r
- } //-- void setGroup(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'. The field 'id' has the\r
* \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(\r
+ final java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'label'. The field 'label' has the\r
* \r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label)\r
- {\r
+ public void setLabel(\r
+ final java.lang.String label) {\r
this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
+ }\r
\r
/**\r
- * Method setLink\r
- * \r
* \r
* \r
* @param index\r
* @param vLink\r
- */\r
- public void setLink(int index, uk.ac.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setLink(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
}\r
- _linkList.setElementAt(vLink, index);\r
- } //-- void setLink(int, uk.ac.vamsas.objects.core.Link) \r
+ \r
+ this._linkList.set(index, vLink);\r
+ }\r
\r
/**\r
- * Method setLink\r
- * \r
* \r
* \r
- * @param linkArray\r
+ * @param vLinkArray\r
*/\r
- public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray)\r
- {\r
+ public void setLink(\r
+ final uk.ac.vamsas.objects.core.Link[] vLinkArray) {\r
//-- copy array\r
- _linkList.removeAllElements();\r
- for (int i = 0; i < linkArray.length; i++) {\r
- _linkList.addElement(linkArray[i]);\r
+ _linkList.clear();\r
+ \r
+ for (int i = 0; i < vLinkArray.length; i++) {\r
+ this._linkList.add(vLinkArray[i]);\r
}\r
- } //-- void setLink(uk.ac.vamsas.objects.core.Link) \r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by copying the given Vector.\r
+ * All elements will be checked for type safety.\r
+ * \r
+ * @param vLinkList the Vector to copy.\r
+ */\r
+ public void setLink(\r
+ final java.util.Vector vLinkList) {\r
+ // copy vector\r
+ this._linkList.clear();\r
+ \r
+ this._linkList.addAll(vLinkList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by setting it to the given\r
+ * Vector. No type checking is performed.\r
+ * @deprecated\r
+ * \r
+ * @param linkVector the Vector to set.\r
+ */\r
+ public void setLinkAsReference(\r
+ final java.util.Vector linkVector) {\r
+ this._linkList = linkVector;\r
+ }\r
\r
/**\r
* Sets the value of field 'modifiable'.\r
* \r
* @param modifiable the value of field 'modifiable'.\r
*/\r
- public void setModifiable(java.lang.String modifiable)\r
- {\r
+ public void setModifiable(\r
+ final java.lang.String modifiable) {\r
this._modifiable = modifiable;\r
- } //-- void setModifiable(java.lang.String) \r
+ }\r
\r
/**\r
- * Method setProperty\r
- * \r
* \r
* \r
* @param index\r
* @param vProperty\r
- */\r
- public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setProperty(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
}\r
- _propertyList.setElementAt(vProperty, index);\r
- } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property) \r
+ \r
+ this._propertyList.set(index, vProperty);\r
+ }\r
\r
/**\r
- * Method setProperty\r
* \r
* \r
- * \r
- * @param propertyArray\r
+ * @param vPropertyArray\r
*/\r
- public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)\r
- {\r
+ public void setProperty(\r
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {\r
//-- copy array\r
- _propertyList.removeAllElements();\r
- for (int i = 0; i < propertyArray.length; i++) {\r
- _propertyList.addElement(propertyArray[i]);\r
+ _propertyList.clear();\r
+ \r
+ for (int i = 0; i < vPropertyArray.length; i++) {\r
+ this._propertyList.add(vPropertyArray[i]);\r
}\r
- } //-- void setProperty(uk.ac.vamsas.objects.core.Property) \r
+ }\r
\r
/**\r
- * Method setScore\r
+ * Sets the value of '_propertyList' by copying the given\r
+ * Vector. All elements will be checked for type safety.\r
* \r
+ * @param vPropertyList the Vector to copy.\r
+ */\r
+ public void setProperty(\r
+ final java.util.Vector vPropertyList) {\r
+ // copy vector\r
+ this._propertyList.clear();\r
+ \r
+ this._propertyList.addAll(vPropertyList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_propertyList' by setting it to the given\r
+ * Vector. No type checking is performed.\r
+ * @deprecated\r
+ * \r
+ * @param propertyVector the Vector to set.\r
+ */\r
+ public void setPropertyAsReference(\r
+ final java.util.Vector propertyVector) {\r
+ this._propertyList = propertyVector;\r
+ }\r
+\r
+ /**\r
* \r
* \r
* @param index\r
* @param vScore\r
- */\r
- public void setScore(int index, uk.ac.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setScore(\r
+ final int index,\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("setScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
}\r
- _scoreList.setElementAt(vScore, index);\r
- } //-- void setScore(int, uk.ac.vamsas.objects.core.Score) \r
+ \r
+ this._scoreList.set(index, vScore);\r
+ }\r
\r
/**\r
- * Method setScore\r
* \r
* \r
- * \r
- * @param scoreArray\r
+ * @param vScoreArray\r
*/\r
- public void setScore(uk.ac.vamsas.objects.core.Score[] scoreArray)\r
- {\r
+ public void setScore(\r
+ final uk.ac.vamsas.objects.core.Score[] vScoreArray) {\r
//-- copy array\r
- _scoreList.removeAllElements();\r
- for (int i = 0; i < scoreArray.length; i++) {\r
- _scoreList.addElement(scoreArray[i]);\r
+ _scoreList.clear();\r
+ \r
+ for (int i = 0; i < vScoreArray.length; i++) {\r
+ this._scoreList.add(vScoreArray[i]);\r
}\r
- } //-- void setScore(uk.ac.vamsas.objects.core.Score) \r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by copying the given Vector.\r
+ * All elements will be checked for type safety.\r
+ * \r
+ * @param vScoreList the Vector to copy.\r
+ */\r
+ public void setScore(\r
+ final java.util.Vector vScoreList) {\r
+ // copy vector\r
+ this._scoreList.clear();\r
+ \r
+ this._scoreList.addAll(vScoreList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by setting it to the given\r
+ * Vector. No type checking is performed.\r
+ * @deprecated\r
+ * \r
+ * @param scoreVector the Vector to set.\r
+ */\r
+ public void setScoreAsReference(\r
+ final java.util.Vector scoreVector) {\r
+ this._scoreList = scoreVector;\r
+ }\r
\r
/**\r
* Sets the value of field 'status'. The field 'status' has the\r
* \r
* @param status the value of field 'status'.\r
*/\r
- public void setStatus(java.lang.String status)\r
- {\r
+ public void setStatus(\r
+ final java.lang.String status) {\r
this._status = status;\r
- } //-- void setStatus(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'type'. The field 'type' has the\r
* \r
* @param type the value of field 'type'.\r
*/\r
- public void setType(java.lang.String type)\r
- {\r
+ public void setType(\r
+ final java.lang.String type) {\r
this._type = type;\r
- } //-- void setType(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return RangeType\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType\r
*/\r
- public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (uk.ac.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
- } //-- uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
git://source.jalview.org / vamsas.git / blobdiff