/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</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
* Class Annotation.\r
//--------------------------/\r
\r
/**\r
- * Field _graph\r
+ * Field _graph.\r
*/\r
private boolean _graph;\r
\r
private boolean _has_graph;\r
\r
/**\r
- * Field _graphType\r
+ * Field _graphType.\r
*/\r
private int _graphType;\r
\r
private boolean _has_graphType;\r
\r
/**\r
- * Field _sequenceRef\r
+ * Field _sequenceRef.\r
*/\r
private java.lang.String _sequenceRef;\r
\r
/**\r
- * Field _graphColour\r
+ * Field _graphColour.\r
*/\r
private int _graphColour;\r
\r
private boolean _has_graphColour;\r
\r
/**\r
- * Field _graphGroup\r
+ * Field _graphGroup.\r
*/\r
private int _graphGroup;\r
\r
private boolean _has_graphGroup;\r
\r
/**\r
- * Field _id\r
+ * Field _id.\r
*/\r
private java.lang.String _id;\r
\r
/**\r
- * Field _scoreOnly\r
+ * Field _scoreOnly.\r
*/\r
private boolean _scoreOnly = false;\r
\r
private boolean _has_scoreOnly;\r
\r
/**\r
- * Field _score\r
+ * Field _score.\r
*/\r
private double _score;\r
\r
private boolean _has_score;\r
\r
/**\r
- * Field _visible\r
+ * Field _visible.\r
*/\r
private boolean _visible;\r
\r
private boolean _has_visible;\r
\r
/**\r
- * Field _annotationElementList\r
+ * Field _annotationElementList.\r
*/\r
private java.util.Vector _annotationElementList;\r
\r
/**\r
- * Field _label\r
+ * Field _label.\r
*/\r
private java.lang.String _label;\r
\r
/**\r
- * Field _description\r
+ * Field _description.\r
*/\r
private java.lang.String _description;\r
\r
/**\r
- * Field _thresholdLine\r
+ * Field _thresholdLine.\r
*/\r
private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
\r
\r
public Annotation() {\r
super();\r
- _annotationElementList = new Vector();\r
- } //-- jalview.schemabinding.version2.Annotation()\r
+ this._annotationElementList = 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(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final jalview.schemabinding.version2.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, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
+ public void addAnnotationElement(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.add(index, vAnnotationElement);\r
+ }\r
\r
/**\r
- * Method deleteGraph\r
- * \r
*/\r
- public void deleteGraph()\r
- {\r
+ public void deleteGraph(\r
+ ) {\r
this._has_graph= false;\r
- } //-- void deleteGraph() \r
+ }\r
\r
/**\r
- * Method deleteGraphColour\r
- * \r
*/\r
- public void deleteGraphColour()\r
- {\r
+ public void deleteGraphColour(\r
+ ) {\r
this._has_graphColour= false;\r
- } //-- void deleteGraphColour() \r
+ }\r
\r
/**\r
- * Method deleteGraphGroup\r
- * \r
*/\r
- public void deleteGraphGroup()\r
- {\r
+ public void deleteGraphGroup(\r
+ ) {\r
this._has_graphGroup= false;\r
- } //-- void deleteGraphGroup() \r
+ }\r
\r
/**\r
- * Method deleteGraphType\r
- * \r
*/\r
- public void deleteGraphType()\r
- {\r
+ public void deleteGraphType(\r
+ ) {\r
this._has_graphType= false;\r
- } //-- void deleteGraphType() \r
+ }\r
\r
/**\r
- * Method deleteScore\r
- * \r
*/\r
- public void deleteScore()\r
- {\r
+ public void deleteScore(\r
+ ) {\r
this._has_score= false;\r
- } //-- void deleteScore() \r
+ }\r
\r
/**\r
- * Method deleteScoreOnly\r
- * \r
*/\r
- public void deleteScoreOnly()\r
- {\r
+ public void deleteScoreOnly(\r
+ ) {\r
this._has_scoreOnly= false;\r
- } //-- void deleteScoreOnly() \r
+ }\r
\r
/**\r
- * Method deleteVisible\r
- * \r
*/\r
- public void deleteVisible()\r
- {\r
+ public void deleteVisible(\r
+ ) {\r
this._has_visible= false;\r
- } //-- void deleteVisible() \r
+ }\r
\r
/**\r
- * Method enumerateAnnotationElement\r
+ * Method enumerateAnnotationElement.\r
* \r
- * \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.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 getAnnotationElement\r
- * \r
- * \r
+ * Method getAnnotationElement.\r
* \r
* @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.schemabinding.version2.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();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.AnnotationElement at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.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 (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) \r
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotationElement\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
- * \r
- * \r
- * @return AnnotationElement\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() \r
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(\r
+ ) {\r
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];\r
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);\r
+ }\r
\r
/**\r
- * Method getAnnotationElementCount\r
- * \r
+ * Method getAnnotationElementCount.\r
* \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'.\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 'graph'.\r
* \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
+ * @return the value of field 'Graph'.\r
*/\r
- public boolean getGraph()\r
- {\r
+ public boolean getGraph(\r
+ ) {\r
return this._graph;\r
- } //-- boolean getGraph() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphColour'.\r
* \r
- * @return int\r
- * @return the value of field 'graphColour'.\r
+ * @return the value of field 'GraphColour'.\r
*/\r
- public int getGraphColour()\r
- {\r
+ public int getGraphColour(\r
+ ) {\r
return this._graphColour;\r
- } //-- int getGraphColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphGroup'.\r
* \r
- * @return int\r
- * @return the value of field 'graphGroup'.\r
+ * @return the value of field 'GraphGroup'.\r
*/\r
- public int getGraphGroup()\r
- {\r
+ public int getGraphGroup(\r
+ ) {\r
return this._graphGroup;\r
- } //-- int getGraphGroup() \r
+ }\r
\r
/**\r
* Returns the value of field 'graphType'.\r
* \r
- * @return int\r
- * @return the value of field 'graphType'.\r
+ * @return the value of field 'GraphType'.\r
*/\r
- public int getGraphType()\r
- {\r
+ public int getGraphType(\r
+ ) {\r
return this._graphType;\r
- } //-- int getGraphType() \r
+ }\r
\r
/**\r
* Returns the value of field 'id'.\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'.\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
* Returns the value of field 'score'.\r
* \r
- * @return double\r
- * @return the value of field 'score'.\r
+ * @return the value of field 'Score'.\r
*/\r
- public double getScore()\r
- {\r
+ public double getScore(\r
+ ) {\r
return this._score;\r
- } //-- double getScore() \r
+ }\r
\r
/**\r
* Returns the value of field 'scoreOnly'.\r
* \r
- * @return boolean\r
- * @return the value of field 'scoreOnly'.\r
+ * @return the value of field 'ScoreOnly'.\r
*/\r
- public boolean getScoreOnly()\r
- {\r
+ public boolean getScoreOnly(\r
+ ) {\r
return this._scoreOnly;\r
- } //-- boolean getScoreOnly() \r
+ }\r
\r
/**\r
* Returns the value of field 'sequenceRef'.\r
* \r
- * @return String\r
- * @return the value of field 'sequenceRef'.\r
+ * @return the value of field 'SequenceRef'.\r
*/\r
- public java.lang.String getSequenceRef()\r
- {\r
+ public java.lang.String getSequenceRef(\r
+ ) {\r
return this._sequenceRef;\r
- } //-- java.lang.String getSequenceRef() \r
+ }\r
\r
/**\r
* Returns the value of field 'thresholdLine'.\r
* \r
- * @return ThresholdLine\r
- * @return the value of field 'thresholdLine'.\r
+ * @return the value of field 'ThresholdLine'.\r
*/\r
- public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
- {\r
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine(\r
+ ) {\r
return this._thresholdLine;\r
- } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() \r
+ }\r
\r
/**\r
* Returns the value of field 'visible'.\r
* \r
- * @return boolean\r
- * @return the value of field 'visible'.\r
+ * @return the value of field 'Visible'.\r
*/\r
- public boolean getVisible()\r
- {\r
+ public boolean getVisible(\r
+ ) {\r
return this._visible;\r
- } //-- boolean getVisible() \r
+ }\r
\r
/**\r
- * Method hasGraph\r
- * \r
- * \r
+ * Method hasGraph.\r
* \r
- * @return boolean\r
+ * @return true if at least one Graph has been added\r
*/\r
- public boolean hasGraph()\r
- {\r
+ public boolean hasGraph(\r
+ ) {\r
return this._has_graph;\r
- } //-- boolean hasGraph() \r
+ }\r
\r
/**\r
- * Method hasGraphColour\r
- * \r
- * \r
+ * Method hasGraphColour.\r
* \r
- * @return boolean\r
+ * @return true if at least one GraphColour has been added\r
*/\r
- public boolean hasGraphColour()\r
- {\r
+ public boolean hasGraphColour(\r
+ ) {\r
return this._has_graphColour;\r
- } //-- boolean hasGraphColour() \r
+ }\r
\r
/**\r
- * Method hasGraphGroup\r
+ * Method hasGraphGroup.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one GraphGroup has been added\r
*/\r
- public boolean hasGraphGroup()\r
- {\r
+ public boolean hasGraphGroup(\r
+ ) {\r
return this._has_graphGroup;\r
- } //-- boolean hasGraphGroup() \r
+ }\r
\r
/**\r
- * Method hasGraphType\r
- * \r
- * \r
+ * Method hasGraphType.\r
* \r
- * @return boolean\r
+ * @return true if at least one GraphType has been added\r
*/\r
- public boolean hasGraphType()\r
- {\r
+ public boolean hasGraphType(\r
+ ) {\r
return this._has_graphType;\r
- } //-- boolean hasGraphType() \r
+ }\r
\r
/**\r
- * Method hasScore\r
+ * Method hasScore.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Score has been added\r
*/\r
- public boolean hasScore()\r
- {\r
+ public boolean hasScore(\r
+ ) {\r
return this._has_score;\r
- } //-- boolean hasScore() \r
+ }\r
\r
/**\r
- * Method hasScoreOnly\r
- * \r
- * \r
+ * Method hasScoreOnly.\r
* \r
- * @return boolean\r
+ * @return true if at least one ScoreOnly has been added\r
*/\r
- public boolean hasScoreOnly()\r
- {\r
+ public boolean hasScoreOnly(\r
+ ) {\r
return this._has_scoreOnly;\r
- } //-- boolean hasScoreOnly() \r
+ }\r
\r
/**\r
- * Method hasVisible\r
+ * Method hasVisible.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one Visible has been added\r
*/\r
- public boolean hasVisible()\r
- {\r
+ public boolean hasVisible(\r
+ ) {\r
return this._has_visible;\r
- } //-- boolean hasVisible() \r
+ }\r
\r
/**\r
- * Method isValid\r
+ * Returns the value of field 'graph'.\r
* \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean isGraph(\r
+ ) {\r
+ return this._graph;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
* \r
+ * @return the value of field 'ScoreOnly'.\r
+ */\r
+ public boolean isScoreOnly(\r
+ ) {\r
+ return this._scoreOnly;\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
+ * Returns the value of field 'visible'.\r
* \r
+ * @return the value of field 'Visible'.\r
+ */\r
+ public boolean isVisible(\r
+ ) {\r
+ return this._visible;\r
+ }\r
+\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 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 jalview.schemabinding.version2.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 jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
return (jalview.schemabinding.version2.AnnotationElement) obj;\r
- } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) \r
+ }\r
\r
/**\r
- * Method setAnnotationElement\r
- * \r
* \r
* \r
* @param index\r
* @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\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 jalview.schemabinding.version2.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, jalview.schemabinding.version2.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(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)\r
- {\r
+ public void setAnnotationElement(\r
+ final jalview.schemabinding.version2.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(jalview.schemabinding.version2.AnnotationElement) \r
+ }\r
\r
/**\r
* Sets the value of field 'description'.\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 'graph'.\r
* \r
* @param graph the value of field 'graph'.\r
*/\r
- public void setGraph(boolean graph)\r
- {\r
+ public void setGraph(\r
+ final boolean graph) {\r
this._graph = graph;\r
this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphColour'.\r
* \r
* @param graphColour the value of field 'graphColour'.\r
*/\r
- public void setGraphColour(int graphColour)\r
- {\r
+ public void setGraphColour(\r
+ final int graphColour) {\r
this._graphColour = graphColour;\r
this._has_graphColour = true;\r
- } //-- void setGraphColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphGroup'.\r
* \r
* @param graphGroup the value of field 'graphGroup'.\r
*/\r
- public void setGraphGroup(int graphGroup)\r
- {\r
+ public void setGraphGroup(\r
+ final int graphGroup) {\r
this._graphGroup = graphGroup;\r
this._has_graphGroup = true;\r
- } //-- void setGraphGroup(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'graphType'.\r
* \r
* @param graphType the value of field 'graphType'.\r
*/\r
- public void setGraphType(int graphType)\r
- {\r
+ public void setGraphType(\r
+ final int graphType) {\r
this._graphType = graphType;\r
this._has_graphType = true;\r
- } //-- void setGraphType(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'id'.\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'.\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
* Sets the value of field 'score'.\r
* \r
* @param score the value of field 'score'.\r
*/\r
- public void setScore(double score)\r
- {\r
+ public void setScore(\r
+ final double score) {\r
this._score = score;\r
this._has_score = true;\r
- } //-- void setScore(double) \r
+ }\r
\r
/**\r
* Sets the value of field 'scoreOnly'.\r
* \r
* @param scoreOnly the value of field 'scoreOnly'.\r
*/\r
- public void setScoreOnly(boolean scoreOnly)\r
- {\r
+ public void setScoreOnly(\r
+ final boolean scoreOnly) {\r
this._scoreOnly = scoreOnly;\r
this._has_scoreOnly = true;\r
- } //-- void setScoreOnly(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'sequenceRef'.\r
* \r
* @param sequenceRef the value of field 'sequenceRef'.\r
*/\r
- public void setSequenceRef(java.lang.String sequenceRef)\r
- {\r
+ public void setSequenceRef(\r
+ final java.lang.String sequenceRef) {\r
this._sequenceRef = sequenceRef;\r
- } //-- void setSequenceRef(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'thresholdLine'.\r
* \r
* @param thresholdLine the value of field 'thresholdLine'.\r
*/\r
- public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)\r
- {\r
+ public void setThresholdLine(\r
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine) {\r
this._thresholdLine = thresholdLine;\r
- } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) \r
+ }\r
\r
/**\r
* Sets the value of field 'visible'.\r
* \r
* @param visible the value of field 'visible'.\r
*/\r
- public void setVisible(boolean visible)\r
- {\r
+ public void setVisible(\r
+ final boolean visible) {\r
this._visible = visible;\r
this._has_visible = true;\r
- } //-- void setVisible(boolean) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\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
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.Annotation\r
+ */\r
+ public static jalview.schemabinding.version2.Annotation unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.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 / jalview.git / blobdiff