/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.util.*;\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
+import org.exolab.castor.xml.*;\r
\r
/**\r
* Class Annotation.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
-public class Annotation implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _graph\r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _graphType\r
- */\r
- private int _graphType;\r
-\r
- /**\r
- * keeps track of state for field: _graphType\r
- */\r
- private boolean _has_graphType;\r
-\r
- /**\r
- * Field _sequenceRef\r
- */\r
- private java.lang.String _sequenceRef;\r
-\r
- /**\r
- * Field _graphColour\r
- */\r
- private int _graphColour;\r
-\r
- /**\r
- * keeps track of state for field: _graphColour\r
- */\r
- private boolean _has_graphColour;\r
-\r
- /**\r
- * Field _graphGroup\r
- */\r
- private int _graphGroup;\r
-\r
- /**\r
- * keeps track of state for field: _graphGroup\r
- */\r
- private boolean _has_graphGroup;\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _annotationElementList\r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Field _label\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _thresholdLine\r
- */\r
- private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Annotation() {\r
- super();\r
- _annotationElementList = new Vector();\r
- } //-- jalview.schemabinding.version2.Annotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param vAnnotationElement\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
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\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
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Method deleteGraphColour\r
- * \r
- */\r
- public void deleteGraphColour()\r
- {\r
- this._has_graphColour= false;\r
- } //-- void deleteGraphColour() \r
-\r
- /**\r
- * Method deleteGraphGroup\r
- * \r
- */\r
- public void deleteGraphGroup()\r
- {\r
- this._has_graphGroup= false;\r
- } //-- void deleteGraphGroup() \r
-\r
- /**\r
- * Method deleteGraphType\r
- * \r
- */\r
- public void deleteGraphType()\r
- {\r
- this._has_graphType= false;\r
- } //-- void deleteGraphType() \r
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \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
- }\r
- \r
- return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @return AnnotationElement\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
-\r
- /**\r
- * Method getAnnotationElementCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'graph'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'graphColour'.\r
- * \r
- * @return int\r
- * @return the value of field 'graphColour'.\r
- */\r
- public int getGraphColour()\r
- {\r
- return this._graphColour;\r
- } //-- int getGraphColour() \r
-\r
- /**\r
- * Returns the value of field 'graphGroup'.\r
- * \r
- * @return int\r
- * @return the value of field 'graphGroup'.\r
- */\r
- public int getGraphGroup()\r
- {\r
- return this._graphGroup;\r
- } //-- int getGraphGroup() \r
-\r
- /**\r
- * Returns the value of field 'graphType'.\r
- * \r
- * @return int\r
- * @return the value of field 'graphType'.\r
- */\r
- public int getGraphType()\r
- {\r
- return this._graphType;\r
- } //-- int getGraphType() \r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'label'.\r
- * \r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel()\r
- {\r
- return this._label;\r
- } //-- java.lang.String getLabel() \r
-\r
- /**\r
- * Returns the value of field 'sequenceRef'.\r
- * \r
- * @return String\r
- * @return the value of field 'sequenceRef'.\r
- */\r
- public java.lang.String getSequenceRef()\r
- {\r
- return this._sequenceRef;\r
- } //-- java.lang.String getSequenceRef() \r
-\r
- /**\r
- * Returns the value of field 'thresholdLine'.\r
- * \r
- * @return ThresholdLine\r
- * @return the value of field 'thresholdLine'.\r
- */\r
- public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
- {\r
- return this._thresholdLine;\r
- } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method hasGraphColour\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraphColour()\r
- {\r
- return this._has_graphColour;\r
- } //-- boolean hasGraphColour() \r
-\r
- /**\r
- * Method hasGraphGroup\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraphGroup()\r
- {\r
- return this._has_graphGroup;\r
- } //-- boolean hasGraphGroup() \r
-\r
- /**\r
- * Method hasGraphType\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraphType()\r
- {\r
- return this._has_graphType;\r
- } //-- boolean hasGraphType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \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
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \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
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllAnnotationElement\r
- * \r
- */\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
-\r
- /**\r
- * Method removeAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.AnnotationElement) obj;\r
- } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) \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
- }\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)\r
- {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
- }\r
- } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \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
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \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
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \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
- this._graphColour = graphColour;\r
- this._has_graphColour = true;\r
- } //-- void setGraphColour(int) \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
- this._graphGroup = graphGroup;\r
- this._has_graphGroup = true;\r
- } //-- void setGraphGroup(int) \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
- this._graphType = graphType;\r
- this._has_graphType = true;\r
- } //-- void setGraphType(int) \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
- this._id = id;\r
- } //-- void setId(java.lang.String) \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
- this._label = label;\r
- } //-- void setLabel(java.lang.String) \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
- this._sequenceRef = sequenceRef;\r
- } //-- void setSequenceRef(java.lang.String) \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
- this._thresholdLine = thresholdLine;\r
- } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \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
- return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
+public class Annotation\r
+ implements java.io.Serializable\r
+{\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _graph\r
+ */\r
+ private boolean _graph;\r
+\r
+ /**\r
+ * keeps track of state for field: _graph\r
+ */\r
+ private boolean _has_graph;\r
+\r
+ /**\r
+ * Field _graphType\r
+ */\r
+ private int _graphType;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphType\r
+ */\r
+ private boolean _has_graphType;\r
+\r
+ /**\r
+ * Field _sequenceRef\r
+ */\r
+ private java.lang.String _sequenceRef;\r
+\r
+ /**\r
+ * Field _graphColour\r
+ */\r
+ private int _graphColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphColour\r
+ */\r
+ private boolean _has_graphColour;\r
+\r
+ /**\r
+ * Field _graphGroup\r
+ */\r
+ private int _graphGroup;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphGroup\r
+ */\r
+ private boolean _has_graphGroup;\r
+\r
+ /**\r
+ * Field _id\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _annotationElementList\r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Field _label\r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Field _description\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _thresholdLine\r
+ */\r
+ private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Annotation()\r
+ {\r
+ super();\r
+ _annotationElementList = new Vector();\r
+ } //-- jalview.schemabinding.version2.Annotation()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(jalview.schemabinding.version2.\r
+ AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.addElement(vAnnotationElement);\r
+ } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement)\r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(int index,\r
+ jalview.schemabinding.version2.AnnotationElement\r
+ vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.insertElementAt(vAnnotationElement, index);\r
+ } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)\r
+\r
+ /**\r
+ * Method deleteGraph\r
+ *\r
+ */\r
+ public void deleteGraph()\r
+ {\r
+ this._has_graph = false;\r
+ } //-- void deleteGraph()\r
+\r
+ /**\r
+ * Method deleteGraphColour\r
+ *\r
+ */\r
+ public void deleteGraphColour()\r
+ {\r
+ this._has_graphColour = false;\r
+ } //-- void deleteGraphColour()\r
+\r
+ /**\r
+ * Method deleteGraphGroup\r
+ *\r
+ */\r
+ public void deleteGraphGroup()\r
+ {\r
+ this._has_graphGroup = false;\r
+ } //-- void deleteGraphGroup()\r
+\r
+ /**\r
+ * Method deleteGraphType\r
+ *\r
+ */\r
+ public void deleteGraphType()\r
+ {\r
+ this._has_graphType = false;\r
+ } //-- void deleteGraphType()\r
+\r
+ /**\r
+ * Method enumerateAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
+ return _annotationElementList.elements();\r
+ } //-- java.util.Enumeration enumerateAnnotationElement()\r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int\r
+ index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ( (index < 0) || (index > _annotationElementList.size()))\r
+ {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.AnnotationElement)\r
+ _annotationElementList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int)\r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement[]\r
+ getAnnotationElement()\r
+ {\r
+ int size = _annotationElementList.size();\r
+ jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.\r
+ schemabinding.version2.AnnotationElement[size];\r
+ for (int index = 0; index < size; index++)\r
+ {\r
+ mArray[index] = (jalview.schemabinding.version2.AnnotationElement)\r
+ _annotationElementList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
+\r
+ /**\r
+ * Method getAnnotationElementCount\r
+ *\r
+ *\r
+ *\r
+ * @return int\r
+ */\r
+ public int getAnnotationElementCount()\r
+ {\r
+ return _annotationElementList.size();\r
+ } //-- int getAnnotationElementCount()\r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ } //-- java.lang.String getDescription()\r
+\r
+ /**\r
+ * Returns the value of field 'graph'.\r
+ *\r
+ * @return boolean\r
+ * @return the value of field 'graph'.\r
+ */\r
+ public boolean getGraph()\r
+ {\r
+ return this._graph;\r
+ } //-- boolean getGraph()\r
+\r
+ /**\r
+ * Returns the value of field 'graphColour'.\r
+ *\r
+ * @return int\r
+ * @return the value of field 'graphColour'.\r
+ */\r
+ public int getGraphColour()\r
+ {\r
+ return this._graphColour;\r
+ } //-- int getGraphColour()\r
+\r
+ /**\r
+ * Returns the value of field 'graphGroup'.\r
+ *\r
+ * @return int\r
+ * @return the value of field 'graphGroup'.\r
+ */\r
+ public int getGraphGroup()\r
+ {\r
+ return this._graphGroup;\r
+ } //-- int getGraphGroup()\r
+\r
+ /**\r
+ * Returns the value of field 'graphType'.\r
+ *\r
+ * @return int\r
+ * @return the value of field 'graphType'.\r
+ */\r
+ public int getGraphType()\r
+ {\r
+ return this._graphType;\r
+ } //-- int getGraphType()\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ } //-- java.lang.String getId()\r
+\r
+ /**\r
+ * Returns the value of field 'label'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'label'.\r
+ */\r
+ public java.lang.String getLabel()\r
+ {\r
+ return this._label;\r
+ } //-- java.lang.String getLabel()\r
+\r
+ /**\r
+ * Returns the value of field 'sequenceRef'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'sequenceRef'.\r
+ */\r
+ public java.lang.String getSequenceRef()\r
+ {\r
+ return this._sequenceRef;\r
+ } //-- java.lang.String getSequenceRef()\r
+\r
+ /**\r
+ * Returns the value of field 'thresholdLine'.\r
+ *\r
+ * @return ThresholdLine\r
+ * @return the value of field 'thresholdLine'.\r
+ */\r
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
+ {\r
+ return this._thresholdLine;\r
+ } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
+\r
+ /**\r
+ * Method hasGraph\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean hasGraph()\r
+ {\r
+ return this._has_graph;\r
+ } //-- boolean hasGraph()\r
+\r
+ /**\r
+ * Method hasGraphColour\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean hasGraphColour()\r
+ {\r
+ return this._has_graphColour;\r
+ } //-- boolean hasGraphColour()\r
+\r
+ /**\r
+ * Method hasGraphGroup\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean hasGraphGroup()\r
+ {\r
+ return this._has_graphGroup;\r
+ } //-- boolean hasGraphGroup()\r
+\r
+ /**\r
+ * Method hasGraphType\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean hasGraphType()\r
+ {\r
+ return this._has_graphType;\r
+ } //-- boolean hasGraphType()\r
+\r
+ /**\r
+ * Method isValid\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try\r
+ {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid()\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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+\r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer)\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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+\r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
+\r
+ /**\r
+ * Method removeAllAnnotationElement\r
+ *\r
+ */\r
+ public void removeAllAnnotationElement()\r
+ {\r
+ _annotationElementList.removeAllElements();\r
+ } //-- void removeAllAnnotationElement()\r
+\r
+ /**\r
+ * Method removeAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement\r
+ removeAnnotationElement(int index)\r
+ {\r
+ java.lang.Object obj = _annotationElementList.elementAt(index);\r
+ _annotationElementList.removeElementAt(index);\r
+ return (jalview.schemabinding.version2.AnnotationElement) obj;\r
+ } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int)\r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void setAnnotationElement(int index,\r
+ jalview.schemabinding.version2.AnnotationElement\r
+ vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ( (index < 0) || (index > _annotationElementList.size()))\r
+ {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _annotationElementList.setElementAt(vAnnotationElement, index);\r
+ } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)\r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param annotationElementArray\r
+ */\r
+ public void setAnnotationElement(jalview.schemabinding.version2.\r
+ AnnotationElement[] annotationElementArray)\r
+ {\r
+ //-- copy array\r
+ _annotationElementList.removeAllElements();\r
+ for (int i = 0; i < annotationElementArray.length; i++)\r
+ {\r
+ _annotationElementList.addElement(annotationElementArray[i]);\r
+ }\r
+ } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement)\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
+ this._description = description;\r
+ } //-- void setDescription(java.lang.String)\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
+ this._graph = graph;\r
+ this._has_graph = true;\r
+ } //-- void setGraph(boolean)\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
+ this._graphColour = graphColour;\r
+ this._has_graphColour = true;\r
+ } //-- void setGraphColour(int)\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
+ this._graphGroup = graphGroup;\r
+ this._has_graphGroup = true;\r
+ } //-- void setGraphGroup(int)\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
+ this._graphType = graphType;\r
+ this._has_graphType = true;\r
+ } //-- void setGraphType(int)\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
+ this._id = id;\r
+ } //-- void setId(java.lang.String)\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
+ this._label = label;\r
+ } //-- void setLabel(java.lang.String)\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
+ this._sequenceRef = sequenceRef;\r
+ } //-- void setSequenceRef(java.lang.String)\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\r
+ thresholdLine)\r
+ {\r
+ this._thresholdLine = thresholdLine;\r
+ } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine)\r
+\r
+ /**\r
+ * Method unmarshal\r
+ *\r
+ *\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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(\r
+ jalview.schemabinding.version2.Annotation.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
+\r
+ /**\r
+ * Method validate\r
+ *\r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
+ Validator();\r
+ validator.validate(this);\r
+ } //-- void validate()\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff