/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\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 org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class Annotation.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\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
+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 _scoreOnly.\r
+ */\r
+ private boolean _scoreOnly = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _scoreOnly\r
+ */\r
+ private boolean _has_scoreOnly;\r
+\r
+ /**\r
+ * Field _score.\r
+ */\r
+ private double _score;\r
+\r
+ /**\r
+ * keeps track of state for field: _score\r
+ */\r
+ private boolean _has_score;\r
+\r
+ /**\r
+ * Field _visible.\r
+ */\r
+ private boolean _visible;\r
+\r
+ /**\r
+ * keeps track of state for field: _visible\r
+ */\r
+ private boolean _has_visible;\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
+ this._annotationElementList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\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(\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
+\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(\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
+ */\r
+ public void deleteGraph(\r
+ ) {\r
+ this._has_graph= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphColour(\r
+ ) {\r
+ this._has_graphColour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphGroup(\r
+ ) {\r
+ this._has_graphGroup= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphType(\r
+ ) {\r
+ this._has_graphType= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScore(\r
+ ) {\r
+ this._has_score= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScoreOnly(\r
+ ) {\r
+ this._has_scoreOnly= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteVisible(\r
+ ) {\r
+ this._has_visible= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAnnotationElement.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AnnotationElement elements\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement(\r
+ ) {\r
+ return this._annotationElementList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.\r
+ * \r
+ * @param index\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.get(index);\r
+ }\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 this collection as an Array\r
+ */\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
+ * @return the size of this collection\r
+ */\r
+ public int getAnnotationElementCount(\r
+ ) {\r
+ return this._annotationElementList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ * \r
+ * @return the value of field 'Description'.\r
+ */\r
+ public java.lang.String getDescription(\r
+ ) {\r
+ return this._description;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graph'.\r
+ * \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean getGraph(\r
+ ) {\r
+ return this._graph;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphColour'.\r
+ * \r
+ * @return the value of field 'GraphColour'.\r
+ */\r
+ public int getGraphColour(\r
+ ) {\r
+ return this._graphColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphGroup'.\r
+ * \r
+ * @return the value of field 'GraphGroup'.\r
+ */\r
+ public int getGraphGroup(\r
+ ) {\r
+ return this._graphGroup;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphType'.\r
+ * \r
+ * @return the value of field 'GraphType'.\r
+ */\r
+ public int getGraphType(\r
+ ) {\r
+ return this._graphType;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId(\r
+ ) {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'label'.\r
+ * \r
+ * @return the value of field 'Label'.\r
+ */\r
+ public java.lang.String getLabel(\r
+ ) {\r
+ return this._label;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'score'.\r
+ * \r
+ * @return the value of field 'Score'.\r
+ */\r
+ public double getScore(\r
+ ) {\r
+ return this._score;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
+ * \r
+ * @return the value of field 'ScoreOnly'.\r
+ */\r
+ public boolean getScoreOnly(\r
+ ) {\r
+ return this._scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequenceRef'.\r
+ * \r
+ * @return the value of field 'SequenceRef'.\r
+ */\r
+ public java.lang.String getSequenceRef(\r
+ ) {\r
+ return this._sequenceRef;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'thresholdLine'.\r
+ * \r
+ * @return the value of field 'ThresholdLine'.\r
+ */\r
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine(\r
+ ) {\r
+ return this._thresholdLine;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'visible'.\r
+ * \r
+ * @return the value of field 'Visible'.\r
+ */\r
+ public boolean getVisible(\r
+ ) {\r
+ return this._visible;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraph.\r
+ * \r
+ * @return true if at least one Graph has been added\r
+ */\r
+ public boolean hasGraph(\r
+ ) {\r
+ return this._has_graph;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphColour.\r
+ * \r
+ * @return true if at least one GraphColour has been added\r
+ */\r
+ public boolean hasGraphColour(\r
+ ) {\r
+ return this._has_graphColour;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphGroup.\r
+ * \r
+ * @return true if at least one GraphGroup has been added\r
+ */\r
+ public boolean hasGraphGroup(\r
+ ) {\r
+ return this._has_graphGroup;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphType.\r
+ * \r
+ * @return true if at least one GraphType has been added\r
+ */\r
+ public boolean hasGraphType(\r
+ ) {\r
+ return this._has_graphType;\r
+ }\r
+\r
+ /**\r
+ * Method hasScore.\r
+ * \r
+ * @return true if at least one Score has been added\r
+ */\r
+ public boolean hasScore(\r
+ ) {\r
+ return this._has_score;\r
+ }\r
+\r
+ /**\r
+ * Method hasScoreOnly.\r
+ * \r
+ * @return true if at least one ScoreOnly has been added\r
+ */\r
+ public boolean hasScoreOnly(\r
+ ) {\r
+ return this._has_scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Method hasVisible.\r
+ * \r
+ * @return true if at least one Visible has been added\r
+ */\r
+ public boolean hasVisible(\r
+ ) {\r
+ return this._has_visible;\r
+ }\r
+\r
+ /**\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 true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\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
+ * @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
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\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
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAnnotationElement(\r
+ ) {\r
+ this._annotationElementList.clear();\r
+ }\r
+\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 the element removed from the collection\r
+ */\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
+ }\r
+\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 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
+ \r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElementArray\r
+ */\r
+ public void setAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {\r
+ //-- copy array\r
+ _annotationElementList.clear();\r
+ \r
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'description'.\r
+ * \r
+ * @param description the value of field 'description'.\r
+ */\r
+ public void setDescription(\r
+ final java.lang.String description) {\r
+ this._description = description;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graph'.\r
+ * \r
+ * @param graph the value of field 'graph'.\r
+ */\r
+ public void setGraph(\r
+ final boolean graph) {\r
+ this._graph = graph;\r
+ this._has_graph = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphColour'.\r
+ * \r
+ * @param graphColour the value of field 'graphColour'.\r
+ */\r
+ public void setGraphColour(\r
+ final int graphColour) {\r
+ this._graphColour = graphColour;\r
+ this._has_graphColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphGroup'.\r
+ * \r
+ * @param graphGroup the value of field 'graphGroup'.\r
+ */\r
+ public void setGraphGroup(\r
+ final int graphGroup) {\r
+ this._graphGroup = graphGroup;\r
+ this._has_graphGroup = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphType'.\r
+ * \r
+ * @param graphType the value of field 'graphType'.\r
+ */\r
+ public void setGraphType(\r
+ final int graphType) {\r
+ this._graphType = graphType;\r
+ this._has_graphType = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(\r
+ final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'label'.\r
+ * \r
+ * @param label the value of field 'label'.\r
+ */\r
+ public void setLabel(\r
+ final java.lang.String label) {\r
+ this._label = label;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'score'.\r
+ * \r
+ * @param score the value of field 'score'.\r
+ */\r
+ public void setScore(\r
+ final double score) {\r
+ this._score = score;\r
+ this._has_score = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'scoreOnly'.\r
+ * \r
+ * @param scoreOnly the value of field 'scoreOnly'.\r
+ */\r
+ public void setScoreOnly(\r
+ final boolean scoreOnly) {\r
+ this._scoreOnly = scoreOnly;\r
+ this._has_scoreOnly = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequenceRef'.\r
+ * \r
+ * @param sequenceRef the value of field 'sequenceRef'.\r
+ */\r
+ public void setSequenceRef(\r
+ final java.lang.String sequenceRef) {\r
+ this._sequenceRef = sequenceRef;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'thresholdLine'.\r
+ * \r
+ * @param thresholdLine the value of field 'thresholdLine'.\r
+ */\r
+ public void setThresholdLine(\r
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine) {\r
+ this._thresholdLine = 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(\r
+ final boolean visible) {\r
+ this._visible = visible;\r
+ this._has_visible = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\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
+ }\r
+\r
+ /**\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
+ )\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
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff