/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\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
+// ---------------------------------/\r
+// - Imported classes and packages -/\r
+// ---------------------------------/\r
+\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
* @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 _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 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 '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 '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 '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 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 'graphType'.\r
- * \r
- * @param graphType the value of field 'graphType'.\r
- */\r
- public void setGraphType(int graphType)\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
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public Annotation()\r
+ {\r
+ super();\r
+ this._annotationElementList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index 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
+ {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index 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
+ {\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\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.AnnotationElement\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size())\r
{\r
- this._graphType = graphType;\r
- this._has_graphType = true;\r
- } //-- void setGraphType(int) \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
+ throw new IndexOutOfBoundsException(\r
+ "getAnnotationElement: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.Returns the contents of the collection in an\r
+ * Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of 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\r
+ .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
{\r
- this._label = label;\r
- } //-- void setLabel(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
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\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
+ 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\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\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
+ {\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
+ {\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\r
+ * if the index 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
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size())\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
+ throw new IndexOutOfBoundsException(\r
+ "setAnnotationElement: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (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
+ {\r
+ // -- copy array\r
+ _annotationElementList.clear();\r
+\r
+ for (int i = 0; i < vAnnotationElementArray.length; i++)\r
{\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'description'.\r
+ * \r
+ * @param description\r
+ * the value of field 'description'.\r
+ */\r
+ public void setDescription(final java.lang.String description)\r
+ {\r
+ this._description = description;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graph'.\r
+ * \r
+ * @param graph\r
+ * the value of field 'graph'.\r
+ */\r
+ public void setGraph(final boolean graph)\r
+ {\r
+ this._graph = graph;\r
+ this._has_graph = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphColour'.\r
+ * \r
+ * @param graphColour\r
+ * the value of field 'graphColour'.\r
+ */\r
+ public void setGraphColour(final int graphColour)\r
+ {\r
+ this._graphColour = graphColour;\r
+ this._has_graphColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphGroup'.\r
+ * \r
+ * @param graphGroup\r
+ * the value of field 'graphGroup'.\r
+ */\r
+ public void setGraphGroup(final int graphGroup)\r
+ {\r
+ this._graphGroup = graphGroup;\r
+ this._has_graphGroup = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphType'.\r
+ * \r
+ * @param graphType\r
+ * the value of field 'graphType'.\r
+ */\r
+ public void setGraphType(final int graphType)\r
+ {\r
+ this._graphType = graphType;\r
+ this._has_graphType = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'label'.\r
+ * \r
+ * @param label\r
+ * the value of field 'label'.\r
+ */\r
+ public void setLabel(final java.lang.String label)\r
+ {\r
+ this._label = label;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'score'.\r
+ * \r
+ * @param score\r
+ * the value of field 'score'.\r
+ */\r
+ public void setScore(final double score)\r
+ {\r
+ this._score = score;\r
+ this._has_score = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'scoreOnly'.\r
+ * \r
+ * @param scoreOnly\r
+ * the value of field 'scoreOnly'.\r
+ */\r
+ public void setScoreOnly(final boolean scoreOnly)\r
+ {\r
+ this._scoreOnly = scoreOnly;\r
+ this._has_scoreOnly = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequenceRef'.\r
+ * \r
+ * @param sequenceRef\r
+ * the value of field 'sequenceRef'.\r
+ */\r
+ public void setSequenceRef(final java.lang.String sequenceRef)\r
+ {\r
+ this._sequenceRef = sequenceRef;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'thresholdLine'.\r
+ * \r
+ * @param thresholdLine\r
+ * the value of field 'thresholdLine'.\r
+ */\r
+ public void setThresholdLine(\r
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine)\r
+ {\r
+ this._thresholdLine = thresholdLine;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'visible'.\r
+ * \r
+ * @param visible\r
+ * the value of field 'visible'.\r
+ */\r
+ public void setVisible(final boolean visible)\r
+ {\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\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ * @return the unmarshaled 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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.Annotation) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.Annotation.class,\r
+ reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ */\r
+ public void validate() 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
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff