-/*\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
-\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
-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 _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
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Annotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Annotation implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _sequenceRef.
+ */
+ private java.lang.String _sequenceRef;
+
+ /**
+ * Field _groupRef.
+ */
+ private java.lang.String _groupRef;
+
+ /**
+ * Field _graphColour.
+ */
+ private int _graphColour;
+
+ /**
+ * keeps track of state for field: _graphColour
+ */
+ private boolean _has_graphColour;
+
+ /**
+ * Field _graphGroup.
+ */
+ private int _graphGroup;
+
+ /**
+ * keeps track of state for field: _graphGroup
+ */
+ private boolean _has_graphGroup;
+
+ /**
+ * height in pixels for the graph if this is a graph-type annotation.
+ */
+ private int _graphHeight;
+
+ /**
+ * keeps track of state for field: _graphHeight
+ */
+ private boolean _has_graphHeight;
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _scoreOnly.
+ */
+ private boolean _scoreOnly = false;
+
+ /**
+ * keeps track of state for field: _scoreOnly
+ */
+ private boolean _has_scoreOnly;
+
+ /**
+ * Field _score.
+ */
+ private double _score;
+
+ /**
+ * keeps track of state for field: _score
+ */
+ private boolean _has_score;
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * Field _centreColLabels.
+ */
+ private boolean _centreColLabels;
+
+ /**
+ * keeps track of state for field: _centreColLabels
+ */
+ private boolean _has_centreColLabels;
+
+ /**
+ * Field _scaleColLabels.
+ */
+ private boolean _scaleColLabels;
+
+ /**
+ * keeps track of state for field: _scaleColLabels
+ */
+ private boolean _has_scaleColLabels;
+
+ /**
+ * Field _showAllColLabels.
+ */
+ private boolean _showAllColLabels;
+
+ /**
+ * keeps track of state for field: _showAllColLabels
+ */
+ private boolean _has_showAllColLabels;
+
+ /**
+ * is an autocalculated annotation row
+ */
+ private boolean _autoCalculated = false;
+
+ /**
+ * keeps track of state for field: _autoCalculated
+ */
+ private boolean _has_autoCalculated;
+
+ /**
+ * is to be shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ */
+ private boolean _belowAlignment = true;
+
+ /**
+ * keeps track of state for field: _belowAlignment
+ */
+ private boolean _has_belowAlignment;
+
+ /**
+ * Optional string identifier used to group sets of annotation produced by a
+ * particular calculation. Values are opaque strings but have semantic meaning
+ * to Jalview's renderer, data importer and calculation system.
+ */
+ private java.lang.String _calcId;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _thresholdLine.
+ */
+ private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Annotation()
+ {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteAutoCalculated()
+ {
+ this._has_autoCalculated = false;
+ }
+
+ /**
+ */
+ public void deleteBelowAlignment()
+ {
+ this._has_belowAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteCentreColLabels()
+ {
+ this._has_centreColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteGraph()
+ {
+ this._has_graph = false;
+ }
+
+ /**
+ */
+ public void deleteGraphColour()
+ {
+ this._has_graphColour = false;
+ }
+
+ /**
+ */
+ public void deleteGraphGroup()
+ {
+ this._has_graphGroup = false;
+ }
+
+ /**
+ */
+ public void deleteGraphHeight()
+ {
+ this._has_graphHeight = false;
+ }
+
+ /**
+ */
+ public void deleteGraphType()
+ {
+ this._has_graphType = false;
+ }
+
+ /**
+ */
+ public void deleteScaleColLabels()
+ {
+ this._has_scaleColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteScore()
+ {
+ this._has_score = false;
+ }
+
+ /**
+ */
+ public void deleteScoreOnly()
+ {
+ this._has_scoreOnly = false;
+ }
+
+ /**
+ */
+ public void deleteShowAllColLabels()
+ {
+ this._has_showAllColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteVisible()
+ {
+ this._has_visible = false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.AnnotationElement
+ * at the given index
+ */
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+ {
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount()
+ {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean getAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean getBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId()
+ {
+ return this._calcId;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean getCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphColour'.
+ *
+ * @return the value of field 'GraphColour'.
+ */
+ public int getGraphColour()
+ {
+ return this._graphColour;
+ }
+
+ /**
+ * Returns the value of field 'graphGroup'.
+ *
+ * @return the value of field 'GraphGroup'.
+ */
+ public int getGraphGroup()
+ {
+ return this._graphGroup;
+ }
+
+ /**
+ * Returns the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @return the value of field 'GraphHeight'.
+ */
+ public int getGraphHeight()
+ {
+ return this._graphHeight;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType()
+ {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'groupRef'.
+ *
+ * @return the value of field 'GroupRef'.
+ */
+ public java.lang.String getGroupRef()
+ {
+ return this._groupRef;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean getScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'score'.
+ *
+ * @return the value of field 'Score'.
+ */
+ public double getScore()
+ {
+ return this._score;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean getScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'sequenceRef'.
+ *
+ * @return the value of field 'SequenceRef'.
+ */
+ public java.lang.String getSequenceRef()
+ {
+ return this._sequenceRef;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean getShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * Returns the value of field 'thresholdLine'.
+ *
+ * @return the value of field 'ThresholdLine'.
+ */
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+ {
+ return this._thresholdLine;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ * Method hasAutoCalculated.
+ *
+ * @return true if at least one AutoCalculated has been added
+ */
+ public boolean hasAutoCalculated()
+ {
+ return this._has_autoCalculated;
+ }
+
+ /**
+ * Method hasBelowAlignment.
+ *
+ * @return true if at least one BelowAlignment has been added
+ */
+ public boolean hasBelowAlignment()
+ {
+ return this._has_belowAlignment;
+ }
+
+ /**
+ * Method hasCentreColLabels.
+ *
+ * @return true if at least one CentreColLabels has been added
+ */
+ public boolean hasCentreColLabels()
+ {
+ return this._has_centreColLabels;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphColour.
+ *
+ * @return true if at least one GraphColour has been added
+ */
+ public boolean hasGraphColour()
+ {
+ return this._has_graphColour;
+ }
+
+ /**
+ * Method hasGraphGroup.
+ *
+ * @return true if at least one GraphGroup has been added
+ */
+ public boolean hasGraphGroup()
+ {
+ return this._has_graphGroup;
+ }
+
+ /**
+ * Method hasGraphHeight.
+ *
+ * @return true if at least one GraphHeight has been added
+ */
+ public boolean hasGraphHeight()
+ {
+ return this._has_graphHeight;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType()
+ {
+ return this._has_graphType;
+ }
+
+ /**
+ * Method hasScaleColLabels.
+ *
+ * @return true if at least one ScaleColLabels has been added
+ */
+ public boolean hasScaleColLabels()
+ {
+ return this._has_scaleColLabels;
+ }
+
+ /**
+ * Method hasScore.
+ *
+ * @return true if at least one Score has been added
+ */
+ public boolean hasScore()
+ {
+ return this._has_score;
+ }
+
+ /**
+ * Method hasScoreOnly.
+ *
+ * @return true if at least one ScoreOnly has been added
+ */
+ public boolean hasScoreOnly()
+ {
+ return this._has_scoreOnly;
+ }
+
+ /**
+ * Method hasShowAllColLabels.
+ *
+ * @return true if at least one ShowAllColLabels has been added
+ */
+ public boolean hasShowAllColLabels()
+ {
+ return this._has_showAllColLabels;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean isAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean isBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean isCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean isScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean isScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean isShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement()
+ {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.schemabinding.version2.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)
+ {
+ // -- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++)
+ {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @param autoCalculated
+ * the value of field 'autoCalculated'.
+ */
+ public void setAutoCalculated(final boolean autoCalculated)
+ {
+ this._autoCalculated = autoCalculated;
+ this._has_autoCalculated = true;
+ }
+
+ /**
+ * Sets the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @param belowAlignment
+ * the value of field 'belowAlignment'.
+ */
+ public void setBelowAlignment(final boolean belowAlignment)
+ {
+ this._belowAlignment = belowAlignment;
+ this._has_belowAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @param calcId
+ * the value of field 'calcId'.
+ */
+ public void setCalcId(final java.lang.String calcId)
+ {
+ this._calcId = calcId;
+ }
+
+ /**
+ * Sets the value of field 'centreColLabels'.
+ *
+ * @param centreColLabels
+ * the value of field 'centreColLabels'.
+ */
+ public void setCentreColLabels(final boolean centreColLabels)
+ {
+ this._centreColLabels = centreColLabels;
+ this._has_centreColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph
+ * the value of field 'graph'.
+ */
+ public void setGraph(final boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphColour'.
+ *
+ * @param graphColour
+ * the value of field 'graphColour'.
+ */
+ public void setGraphColour(final int graphColour)
+ {
+ this._graphColour = graphColour;
+ this._has_graphColour = true;
+ }
+
+ /**
+ * Sets the value of field 'graphGroup'.
+ *
+ * @param graphGroup
+ * the value of field 'graphGroup'.
+ */
+ public void setGraphGroup(final int graphGroup)
+ {
+ this._graphGroup = graphGroup;
+ this._has_graphGroup = true;
+ }
+
+ /**
+ * Sets the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @param graphHeight
+ * the value of field 'graphHeight'.
+ */
+ public void setGraphHeight(final int graphHeight)
+ {
+ this._graphHeight = graphHeight;
+ this._has_graphHeight = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType
+ * the value of field 'graphType'.
+ */
+ public void setGraphType(final int graphType)
+ {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'groupRef'.
+ *
+ * @param groupRef
+ * the value of field 'groupRef'.
+ */
+ public void setGroupRef(final java.lang.String groupRef)
+ {
+ this._groupRef = groupRef;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label
+ * the value of field 'label'.
+ */
+ public void setLabel(final java.lang.String label)
+ {
+ this._label = label;
+ }
+
+ /**
+ * Sets the value of field 'scaleColLabels'.
+ *
+ * @param scaleColLabels
+ * the value of field 'scaleColLabels'.
+ */
+ public void setScaleColLabels(final boolean scaleColLabels)
+ {
+ this._scaleColLabels = scaleColLabels;
+ this._has_scaleColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'score'.
+ *
+ * @param score
+ * the value of field 'score'.
+ */
+ public void setScore(final double score)
+ {
+ this._score = score;
+ this._has_score = true;
+ }
+
+ /**
+ * Sets the value of field 'scoreOnly'.
+ *
+ * @param scoreOnly
+ * the value of field 'scoreOnly'.
+ */
+ public void setScoreOnly(final boolean scoreOnly)
+ {
+ this._scoreOnly = scoreOnly;
+ this._has_scoreOnly = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceRef'.
+ *
+ * @param sequenceRef
+ * the value of field 'sequenceRef'.
+ */
+ public void setSequenceRef(final java.lang.String sequenceRef)
+ {
+ this._sequenceRef = sequenceRef;
+ }
+
+ /**
+ * Sets the value of field 'showAllColLabels'.
+ *
+ * @param showAllColLabels
+ * the value of field 'showAllColLabels'
+ */
+ public void setShowAllColLabels(final boolean showAllColLabels)
+ {
+ this._showAllColLabels = showAllColLabels;
+ this._has_showAllColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'thresholdLine'.
+ *
+ * @param thresholdLine
+ * the value of field 'thresholdLine'.
+ */
+ public void setThresholdLine(
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine)
+ {
+ this._thresholdLine = thresholdLine;
+ }
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible
+ * the value of field 'visible'.
+ */
+ public void setVisible(final boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Annotation
+ */
+ public static jalview.schemabinding.version2.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Annotation) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Annotation.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff