viewId will appear for each instance.</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="linkAlignPanel" type="xs:boolean" use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag set if the alignment panel containing this JSeq should be explicitly linked to the Jmol view referred to/created by this structureState (since Jalview 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Alignment implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _annotation.
- */
- private jalview.binding.Annotation _annotation;
-
- /**
- * Field _sequenceSet.
- */
- private jalview.binding.SequenceSet _sequenceSet;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Alignment()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public jalview.binding.Annotation getAnnotation()
- {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'sequenceSet'.
- *
- * @return the value of field 'SequenceSet'.
- */
- public jalview.binding.SequenceSet getSequenceSet()
- {
- return this._sequenceSet;
- }
-
- /**
- * 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;
+public class Alignment implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _annotation.
+ */
+ private jalview.binding.Annotation _annotation;
+
+ /**
+ * Field _sequenceSet.
+ */
+ private jalview.binding.SequenceSet _sequenceSet;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Alignment() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public jalview.binding.Annotation getAnnotation(
+ ) {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSet'.
+ *
+ * @return the value of field 'SequenceSet'.
+ */
+ public jalview.binding.SequenceSet getSequenceSet(
+ ) {
+ return this._sequenceSet;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation the value of field 'annotation'.
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation annotation) {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSet'.
+ *
+ * @param sequenceSet the value of field 'sequenceSet'.
+ */
+ public void setSequenceSet(
+ final jalview.binding.SequenceSet sequenceSet) {
+ this._sequenceSet = sequenceSet;
+ }
+
+ /**
+ * 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.binding.Alignment
+ */
+ public static jalview.binding.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation
- * the value of field 'annotation'.
- */
- public void setAnnotation(final jalview.binding.Annotation annotation)
- {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'sequenceSet'.
- *
- * @param sequenceSet
- * the value of field 'sequenceSet'.
- */
- public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
- {
- this._sequenceSet = sequenceSet;
- }
-
- /**
- * 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.binding.Alignment
- */
- public static jalview.binding.Alignment unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(
- jalview.binding.Alignment.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @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 _annotationElementList.
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- // ----------------/
- // - 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.binding.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.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationElementList.add(index, vAnnotationElement);
- }
-
- /**
- */
- public void deleteGraph()
- {
- this._has_graph = false;
- }
-
- /**
- */
- public void deleteGraphType()
- {
- this._has_graphType = false;
- }
-
- /**
- * Method enumerateAnnotationElement.
- *
- * @return an Enumeration over all jalview.binding.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.binding.AnnotationElement at the given
- * index
- */
- public jalview.binding.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) + "]");
+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 _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Annotation() {
+ super();
+ this._annotationElementList = new java.util.Vector();
}
- return (jalview.binding.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.binding.AnnotationElement[] getAnnotationElement()
- {
- jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
- return (jalview.binding.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 '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 'graphType'.
- *
- * @return the value of field 'GraphType'.
- */
- public int getGraphType()
- {
- return this._graphType;
- }
-
- /**
- * Returns the value of field 'label'.
- *
- * @return the value of field 'Label'.
- */
- public java.lang.String getLabel()
- {
- return this._label;
- }
-
- /**
- * Method hasGraph.
- *
- * @return true if at least one Graph has been added
- */
- public boolean hasGraph()
- {
- return this._has_graph;
- }
-
- /**
- * Method hasGraphType.
- *
- * @return true if at least one GraphType has been added
- */
- public boolean hasGraphType()
- {
- return this._has_graphType;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean isGraph()
- {
- return this._graph;
- }
-
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.addElement(vAnnotationElement);
}
- return true;
- }
-
- /**
- *
- *
- * @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.binding.AnnotationElement vAnnotationElement)
- {
- boolean removed = _annotationElementList.remove(vAnnotationElement);
- return removed;
- }
-
- /**
- * Method removeAnnotationElementAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.AnnotationElement removeAnnotationElementAt(
- final int index)
- {
- java.lang.Object obj = this._annotationElementList.remove(index);
- return (jalview.binding.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.binding.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) + "]");
+
+ /**
+ *
+ *
+ * @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.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph(
+ ) {
+ this._has_graph= false;
+ }
+
+ /**
+ */
+ public void deleteGraphType(
+ ) {
+ this._has_graphType= false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.binding.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.binding.AnnotationElement
+ * at the given index
+ */
+ public jalview.binding.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.binding.AnnotationElement) _annotationElementList.get(index);
}
- this._annotationElementList.set(index, vAnnotationElement);
- }
-
- /**
- *
- *
- * @param vAnnotationElementArray
- */
- public void setAnnotationElement(
- final jalview.binding.AnnotationElement[] vAnnotationElementArray)
- {
- // -- copy array
- _annotationElementList.clear();
-
- for (int i = 0; i < vAnnotationElementArray.length; i++)
- {
- this._annotationElementList.add(vAnnotationElementArray[i]);
+ /**
+ * 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.binding.AnnotationElement[] getAnnotationElement(
+ ) {
+ jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+ return (jalview.binding.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 '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 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType(
+ ) {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel(
+ ) {
+ return this._label;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph(
+ ) {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType(
+ ) {
+ return this._has_graphType;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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.binding.AnnotationElement vAnnotationElement) {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.AnnotationElement removeAnnotationElementAt(
+ final int index) {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.binding.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.binding.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.binding.AnnotationElement[] vAnnotationElementArray) {
+ //-- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * 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 '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 'label'.
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(
+ final java.lang.String label) {
+ this._label = label;
+ }
+
+ /**
+ * 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.binding.Annotation
+ */
+ public static jalview.binding.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.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);
}
- }
-
- /**
- * 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 '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 'label'.
- *
- * @param label
- * the value of field 'label'.
- */
- public void setLabel(final java.lang.String label)
- {
- this._label = label;
- }
-
- /**
- * 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.binding.Annotation
- */
- public static jalview.binding.Annotation unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(
- jalview.binding.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationElement implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _position.
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * Field _displayCharacter.
- */
- private java.lang.String _displayCharacter;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _secondaryStructure.
- */
- private java.lang.String _secondaryStructure;
-
- /**
- * Field _value.
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public AnnotationElement()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class AnnotationElement implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _position.
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _displayCharacter.
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure.
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationElement() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deletePosition(
+ ) {
+ this._has_position= false;
+ }
+
+ /**
+ */
+ public void deleteValue(
+ ) {
+ this._has_value= false;
+ }
+
+ /**
+ * 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 'displayCharacter'.
+ *
+ * @return the value of field 'DisplayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter(
+ ) {
+ return this._displayCharacter;
+ }
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return the value of field 'Position'.
*/
- public void deletePosition()
- {
- this._has_position = false;
- }
+ public int getPosition(
+ ) {
+ return this._position;
+ }
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return the value of field 'SecondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure(
+ ) {
+ return this._secondaryStructure;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition(
+ ) {
+ return this._has_position;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue(
+ ) {
+ return this._has_value;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * 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 'displayCharacter'.
+ *
+ * @param displayCharacter the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(
+ final java.lang.String displayCharacter) {
+ this._displayCharacter = displayCharacter;
+ }
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position the value of field 'position'.
+ */
+ public void setPosition(
+ final int position) {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure the value of field
+ * 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(
+ final java.lang.String secondaryStructure) {
+ this._secondaryStructure = secondaryStructure;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final float value) {
+ this._value = value;
+ this._has_value = 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.binding.AnnotationElement
+ */
+ public static jalview.binding.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteValue()
- {
- this._has_value = false;
- }
-
- /**
- * 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 'displayCharacter'.
- *
- * @return the value of field 'DisplayCharacter'.
- */
- public java.lang.String getDisplayCharacter()
- {
- return this._displayCharacter;
- }
-
- /**
- * Returns the value of field 'position'.
- *
- * @return the value of field 'Position'.
- */
- public int getPosition()
- {
- return this._position;
- }
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return the value of field 'SecondaryStructure'.
- */
- public java.lang.String getSecondaryStructure()
- {
- return this._secondaryStructure;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public float getValue()
- {
- return this._value;
- }
-
- /**
- * Method hasPosition.
- *
- * @return true if at least one Position has been added
- */
- public boolean hasPosition()
- {
- return this._has_position;
- }
-
- /**
- * Method hasValue.
- *
- * @return true if at least one Value has been added
- */
- public boolean hasValue()
- {
- return this._has_value;
- }
-
- /**
- * 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;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * 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 'displayCharacter'.
- *
- * @param displayCharacter
- * the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(final java.lang.String displayCharacter)
- {
- this._displayCharacter = displayCharacter;
- }
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position
- * the value of field 'position'.
- */
- public void setPosition(final int position)
- {
- this._position = position;
- this._has_position = true;
- }
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure
- * the value of field 'secondaryStructure'.
- */
- public void setSecondaryStructure(
- final java.lang.String secondaryStructure)
- {
- this._secondaryStructure = secondaryStructure;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value
- * the value of field 'value'.
- */
- public void setValue(final float value)
- {
- this._value = value;
- this._has_value = 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.binding.AnnotationElement
- */
- public static jalview.binding.AnnotationElement unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
- jalview.binding.AnnotationElement.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Colour implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _RGB.
- */
- private java.lang.String _RGB;
-
- /**
- * Field _minRGB.
- */
- private java.lang.String _minRGB;
-
- /**
- * loosely specified enumeration: NONE,ABOVE, or BELOW
- */
- private java.lang.String _threshType;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _max.
- */
- private float _max;
-
- /**
- * keeps track of state for field: _max
- */
- private boolean _has_max;
-
- /**
- * Field _min.
- */
- private float _min;
-
- /**
- * keeps track of state for field: _min
- */
- private boolean _has_min;
-
- /**
- * Field _colourByLabel.
- */
- private boolean _colourByLabel;
-
- /**
- * keeps track of state for field: _colourByLabel
- */
- private boolean _has_colourByLabel;
-
- /**
- * Field _autoScale.
- */
- private boolean _autoScale;
-
- /**
- * keeps track of state for field: _autoScale
- */
- private boolean _has_autoScale;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Colour()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteAutoScale()
- {
- this._has_autoScale = false;
- }
-
- /**
- */
- public void deleteColourByLabel()
- {
- this._has_colourByLabel = false;
- }
-
- /**
- */
- public void deleteMax()
- {
- this._has_max = false;
- }
-
- /**
- */
- public void deleteMin()
- {
- this._has_min = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean getAutoScale()
- {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean getColourByLabel()
- {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'max'.
- *
- * @return the value of field 'Max'.
- */
- public float getMax()
- {
- return this._max;
- }
-
- /**
- * Returns the value of field 'min'.
- *
- * @return the value of field 'Min'.
- */
- public float getMin()
- {
- return this._min;
- }
-
- /**
- * Returns the value of field 'minRGB'.
- *
- * @return the value of field 'MinRGB'.
- */
- public java.lang.String getMinRGB()
- {
- return this._minRGB;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'RGB'.
- *
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB()
- {
- return this._RGB;
- }
-
- /**
- * Returns the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
- *
- * @return the value of field 'ThreshType'.
- */
- public java.lang.String getThreshType()
- {
- return this._threshType;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Method hasAutoScale.
- *
- * @return true if at least one AutoScale has been added
- */
- public boolean hasAutoScale()
- {
- return this._has_autoScale;
- }
-
- /**
- * Method hasColourByLabel.
- *
- * @return true if at least one ColourByLabel has been added
- */
- public boolean hasColourByLabel()
- {
- return this._has_colourByLabel;
- }
-
- /**
- * Method hasMax.
- *
- * @return true if at least one Max has been added
- */
- public boolean hasMax()
- {
- return this._has_max;
- }
-
- /**
- * Method hasMin.
- *
- * @return true if at least one Min has been added
- */
- public boolean hasMin()
- {
- return this._has_min;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean isAutoScale()
- {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean isColourByLabel()
- {
- return this._colourByLabel;
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'autoScale'.
- *
- * @param autoScale
- * the value of field 'autoScale'.
- */
- public void setAutoScale(final boolean autoScale)
- {
- this._autoScale = autoScale;
- this._has_autoScale = true;
- }
-
- /**
- * Sets the value of field 'colourByLabel'.
- *
- * @param colourByLabel
- * the value of field 'colourByLabel'.
- */
- public void setColourByLabel(final boolean colourByLabel)
- {
- this._colourByLabel = colourByLabel;
- this._has_colourByLabel = true;
- }
-
- /**
- * Sets the value of field 'max'.
- *
- * @param max
- * the value of field 'max'.
- */
- public void setMax(final float max)
- {
- this._max = max;
- this._has_max = true;
- }
-
- /**
- * Sets the value of field 'min'.
- *
- * @param min
- * the value of field 'min'.
- */
- public void setMin(final float min)
- {
- this._min = min;
- this._has_min = true;
- }
-
- /**
- * Sets the value of field 'minRGB'.
- *
- * @param minRGB
- * the value of field 'minRGB'.
- */
- public void setMinRGB(final java.lang.String minRGB)
- {
- this._minRGB = minRGB;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB
- * the value of field 'RGB'.
- */
- public void setRGB(final java.lang.String RGB)
- {
- this._RGB = RGB;
- }
-
- /**
- * Sets the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
- *
- * @param threshType
- * the value of field 'threshType'.
- */
- public void setThreshType(final java.lang.String threshType)
- {
- this._threshType = threshType;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = 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.binding.Colour
- */
- public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Colour) Unmarshaller.unmarshal(
- jalview.binding.Colour.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);
- }
+public class Colour implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+
+ /**
+ * loosely specified enumeration: NONE,ABOVE, or BELOW
+ */
+ private java.lang.String _threshType;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Colour() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAutoScale(
+ ) {
+ this._has_autoScale= false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel(
+ ) {
+ this._has_colourByLabel= false;
+ }
+
+ /**
+ */
+ public void deleteMax(
+ ) {
+ this._has_max= false;
+ }
+
+ /**
+ */
+ public void deleteMin(
+ ) {
+ this._has_min= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax(
+ ) {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin(
+ ) {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB(
+ ) {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB(
+ ) {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'. The field
+ * 'threshType' has the following description: loosely
+ * specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public java.lang.String getThreshType(
+ ) {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale(
+ ) {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel(
+ ) {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax(
+ ) {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin(
+ ) {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale the value of field 'autoScale'.
+ */
+ public void setAutoScale(
+ final boolean autoScale) {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(
+ final boolean colourByLabel) {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max the value of field 'max'.
+ */
+ public void setMax(
+ final float max) {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min the value of field 'min'.
+ */
+ public void setMin(
+ final float min) {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB the value of field 'minRGB'.
+ */
+ public void setMinRGB(
+ final java.lang.String minRGB) {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB the value of field 'RGB'.
+ */
+ public void setRGB(
+ final java.lang.String RGB) {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'. The field 'threshType'
+ * has the following description: loosely specified
+ * enumeration: NONE,ABOVE, or BELOW
+ *
+ * @param threshType the value of field 'threshType'.
+ */
+ public void setThreshType(
+ final java.lang.String threshType) {
+ this._threshType = threshType;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = 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.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Feature implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _begin.
- */
- private int _begin;
-
- /**
- * keeps track of state for field: _begin
- */
- private boolean _has_begin;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _status.
- */
- private java.lang.String _status;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Feature()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class Feature implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Feature() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteBegin(
+ ) {
+ this._has_begin= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin(
+ ) {
+ return this._begin;
+ }
+
+ /**
+ * 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 'end'.
+ *
+ * @return the value of field 'End'.
*/
- public void deleteBegin()
- {
- this._has_begin = false;
- }
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus(
+ ) {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin(
+ ) {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin the value of field 'begin'.
+ */
+ public void setBegin(
+ final int begin) {
+ this._begin = begin;
+ this._has_begin = 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 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(
+ final java.lang.String status) {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * 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.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return the value of field 'Begin'.
- */
- public int getBegin()
- {
- return this._begin;
- }
-
- /**
- * 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 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Returns the value of field 'status'.
- *
- * @return the value of field 'Status'.
- */
- public java.lang.String getStatus()
- {
- return this._status;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * Method hasBegin.
- *
- * @return true if at least one Begin has been added
- */
- public boolean hasBegin()
- {
- return this._has_begin;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * 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;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin
- * the value of field 'begin'.
- */
- public void setBegin(final int begin)
- {
- this._begin = begin;
- this._has_begin = 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 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'status'.
- *
- * @param status
- * the value of field 'status'.
- */
- public void setStatus(final java.lang.String status)
- {
- this._status = status;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * 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.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Feature.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class FeatureSettings implements java.io.Serializable
-{
+public class FeatureSettings implements java.io.Serializable {
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
- /**
- * Field _settingList.
- */
- private java.util.Vector _settingList;
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
- // ----------------/
- // - Constructors -/
- // ----------------/
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
- public FeatureSettings()
- {
- super();
- this._settingList = new java.util.Vector();
- }
- // -----------/
- // - Methods -/
- // -----------/
+ //----------------/
+ //- Constructors -/
+ //----------------/
- /**
- *
- *
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSetting(final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- this._settingList.addElement(vSetting);
- }
+ public FeatureSettings() {
+ super();
+ this._settingList = new java.util.Vector();
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSetting(final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- this._settingList.add(index, vSetting);
- }
- /**
- * Method enumerateSetting.
- *
- * @return an Enumeration over all jalview.binding.Setting elements
- */
- public java.util.Enumeration enumerateSetting()
- {
- return this._settingList.elements();
- }
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method getSetting.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Setting at the given index
- */
- public jalview.binding.Setting getSetting(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size())
- {
- throw new IndexOutOfBoundsException("getSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.addElement(vSetting);
}
- return (jalview.binding.Setting) _settingList.get(index);
- }
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.add(index, vSetting);
+ }
- /**
- * Method getSetting.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.binding.Setting[] getSetting()
- {
- jalview.binding.Setting[] array = new jalview.binding.Setting[0];
- return (jalview.binding.Setting[]) this._settingList.toArray(array);
- }
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.binding.Setting
+ * elements
+ */
+ public java.util.Enumeration enumerateSetting(
+ ) {
+ return this._settingList.elements();
+ }
- /**
- * Method getSettingCount.
- *
- * @return the size of this collection
- */
- public int getSettingCount()
- {
- return this._settingList.size();
- }
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Setting at the
+ * given index
+ */
+ public jalview.binding.Setting getSetting(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Setting) _settingList.get(index);
+ }
- /**
- * 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;
+ /**
+ * Method getSetting.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.binding.Setting[] getSetting(
+ ) {
+ jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+ return (jalview.binding.Setting[]) this._settingList.toArray(array);
}
- return true;
- }
- /**
- *
- *
- * @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);
- }
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount(
+ ) {
+ return this._settingList.size();
+ }
- /**
- *
- *
- * @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);
- }
+ /**
+ * 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;
+ }
- /**
+ /**
+ *
+ *
+ * @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 removeAllSetting()
- {
- this._settingList.clear();
- }
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- * Method removeSetting.
- *
- * @param vSetting
- * @return true if the object was removed from the collection.
- */
- public boolean removeSetting(final jalview.binding.Setting vSetting)
- {
- boolean removed = _settingList.remove(vSetting);
- return removed;
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * Method removeSettingAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Setting removeSettingAt(final int index)
- {
- java.lang.Object obj = this._settingList.remove(index);
- return (jalview.binding.Setting) obj;
- }
+ /**
+ */
+ public void removeAllSetting(
+ ) {
+ this._settingList.clear();
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSetting(final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size())
- {
- throw new IndexOutOfBoundsException("setSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(
+ final jalview.binding.Setting vSetting) {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
}
- this._settingList.set(index, vSetting);
- }
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Setting removeSettingAt(
+ final int index) {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.binding.Setting) obj;
+ }
- /**
- *
- *
- * @param vSettingArray
- */
- public void setSetting(final jalview.binding.Setting[] vSettingArray)
- {
- // -- copy array
- _settingList.clear();
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ this._settingList.set(index, vSetting);
+ }
- for (int i = 0; i < vSettingArray.length; i++)
- {
- this._settingList.add(vSettingArray[i]);
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(
+ final jalview.binding.Setting[] vSettingArray) {
+ //-- copy array
+ _settingList.clear();
+
+ for (int i = 0; i < vSettingArray.length; i++) {
+ this._settingList.add(vSettingArray[i]);
+ }
}
- }
- /**
- * 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.binding.FeatureSettings
- */
- public static jalview.binding.FeatureSettings unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
- jalview.binding.FeatureSettings.class, reader);
- }
+ /**
+ * 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.binding.FeatureSettings
+ */
+ public static jalview.binding.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Features extends Feature implements java.io.Serializable
+public class Features extends Feature
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Features()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
- // -----------/
- // - Methods -/
- // -----------/
+ public Features() {
+ super();
+ }
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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;
}
- return true;
- }
- /**
- *
- *
- * @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 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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Features.class, reader);
- }
+ /**
+ * 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.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JGroup implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _colour.
- */
- private java.lang.String _colour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _outlineColour.
- */
- private int _outlineColour;
-
- /**
- * keeps track of state for field: _outlineColour
- */
- private boolean _has_outlineColour;
-
- /**
- * Field _displayBoxes.
- */
- private boolean _displayBoxes;
-
- /**
- * keeps track of state for field: _displayBoxes
- */
- private boolean _has_displayBoxes;
-
- /**
- * Field _displayText.
- */
- private boolean _displayText;
-
- /**
- * keeps track of state for field: _displayText
- */
- private boolean _has_displayText;
-
- /**
- * Field _colourText.
- */
- private boolean _colourText;
-
- /**
- * keeps track of state for field: _colourText
- */
- private boolean _has_colourText;
-
- /**
- * Field _seqList.
- */
- private java.util.Vector _seqList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JGroup()
- {
- super();
- this._seqList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSeq(final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._seqList.addElement(new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSeq(final int index, final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._seqList.add(index, new java.lang.Integer(vSeq));
- }
-
- /**
- */
- public void deleteColourText()
- {
- this._has_colourText = false;
- }
-
- /**
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
-
- /**
- */
- public void deleteDisplayBoxes()
- {
- this._has_displayBoxes = false;
- }
-
- /**
- */
- public void deleteDisplayText()
- {
- this._has_displayText = false;
- }
-
- /**
- */
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- */
- public void deleteOutlineColour()
- {
- this._has_outlineColour = false;
- }
-
- /**
- */
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
-
- /**
- */
- public void deleteStart()
- {
- this._has_start = false;
- }
-
- /**
- * Method enumerateSeq.
- *
- * @return an Enumeration over all int elements
- */
- public java.util.Enumeration enumerateSeq()
- {
- return this._seqList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public java.lang.String getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean getColourText()
- {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean getDisplayBoxes()
- {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean getDisplayText()
- {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return the value of field 'OutlineColour'.
- */
- public int getOutlineColour()
- {
- return this._outlineColour;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Method getSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the int at the given index
- */
- public int getSeq(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size())
- {
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- return ((java.lang.Integer) _seqList.get(index)).intValue();
- }
-
- /**
- * Method getSeq.Returns the contents of the collection in an Array.
- *
- * @return this collection as an Array
- */
- public int[] getSeq()
- {
- int size = this._seqList.size();
- int[] array = new int[size];
- java.util.Iterator iter = _seqList.iterator();
- for (int index = 0; index < size; index++)
- {
- array[index] = ((java.lang.Integer) iter.next()).intValue();
- }
- return array;
- }
-
- /**
- * Method getSeqCount.
- *
- * @return the size of this collection
- */
- public int getSeqCount()
- {
- return this._seqList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart()
- {
- return this._start;
- }
-
- /**
- * Method hasColourText.
- *
- * @return true if at least one ColourText has been added
- */
- public boolean hasColourText()
- {
- return this._has_colourText;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasDisplayBoxes.
- *
- * @return true if at least one DisplayBoxes has been added
- */
- public boolean hasDisplayBoxes()
- {
- return this._has_displayBoxes;
- }
-
- /**
- * Method hasDisplayText.
- *
- * @return true if at least one DisplayText has been added
- */
- public boolean hasDisplayText()
- {
- return this._has_displayText;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * Method hasOutlineColour.
- *
- * @return true if at least one OutlineColour has been added
- */
- public boolean hasOutlineColour()
- {
- return this._has_outlineColour;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart()
- {
- return this._has_start;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean isColourText()
- {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean isDisplayBoxes()
- {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean isDisplayText()
- {
- return this._displayText;
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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 removeAllSeq()
- {
- this._seqList.clear();
- }
-
- /**
- * Method removeSeq.
- *
- * @param vSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeSeq(final int vSeq)
- {
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
- return removed;
- }
-
- /**
- * Method removeSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public int removeSeqAt(final int index)
- {
- java.lang.Object obj = this._seqList.remove(index);
- return ((java.lang.Integer) obj).intValue();
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final java.lang.String colour)
- {
- this._colour = colour;
- }
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText
- * the value of field 'colourText'.
- */
- public void setColourText(final boolean colourText)
- {
- this._colourText = colourText;
- this._has_colourText = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes
- * the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(final boolean displayBoxes)
- {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- }
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText
- * the value of field 'displayText'.
- */
- public void setDisplayText(final boolean displayText)
- {
- this._displayText = displayText;
- this._has_displayText = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour
- * the value of field 'outlineColour'.
- */
- public void setOutlineColour(final int outlineColour)
- {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSeq(final int index, final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size())
- {
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- this._seqList.set(index, new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param vSeqArray
- */
- public void setSeq(final int[] vSeqArray)
- {
- // -- copy array
- _seqList.clear();
-
- for (int i = 0; i < vSeqArray.length; i++)
- {
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start
- * the value of field 'start'.
- */
- public void setStart(final int start)
- {
- this._start = start;
- this._has_start = 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.binding.JGroup
- */
- public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(
- jalview.binding.JGroup.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);
- }
+public class JGroup implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JGroup() {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText(
+ ) {
+ this._has_colourText= false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes(
+ ) {
+ this._has_displayBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText(
+ ) {
+ this._has_displayText= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour(
+ ) {
+ this._has_outlineColour= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq(
+ ) {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour(
+ ) {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an
+ * Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq(
+ ) {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++) {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount(
+ ) {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText(
+ ) {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes(
+ ) {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText(
+ ) {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour(
+ ) {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllSeq(
+ ) {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(
+ final int vSeq) {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(
+ final int index) {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final java.lang.String colour) {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText the value of field 'colourText'.
+ */
+ public void setColourText(
+ final boolean colourText) {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(
+ final boolean displayBoxes) {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText the value of field 'displayText'.
+ */
+ public void setDisplayText(
+ final boolean displayText) {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(
+ final int outlineColour) {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(
+ final int[] vSeqArray) {
+ //-- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++) {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = 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.binding.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JSeq implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _id.
- */
- private int _id;
-
- /**
- * keeps track of state for field: _id
- */
- private boolean _has_id;
-
- /**
- * Field _featuresList.
- */
- private java.util.Vector _featuresList;
-
- /**
- * Field _pdbidsList.
- */
- private java.util.Vector _pdbidsList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JSeq()
- {
- super();
- this._featuresList = new java.util.Vector();
- this._pdbidsList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addFeatures(final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- this._featuresList.addElement(vFeatures);
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addFeatures(final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- this._featuresList.add(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbids(final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- this._pdbidsList.addElement(vPdbids);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbids(final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- this._pdbidsList.add(index, vPdbids);
- }
-
- /**
- */
- public void deleteColour()
- {
- this._has_colour = false;
- }
-
- /**
- */
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- */
- public void deleteId()
- {
- this._has_id = false;
- }
-
- /**
- */
- public void deleteStart()
- {
- this._has_start = false;
- }
-
- /**
- * Method enumerateFeatures.
- *
- * @return an Enumeration over all jalview.binding.Features elements
- */
- public java.util.Enumeration enumerateFeatures()
- {
- return this._featuresList.elements();
- }
-
- /**
- * Method enumeratePdbids.
- *
- * @return an Enumeration over all jalview.binding.Pdbids elements
- */
- public java.util.Enumeration enumeratePdbids()
- {
- return this._pdbidsList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Method getFeatures.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Features at the given index
- */
- public jalview.binding.Features getFeatures(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size())
- {
- throw new IndexOutOfBoundsException("getFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
- }
-
- return (jalview.binding.Features) _featuresList.get(index);
- }
-
- /**
- * Method getFeatures.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.binding.Features[] getFeatures()
- {
- jalview.binding.Features[] array = new jalview.binding.Features[0];
- return (jalview.binding.Features[]) this._featuresList.toArray(array);
- }
-
- /**
- * Method getFeaturesCount.
- *
- * @return the size of this collection
- */
- public int getFeaturesCount()
- {
- return this._featuresList.size();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public int getId()
- {
- return this._id;
- }
-
- /**
- * Method getPdbids.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Pdbids at the given index
- */
- public jalview.binding.Pdbids getPdbids(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size())
- {
- throw new IndexOutOfBoundsException("getPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
- }
-
- return (jalview.binding.Pdbids) _pdbidsList.get(index);
- }
-
- /**
- * Method getPdbids.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.binding.Pdbids[] getPdbids()
- {
- jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
- return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
- }
-
- /**
- * Method getPdbidsCount.
- *
- * @return the size of this collection
- */
- public int getPdbidsCount()
- {
- return this._pdbidsList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart()
- {
- return this._start;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour()
- {
- return this._has_colour;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * Method hasId.
- *
- * @return true if at least one Id has been added
- */
- public boolean hasId()
- {
- return this._has_id;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart()
- {
- return this._has_start;
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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 removeAllFeatures()
- {
- this._featuresList.clear();
- }
-
- /**
- */
- public void removeAllPdbids()
- {
- this._pdbidsList.clear();
- }
-
- /**
- * Method removeFeatures.
- *
- * @param vFeatures
- * @return true if the object was removed from the collection.
- */
- public boolean removeFeatures(final jalview.binding.Features vFeatures)
- {
- boolean removed = _featuresList.remove(vFeatures);
- return removed;
- }
-
- /**
- * Method removeFeaturesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Features removeFeaturesAt(final int index)
- {
- java.lang.Object obj = this._featuresList.remove(index);
- return (jalview.binding.Features) obj;
- }
-
- /**
- * Method removePdbids.
- *
- * @param vPdbids
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbids(final jalview.binding.Pdbids vPdbids)
- {
- boolean removed = _pdbidsList.remove(vPdbids);
- return removed;
- }
-
- /**
- * Method removePdbidsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Pdbids removePdbidsAt(final int index)
- {
- java.lang.Object obj = this._pdbidsList.remove(index);
- return (jalview.binding.Pdbids) obj;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final int colour)
- {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setFeatures(final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size())
- {
- throw new IndexOutOfBoundsException("setFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
- }
-
- this._featuresList.set(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vFeaturesArray
- */
- public void setFeatures(final jalview.binding.Features[] vFeaturesArray)
- {
- // -- copy array
- _featuresList.clear();
-
- for (int i = 0; i < vFeaturesArray.length; i++)
- {
- this._featuresList.add(vFeaturesArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final int id)
- {
- this._id = id;
- this._has_id = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setPdbids(final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size())
- {
- throw new IndexOutOfBoundsException("setPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
- }
-
- this._pdbidsList.set(index, vPdbids);
- }
-
- /**
- *
- *
- * @param vPdbidsArray
- */
- public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray)
- {
- // -- copy array
- _pdbidsList.clear();
-
- for (int i = 0; i < vPdbidsArray.length; i++)
- {
- this._pdbidsList.add(vPdbidsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start
- * the value of field 'start'.
- */
- public void setStart(final int start)
- {
- this._start = start;
- this._has_start = 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.binding.JSeq
- */
- public static jalview.binding.JSeq unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(
- jalview.binding.JSeq.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);
- }
+public class JSeq implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _id.
+ */
+ private int _id;
+
+ /**
+ * keeps track of state for field: _id
+ */
+ private boolean _has_id;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JSeq() {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ */
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteId(
+ ) {
+ this._has_id= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.binding.Features
+ * elements
+ */
+ public java.util.Enumeration enumerateFeatures(
+ ) {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.binding.Pdbids
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbids(
+ ) {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Features at the
+ * given index
+ */
+ public jalview.binding.Features getFeatures(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.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.binding.Features[] getFeatures(
+ ) {
+ jalview.binding.Features[] array = new jalview.binding.Features[0];
+ return (jalview.binding.Features[]) this._featuresList.toArray(array);
+ }
+
+ /**
+ * Method getFeaturesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFeaturesCount(
+ ) {
+ return this._featuresList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public int getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbids.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Pdbids at the given
+ * index
+ */
+ public jalview.binding.Pdbids getPdbids(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.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.binding.Pdbids[] getPdbids(
+ ) {
+ jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+ return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+ }
+
+ /**
+ * Method getPdbidsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbidsCount(
+ ) {
+ return this._pdbidsList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasId.
+ *
+ * @return true if at least one Id has been added
+ */
+ public boolean hasId(
+ ) {
+ return this._has_id;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllFeatures(
+ ) {
+ this._featuresList.clear();
+ }
+
+ /**
+ */
+ public void removeAllPdbids(
+ ) {
+ this._pdbidsList.clear();
+ }
+
+ /**
+ * Method removeFeatures.
+ *
+ * @param vFeatures
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFeatures(
+ final jalview.binding.Features vFeatures) {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Features removeFeaturesAt(
+ final int index) {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.binding.Features) obj;
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(
+ final jalview.binding.Pdbids vPdbids) {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Pdbids removePdbidsAt(
+ final int index) {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.binding.Pdbids) obj;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(
+ final jalview.binding.Features[] vFeaturesArray) {
+ //-- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++) {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final int id) {
+ this._id = id;
+ this._has_id = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(
+ final jalview.binding.Pdbids[] vPdbidsArray) {
+ //-- copy array
+ _pdbidsList.clear();
+
+ for (int i = 0; i < vPdbidsArray.length; i++) {
+ this._pdbidsList.add(vPdbidsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = 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.binding.JSeq
+ */
+ public static jalview.binding.JSeq unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModel implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _creationDate.
- */
- private java.util.Date _creationDate;
-
- /**
- * Field _version.
- */
- private java.lang.String _version;
-
- /**
- * Field _vamsasModel.
- */
- private jalview.binding.VamsasModel _vamsasModel;
-
- /**
- * Field _jalviewModelSequence.
- */
- private jalview.binding.JalviewModelSequence _jalviewModelSequence;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewModel()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'creationDate'.
- *
- * @return the value of field 'CreationDate'.
- */
- public java.util.Date getCreationDate()
- {
- return this._creationDate;
- }
-
- /**
- * Returns the value of field 'jalviewModelSequence'.
- *
- * @return the value of field 'JalviewModelSequence'.
- */
- public jalview.binding.JalviewModelSequence getJalviewModelSequence()
- {
- return this._jalviewModelSequence;
- }
-
- /**
- * Returns the value of field 'vamsasModel'.
- *
- * @return the value of field 'VamsasModel'.
- */
- public jalview.binding.VamsasModel getVamsasModel()
- {
- return this._vamsasModel;
- }
-
- /**
- * Returns the value of field 'version'.
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- }
-
- /**
- * 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;
+public class JalviewModel implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _creationDate.
+ */
+ private java.util.Date _creationDate;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _vamsasModel.
+ */
+ private jalview.binding.VamsasModel _vamsasModel;
+
+ /**
+ * Field _jalviewModelSequence.
+ */
+ private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModel() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'creationDate'.
+ *
+ * @return the value of field 'CreationDate'.
+ */
+ public java.util.Date getCreationDate(
+ ) {
+ return this._creationDate;
+ }
+
+ /**
+ * Returns the value of field 'jalviewModelSequence'.
+ *
+ * @return the value of field 'JalviewModelSequence'.
+ */
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence(
+ ) {
+ return this._jalviewModelSequence;
+ }
+
+ /**
+ * Returns the value of field 'vamsasModel'.
+ *
+ * @return the value of field 'VamsasModel'.
+ */
+ public jalview.binding.VamsasModel getVamsasModel(
+ ) {
+ return this._vamsasModel;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'creationDate'.
+ *
+ * @param creationDate the value of field 'creationDate'.
+ */
+ public void setCreationDate(
+ final java.util.Date creationDate) {
+ this._creationDate = creationDate;
+ }
+
+ /**
+ * Sets the value of field 'jalviewModelSequence'.
+ *
+ * @param jalviewModelSequence the value of field
+ * 'jalviewModelSequence'.
+ */
+ public void setJalviewModelSequence(
+ final jalview.binding.JalviewModelSequence jalviewModelSequence) {
+ this._jalviewModelSequence = jalviewModelSequence;
+ }
+
+ /**
+ * Sets the value of field 'vamsasModel'.
+ *
+ * @param vamsasModel the value of field 'vamsasModel'.
+ */
+ public void setVamsasModel(
+ final jalview.binding.VamsasModel vamsasModel) {
+ this._vamsasModel = vamsasModel;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * 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.binding.JalviewModel
+ */
+ public static jalview.binding.JalviewModel unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'creationDate'.
- *
- * @param creationDate
- * the value of field 'creationDate'.
- */
- public void setCreationDate(final java.util.Date creationDate)
- {
- this._creationDate = creationDate;
- }
-
- /**
- * Sets the value of field 'jalviewModelSequence'.
- *
- * @param jalviewModelSequence
- * the value of field 'jalviewModelSequence'.
- */
- public void setJalviewModelSequence(
- final jalview.binding.JalviewModelSequence jalviewModelSequence)
- {
- this._jalviewModelSequence = jalviewModelSequence;
- }
-
- /**
- * Sets the value of field 'vamsasModel'.
- *
- * @param vamsasModel
- * the value of field 'vamsasModel'.
- */
- public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel)
- {
- this._vamsasModel = vamsasModel;
- }
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version
- * the value of field 'version'.
- */
- public void setVersion(final java.lang.String version)
- {
- this._version = version;
- }
-
- /**
- * 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.binding.JalviewModel
- */
- public static jalview.binding.JalviewModel unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
- jalview.binding.JalviewModel.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequence implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _JSeqList.
- */
- private java.util.Vector _JSeqList;
-
- /**
- * Field _JGroupList.
- */
- private java.util.Vector _JGroupList;
-
- /**
- * Field _viewportList.
- */
- private java.util.Vector _viewportList;
-
- /**
- * Field _userColoursList.
- */
- private java.util.Vector _userColoursList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _featureSettings.
- */
- private jalview.binding.FeatureSettings _featureSettings;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewModelSequence()
- {
- super();
- this._JSeqList = new java.util.Vector();
- this._JGroupList = new java.util.Vector();
- this._viewportList = new java.util.Vector();
- this._userColoursList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJGroup(final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JGroupList.addElement(vJGroup);
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJGroup(final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JGroupList.add(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJSeq(final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JSeqList.addElement(vJSeq);
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JSeqList.add(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final int index, final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.add(index, vTree);
- }
-
- /**
- *
- *
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addUserColours(final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- this._userColoursList.addElement(vUserColours);
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addUserColours(final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- this._userColoursList.add(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addViewport(final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- this._viewportList.addElement(vViewport);
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addViewport(final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- this._viewportList.add(index, vViewport);
- }
-
- /**
- * Method enumerateJGroup.
- *
- * @return an Enumeration over all jalview.binding.JGroup elements
- */
- public java.util.Enumeration enumerateJGroup()
- {
- return this._JGroupList.elements();
- }
-
- /**
- * Method enumerateJSeq.
- *
- * @return an Enumeration over all jalview.binding.JSeq elements
- */
- public java.util.Enumeration enumerateJSeq()
- {
- return this._JSeqList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all jalview.binding.Tree elements
- */
- public java.util.Enumeration enumerateTree()
- {
- return this._treeList.elements();
- }
-
- /**
- * Method enumerateUserColours.
- *
- * @return an Enumeration over all jalview.binding.UserColours elements
- */
- public java.util.Enumeration enumerateUserColours()
- {
- return this._userColoursList.elements();
- }
-
- /**
- * Method enumerateViewport.
- *
- * @return an Enumeration over all jalview.binding.Viewport elements
- */
- public java.util.Enumeration enumerateViewport()
- {
- return this._viewportList.elements();
- }
-
- /**
- * Returns the value of field 'featureSettings'.
- *
- * @return the value of field 'FeatureSettings'.
- */
- public jalview.binding.FeatureSettings getFeatureSettings()
- {
- return this._featureSettings;
- }
-
- /**
- * Method getJGroup.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.JGroup at the given index
- */
- public jalview.binding.JGroup getJGroup(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size())
- {
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
- }
-
- return (jalview.binding.JGroup) _JGroupList.get(index);
- }
-
- /**
- * Method getJGroup.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.binding.JGroup[] getJGroup()
- {
- jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
- return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
- }
-
- /**
- * Method getJGroupCount.
- *
- * @return the size of this collection
- */
- public int getJGroupCount()
- {
- return this._JGroupList.size();
- }
-
- /**
- * Method getJSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.JSeq at the given index
- */
- public jalview.binding.JSeq getJSeq(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size())
- {
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- return (jalview.binding.JSeq) _JSeqList.get(index);
- }
-
- /**
- * Method getJSeq.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.binding.JSeq[] getJSeq()
- {
- jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
- return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
- }
-
- /**
- * Method getJSeqCount.
- *
- * @return the size of this collection
- */
- public int getJSeqCount()
- {
- return this._JSeqList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Tree at the given index
- */
- public jalview.binding.Tree getTree(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (jalview.binding.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.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.binding.Tree[] getTree()
- {
- jalview.binding.Tree[] array = new jalview.binding.Tree[0];
- return (jalview.binding.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount()
- {
- return this._treeList.size();
- }
-
- /**
- * Method getUserColours.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.UserColours at the given index
- */
- public jalview.binding.UserColours getUserColours(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size())
- {
- throw new IndexOutOfBoundsException("getUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
- }
-
- return (jalview.binding.UserColours) _userColoursList.get(index);
- }
-
- /**
- * Method getUserColours.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.binding.UserColours[] getUserColours()
- {
- jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
- return (jalview.binding.UserColours[]) this._userColoursList
- .toArray(array);
- }
-
- /**
- * Method getUserColoursCount.
- *
- * @return the size of this collection
- */
- public int getUserColoursCount()
- {
- return this._userColoursList.size();
- }
-
- /**
- * Method getViewport.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Viewport at the given index
- */
- public jalview.binding.Viewport getViewport(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size())
- {
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
- }
-
- return (jalview.binding.Viewport) _viewportList.get(index);
- }
-
- /**
- * Method getViewport.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.binding.Viewport[] getViewport()
- {
- jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
- return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
- }
-
- /**
- * Method getViewportCount.
- *
- * @return the size of this collection
- */
- public int getViewportCount()
- {
- return this._viewportList.size();
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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 removeAllJGroup()
- {
- this._JGroupList.clear();
- }
-
- /**
- */
- public void removeAllJSeq()
- {
- this._JSeqList.clear();
- }
-
- /**
- */
- public void removeAllTree()
- {
- this._treeList.clear();
- }
-
- /**
- */
- public void removeAllUserColours()
- {
- this._userColoursList.clear();
- }
-
- /**
- */
- public void removeAllViewport()
- {
- this._viewportList.clear();
- }
-
- /**
- * Method removeJGroup.
- *
- * @param vJGroup
- * @return true if the object was removed from the collection.
- */
- public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
- {
- boolean removed = _JGroupList.remove(vJGroup);
- return removed;
- }
-
- /**
- * Method removeJGroupAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JGroup removeJGroupAt(final int index)
- {
- java.lang.Object obj = this._JGroupList.remove(index);
- return (jalview.binding.JGroup) obj;
- }
-
- /**
- * Method removeJSeq.
- *
- * @param vJSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
- {
- boolean removed = _JSeqList.remove(vJSeq);
- return removed;
- }
-
- /**
- * Method removeJSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JSeq removeJSeqAt(final int index)
- {
- java.lang.Object obj = this._JSeqList.remove(index);
- return (jalview.binding.JSeq) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(final jalview.binding.Tree vTree)
- {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Tree removeTreeAt(final int index)
- {
- java.lang.Object obj = this._treeList.remove(index);
- return (jalview.binding.Tree) obj;
- }
-
- /**
- * Method removeUserColours.
- *
- * @param vUserColours
- * @return true if the object was removed from the collection.
- */
- public boolean removeUserColours(
- final jalview.binding.UserColours vUserColours)
- {
- boolean removed = _userColoursList.remove(vUserColours);
- return removed;
- }
-
- /**
- * Method removeUserColoursAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.UserColours removeUserColoursAt(final int index)
- {
- java.lang.Object obj = this._userColoursList.remove(index);
- return (jalview.binding.UserColours) obj;
- }
-
- /**
- * Method removeViewport.
- *
- * @param vViewport
- * @return true if the object was removed from the collection.
- */
- public boolean removeViewport(final jalview.binding.Viewport vViewport)
- {
- boolean removed = _viewportList.remove(vViewport);
- return removed;
- }
-
- /**
- * Method removeViewportAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Viewport removeViewportAt(final int index)
- {
- java.lang.Object obj = this._viewportList.remove(index);
- return (jalview.binding.Viewport) obj;
- }
-
- /**
- * Sets the value of field 'featureSettings'.
- *
- * @param featureSettings
- * the value of field 'featureSettings'.
- */
- public void setFeatureSettings(
- final jalview.binding.FeatureSettings featureSettings)
- {
- this._featureSettings = featureSettings;
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setJGroup(final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size())
- {
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
- }
-
- this._JGroupList.set(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJGroupArray
- */
- public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
- {
- // -- copy array
- _JGroupList.clear();
-
- for (int i = 0; i < vJGroupArray.length; i++)
- {
- this._JGroupList.add(vJGroupArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size())
- {
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
- }
-
- this._JSeqList.set(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vJSeqArray
- */
- public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
- {
- // -- copy array
- _JSeqList.clear();
-
- for (int i = 0; i < vJSeqArray.length; i++)
- {
- this._JSeqList.add(vJSeqArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setTree(final int index, final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(final jalview.binding.Tree[] vTreeArray)
- {
- // -- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++)
- {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setUserColours(final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size())
- {
- throw new IndexOutOfBoundsException("setUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
- }
-
- this._userColoursList.set(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vUserColoursArray
- */
- public void setUserColours(
- final jalview.binding.UserColours[] vUserColoursArray)
- {
- // -- copy array
- _userColoursList.clear();
-
- for (int i = 0; i < vUserColoursArray.length; i++)
- {
- this._userColoursList.add(vUserColoursArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setViewport(final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size())
- {
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
- }
-
- this._viewportList.set(index, vViewport);
- }
-
- /**
- *
- *
- * @param vViewportArray
- */
- public void setViewport(final jalview.binding.Viewport[] vViewportArray)
- {
- // -- copy array
- _viewportList.clear();
-
- for (int i = 0; i < vViewportArray.length; i++)
- {
- this._viewportList.add(vViewportArray[i]);
- }
- }
-
- /**
- * 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.binding.JalviewModelSequence
- */
- public static jalview.binding.JalviewModelSequence unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
- jalview.binding.JalviewModelSequence.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);
- }
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.binding.FeatureSettings _featureSettings;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModelSequence() {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.binding.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup(
+ ) {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.binding.JSeq elements
+ */
+ public java.util.Enumeration enumerateJSeq(
+ ) {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.binding.Tree elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.binding.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours(
+ ) {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.binding.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport(
+ ) {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.binding.FeatureSettings getFeatureSettings(
+ ) {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JGroup at the given
+ * index
+ */
+ public jalview.binding.JGroup getJGroup(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.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.binding.JGroup[] getJGroup(
+ ) {
+ jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+ return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount(
+ ) {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JSeq at the given
+ * index
+ */
+ public jalview.binding.JSeq getJSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.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.binding.JSeq[] getJSeq(
+ ) {
+ jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+ return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount(
+ ) {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Tree at the given
+ * index
+ */
+ public jalview.binding.Tree getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.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.binding.Tree[] getTree(
+ ) {
+ jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+ return (jalview.binding.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.UserColours at the
+ * given index
+ */
+ public jalview.binding.UserColours getUserColours(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.UserColours) _userColoursList.get(index);
+ }
+
+ /**
+ * Method getUserColours.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.binding.UserColours[] getUserColours(
+ ) {
+ jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+ return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount(
+ ) {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Viewport at the
+ * given index
+ */
+ public jalview.binding.Viewport getViewport(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Viewport) _viewportList.get(index);
+ }
+
+ /**
+ * Method getViewport.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.binding.Viewport[] getViewport(
+ ) {
+ jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+ return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount(
+ ) {
+ return this._viewportList.size();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllJGroup(
+ ) {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq(
+ ) {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours(
+ ) {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport(
+ ) {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.binding.JGroup vJGroup) {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JGroup removeJGroupAt(
+ final int index) {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.binding.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(
+ final jalview.binding.JSeq vJSeq) {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JSeq removeJSeqAt(
+ final int index) {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.binding.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final jalview.binding.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Tree removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.binding.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.binding.UserColours vUserColours) {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.UserColours removeUserColoursAt(
+ final int index) {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.binding.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.binding.Viewport vViewport) {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Viewport removeViewportAt(
+ final int index) {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.binding.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.binding.FeatureSettings featureSettings) {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.binding.JGroup[] vJGroupArray) {
+ //-- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++) {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(
+ final jalview.binding.JSeq[] vJSeqArray) {
+ //-- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++) {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final jalview.binding.Tree[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.binding.UserColours[] vUserColoursArray) {
+ //-- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++) {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.binding.Viewport[] vViewportArray) {
+ //-- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++) {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * 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.binding.JalviewModelSequence
+ */
+ public static jalview.binding.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewUserColours implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _schemeName.
- */
- private java.lang.String _schemeName;
-
- /**
- * Jalview colour scheme document version.
- *
- */
- private java.lang.String _version;
-
- /**
- * Field _colourList.
- */
- private java.util.Vector _colourList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewUserColours()
- {
- super();
- this._colourList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addColour(final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- this._colourList.addElement(vColour);
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addColour(final int index, final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- this._colourList.add(index, vColour);
- }
-
- /**
- * Method enumerateColour.
- *
- * @return an Enumeration over all Colour elements
- */
- public java.util.Enumeration enumerateColour()
- {
- return this._colourList.elements();
- }
-
- /**
- * Method getColour.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the Colour at the given index
- */
- public Colour getColour(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size())
- {
- throw new IndexOutOfBoundsException("getColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+public class JalviewUserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewUserColours() {
+ super();
+ this._colourList = new java.util.Vector();
}
- return (Colour) _colourList.get(index);
- }
-
- /**
- * Method getColour.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 Colour[] getColour()
- {
- Colour[] array = new Colour[0];
- return (Colour[]) this._colourList.toArray(array);
- }
-
- /**
- * Method getColourCount.
- *
- * @return the size of this collection
- */
- public int getColourCount()
- {
- return this._colourList.size();
- }
-
- /**
- * Returns the value of field 'schemeName'.
- *
- * @return the value of field 'SchemeName'.
- */
- public java.lang.String getSchemeName()
- {
- return this._schemeName;
- }
-
- /**
- * Returns the value of field 'version'. The field 'version' has the following
- * description: Jalview colour scheme document version.
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- }
-
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour(
+ ) {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ return (Colour) _colourList.get(index);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
+
+ /**
+ * Method getColour.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 Colour[] getColour(
+ ) {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
*/
- public void removeAllColour()
- {
- this._colourList.clear();
- }
-
- /**
- * Method removeColour.
- *
- * @param vColour
- * @return true if the object was removed from the collection.
- */
- public boolean removeColour(final Colour vColour)
- {
- boolean removed = _colourList.remove(vColour);
- return removed;
- }
-
- /**
- * Method removeColourAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Colour removeColourAt(final int index)
- {
- java.lang.Object obj = this._colourList.remove(index);
- return (Colour) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setColour(final int index, final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size())
- {
- throw new IndexOutOfBoundsException("setColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ public int getColourCount(
+ ) {
+ return this._colourList.size();
}
- this._colourList.set(index, vColour);
- }
-
- /**
- *
- *
- * @param vColourArray
- */
- public void setColour(final Colour[] vColourArray)
- {
- // -- copy array
- _colourList.clear();
-
- for (int i = 0; i < vColourArray.length; i++)
- {
- this._colourList.add(vColourArray[i]);
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName(
+ ) {
+ return this._schemeName;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Jalview colour scheme
+ * document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllColour(
+ ) {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(
+ final Colour vColour) {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(
+ final int index) {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(
+ final Colour[] vColourArray) {
+ //-- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++) {
+ this._colourList.add(vColourArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName the value of field 'schemeName'.
+ */
+ public void setSchemeName(
+ final java.lang.String schemeName) {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Jalview colour scheme document
+ * version.
+ *
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * 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.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.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);
}
- }
-
- /**
- * Sets the value of field 'schemeName'.
- *
- * @param schemeName
- * the value of field 'schemeName'.
- */
- public void setSchemeName(final java.lang.String schemeName)
- {
- this._schemeName = schemeName;
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has the following
- * description: Jalview colour scheme document version.
- *
- *
- * @param version
- * the value of field 'version'.
- */
- public void setVersion(final java.lang.String version)
- {
- this._version = version;
- }
-
- /**
- * 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.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.JalviewUserColours.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbentry implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _items.
- */
- private java.util.Vector _items;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Pdbentry()
- {
- super();
- this._items = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- this._items.addElement(vPdbentryItem);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbentryItem(final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- this._items.add(index, vPdbentryItem);
- }
-
- /**
- * Method enumeratePdbentryItem.
- *
- * @return an Enumeration over all jalview.binding.PdbentryItem elements
- */
- public java.util.Enumeration enumeratePdbentryItem()
- {
- return this._items.elements();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Method getPdbentryItem.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.PdbentryItem at the given index
- */
- public jalview.binding.PdbentryItem getPdbentryItem(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._items.size())
- {
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+public class Pdbentry implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbentry() {
+ super();
+ this._items = new java.util.Vector();
}
- return (jalview.binding.PdbentryItem) _items.get(index);
- }
-
- /**
- * Method getPdbentryItem.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.binding.PdbentryItem[] getPdbentryItem()
- {
- jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
- return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
- }
-
- /**
- * Method getPdbentryItemCount.
- *
- * @return the size of this collection
- */
- public int getPdbentryItemCount()
- {
- return this._items.size();
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all jalview.binding.PdbentryItem
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem(
+ ) {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.PdbentryItem at the
+ * given index
+ */
+ public jalview.binding.PdbentryItem getPdbentryItem(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ return (jalview.binding.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.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 void removeAllPdbentryItem()
- {
- this._items.clear();
- }
-
- /**
- * Method removePdbentryItem.
- *
- * @param vPdbentryItem
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem)
- {
- boolean removed = _items.remove(vPdbentryItem);
- return removed;
- }
-
- /**
- * Method removePdbentryItemAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
- {
- java.lang.Object obj = this._items.remove(index);
- return (jalview.binding.PdbentryItem) obj;
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setPdbentryItem(final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._items.size())
- {
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+ public jalview.binding.PdbentryItem[] getPdbentryItem(
+ ) {
+ jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+ return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
}
- this._items.set(index, vPdbentryItem);
- }
-
- /**
- *
- *
- * @param vPdbentryItemArray
- */
- public void setPdbentryItem(
- final jalview.binding.PdbentryItem[] vPdbentryItemArray)
- {
- // -- copy array
- _items.clear();
-
- for (int i = 0; i < vPdbentryItemArray.length; i++)
- {
- this._items.add(vPdbentryItemArray[i]);
+ /**
+ * Method getPdbentryItemCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbentryItemCount(
+ ) {
+ return this._items.size();
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllPdbentryItem(
+ ) {
+ this._items.clear();
+ }
+
+ /**
+ * Method removePdbentryItem.
+ *
+ * @param vPdbentryItem
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem) {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.PdbentryItem removePdbentryItemAt(
+ final int index) {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.binding.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
+ //-- copy array
+ _items.clear();
+
+ for (int i = 0; i < vPdbentryItemArray.length; i++) {
+ this._items.add(vPdbentryItemArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * 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.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.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);
}
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * 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.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbentry.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
/**
*
* @version $Revision$ $Date$
*/
-public class PdbentryItem implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public PdbentryItem()
- {
- super();
- this._propertyList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addProperty(final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addProperty(final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all jalview.binding.Property elements
- */
- public java.util.Enumeration enumerateProperty()
- {
- return this._propertyList.elements();
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Property at the given index
- */
- public jalview.binding.Property getProperty(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size())
- {
- throw new IndexOutOfBoundsException("getProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+public class PdbentryItem implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public PdbentryItem() {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.binding.Property
+ * elements
+ */
+ public java.util.Enumeration enumerateProperty(
+ ) {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Property at the
+ * given index
+ */
+ public jalview.binding.Property getProperty(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.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.binding.Property[] getProperty(
+ ) {
+ jalview.binding.Property[] array = new jalview.binding.Property[0];
+ return (jalview.binding.Property[]) this._propertyList.toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount(
+ ) {
+ return this._propertyList.size();
}
- return (jalview.binding.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.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.binding.Property[] getProperty()
- {
- jalview.binding.Property[] array = new jalview.binding.Property[0];
- return (jalview.binding.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount()
- {
- return this._propertyList.size();
- }
-
- /**
+ /**
*/
- public void removeAllProperty()
- {
- this._propertyList.clear();
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(final jalview.binding.Property vProperty)
- {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Property removePropertyAt(final int index)
- {
- java.lang.Object obj = this._propertyList.remove(index);
- return (jalview.binding.Property) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setProperty(final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size())
- {
- throw new IndexOutOfBoundsException("setProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ public void removeAllProperty(
+ ) {
+ this._propertyList.clear();
}
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(final jalview.binding.Property[] vPropertyArray)
- {
- // -- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++)
- {
- this._propertyList.add(vPropertyArray[i]);
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.binding.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Property removePropertyAt(
+ final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.binding.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.binding.Property[] vPropertyArray) {
+ //-- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
}
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbids extends Pdbentry implements java.io.Serializable
+public class Pdbids extends Pdbentry
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Pdbids()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
- // -----------/
- // - Methods -/
- // -----------/
+ public Pdbids() {
+ super();
+ }
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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;
}
- return true;
- }
- /**
- *
- *
- * @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 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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbids.class, reader);
- }
+ /**
+ * 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.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Property implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Property()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue()
- {
- return this._value;
- }
-
- /**
- * 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;
+public class Property implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Property() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final java.lang.String value) {
+ this._value = value;
+ }
+
+ /**
+ * 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.binding.Property
+ */
+ public static jalview.binding.Property unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value
- * the value of field 'value'.
- */
- public void setValue(final java.lang.String value)
- {
- this._value = value;
- }
-
- /**
- * 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.binding.Property
- */
- public static jalview.binding.Property unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Property) Unmarshaller.unmarshal(
- jalview.binding.Property.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Sequence extends SequenceType implements java.io.Serializable
+public class Sequence extends SequenceType
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Sequence()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
- // -----------/
- // - Methods -/
- // -----------/
+ public Sequence() {
+ super();
+ }
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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;
}
- return true;
- }
- /**
- *
- *
- * @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 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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.Sequence.class, reader);
- }
+ /**
+ * 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.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSet implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _gapChar.
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned.
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
- * Field _sequenceList.
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList.
- */
- private java.util.Vector _annotationList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceSet()
- {
- super();
- this._sequenceList = new java.util.Vector();
- this._annotationList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotation(final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationList.addElement(vAnnotation);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotation(final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationList.add(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequence(final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceList.addElement(vSequence);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequence(final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceList.add(index, vSequence);
- }
-
- /**
- */
- public void deleteAligned()
- {
- this._has_aligned = false;
- }
-
- /**
- * Method enumerateAnnotation.
- *
- * @return an Enumeration over all jalview.binding.Annotation elements
- */
- public java.util.Enumeration enumerateAnnotation()
- {
- return this._annotationList.elements();
- }
-
- /**
- * Method enumerateSequence.
- *
- * @return an Enumeration over all jalview.binding.Sequence elements
- */
- public java.util.Enumeration enumerateSequence()
- {
- return this._sequenceList.elements();
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean getAligned()
- {
- return this._aligned;
- }
-
- /**
- * Method getAnnotation.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Annotation at the given index
- */
- public jalview.binding.Annotation getAnnotation(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size())
- {
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
- }
-
- return (jalview.binding.Annotation) _annotationList.get(index);
- }
-
- /**
- * Method getAnnotation.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.binding.Annotation[] getAnnotation()
- {
- jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
- return (jalview.binding.Annotation[]) this._annotationList
- .toArray(array);
- }
-
- /**
- * Method getAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationCount()
- {
- return this._annotationList.size();
- }
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return the value of field 'GapChar'.
- */
- public java.lang.String getGapChar()
- {
- return this._gapChar;
- }
-
- /**
- * Method getSequence.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Sequence at the given index
- */
- public jalview.binding.Sequence getSequence(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size())
- {
- throw new IndexOutOfBoundsException("getSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
- }
-
- return (jalview.binding.Sequence) _sequenceList.get(index);
- }
-
- /**
- * Method getSequence.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.binding.Sequence[] getSequence()
- {
- jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
- return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
- }
-
- /**
- * Method getSequenceCount.
- *
- * @return the size of this collection
- */
- public int getSequenceCount()
- {
- return this._sequenceList.size();
- }
-
- /**
- * Method hasAligned.
- *
- * @return true if at least one Aligned has been added
- */
- public boolean hasAligned()
- {
- return this._has_aligned;
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean isAligned()
- {
- return this._aligned;
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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 removeAllAnnotation()
- {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence()
- {
- this._sequenceList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.binding.Annotation vAnnotation)
- {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Annotation removeAnnotationAt(final int index)
- {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.binding.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(final jalview.binding.Sequence vSequence)
- {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Sequence removeSequenceAt(final int index)
- {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.binding.Sequence) obj;
- }
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned
- * the value of field 'aligned'.
- */
- public void setAligned(final boolean aligned)
- {
- this._aligned = aligned;
- this._has_aligned = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAnnotation(final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size())
- {
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
- }
-
- this._annotationList.set(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vAnnotationArray
- */
- public void setAnnotation(
- final jalview.binding.Annotation[] vAnnotationArray)
- {
- // -- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++)
- {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar
- * the value of field 'gapChar'.
- */
- public void setGapChar(final java.lang.String gapChar)
- {
- this._gapChar = gapChar;
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequence(final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size())
- {
- throw new IndexOutOfBoundsException("setSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
- }
-
- this._sequenceList.set(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceArray
- */
- public void setSequence(final jalview.binding.Sequence[] vSequenceArray)
- {
- // -- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++)
- {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- * 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.binding.SequenceSet
- */
- public static jalview.binding.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
- jalview.binding.SequenceSet.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);
- }
+public class SequenceSet implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned.
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet() {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ */
+ public void deleteAligned(
+ ) {
+ this._has_aligned= false;
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.binding.Annotation
+ * elements
+ */
+ public java.util.Enumeration enumerateAnnotation(
+ ) {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.binding.Sequence
+ * elements
+ */
+ public java.util.Enumeration enumerateSequence(
+ ) {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean getAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Annotation at the
+ * given index
+ */
+ public jalview.binding.Annotation getAnnotation(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Annotation) _annotationList.get(index);
+ }
+
+ /**
+ * Method getAnnotation.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.binding.Annotation[] getAnnotation(
+ ) {
+ jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+ return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationCount(
+ ) {
+ return this._annotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar(
+ ) {
+ return this._gapChar;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Sequence at the
+ * given index
+ */
+ public jalview.binding.Sequence getSequence(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Sequence) _sequenceList.get(index);
+ }
+
+ /**
+ * Method getSequence.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.binding.Sequence[] getSequence(
+ ) {
+ jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+ return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount(
+ ) {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method hasAligned.
+ *
+ * @return true if at least one Aligned has been added
+ */
+ public boolean hasAligned(
+ ) {
+ return this._has_aligned;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean isAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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 removeAllAnnotation(
+ ) {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence(
+ ) {
+ this._sequenceList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.binding.Annotation vAnnotation) {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Annotation removeAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.binding.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.binding.Sequence vSequence) {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Sequence removeSequenceAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.binding.Sequence) obj;
+ }
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(
+ final boolean aligned) {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ this._annotationList.set(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationArray
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation[] vAnnotationArray) {
+ //-- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++) {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar the value of field 'gapChar'.
+ */
+ public void setGapChar(
+ final java.lang.String gapChar) {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(
+ final jalview.binding.Sequence[] vSequenceArray) {
+ //-- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++) {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ * 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.binding.SequenceSet
+ */
+ public static jalview.binding.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceType implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _sequence.
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceType()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * 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 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public java.lang.String getSequence()
- {
- return this._sequence;
- }
-
- /**
- * 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;
+public class SequenceType implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceType() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence(
+ ) {
+ return this._sequence;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * 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 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence the value of field 'sequence'.
+ */
+ public void setSequence(
+ final java.lang.String sequence) {
+ this._sequence = sequence;
+ }
+
+ /**
+ * 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.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * 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 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence
- * the value of field 'sequence'.
- */
- public void setSequence(final java.lang.String sequence)
- {
- this._sequence = sequence;
- }
-
- /**
- * 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.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.SequenceType.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Setting implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _display.
- */
- private boolean _display;
-
- /**
- * keeps track of state for field: _display
- */
- private boolean _has_display;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Setting()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class Setting implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Setting() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteDisplay(
+ ) {
+ this._has_display= false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
*/
- public void deleteColour()
- {
- this._has_colour = false;
- }
+ public boolean getDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay(
+ ) {
+ return this._has_display;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display the value of field 'display'.
+ */
+ public void setDisplay(
+ final boolean display) {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * 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.binding.Setting
+ */
+ public static jalview.binding.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteDisplay()
- {
- this._has_display = false;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean getDisplay()
- {
- return this._display;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour()
- {
- return this._has_colour;
- }
-
- /**
- * Method hasDisplay.
- *
- * @return true if at least one Display has been added
- */
- public boolean hasDisplay()
- {
- return this._has_display;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean isDisplay()
- {
- return this._display;
- }
-
- /**
- * 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;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final int colour)
- {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'display'.
- *
- * @param display
- * the value of field 'display'.
- */
- public void setDisplay(final boolean display)
- {
- this._display = display;
- this._has_display = true;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * 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.binding.Setting
- */
- public static jalview.binding.Setting unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Setting) Unmarshaller.unmarshal(
- jalview.binding.Setting.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Tree implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _showBootstrap.
- */
- private boolean _showBootstrap;
-
- /**
- * keeps track of state for field: _showBootstrap
- */
- private boolean _has_showBootstrap;
-
- /**
- * Field _showDistances.
- */
- private boolean _showDistances;
-
- /**
- * keeps track of state for field: _showDistances
- */
- private boolean _has_showDistances;
-
- /**
- * Field _markUnlinked.
- */
- private boolean _markUnlinked;
-
- /**
- * keeps track of state for field: _markUnlinked
- */
- private boolean _has_markUnlinked;
-
- /**
- * Field _fitToWindow.
- */
- private boolean _fitToWindow;
-
- /**
- * keeps track of state for field: _fitToWindow
- */
- private boolean _has_fitToWindow;
-
- /**
- * Field _currentTree.
- */
- private boolean _currentTree;
-
- /**
- * keeps track of state for field: _currentTree
- */
- private boolean _has_currentTree;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newick.
- */
- private java.lang.String _newick;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Tree()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteCurrentTree()
- {
- this._has_currentTree = false;
- }
-
- /**
- */
- public void deleteFitToWindow()
- {
- this._has_fitToWindow = false;
- }
-
- /**
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
-
- /**
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
-
- /**
- */
- public void deleteMarkUnlinked()
- {
- this._has_markUnlinked = false;
- }
-
- /**
- */
- public void deleteShowBootstrap()
- {
- this._has_showBootstrap = false;
- }
-
- /**
- */
- public void deleteShowDistances()
- {
- this._has_showDistances = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean getCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean getFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean getMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return the value of field 'Newick'.
- */
- public java.lang.String getNewick()
- {
- return this._newick;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean getShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean getShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasCurrentTree.
- *
- * @return true if at least one CurrentTree has been added
- */
- public boolean hasCurrentTree()
- {
- return this._has_currentTree;
- }
-
- /**
- * Method hasFitToWindow.
- *
- * @return true if at least one FitToWindow has been added
- */
- public boolean hasFitToWindow()
- {
- return this._has_fitToWindow;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasMarkUnlinked.
- *
- * @return true if at least one MarkUnlinked has been added
- */
- public boolean hasMarkUnlinked()
- {
- return this._has_markUnlinked;
- }
-
- /**
- * Method hasShowBootstrap.
- *
- * @return true if at least one ShowBootstrap has been added
- */
- public boolean hasShowBootstrap()
- {
- return this._has_showBootstrap;
- }
-
- /**
- * Method hasShowDistances.
- *
- * @return true if at least one ShowDistances has been added
- */
- public boolean hasShowDistances()
- {
- return this._has_showDistances;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean isCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean isFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean isMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean isShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean isShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'currentTree'.
- *
- * @param currentTree
- * the value of field 'currentTree'.
- */
- public void setCurrentTree(final boolean currentTree)
- {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- }
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow
- * the value of field 'fitToWindow'.
- */
- public void setFitToWindow(final boolean fitToWindow)
- {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked
- * the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(final boolean markUnlinked)
- {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- }
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick
- * the value of field 'newick'.
- */
- public void setNewick(final java.lang.String newick)
- {
- this._newick = newick;
- }
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap
- * the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(final boolean showBootstrap)
- {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- }
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances
- * the value of field 'showDistances'.
- */
- public void setShowDistances(final boolean showDistances)
- {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = 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.binding.Tree
- */
- public static jalview.binding.Tree unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Tree) Unmarshaller.unmarshal(
- jalview.binding.Tree.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);
- }
+public class Tree implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteCurrentTree(
+ ) {
+ this._has_currentTree= false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow(
+ ) {
+ this._has_fitToWindow= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked(
+ ) {
+ this._has_markUnlinked= false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap(
+ ) {
+ this._has_showBootstrap= false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances(
+ ) {
+ this._has_showDistances= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick(
+ ) {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree(
+ ) {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow(
+ ) {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked(
+ ) {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap(
+ ) {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances(
+ ) {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree the value of field 'currentTree'.
+ */
+ public void setCurrentTree(
+ final boolean currentTree) {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(
+ final boolean fitToWindow) {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(
+ final boolean markUnlinked) {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick the value of field 'newick'.
+ */
+ public void setNewick(
+ final java.lang.String newick) {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(
+ final boolean showBootstrap) {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances the value of field 'showDistances'.
+ */
+ public void setShowDistances(
+ final boolean showDistances) {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = 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.binding.Tree
+ */
+ public static jalview.binding.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColourScheme extends JalviewUserColours implements
- java.io.Serializable
+public class UserColourScheme extends JalviewUserColours
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public UserColourScheme()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
- // -----------/
- // - Methods -/
- // -----------/
+ public UserColourScheme() {
+ super();
+ }
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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;
}
- return true;
- }
- /**
- *
- *
- * @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 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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColourScheme.class, reader);
- }
+ /**
+ * 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.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColours implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _userColourScheme.
- */
- private jalview.binding.UserColourScheme _userColourScheme;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public UserColours()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * 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 'userColourScheme'.
- *
- * @return the value of field 'UserColourScheme'.
- */
- public jalview.binding.UserColourScheme getUserColourScheme()
- {
- return this._userColourScheme;
- }
-
- /**
- * 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;
+public class UserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _userColourScheme.
+ */
+ private jalview.binding.UserColourScheme _userColourScheme;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public UserColours() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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 'userColourScheme'.
+ *
+ * @return the value of field 'UserColourScheme'.
+ */
+ public jalview.binding.UserColourScheme getUserColourScheme(
+ ) {
+ return this._userColourScheme;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * 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 'userColourScheme'.
+ *
+ * @param userColourScheme the value of field 'userColourScheme'
+ */
+ public void setUserColourScheme(
+ final jalview.binding.UserColourScheme userColourScheme) {
+ this._userColourScheme = userColourScheme;
+ }
+
+ /**
+ * 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.binding.UserColours
+ */
+ public static jalview.binding.UserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * 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 'userColourScheme'.
- *
- * @param userColourScheme
- * the value of field 'userColourScheme'
- */
- public void setUserColourScheme(
- final jalview.binding.UserColourScheme userColourScheme)
- {
- this._userColourScheme = userColourScheme;
- }
-
- /**
- * 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.binding.UserColours
- */
- public static jalview.binding.UserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColours.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);
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VAMSAS implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _alignmentList.
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList.
- */
- private java.util.Vector _sequenceSetList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public VAMSAS()
- {
- super();
- this._alignmentList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- this._sequenceSetList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlignment(final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alignmentList.addElement(vAlignment);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlignment(final int index, final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alignmentList.add(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSet(final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetList.addElement(vSequenceSet);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetList.add(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final int index, final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.add(index, vTree);
- }
-
- /**
- * Method enumerateAlignment.
- *
- * @return an Enumeration over all Alignment elements
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return this._alignmentList.elements();
- }
-
- /**
- * Method enumerateSequenceSet.
- *
- * @return an Enumeration over all SequenceSet elements
- */
- public java.util.Enumeration enumerateSequenceSet()
- {
- return this._sequenceSetList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateTree()
- {
- return this._treeList.elements();
- }
-
- /**
- * Method getAlignment.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the Alignment at the given index
- */
- public Alignment getAlignment(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size())
- {
- throw new IndexOutOfBoundsException("getAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
- }
-
- return (Alignment) _alignmentList.get(index);
- }
-
- /**
- * Method getAlignment.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 Alignment[] getAlignment()
- {
- Alignment[] array = new Alignment[0];
- return (Alignment[]) this._alignmentList.toArray(array);
- }
-
- /**
- * Method getAlignmentCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentCount()
- {
- return this._alignmentList.size();
- }
-
- /**
- * Method getSequenceSet.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the SequenceSet at the given index
- */
- public SequenceSet getSequenceSet(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size())
- {
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
- }
-
- return (SequenceSet) _sequenceSetList.get(index);
- }
-
- /**
- * Method getSequenceSet.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 SequenceSet[] getSequenceSet()
- {
- SequenceSet[] array = new SequenceSet[0];
- return (SequenceSet[]) this._sequenceSetList.toArray(array);
- }
-
- /**
- * Method getSequenceSetCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetCount()
- {
- return this._sequenceSetList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getTree(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (java.lang.String) _treeList.get(index);
- }
-
- /**
- * Method getTree.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 java.lang.String[] getTree()
- {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount()
- {
- return this._treeList.size();
- }
-
- /**
- * 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;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Method removeAlignment.
- *
- * @param vAlignment
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignment(final Alignment vAlignment)
- {
- boolean removed = _alignmentList.remove(vAlignment);
- return removed;
- }
-
- /**
- * Method removeAlignmentAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Alignment removeAlignmentAt(final int index)
- {
- java.lang.Object obj = this._alignmentList.remove(index);
- return (Alignment) obj;
- }
-
- /**
- */
- public void removeAllAlignment()
- {
- this._alignmentList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSet()
- {
- this._sequenceSetList.clear();
- }
-
- /**
- */
- public void removeAllTree()
- {
- this._treeList.clear();
- }
-
- /**
- * Method removeSequenceSet.
- *
- * @param vSequenceSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSet(final SequenceSet vSequenceSet)
- {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public SequenceSet removeSequenceSetAt(final int index)
- {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (SequenceSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(final java.lang.String vTree)
- {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeTreeAt(final int index)
- {
- java.lang.Object obj = this._treeList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlignment(final int index, final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size())
- {
- throw new IndexOutOfBoundsException("setAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
- }
-
- this._alignmentList.set(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vAlignmentArray
- */
- public void setAlignment(final Alignment[] vAlignmentArray)
- {
- // -- copy array
- _alignmentList.clear();
-
- for (int i = 0; i < vAlignmentArray.length; i++)
- {
- this._alignmentList.add(vAlignmentArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size())
- {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
- }
-
- this._sequenceSetList.set(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vSequenceSetArray
- */
- public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
- {
- // -- copy array
- _sequenceSetList.clear();
-
- for (int i = 0; i < vSequenceSetArray.length; i++)
- {
- this._sequenceSetList.add(vSequenceSetArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setTree(final int index, final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(final java.lang.String[] vTreeArray)
- {
- // -- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++)
- {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- * 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.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VAMSAS.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);
- }
+public class VAMSAS implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _alignmentList.
+ */
+ private java.util.Vector _alignmentList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VAMSAS() {
+ super();
+ this._alignmentList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.addElement(vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.add(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.addElement(vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.add(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateAlignment.
+ *
+ * @return an Enumeration over all Alignment elements
+ */
+ public java.util.Enumeration enumerateAlignment(
+ ) {
+ return this._alignmentList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSet.
+ *
+ * @return an Enumeration over all SequenceSet elements
+ */
+ public java.util.Enumeration enumerateSequenceSet(
+ ) {
+ return this._sequenceSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method getAlignment.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Alignment at the given index
+ */
+ public Alignment getAlignment(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ return (Alignment) _alignmentList.get(index);
+ }
+
+ /**
+ * Method getAlignment.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 Alignment[] getAlignment(
+ ) {
+ Alignment[] array = new Alignment[0];
+ return (Alignment[]) this._alignmentList.toArray(array);
+ }
+
+ /**
+ * Method getAlignmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentCount(
+ ) {
+ return this._alignmentList.size();
+ }
+
+ /**
+ * Method getSequenceSet.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the SequenceSet at the given index
+ */
+ public SequenceSet getSequenceSet(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ return (SequenceSet) _sequenceSetList.get(index);
+ }
+
+ /**
+ * Method getSequenceSet.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 SequenceSet[] getSequenceSet(
+ ) {
+ SequenceSet[] array = new SequenceSet[0];
+ return (SequenceSet[]) this._sequenceSetList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetCount(
+ ) {
+ return this._sequenceSetList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.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 java.lang.String[] getTree(
+ ) {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Method removeAlignment.
+ *
+ * @param vAlignment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignment(
+ final Alignment vAlignment) {
+ boolean removed = _alignmentList.remove(vAlignment);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Alignment removeAlignmentAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentList.remove(index);
+ return (Alignment) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignment(
+ ) {
+ this._alignmentList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSet(
+ ) {
+ this._sequenceSetList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(
+ final SequenceSet vSequenceSet) {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public SequenceSet removeSequenceSetAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (SequenceSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final java.lang.String vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ this._alignmentList.set(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentArray
+ */
+ public void setAlignment(
+ final Alignment[] vAlignmentArray) {
+ //-- copy array
+ _alignmentList.clear();
+
+ for (int i = 0; i < vAlignmentArray.length; i++) {
+ this._alignmentList.add(vAlignmentArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(
+ final SequenceSet[] vSequenceSetArray) {
+ //-- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++) {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final java.lang.String[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * 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.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VamsasModel extends VAMSAS implements java.io.Serializable
+public class VamsasModel extends VAMSAS
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public VamsasModel()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
- // -----------/
- // - Methods -/
- // -----------/
+ public VamsasModel() {
+ super();
+ }
- /**
- * 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;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * 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;
}
- return true;
- }
- /**
- *
- *
- * @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 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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
- /**
- * 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.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VamsasModel.class, reader);
- }
+ /**
+ * 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.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.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);
- }
+ /**
+ *
+ *
+ * @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);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
-
- /**
- * Field _showText.
- */
- private boolean _showText;
-
- /**
- * keeps track of state for field: _showText
- */
- private boolean _has_showText;
-
- /**
- * Field _showColourText.
- */
- private boolean _showColourText;
-
- /**
- * keeps track of state for field: _showColourText
- */
- private boolean _has_showColourText;
-
- /**
- * Field _showBoxes.
- */
- private boolean _showBoxes;
-
- /**
- * keeps track of state for field: _showBoxes
- */
- private boolean _has_showBoxes;
-
- /**
- * Field _wrapAlignment.
- */
- private boolean _wrapAlignment;
-
- /**
- * keeps track of state for field: _wrapAlignment
- */
- private boolean _has_wrapAlignment;
-
- /**
- * Field _renderGaps.
- */
- private boolean _renderGaps;
-
- /**
- * keeps track of state for field: _renderGaps
- */
- private boolean _has_renderGaps;
-
- /**
- * Field _showSequenceFeatures.
- */
- private boolean _showSequenceFeatures;
-
- /**
- * keeps track of state for field: _showSequenceFeatures
- */
- private boolean _has_showSequenceFeatures;
-
- /**
- * Field _showAnnotation.
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * Field _showConservation.
- */
- private boolean _showConservation;
-
- /**
- * keeps track of state for field: _showConservation
- */
- private boolean _has_showConservation;
-
- /**
- * Field _showQuality.
- */
- private boolean _showQuality;
-
- /**
- * keeps track of state for field: _showQuality
- */
- private boolean _has_showQuality;
-
- /**
- * Field _showIdentity.
- */
- private boolean _showIdentity;
-
- /**
- * keeps track of state for field: _showIdentity
- */
- private boolean _has_showIdentity;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Viewport()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
+public class Viewport implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _showConservation.
+ */
+ private boolean _showConservation;
+
+ /**
+ * keeps track of state for field: _showConservation
+ */
+ private boolean _has_showConservation;
+
+ /**
+ * Field _showQuality.
+ */
+ private boolean _showQuality;
+
+ /**
+ * keeps track of state for field: _showQuality
+ */
+ private boolean _has_showQuality;
+
+ /**
+ * Field _showIdentity.
+ */
+ private boolean _showIdentity;
+
+ /**
+ * keeps track of state for field: _showIdentity
+ */
+ private boolean _has_showIdentity;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Viewport() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected(
+ ) {
+ this._has_conservationSelected= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deletePidSelected(
+ ) {
+ this._has_pidSelected= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteRenderGaps(
+ ) {
+ this._has_renderGaps= false;
+ }
+
+ /**
+ */
+ public void deleteShowAnnotation(
+ ) {
+ this._has_showAnnotation= false;
+ }
+
+ /**
+ */
+ public void deleteShowBoxes(
+ ) {
+ this._has_showBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteShowColourText(
+ ) {
+ this._has_showColourText= false;
+ }
+
+ /**
+ */
+ public void deleteShowConservation(
+ ) {
+ this._has_showConservation= false;
+ }
+
+ /**
+ */
+ public void deleteShowFullId(
+ ) {
+ this._has_showFullId= false;
+ }
+
+ /**
+ */
+ public void deleteShowIdentity(
+ ) {
+ this._has_showIdentity= false;
+ }
+
+ /**
+ */
+ public void deleteShowQuality(
+ ) {
+ this._has_showQuality= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures(
+ ) {
+ this._has_showSequenceFeatures= false;
+ }
+
+ /**
+ */
+ public void deleteShowText(
+ ) {
+ this._has_showText= false;
+ }
+
+ /**
+ */
+ public void deleteStartRes(
+ ) {
+ this._has_startRes= false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq(
+ ) {
+ this._has_startSeq= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment(
+ ) {
+ this._has_wrapAlignment= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour(
+ ) {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean getShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean getShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean getShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes(
+ ) {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq(
+ ) {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been
+ * added
+ */
+ public boolean hasConservationSelected(
+ ) {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected(
+ ) {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps(
+ ) {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation(
+ ) {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes(
+ ) {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText(
+ ) {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConservation.
+ *
+ * @return true if at least one ShowConservation has been added
+ */
+ public boolean hasShowConservation(
+ ) {
+ return this._has_showConservation;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId(
+ ) {
+ return this._has_showFullId;
+ }
- /**
+ /**
+ * Method hasShowIdentity.
+ *
+ * @return true if at least one ShowIdentity has been added
*/
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
+ public boolean hasShowIdentity(
+ ) {
+ return this._has_showIdentity;
+ }
- /**
+ /**
+ * Method hasShowQuality.
+ *
+ * @return true if at least one ShowQuality has been added
*/
- public void deleteConservationSelected()
- {
- this._has_conservationSelected = false;
- }
+ public boolean hasShowQuality(
+ ) {
+ return this._has_showQuality;
+ }
- /**
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been
+ * added
*/
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
+ public boolean hasShowSequenceFeatures(
+ ) {
+ return this._has_showSequenceFeatures;
+ }
- /**
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
*/
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
+ public boolean hasShowText(
+ ) {
+ return this._has_showText;
+ }
- /**
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
*/
- public void deleteHeight()
- {
- this._has_height = false;
- }
+ public boolean hasStartRes(
+ ) {
+ return this._has_startRes;
+ }
- /**
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
*/
- public void deletePidSelected()
- {
- this._has_pidSelected = false;
- }
+ public boolean hasStartSeq(
+ ) {
+ return this._has_startSeq;
+ }
- /**
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
*/
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
- /**
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
*/
- public void deleteRenderGaps()
- {
- this._has_renderGaps = false;
- }
+ public boolean hasWrapAlignment(
+ ) {
+ return this._has_wrapAlignment;
+ }
- /**
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
*/
- public void deleteShowAnnotation()
- {
- this._has_showAnnotation = false;
- }
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
- /**
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
*/
- public void deleteShowBoxes()
- {
- this._has_showBoxes = false;
- }
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
- /**
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
*/
- public void deleteShowColourText()
- {
- this._has_showColourText = false;
- }
+ public boolean isConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
- /**
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
*/
- public void deleteShowConservation()
- {
- this._has_showConservation = false;
- }
+ public boolean isPidSelected(
+ ) {
+ return this._pidSelected;
+ }
- /**
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
*/
- public void deleteShowFullId()
- {
- this._has_showFullId = false;
- }
+ public boolean isRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
- /**
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
*/
- public void deleteShowIdentity()
- {
- this._has_showIdentity = false;
- }
+ public boolean isShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
- /**
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
*/
- public void deleteShowQuality()
- {
- this._has_showQuality = false;
- }
-
- /**
- */
- public void deleteShowSequenceFeatures()
- {
- this._has_showSequenceFeatures = false;
- }
-
- /**
- */
- public void deleteShowText()
- {
- this._has_showText = false;
- }
-
- /**
- */
- public void deleteStartRes()
- {
- this._has_startRes = false;
- }
-
- /**
- */
- public void deleteStartSeq()
- {
- this._has_startSeq = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteWrapAlignment()
- {
- this._has_wrapAlignment = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour()
- {
- return this._bgColour;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean getShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean getShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean getShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText()
- {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes()
- {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq()
- {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been added
- */
- public boolean hasConservationSelected()
- {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected()
- {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps()
- {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation()
- {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes()
- {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText()
- {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConservation.
- *
- * @return true if at least one ShowConservation has been added
- */
- public boolean hasShowConservation()
- {
- return this._has_showConservation;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowIdentity.
- *
- * @return true if at least one ShowIdentity has been added
- */
- public boolean hasShowIdentity()
- {
- return this._has_showIdentity;
- }
-
- /**
- * Method hasShowQuality.
- *
- * @return true if at least one ShowQuality has been added
- */
- public boolean hasShowQuality()
- {
- return this._has_showQuality;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been added
- */
- public boolean hasShowSequenceFeatures()
- {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText()
- {
- return this._has_showText;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes()
- {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq()
- {
- return this._has_startSeq;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment()
- {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean isShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean isShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean isShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText()
- {
- return this._showText;
- }
-
- /**
- * 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 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour
- * the value of field 'bgColour'.
- */
- public void setBgColour(final java.lang.String bgColour)
- {
- this._bgColour = bgColour;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected
- * the value of field 'conservationSelected'.
- */
- public void setConservationSelected(final boolean conservationSelected)
- {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected
- * the value of field 'pidSelected'.
- */
- public void setPidSelected(final boolean pidSelected)
- {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps
- * the value of field 'renderGaps'.
- */
- public void setRenderGaps(final boolean renderGaps)
- {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation
- * the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(final boolean showAnnotation)
- {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes
- * the value of field 'showBoxes'.
- */
- public void setShowBoxes(final boolean showBoxes)
- {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText
- * the value of field 'showColourText'.
- */
- public void setShowColourText(final boolean showColourText)
- {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConservation'.
- *
- * @param showConservation
- * the value of field 'showConservation'
- */
- public void setShowConservation(final boolean showConservation)
- {
- this._showConservation = showConservation;
- this._has_showConservation = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId
- * the value of field 'showFullId'.
- */
- public void setShowFullId(final boolean showFullId)
- {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showIdentity'.
- *
- * @param showIdentity
- * the value of field 'showIdentity'.
- */
- public void setShowIdentity(final boolean showIdentity)
- {
- this._showIdentity = showIdentity;
- this._has_showIdentity = true;
- }
-
- /**
- * Sets the value of field 'showQuality'.
- *
- * @param showQuality
- * the value of field 'showQuality'.
- */
- public void setShowQuality(final boolean showQuality)
- {
- this._showQuality = showQuality;
- this._has_showQuality = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures
- * the value of field 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(final boolean showSequenceFeatures)
- {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText
- * the value of field 'showText'.
- */
- public void setShowText(final boolean showText)
- {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes
- * the value of field 'startRes'.
- */
- public void setStartRes(final int startRes)
- {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq
- * the value of field 'startSeq'.
- */
- public void setStartSeq(final int startSeq)
- {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment
- * the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(final boolean wrapAlignment)
- {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = 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.binding.Viewport
- */
- public static jalview.binding.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(
- jalview.binding.Viewport.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);
- }
+ public boolean isShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean isShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean isShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean isShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * 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 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour the value of field 'bgColour'.
+ */
+ public void setBgColour(
+ final java.lang.String bgColour) {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected the value of field
+ * 'conservationSelected'.
+ */
+ public void setConservationSelected(
+ final boolean conservationSelected) {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected the value of field 'pidSelected'.
+ */
+ public void setPidSelected(
+ final boolean pidSelected) {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(
+ final boolean renderGaps) {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(
+ final boolean showAnnotation) {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(
+ final boolean showBoxes) {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText the value of field 'showColourText'.
+ */
+ public void setShowColourText(
+ final boolean showColourText) {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConservation'.
+ *
+ * @param showConservation the value of field 'showConservation'
+ */
+ public void setShowConservation(
+ final boolean showConservation) {
+ this._showConservation = showConservation;
+ this._has_showConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId the value of field 'showFullId'.
+ */
+ public void setShowFullId(
+ final boolean showFullId) {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showIdentity'.
+ *
+ * @param showIdentity the value of field 'showIdentity'.
+ */
+ public void setShowIdentity(
+ final boolean showIdentity) {
+ this._showIdentity = showIdentity;
+ this._has_showIdentity = true;
+ }
+
+ /**
+ * Sets the value of field 'showQuality'.
+ *
+ * @param showQuality the value of field 'showQuality'.
+ */
+ public void setShowQuality(
+ final boolean showQuality) {
+ this._showQuality = showQuality;
+ this._has_showQuality = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures the value of field
+ * 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(
+ final boolean showSequenceFeatures) {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText the value of field 'showText'.
+ */
+ public void setShowText(
+ final boolean showText) {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes the value of field 'startRes'.
+ */
+ public void setStartRes(
+ final int startRes) {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq the value of field 'startSeq'.
+ */
+ public void setStartSeq(
+ final int startSeq) {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(
+ final boolean wrapAlignment) {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = 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.binding.Viewport
+ */
+ public static jalview.binding.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.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);
+ }
}
-#Mon Sep 06 13:16:48 BST 2010\r
+#Tue Feb 15 17:12:42 GMT 2011\r
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlcodMap implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * internal jalview id for the dnasq for this mapping.\r
- * \r
- */\r
- private java.lang.String _dnasq;\r
-\r
- /**\r
- * a Mapping entry and an associated protein sequence\r
- * \r
- */\r
- private jalview.schemabinding.version2.Mapping _mapping;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AlcodMap()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'dnasq'. The field 'dnasq' has the following\r
- * description: internal jalview id for the dnasq for this mapping.\r
- * \r
- * \r
- * @return the value of field 'Dnasq'.\r
- */\r
- public java.lang.String getDnasq()\r
- {\r
- return this._dnasq;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapping'. The field 'mapping' has the following\r
- * description: a Mapping entry and an associated protein sequence\r
- * \r
- * \r
- * @return the value of field 'Mapping'.\r
- */\r
- public jalview.schemabinding.version2.Mapping getMapping()\r
- {\r
- return this._mapping;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class AlcodMap implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * internal jalview id for the dnasq for this mapping.\r
+ * \r
+ */\r
+ private java.lang.String _dnasq;\r
+\r
+ /**\r
+ * a Mapping entry and an associated protein sequence\r
+ * \r
+ */\r
+ private jalview.schemabinding.version2.Mapping _mapping;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodMap() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'dnasq'. The field 'dnasq' has\r
+ * the following description: internal jalview id for the dnasq\r
+ * for this mapping.\r
+ * \r
+ * \r
+ * @return the value of field 'Dnasq'.\r
+ */\r
+ public java.lang.String getDnasq(\r
+ ) {\r
+ return this._dnasq;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapping'. The field 'mapping'\r
+ * has the following description: a Mapping entry and an\r
+ * associated protein sequence\r
+ * \r
+ * \r
+ * @return the value of field 'Mapping'.\r
+ */\r
+ public jalview.schemabinding.version2.Mapping getMapping(\r
+ ) {\r
+ return this._mapping;\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
+ * \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
+ * Sets the value of field 'dnasq'. The field 'dnasq' has the\r
+ * following description: internal jalview id for the dnasq for\r
+ * this mapping.\r
+ * \r
+ * \r
+ * @param dnasq the value of field 'dnasq'.\r
+ */\r
+ public void setDnasq(\r
+ final java.lang.String dnasq) {\r
+ this._dnasq = dnasq;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapping'. The field 'mapping' has\r
+ * the following description: a Mapping entry and an associated\r
+ * protein sequence\r
+ * \r
+ * \r
+ * @param mapping the value of field 'mapping'.\r
+ */\r
+ public void setMapping(\r
+ final jalview.schemabinding.version2.Mapping mapping) {\r
+ this._mapping = mapping;\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.AlcodMap\r
+ */\r
+ public static jalview.schemabinding.version2.AlcodMap unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.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
- return true;\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 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 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
- * Sets the value of field 'dnasq'. The field 'dnasq' has the following\r
- * description: internal jalview id for the dnasq for this mapping.\r
- * \r
- * \r
- * @param dnasq\r
- * the value of field 'dnasq'.\r
- */\r
- public void setDnasq(final java.lang.String dnasq)\r
- {\r
- this._dnasq = dnasq;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapping'. The field 'mapping' has the following\r
- * description: a Mapping entry and an associated protein sequence\r
- * \r
- * \r
- * @param mapping\r
- * the value of field 'mapping'.\r
- */\r
- public void setMapping(\r
- final jalview.schemabinding.version2.Mapping mapping)\r
- {\r
- this._mapping = mapping;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.AlcodMap\r
- */\r
- public static jalview.schemabinding.version2.AlcodMap 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.AlcodMap) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.AlcodMap.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Alcodon implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _pos1.\r
- */\r
- private long _pos1;\r
-\r
- /**\r
- * keeps track of state for field: _pos1\r
- */\r
- private boolean _has_pos1;\r
-\r
- /**\r
- * Field _pos2.\r
- */\r
- private long _pos2;\r
-\r
- /**\r
- * keeps track of state for field: _pos2\r
- */\r
- private boolean _has_pos2;\r
-\r
- /**\r
- * Field _pos3.\r
- */\r
- private long _pos3;\r
-\r
- /**\r
- * keeps track of state for field: _pos3\r
- */\r
- private boolean _has_pos3;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Alcodon()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
+public class Alcodon implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _pos1.\r
+ */\r
+ private long _pos1;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos1\r
+ */\r
+ private boolean _has_pos1;\r
+\r
+ /**\r
+ * Field _pos2.\r
+ */\r
+ private long _pos2;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos2\r
+ */\r
+ private boolean _has_pos2;\r
+\r
+ /**\r
+ * Field _pos3.\r
+ */\r
+ private long _pos3;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos3\r
+ */\r
+ private boolean _has_pos3;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Alcodon() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
*/\r
- public void deletePos1()\r
- {\r
- this._has_pos1 = false;\r
- }\r
+ public void deletePos1(\r
+ ) {\r
+ this._has_pos1= false;\r
+ }\r
\r
- /**\r
+ /**\r
*/\r
- public void deletePos2()\r
- {\r
- this._has_pos2 = false;\r
- }\r
+ public void deletePos2(\r
+ ) {\r
+ this._has_pos2= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePos3(\r
+ ) {\r
+ this._has_pos3= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos1'.\r
+ * \r
+ * @return the value of field 'Pos1'.\r
+ */\r
+ public long getPos1(\r
+ ) {\r
+ return this._pos1;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos2'.\r
+ * \r
+ * @return the value of field 'Pos2'.\r
+ */\r
+ public long getPos2(\r
+ ) {\r
+ return this._pos2;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos3'.\r
+ * \r
+ * @return the value of field 'Pos3'.\r
+ */\r
+ public long getPos3(\r
+ ) {\r
+ return this._pos3;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos1.\r
+ * \r
+ * @return true if at least one Pos1 has been added\r
+ */\r
+ public boolean hasPos1(\r
+ ) {\r
+ return this._has_pos1;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos2.\r
+ * \r
+ * @return true if at least one Pos2 has been added\r
+ */\r
+ public boolean hasPos2(\r
+ ) {\r
+ return this._has_pos2;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos3.\r
+ * \r
+ * @return true if at least one Pos3 has been added\r
+ */\r
+ public boolean hasPos3(\r
+ ) {\r
+ return this._has_pos3;\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
+ * \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
+ * Sets the value of field 'pos1'.\r
+ * \r
+ * @param pos1 the value of field 'pos1'.\r
+ */\r
+ public void setPos1(\r
+ final long pos1) {\r
+ this._pos1 = pos1;\r
+ this._has_pos1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pos2'.\r
+ * \r
+ * @param pos2 the value of field 'pos2'.\r
+ */\r
+ public void setPos2(\r
+ final long pos2) {\r
+ this._pos2 = pos2;\r
+ this._has_pos2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pos3'.\r
+ * \r
+ * @param pos3 the value of field 'pos3'.\r
+ */\r
+ public void setPos3(\r
+ final long pos3) {\r
+ this._pos3 = pos3;\r
+ this._has_pos3 = 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 jalview.schemabinding.version2.Alcodo\r
+ */\r
+ public static jalview.schemabinding.version2.Alcodon unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader);\r
+ }\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 deletePos3()\r
- {\r
- this._has_pos3 = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pos1'.\r
- * \r
- * @return the value of field 'Pos1'.\r
- */\r
- public long getPos1()\r
- {\r
- return this._pos1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pos2'.\r
- * \r
- * @return the value of field 'Pos2'.\r
- */\r
- public long getPos2()\r
- {\r
- return this._pos2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pos3'.\r
- * \r
- * @return the value of field 'Pos3'.\r
- */\r
- public long getPos3()\r
- {\r
- return this._pos3;\r
- }\r
-\r
- /**\r
- * Method hasPos1.\r
- * \r
- * @return true if at least one Pos1 has been added\r
- */\r
- public boolean hasPos1()\r
- {\r
- return this._has_pos1;\r
- }\r
-\r
- /**\r
- * Method hasPos2.\r
- * \r
- * @return true if at least one Pos2 has been added\r
- */\r
- public boolean hasPos2()\r
- {\r
- return this._has_pos2;\r
- }\r
-\r
- /**\r
- * Method hasPos3.\r
- * \r
- * @return true if at least one Pos3 has been added\r
- */\r
- public boolean hasPos3()\r
- {\r
- return this._has_pos3;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
- return true;\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 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 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
- * Sets the value of field 'pos1'.\r
- * \r
- * @param pos1\r
- * the value of field 'pos1'.\r
- */\r
- public void setPos1(final long pos1)\r
- {\r
- this._pos1 = pos1;\r
- this._has_pos1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pos2'.\r
- * \r
- * @param pos2\r
- * the value of field 'pos2'.\r
- */\r
- public void setPos2(final long pos2)\r
- {\r
- this._pos2 = pos2;\r
- this._has_pos2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pos3'.\r
- * \r
- * @param pos3\r
- * the value of field 'pos3'.\r
- */\r
- public void setPos3(final long pos3)\r
- {\r
- this._pos3 = pos3;\r
- this._has_pos3 = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Alcodo\r
- */\r
- public static jalview.schemabinding.version2.Alcodon 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.Alcodon) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Alcodon.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlcodonFrame implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _alcodonList.\r
- */\r
- private java.util.Vector _alcodonList;\r
-\r
- /**\r
- * Field _alcodMapList.\r
- */\r
- private java.util.Vector _alcodMapList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AlcodonFrame()\r
- {\r
- super();\r
- this._alcodonList = new java.util.Vector();\r
- this._alcodMapList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodMapList.addElement(vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodMap(final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodMapList.add(index, vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodon(\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonList.addElement(vAlcodon);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodon(final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonList.add(index, vAlcodon);\r
- }\r
-\r
- /**\r
- * Method enumerateAlcodMap.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAlcodMap()\r
- {\r
- return this._alcodMapList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateAlcodon.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Alcodon\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAlcodon()\r
- {\r
- return this._alcodonList.elements();\r
- }\r
-\r
- /**\r
- * Method getAlcodMap.\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.AlcodMap at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAlcodMap: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodMapList.size() - 1) + "]");\r
+public class AlcodonFrame implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _alcodonList.\r
+ */\r
+ private java.util.Vector _alcodonList;\r
+\r
+ /**\r
+ * Field _alcodMapList.\r
+ */\r
+ private java.util.Vector _alcodMapList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodonFrame() {\r
+ super();\r
+ this._alcodonList = new java.util.Vector();\r
+ this._alcodMapList = new java.util.Vector();\r
}\r
\r
- return (jalview.schemabinding.version2.AlcodMap) _alcodMapList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodMap.Returns the contents of the collection in an 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.AlcodMap[] getAlcodMap()\r
- {\r
- jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];\r
- return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAlcodMapCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAlcodMapCount()\r
- {\r
- return this._alcodMapList.size();\r
- }\r
-\r
- /**\r
- * Method getAlcodon.\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.Alcodon at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Alcodon getAlcodon(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAlcodon: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonList.size() - 1) + "]");\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodMapList.addElement(vAlcodMap);\r
}\r
\r
- return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodon.Returns the contents of the collection in an 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.Alcodon[] getAlcodon()\r
- {\r
- jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];\r
- return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAlcodonCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAlcodonCount()\r
- {\r
- return this._alcodonList.size();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodMap(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodMapList.add(index, vAlcodMap);\r
}\r
- return true;\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 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 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
- * Method removeAlcodMap.\r
- * \r
- * @param vAlcodMap\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- {\r
- boolean removed = _alcodMapList.remove(vAlcodMap);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAlcodMapAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._alcodMapList.remove(index);\r
- return (jalview.schemabinding.version2.AlcodMap) obj;\r
- }\r
-\r
- /**\r
- * Method removeAlcodon.\r
- * \r
- * @param vAlcodon\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodon(\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- {\r
- boolean removed = _alcodonList.remove(vAlcodon);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAlcodonAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Alcodon removeAlcodonAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._alcodonList.remove(index);\r
- return (jalview.schemabinding.version2.Alcodon) obj;\r
- }\r
-\r
- /**\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllAlcodMap()\r
- {\r
- this._alcodMapList.clear();\r
- }\r
+ public void addAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonList.addElement(vAlcodon);\r
+ }\r
\r
- /**\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllAlcodon()\r
- {\r
- this._alcodonList.clear();\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAlcodMap(final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodMapList.size() - 1) + "]");\r
+ public void addAlcodon(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonList.add(index, vAlcodon);\r
}\r
\r
- this._alcodMapList.set(index, vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodMapArray\r
- */\r
- public void setAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)\r
- {\r
- // -- copy array\r
- _alcodMapList.clear();\r
-\r
- for (int i = 0; i < vAlcodMapArray.length; i++)\r
- {\r
- this._alcodMapList.add(vAlcodMapArray[i]);\r
+ /**\r
+ * Method enumerateAlcodMap.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AlcodMap elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodMap(\r
+ ) {\r
+ return this._alcodMapList.elements();\r
}\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAlcodon(final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAlcodon: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonList.size() - 1) + "]");\r
+\r
+ /**\r
+ * Method enumerateAlcodon.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Alcodon elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodon(\r
+ ) {\r
+ return this._alcodonList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMap.\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.AlcodMap at the given index\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap getAlcodMap(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodMapList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMap.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap[] getAlcodMap(\r
+ ) {\r
+ jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];\r
+ return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMapCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodMapCount(\r
+ ) {\r
+ return this._alcodMapList.size();\r
}\r
\r
- this._alcodonList.set(index, vAlcodon);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodonArray\r
- */\r
- public void setAlcodon(\r
- final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)\r
- {\r
- // -- copy array\r
- _alcodonList.clear();\r
-\r
- for (int i = 0; i < vAlcodonArray.length; i++)\r
- {\r
- this._alcodonList.add(vAlcodonArray[i]);\r
+ /**\r
+ * Method getAlcodon.\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.Alcodon at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon getAlcodon(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodon.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon[] getAlcodon(\r
+ ) {\r
+ jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];\r
+ return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonCount(\r
+ ) {\r
+ return this._alcodonList.size();\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
+ * \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
+ * Method removeAlcodMap.\r
+ * \r
+ * @param vAlcodMap\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap) {\r
+ boolean removed = _alcodMapList.remove(vAlcodMap);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodMapAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodMapList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodMap) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodon.\r
+ * \r
+ * @param vAlcodon\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon) {\r
+ boolean removed = _alcodonList.remove(vAlcodon);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodonAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon removeAlcodonAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodonList.remove(index);\r
+ return (jalview.schemabinding.version2.Alcodon) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodMap(\r
+ ) {\r
+ this._alcodMapList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodon(\r
+ ) {\r
+ this._alcodonList.clear();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodMap(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodMapList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodMapList.set(index, vAlcodMap);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodMapArray\r
+ */\r
+ public void setAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {\r
+ //-- copy array\r
+ _alcodMapList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodMapArray.length; i++) {\r
+ this._alcodMapList.add(vAlcodMapArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodon(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodonList.set(index, vAlcodon);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonArray\r
+ */\r
+ public void setAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {\r
+ //-- copy array\r
+ _alcodonList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodonArray.length; i++) {\r
+ this._alcodonList.add(vAlcodonArray[i]);\r
+ }\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.AlcodonFrame\r
+ */\r
+ public static jalview.schemabinding.version2.AlcodonFrame unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.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
- /**\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame\r
- */\r
- public static jalview.schemabinding.version2.AlcodonFrame 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.AlcodonFrame) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\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 _groupRef.\r
- */\r
- private java.lang.String _groupRef;\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 _centreColLabels.\r
- */\r
- private boolean _centreColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _centreColLabels\r
- */\r
- private boolean _has_centreColLabels;\r
-\r
- /**\r
- * Field _scaleColLabels.\r
- */\r
- private boolean _scaleColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _scaleColLabels\r
- */\r
- private boolean _has_scaleColLabels;\r
-\r
- /**\r
- * Field _showAllColLabels.\r
- */\r
- private boolean _showAllColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _showAllColLabels\r
- */\r
- private boolean _has_showAllColLabels;\r
-\r
- /**\r
- * is an autocalculated annotation row\r
- */\r
- private boolean _autoCalculated = false;\r
-\r
- /**\r
- * keeps track of state for field: _autoCalculated\r
- */\r
- private boolean _has_autoCalculated;\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 deleteAutoCalculated()\r
- {\r
- this._has_autoCalculated = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteCentreColLabels()\r
- {\r
- this._has_centreColLabels = false;\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 deleteScaleColLabels()\r
- {\r
- this._has_scaleColLabels = 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 deleteShowAllColLabels()\r
- {\r
- this._has_showAllColLabels = 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
- 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 'autoCalculated'. The field 'autoCalculated' has\r
- * the following description: is an autocalculated annotation row\r
- * \r
- * @return the value of field 'AutoCalculated'.\r
- */\r
- public boolean getAutoCalculated()\r
- {\r
- return this._autoCalculated;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColLabels'.\r
- * \r
- * @return the value of field 'CentreColLabels'.\r
- */\r
- public boolean getCentreColLabels()\r
- {\r
- return this._centreColLabels;\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 'groupRef'.\r
- * \r
- * @return the value of field 'GroupRef'.\r
- */\r
- public java.lang.String getGroupRef()\r
- {\r
- return this._groupRef;\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 'scaleColLabels'.\r
- * \r
- * @return the value of field 'ScaleColLabels'.\r
- */\r
- public boolean getScaleColLabels()\r
- {\r
- return this._scaleColLabels;\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 'showAllColLabels'.\r
- * \r
- * @return the value of field 'ShowAllColLabels'.\r
- */\r
- public boolean getShowAllColLabels()\r
- {\r
- return this._showAllColLabels;\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 hasAutoCalculated.\r
- * \r
- * @return true if at least one AutoCalculated has been added\r
- */\r
- public boolean hasAutoCalculated()\r
- {\r
- return this._has_autoCalculated;\r
- }\r
-\r
- /**\r
- * Method hasCentreColLabels.\r
- * \r
- * @return true if at least one CentreColLabels has been added\r
- */\r
- public boolean hasCentreColLabels()\r
- {\r
- return this._has_centreColLabels;\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 hasScaleColLabels.\r
- * \r
- * @return true if at least one ScaleColLabels has been added\r
- */\r
- public boolean hasScaleColLabels()\r
- {\r
- return this._has_scaleColLabels;\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 hasShowAllColLabels.\r
- * \r
- * @return true if at least one ShowAllColLabels has been added\r
- */\r
- public boolean hasShowAllColLabels()\r
- {\r
- return this._has_showAllColLabels;\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 'autoCalculated'. The field 'autoCalculated' has\r
- * the following description: is an autocalculated annotation row\r
- * \r
- * @return the value of field 'AutoCalculated'.\r
- */\r
- public boolean isAutoCalculated()\r
- {\r
- return this._autoCalculated;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColLabels'.\r
- * \r
- * @return the value of field 'CentreColLabels'.\r
- */\r
- public boolean isCentreColLabels()\r
- {\r
- return this._centreColLabels;\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 'scaleColLabels'.\r
- * \r
- * @return the value of field 'ScaleColLabels'.\r
- */\r
- public boolean isScaleColLabels()\r
- {\r
- return this._scaleColLabels;\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
- * Returns the value of field 'showAllColLabels'.\r
- * \r
- * @return the value of field 'ShowAllColLabels'.\r
- */\r
- public boolean isShowAllColLabels()\r
- {\r
- return this._showAllColLabels;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\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 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 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
- 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
- this._annotationElementList.add(vAnnotationElementArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has\r
- * the following description: is an autocalculated annotation row\r
- * \r
- * @param autoCalculated\r
- * the value of field 'autoCalculated'.\r
- */\r
- public void setAutoCalculated(final boolean autoCalculated)\r
- {\r
- this._autoCalculated = autoCalculated;\r
- this._has_autoCalculated = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'centreColLabels'.\r
- * \r
- * @param centreColLabels\r
- * the value of field 'centreColLabels'.\r
- */\r
- public void setCentreColLabels(final boolean centreColLabels)\r
- {\r
- this._centreColLabels = centreColLabels;\r
- this._has_centreColLabels = true;\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 'groupRef'.\r
- * \r
- * @param groupRef\r
- * the value of field 'groupRef'.\r
- */\r
- public void setGroupRef(final java.lang.String groupRef)\r
- {\r
- this._groupRef = groupRef;\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 'scaleColLabels'.\r
- * \r
- * @param scaleColLabels\r
- * the value of field 'scaleColLabels'.\r
- */\r
- public void setScaleColLabels(final boolean scaleColLabels)\r
- {\r
- this._scaleColLabels = scaleColLabels;\r
- this._has_scaleColLabels = true;\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 'showAllColLabels'.\r
- * \r
- * @param showAllColLabels\r
- * the value of field 'showAllColLabels'\r
- */\r
- public void setShowAllColLabels(final boolean showAllColLabels)\r
- {\r
- this._showAllColLabels = showAllColLabels;\r
- this._has_showAllColLabels = true;\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 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 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
+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 _groupRef.\r
+ */\r
+ private java.lang.String _groupRef;\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 _centreColLabels.\r
+ */\r
+ private boolean _centreColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _centreColLabels\r
+ */\r
+ private boolean _has_centreColLabels;\r
+\r
+ /**\r
+ * Field _scaleColLabels.\r
+ */\r
+ private boolean _scaleColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _scaleColLabels\r
+ */\r
+ private boolean _has_scaleColLabels;\r
+\r
+ /**\r
+ * Field _showAllColLabels.\r
+ */\r
+ private boolean _showAllColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _showAllColLabels\r
+ */\r
+ private boolean _has_showAllColLabels;\r
+\r
+ /**\r
+ * is an autocalculated annotation row\r
+ */\r
+ private boolean _autoCalculated = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _autoCalculated\r
+ */\r
+ private boolean _has_autoCalculated;\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 deleteAutoCalculated(\r
+ ) {\r
+ this._has_autoCalculated= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteCentreColLabels(\r
+ ) {\r
+ this._has_centreColLabels= false;\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 deleteScaleColLabels(\r
+ ) {\r
+ this._has_scaleColLabels= 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 deleteShowAllColLabels(\r
+ ) {\r
+ this._has_showAllColLabels= 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 'autoCalculated'. The field\r
+ * 'autoCalculated' has the following description: is an\r
+ * autocalculated annotation row\r
+ * \r
+ * @return the value of field 'AutoCalculated'.\r
+ */\r
+ public boolean getAutoCalculated(\r
+ ) {\r
+ return this._autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColLabels'.\r
+ * \r
+ * @return the value of field 'CentreColLabels'.\r
+ */\r
+ public boolean getCentreColLabels(\r
+ ) {\r
+ return this._centreColLabels;\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 'groupRef'.\r
+ * \r
+ * @return the value of field 'GroupRef'.\r
+ */\r
+ public java.lang.String getGroupRef(\r
+ ) {\r
+ return this._groupRef;\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 'scaleColLabels'.\r
+ * \r
+ * @return the value of field 'ScaleColLabels'.\r
+ */\r
+ public boolean getScaleColLabels(\r
+ ) {\r
+ return this._scaleColLabels;\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 'showAllColLabels'.\r
+ * \r
+ * @return the value of field 'ShowAllColLabels'.\r
+ */\r
+ public boolean getShowAllColLabels(\r
+ ) {\r
+ return this._showAllColLabels;\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 hasAutoCalculated.\r
+ * \r
+ * @return true if at least one AutoCalculated has been added\r
+ */\r
+ public boolean hasAutoCalculated(\r
+ ) {\r
+ return this._has_autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Method hasCentreColLabels.\r
+ * \r
+ * @return true if at least one CentreColLabels has been added\r
+ */\r
+ public boolean hasCentreColLabels(\r
+ ) {\r
+ return this._has_centreColLabels;\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 hasScaleColLabels.\r
+ * \r
+ * @return true if at least one ScaleColLabels has been added\r
+ */\r
+ public boolean hasScaleColLabels(\r
+ ) {\r
+ return this._has_scaleColLabels;\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 hasShowAllColLabels.\r
+ * \r
+ * @return true if at least one ShowAllColLabels has been added\r
+ */\r
+ public boolean hasShowAllColLabels(\r
+ ) {\r
+ return this._has_showAllColLabels;\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 'autoCalculated'. The field\r
+ * 'autoCalculated' has the following description: is an\r
+ * autocalculated annotation row\r
+ * \r
+ * @return the value of field 'AutoCalculated'.\r
+ */\r
+ public boolean isAutoCalculated(\r
+ ) {\r
+ return this._autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColLabels'.\r
+ * \r
+ * @return the value of field 'CentreColLabels'.\r
+ */\r
+ public boolean isCentreColLabels(\r
+ ) {\r
+ return this._centreColLabels;\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 'scaleColLabels'.\r
+ * \r
+ * @return the value of field 'ScaleColLabels'.\r
+ */\r
+ public boolean isScaleColLabels(\r
+ ) {\r
+ return this._scaleColLabels;\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
+ * Returns the value of field 'showAllColLabels'.\r
+ * \r
+ * @return the value of field 'ShowAllColLabels'.\r
+ */\r
+ public boolean isShowAllColLabels(\r
+ ) {\r
+ return this._showAllColLabels;\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 'autoCalculated'. The field\r
+ * 'autoCalculated' has the following description: is an\r
+ * autocalculated annotation row\r
+ * \r
+ * @param autoCalculated the value of field 'autoCalculated'.\r
+ */\r
+ public void setAutoCalculated(\r
+ final boolean autoCalculated) {\r
+ this._autoCalculated = autoCalculated;\r
+ this._has_autoCalculated = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'centreColLabels'.\r
+ * \r
+ * @param centreColLabels the value of field 'centreColLabels'.\r
+ */\r
+ public void setCentreColLabels(\r
+ final boolean centreColLabels) {\r
+ this._centreColLabels = centreColLabels;\r
+ this._has_centreColLabels = true;\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 'groupRef'.\r
+ * \r
+ * @param groupRef the value of field 'groupRef'.\r
+ */\r
+ public void setGroupRef(\r
+ final java.lang.String groupRef) {\r
+ this._groupRef = groupRef;\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 'scaleColLabels'.\r
+ * \r
+ * @param scaleColLabels the value of field 'scaleColLabels'.\r
+ */\r
+ public void setScaleColLabels(\r
+ final boolean scaleColLabels) {\r
+ this._scaleColLabels = scaleColLabels;\r
+ this._has_scaleColLabels = true;\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 'showAllColLabels'.\r
+ * \r
+ * @param showAllColLabels the value of field 'showAllColLabels'\r
+ */\r
+ public void setShowAllColLabels(\r
+ final boolean showAllColLabels) {\r
+ this._showAllColLabels = showAllColLabels;\r
+ this._has_showAllColLabels = true;\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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationColours implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _aboveThreshold.\r
- */\r
- private int _aboveThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _aboveThreshold\r
- */\r
- private boolean _has_aboveThreshold;\r
-\r
- /**\r
- * Field _annotation.\r
- */\r
- private java.lang.String _annotation;\r
-\r
- /**\r
- * Field _minColour.\r
- */\r
- private int _minColour;\r
-\r
- /**\r
- * keeps track of state for field: _minColour\r
- */\r
- private boolean _has_minColour;\r
-\r
- /**\r
- * Field _maxColour.\r
- */\r
- private int _maxColour;\r
-\r
- /**\r
- * keeps track of state for field: _maxColour\r
- */\r
- private boolean _has_maxColour;\r
-\r
- /**\r
- * Field _colourScheme.\r
- */\r
- private java.lang.String _colourScheme;\r
-\r
- /**\r
- * Field _threshold.\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationColours()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteAboveThreshold()\r
- {\r
- this._has_aboveThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMaxColour()\r
- {\r
- this._has_maxColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMinColour()\r
- {\r
- this._has_minColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'aboveThreshold'.\r
- * \r
- * @return the value of field 'AboveThreshold'.\r
- */\r
- public int getAboveThreshold()\r
- {\r
- return this._aboveThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'annotation'.\r
- * \r
- * @return the value of field 'Annotation'.\r
- */\r
- public java.lang.String getAnnotation()\r
- {\r
- return this._annotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourScheme'.\r
- * \r
- * @return the value of field 'ColourScheme'.\r
- */\r
- public java.lang.String getColourScheme()\r
- {\r
- return this._colourScheme;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'maxColour'.\r
- * \r
- * @return the value of field 'MaxColour'.\r
- */\r
- public int getMaxColour()\r
- {\r
- return this._maxColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'minColour'.\r
- * \r
- * @return the value of field 'MinColour'.\r
- */\r
- public int getMinColour()\r
- {\r
- return this._minColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- }\r
-\r
- /**\r
- * Method hasAboveThreshold.\r
- * \r
- * @return true if at least one AboveThreshold has been added\r
- */\r
- public boolean hasAboveThreshold()\r
- {\r
- return this._has_aboveThreshold;\r
- }\r
-\r
- /**\r
- * Method hasMaxColour.\r
- * \r
- * @return true if at least one MaxColour has been added\r
- */\r
- public boolean hasMaxColour()\r
- {\r
- return this._has_maxColour;\r
- }\r
-\r
- /**\r
- * Method hasMinColour.\r
- * \r
- * @return true if at least one MinColour has been added\r
- */\r
- public boolean hasMinColour()\r
- {\r
- return this._has_minColour;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class AnnotationColours implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _aboveThreshold.\r
+ */\r
+ private int _aboveThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _aboveThreshold\r
+ */\r
+ private boolean _has_aboveThreshold;\r
+\r
+ /**\r
+ * Field _annotation.\r
+ */\r
+ private java.lang.String _annotation;\r
+\r
+ /**\r
+ * Field _minColour.\r
+ */\r
+ private int _minColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _minColour\r
+ */\r
+ private boolean _has_minColour;\r
+\r
+ /**\r
+ * Field _maxColour.\r
+ */\r
+ private int _maxColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _maxColour\r
+ */\r
+ private boolean _has_maxColour;\r
+\r
+ /**\r
+ * Field _colourScheme.\r
+ */\r
+ private java.lang.String _colourScheme;\r
+\r
+ /**\r
+ * Field _threshold.\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationColours() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteAboveThreshold(\r
+ ) {\r
+ this._has_aboveThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMaxColour(\r
+ ) {\r
+ this._has_maxColour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMinColour(\r
+ ) {\r
+ this._has_minColour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'aboveThreshold'.\r
+ * \r
+ * @return the value of field 'AboveThreshold'.\r
+ */\r
+ public int getAboveThreshold(\r
+ ) {\r
+ return this._aboveThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'annotation'.\r
+ * \r
+ * @return the value of field 'Annotation'.\r
+ */\r
+ public java.lang.String getAnnotation(\r
+ ) {\r
+ return this._annotation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourScheme'.\r
+ * \r
+ * @return the value of field 'ColourScheme'.\r
+ */\r
+ public java.lang.String getColourScheme(\r
+ ) {\r
+ return this._colourScheme;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'maxColour'.\r
+ * \r
+ * @return the value of field 'MaxColour'.\r
+ */\r
+ public int getMaxColour(\r
+ ) {\r
+ return this._maxColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'minColour'.\r
+ * \r
+ * @return the value of field 'MinColour'.\r
+ */\r
+ public int getMinColour(\r
+ ) {\r
+ return this._minColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshold'.\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasAboveThreshold.\r
+ * \r
+ * @return true if at least one AboveThreshold has been added\r
+ */\r
+ public boolean hasAboveThreshold(\r
+ ) {\r
+ return this._has_aboveThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasMaxColour.\r
+ * \r
+ * @return true if at least one MaxColour has been added\r
+ */\r
+ public boolean hasMaxColour(\r
+ ) {\r
+ return this._has_maxColour;\r
+ }\r
+\r
+ /**\r
+ * Method hasMinColour.\r
+ * \r
+ * @return true if at least one MinColour has been added\r
+ */\r
+ public boolean hasMinColour(\r
+ ) {\r
+ return this._has_minColour;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\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
+ * \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
+ * Sets the value of field 'aboveThreshold'.\r
+ * \r
+ * @param aboveThreshold the value of field 'aboveThreshold'.\r
+ */\r
+ public void setAboveThreshold(\r
+ final int aboveThreshold) {\r
+ this._aboveThreshold = aboveThreshold;\r
+ this._has_aboveThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'annotation'.\r
+ * \r
+ * @param annotation the value of field 'annotation'.\r
+ */\r
+ public void setAnnotation(\r
+ final java.lang.String annotation) {\r
+ this._annotation = annotation;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colourScheme'.\r
+ * \r
+ * @param colourScheme the value of field 'colourScheme'.\r
+ */\r
+ public void setColourScheme(\r
+ final java.lang.String colourScheme) {\r
+ this._colourScheme = colourScheme;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'maxColour'.\r
+ * \r
+ * @param maxColour the value of field 'maxColour'.\r
+ */\r
+ public void setMaxColour(\r
+ final int maxColour) {\r
+ this._maxColour = maxColour;\r
+ this._has_maxColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'minColour'.\r
+ * \r
+ * @param minColour the value of field 'minColour'.\r
+ */\r
+ public void setMinColour(\r
+ final int minColour) {\r
+ this._minColour = minColour;\r
+ this._has_minColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshold'.\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = 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.AnnotationColours\r
+ */\r
+ public static jalview.schemabinding.version2.AnnotationColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.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
- return true;\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 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 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
- * Sets the value of field 'aboveThreshold'.\r
- * \r
- * @param aboveThreshold\r
- * the value of field 'aboveThreshold'.\r
- */\r
- public void setAboveThreshold(final int aboveThreshold)\r
- {\r
- this._aboveThreshold = aboveThreshold;\r
- this._has_aboveThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'annotation'.\r
- * \r
- * @param annotation\r
- * the value of field 'annotation'.\r
- */\r
- public void setAnnotation(final java.lang.String annotation)\r
- {\r
- this._annotation = annotation;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourScheme'.\r
- * \r
- * @param colourScheme\r
- * the value of field 'colourScheme'.\r
- */\r
- public void setColourScheme(final java.lang.String colourScheme)\r
- {\r
- this._colourScheme = colourScheme;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'maxColour'.\r
- * \r
- * @param maxColour\r
- * the value of field 'maxColour'.\r
- */\r
- public void setMaxColour(final int maxColour)\r
- {\r
- this._maxColour = maxColour;\r
- this._has_maxColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'minColour'.\r
- * \r
- * @param minColour\r
- * the value of field 'minColour'.\r
- */\r
- public void setMinColour(final int minColour)\r
- {\r
- this._minColour = minColour;\r
- this._has_minColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.AnnotationColours\r
- */\r
- public static jalview.schemabinding.version2.AnnotationColours 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.AnnotationColours) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.AnnotationColours.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationElement implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _position.\r
- */\r
- private int _position;\r
-\r
- /**\r
- * keeps track of state for field: _position\r
- */\r
- private boolean _has_position;\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _displayCharacter.\r
- */\r
- private java.lang.String _displayCharacter;\r
-\r
- /**\r
- * Field _description.\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _secondaryStructure.\r
- */\r
- private java.lang.String _secondaryStructure;\r
-\r
- /**\r
- * Field _value.\r
- */\r
- private float _value;\r
-\r
- /**\r
- * keeps track of state for field: _value\r
- */\r
- private boolean _has_value;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationElement()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePosition()\r
- {\r
- this._has_position = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteValue()\r
- {\r
- this._has_value = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\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 'displayCharacter'.\r
- * \r
- * @return the value of field 'DisplayCharacter'.\r
- */\r
- public java.lang.String getDisplayCharacter()\r
- {\r
- return this._displayCharacter;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'position'.\r
- * \r
- * @return the value of field 'Position'.\r
- */\r
- public int getPosition()\r
- {\r
- return this._position;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'secondaryStructure'.\r
- * \r
- * @return the value of field 'SecondaryStructure'.\r
- */\r
- public java.lang.String getSecondaryStructure()\r
- {\r
- return this._secondaryStructure;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return the value of field 'Value'.\r
- */\r
- public float getValue()\r
- {\r
- return this._value;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasPosition.\r
- * \r
- * @return true if at least one Position has been added\r
- */\r
- public boolean hasPosition()\r
- {\r
- return this._has_position;\r
- }\r
-\r
- /**\r
- * Method hasValue.\r
- * \r
- * @return true if at least one Value has been added\r
- */\r
- public boolean hasValue()\r
- {\r
- return this._has_value;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class AnnotationElement implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _position.\r
+ */\r
+ private int _position;\r
+\r
+ /**\r
+ * keeps track of state for field: _position\r
+ */\r
+ private boolean _has_position;\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
+ * Field _displayCharacter.\r
+ */\r
+ private java.lang.String _displayCharacter;\r
+\r
+ /**\r
+ * Field _description.\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _secondaryStructure.\r
+ */\r
+ private java.lang.String _secondaryStructure;\r
+\r
+ /**\r
+ * Field _value.\r
+ */\r
+ private float _value;\r
+\r
+ /**\r
+ * keeps track of state for field: _value\r
+ */\r
+ private boolean _has_value;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationElement() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteColour(\r
+ ) {\r
+ this._has_colour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePosition(\r
+ ) {\r
+ this._has_position= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteValue(\r
+ ) {\r
+ this._has_value= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour(\r
+ ) {\r
+ return this._colour;\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 'displayCharacter'.\r
+ * \r
+ * @return the value of field 'DisplayCharacter'.\r
+ */\r
+ public java.lang.String getDisplayCharacter(\r
+ ) {\r
+ return this._displayCharacter;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'position'.\r
+ * \r
+ * @return the value of field 'Position'.\r
+ */\r
+ public int getPosition(\r
+ ) {\r
+ return this._position;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'secondaryStructure'.\r
+ * \r
+ * @return the value of field 'SecondaryStructure'.\r
+ */\r
+ public java.lang.String getSecondaryStructure(\r
+ ) {\r
+ return this._secondaryStructure;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'value'.\r
+ * \r
+ * @return the value of field 'Value'.\r
+ */\r
+ public float getValue(\r
+ ) {\r
+ return this._value;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour(\r
+ ) {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasPosition.\r
+ * \r
+ * @return true if at least one Position has been added\r
+ */\r
+ public boolean hasPosition(\r
+ ) {\r
+ return this._has_position;\r
+ }\r
+\r
+ /**\r
+ * Method hasValue.\r
+ * \r
+ * @return true if at least one Value has been added\r
+ */\r
+ public boolean hasValue(\r
+ ) {\r
+ return this._has_value;\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
+ * \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
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final int colour) {\r
+ this._colour = colour;\r
+ this._has_colour = true;\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 'displayCharacter'.\r
+ * \r
+ * @param displayCharacter the value of field 'displayCharacter'\r
+ */\r
+ public void setDisplayCharacter(\r
+ final java.lang.String displayCharacter) {\r
+ this._displayCharacter = displayCharacter;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'position'.\r
+ * \r
+ * @param position the value of field 'position'.\r
+ */\r
+ public void setPosition(\r
+ final int position) {\r
+ this._position = position;\r
+ this._has_position = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'secondaryStructure'.\r
+ * \r
+ * @param secondaryStructure the value of field\r
+ * 'secondaryStructure'.\r
+ */\r
+ public void setSecondaryStructure(\r
+ final java.lang.String secondaryStructure) {\r
+ this._secondaryStructure = secondaryStructure;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'value'.\r
+ * \r
+ * @param value the value of field 'value'.\r
+ */\r
+ public void setValue(\r
+ final float value) {\r
+ this._value = value;\r
+ this._has_value = 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.AnnotationElement\r
+ */\r
+ public static jalview.schemabinding.version2.AnnotationElement unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.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
- return true;\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 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 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
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\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 'displayCharacter'.\r
- * \r
- * @param displayCharacter\r
- * the value of field 'displayCharacter'\r
- */\r
- public void setDisplayCharacter(final java.lang.String displayCharacter)\r
- {\r
- this._displayCharacter = displayCharacter;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'position'.\r
- * \r
- * @param position\r
- * the value of field 'position'.\r
- */\r
- public void setPosition(final int position)\r
- {\r
- this._position = position;\r
- this._has_position = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'secondaryStructure'.\r
- * \r
- * @param secondaryStructure\r
- * the value of field 'secondaryStructure'.\r
- */\r
- public void setSecondaryStructure(\r
- final java.lang.String secondaryStructure)\r
- {\r
- this._secondaryStructure = secondaryStructure;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value\r
- * the value of field 'value'.\r
- */\r
- public void setValue(final float value)\r
- {\r
- this._value = value;\r
- this._has_value = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement\r
- */\r
- public static jalview.schemabinding.version2.AnnotationElement 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.AnnotationElement) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.AnnotationElement.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Colour implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _RGB.\r
- */\r
- private java.lang.String _RGB;\r
-\r
- /**\r
- * Field _minRGB.\r
- */\r
- private java.lang.String _minRGB;\r
-\r
- /**\r
- * loosely specified enumeration: NONE,ABOVE, or BELOW\r
- */\r
- private java.lang.String _threshType;\r
-\r
- /**\r
- * Field _threshold.\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- /**\r
- * Field _max.\r
- */\r
- private float _max;\r
-\r
- /**\r
- * keeps track of state for field: _max\r
- */\r
- private boolean _has_max;\r
-\r
- /**\r
- * Field _min.\r
- */\r
- private float _min;\r
-\r
- /**\r
- * keeps track of state for field: _min\r
- */\r
- private boolean _has_min;\r
-\r
- /**\r
- * Field _colourByLabel.\r
- */\r
- private boolean _colourByLabel;\r
-\r
- /**\r
- * keeps track of state for field: _colourByLabel\r
- */\r
- private boolean _has_colourByLabel;\r
-\r
- /**\r
- * Field _autoScale.\r
- */\r
- private boolean _autoScale;\r
-\r
- /**\r
- * keeps track of state for field: _autoScale\r
- */\r
- private boolean _has_autoScale;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Colour()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteAutoScale()\r
- {\r
- this._has_autoScale = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColourByLabel()\r
- {\r
- this._has_colourByLabel = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMax()\r
- {\r
- this._has_max = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMin()\r
- {\r
- this._has_min = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoScale'.\r
- * \r
- * @return the value of field 'AutoScale'.\r
- */\r
- public boolean getAutoScale()\r
- {\r
- return this._autoScale;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourByLabel'.\r
- * \r
- * @return the value of field 'ColourByLabel'.\r
- */\r
- public boolean getColourByLabel()\r
- {\r
- return this._colourByLabel;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'max'.\r
- * \r
- * @return the value of field 'Max'.\r
- */\r
- public float getMax()\r
- {\r
- return this._max;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'min'.\r
- * \r
- * @return the value of field 'Min'.\r
- */\r
- public float getMin()\r
- {\r
- return this._min;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'minRGB'.\r
- * \r
- * @return the value of field 'MinRGB'.\r
- */\r
- public java.lang.String getMinRGB()\r
- {\r
- return this._minRGB;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'RGB'.\r
- * \r
- * @return the value of field 'RGB'.\r
- */\r
- public java.lang.String getRGB()\r
- {\r
- return this._RGB;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshType'. The field 'threshType' has the\r
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW\r
- * \r
- * @return the value of field 'ThreshType'.\r
- */\r
- public java.lang.String getThreshType()\r
- {\r
- return this._threshType;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- }\r
-\r
- /**\r
- * Method hasAutoScale.\r
- * \r
- * @return true if at least one AutoScale has been added\r
- */\r
- public boolean hasAutoScale()\r
- {\r
- return this._has_autoScale;\r
- }\r
-\r
- /**\r
- * Method hasColourByLabel.\r
- * \r
- * @return true if at least one ColourByLabel has been added\r
- */\r
- public boolean hasColourByLabel()\r
- {\r
- return this._has_colourByLabel;\r
- }\r
-\r
- /**\r
- * Method hasMax.\r
- * \r
- * @return true if at least one Max has been added\r
- */\r
- public boolean hasMax()\r
- {\r
- return this._has_max;\r
- }\r
-\r
- /**\r
- * Method hasMin.\r
- * \r
- * @return true if at least one Min has been added\r
- */\r
- public boolean hasMin()\r
- {\r
- return this._has_min;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoScale'.\r
- * \r
- * @return the value of field 'AutoScale'.\r
- */\r
- public boolean isAutoScale()\r
- {\r
- return this._autoScale;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourByLabel'.\r
- * \r
- * @return the value of field 'ColourByLabel'.\r
- */\r
- public boolean isColourByLabel()\r
- {\r
- return this._colourByLabel;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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
- * Sets the value of field 'autoScale'.\r
- * \r
- * @param autoScale\r
- * the value of field 'autoScale'.\r
- */\r
- public void setAutoScale(final boolean autoScale)\r
- {\r
- this._autoScale = autoScale;\r
- this._has_autoScale = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourByLabel'.\r
- * \r
- * @param colourByLabel\r
- * the value of field 'colourByLabel'.\r
- */\r
- public void setColourByLabel(final boolean colourByLabel)\r
- {\r
- this._colourByLabel = colourByLabel;\r
- this._has_colourByLabel = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'max'.\r
- * \r
- * @param max\r
- * the value of field 'max'.\r
- */\r
- public void setMax(final float max)\r
- {\r
- this._max = max;\r
- this._has_max = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'min'.\r
- * \r
- * @param min\r
- * the value of field 'min'.\r
- */\r
- public void setMin(final float min)\r
- {\r
- this._min = min;\r
- this._has_min = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'minRGB'.\r
- * \r
- * @param minRGB\r
- * the value of field 'minRGB'.\r
- */\r
- public void setMinRGB(final java.lang.String minRGB)\r
- {\r
- this._minRGB = minRGB;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'RGB'.\r
- * \r
- * @param RGB\r
- * the value of field 'RGB'.\r
- */\r
- public void setRGB(final java.lang.String RGB)\r
- {\r
- this._RGB = RGB;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshType'. The field 'threshType' has the\r
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW\r
- * \r
- * @param threshType\r
- * the value of field 'threshType'.\r
- */\r
- public void setThreshType(final java.lang.String threshType)\r
- {\r
- this._threshType = threshType;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Colour\r
- */\r
- public static jalview.schemabinding.version2.Colour 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.Colour) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Colour.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class Colour implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _name.\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _RGB.\r
+ */\r
+ private java.lang.String _RGB;\r
+\r
+ /**\r
+ * Field _minRGB.\r
+ */\r
+ private java.lang.String _minRGB;\r
+\r
+ /**\r
+ * loosely specified enumeration: NONE,ABOVE, or BELOW\r
+ */\r
+ private java.lang.String _threshType;\r
+\r
+ /**\r
+ * Field _threshold.\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+ /**\r
+ * Field _max.\r
+ */\r
+ private float _max;\r
+\r
+ /**\r
+ * keeps track of state for field: _max\r
+ */\r
+ private boolean _has_max;\r
+\r
+ /**\r
+ * Field _min.\r
+ */\r
+ private float _min;\r
+\r
+ /**\r
+ * keeps track of state for field: _min\r
+ */\r
+ private boolean _has_min;\r
+\r
+ /**\r
+ * Field _colourByLabel.\r
+ */\r
+ private boolean _colourByLabel;\r
+\r
+ /**\r
+ * keeps track of state for field: _colourByLabel\r
+ */\r
+ private boolean _has_colourByLabel;\r
+\r
+ /**\r
+ * Field _autoScale.\r
+ */\r
+ private boolean _autoScale;\r
+\r
+ /**\r
+ * keeps track of state for field: _autoScale\r
+ */\r
+ private boolean _has_autoScale;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Colour() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteAutoScale(\r
+ ) {\r
+ this._has_autoScale= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColourByLabel(\r
+ ) {\r
+ this._has_colourByLabel= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMax(\r
+ ) {\r
+ this._has_max= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMin(\r
+ ) {\r
+ this._has_min= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean getAutoScale(\r
+ ) {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean getColourByLabel(\r
+ ) {\r
+ return this._colourByLabel;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'max'.\r
+ * \r
+ * @return the value of field 'Max'.\r
+ */\r
+ public float getMax(\r
+ ) {\r
+ return this._max;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'min'.\r
+ * \r
+ * @return the value of field 'Min'.\r
+ */\r
+ public float getMin(\r
+ ) {\r
+ return this._min;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'minRGB'.\r
+ * \r
+ * @return the value of field 'MinRGB'.\r
+ */\r
+ public java.lang.String getMinRGB(\r
+ ) {\r
+ return this._minRGB;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return the value of field 'Name'.\r
+ */\r
+ public java.lang.String getName(\r
+ ) {\r
+ return this._name;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'RGB'.\r
+ * \r
+ * @return the value of field 'RGB'.\r
+ */\r
+ public java.lang.String getRGB(\r
+ ) {\r
+ return this._RGB;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshType'. The field\r
+ * 'threshType' has the following description: loosely\r
+ * specified enumeration: NONE,ABOVE, or BELOW\r
+ * \r
+ * @return the value of field 'ThreshType'.\r
+ */\r
+ public java.lang.String getThreshType(\r
+ ) {\r
+ return this._threshType;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshold'.\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasAutoScale.\r
+ * \r
+ * @return true if at least one AutoScale has been added\r
+ */\r
+ public boolean hasAutoScale(\r
+ ) {\r
+ return this._has_autoScale;\r
+ }\r
+\r
+ /**\r
+ * Method hasColourByLabel.\r
+ * \r
+ * @return true if at least one ColourByLabel has been added\r
+ */\r
+ public boolean hasColourByLabel(\r
+ ) {\r
+ return this._has_colourByLabel;\r
+ }\r
+\r
+ /**\r
+ * Method hasMax.\r
+ * \r
+ * @return true if at least one Max has been added\r
+ */\r
+ public boolean hasMax(\r
+ ) {\r
+ return this._has_max;\r
+ }\r
+\r
+ /**\r
+ * Method hasMin.\r
+ * \r
+ * @return true if at least one Min has been added\r
+ */\r
+ public boolean hasMin(\r
+ ) {\r
+ return this._has_min;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean isAutoScale(\r
+ ) {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean isColourByLabel(\r
+ ) {\r
+ return this._colourByLabel;\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
+ * \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
+ * Sets the value of field 'autoScale'.\r
+ * \r
+ * @param autoScale the value of field 'autoScale'.\r
+ */\r
+ public void setAutoScale(\r
+ final boolean autoScale) {\r
+ this._autoScale = autoScale;\r
+ this._has_autoScale = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colourByLabel'.\r
+ * \r
+ * @param colourByLabel the value of field 'colourByLabel'.\r
+ */\r
+ public void setColourByLabel(\r
+ final boolean colourByLabel) {\r
+ this._colourByLabel = colourByLabel;\r
+ this._has_colourByLabel = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'max'.\r
+ * \r
+ * @param max the value of field 'max'.\r
+ */\r
+ public void setMax(\r
+ final float max) {\r
+ this._max = max;\r
+ this._has_max = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'min'.\r
+ * \r
+ * @param min the value of field 'min'.\r
+ */\r
+ public void setMin(\r
+ final float min) {\r
+ this._min = min;\r
+ this._has_min = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'minRGB'.\r
+ * \r
+ * @param minRGB the value of field 'minRGB'.\r
+ */\r
+ public void setMinRGB(\r
+ final java.lang.String minRGB) {\r
+ this._minRGB = minRGB;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(\r
+ final java.lang.String name) {\r
+ this._name = name;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'RGB'.\r
+ * \r
+ * @param RGB the value of field 'RGB'.\r
+ */\r
+ public void setRGB(\r
+ final java.lang.String RGB) {\r
+ this._RGB = RGB;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshType'. The field 'threshType'\r
+ * has the following description: loosely specified\r
+ * enumeration: NONE,ABOVE, or BELOW\r
+ * \r
+ * @param threshType the value of field 'threshType'.\r
+ */\r
+ public void setThreshType(\r
+ final java.lang.String threshType) {\r
+ this._threshType = threshType;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshold'.\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = 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 jalview.schemabinding.version2.Colour\r
+ */\r
+ public static jalview.schemabinding.version2.Colour unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class DBRef implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _source.\r
- */\r
- private java.lang.String _source;\r
-\r
- /**\r
- * Field _version.\r
- */\r
- private java.lang.String _version;\r
-\r
- /**\r
- * Field _accessionId.\r
- */\r
- private java.lang.String _accessionId;\r
-\r
- /**\r
- * Field _mapping.\r
- */\r
- private jalview.schemabinding.version2.Mapping _mapping;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public DBRef()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'accessionId'.\r
- * \r
- * @return the value of field 'AccessionId'.\r
- */\r
- public java.lang.String getAccessionId()\r
- {\r
- return this._accessionId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapping'.\r
- * \r
- * @return the value of field 'Mapping'.\r
- */\r
- public jalview.schemabinding.version2.Mapping getMapping()\r
- {\r
- return this._mapping;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'source'.\r
- * \r
- * @return the value of field 'Source'.\r
- */\r
- public java.lang.String getSource()\r
- {\r
- return this._source;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'version'.\r
- * \r
- * @return the value of field 'Version'.\r
- */\r
- public java.lang.String getVersion()\r
- {\r
- return this._version;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class DBRef implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _source.\r
+ */\r
+ private java.lang.String _source;\r
+\r
+ /**\r
+ * Field _version.\r
+ */\r
+ private java.lang.String _version;\r
+\r
+ /**\r
+ * Field _accessionId.\r
+ */\r
+ private java.lang.String _accessionId;\r
+\r
+ /**\r
+ * Field _mapping.\r
+ */\r
+ private jalview.schemabinding.version2.Mapping _mapping;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public DBRef() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'accessionId'.\r
+ * \r
+ * @return the value of field 'AccessionId'.\r
+ */\r
+ public java.lang.String getAccessionId(\r
+ ) {\r
+ return this._accessionId;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapping'.\r
+ * \r
+ * @return the value of field 'Mapping'.\r
+ */\r
+ public jalview.schemabinding.version2.Mapping getMapping(\r
+ ) {\r
+ return this._mapping;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'source'.\r
+ * \r
+ * @return the value of field 'Source'.\r
+ */\r
+ public java.lang.String getSource(\r
+ ) {\r
+ return this._source;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'version'.\r
+ * \r
+ * @return the value of field 'Version'.\r
+ */\r
+ public java.lang.String getVersion(\r
+ ) {\r
+ return this._version;\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
+ * \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
+ * Sets the value of field 'accessionId'.\r
+ * \r
+ * @param accessionId the value of field 'accessionId'.\r
+ */\r
+ public void setAccessionId(\r
+ final java.lang.String accessionId) {\r
+ this._accessionId = accessionId;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapping'.\r
+ * \r
+ * @param mapping the value of field 'mapping'.\r
+ */\r
+ public void setMapping(\r
+ final jalview.schemabinding.version2.Mapping mapping) {\r
+ this._mapping = mapping;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'source'.\r
+ * \r
+ * @param source the value of field 'source'.\r
+ */\r
+ public void setSource(\r
+ final java.lang.String source) {\r
+ this._source = source;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'version'.\r
+ * \r
+ * @param version the value of field 'version'.\r
+ */\r
+ public void setVersion(\r
+ final java.lang.String version) {\r
+ this._version = version;\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 jalview.schemabinding.version2.DBRef\r
+ */\r
+ public static jalview.schemabinding.version2.DBRef unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.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
- return true;\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 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 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
- * Sets the value of field 'accessionId'.\r
- * \r
- * @param accessionId\r
- * the value of field 'accessionId'.\r
- */\r
- public void setAccessionId(final java.lang.String accessionId)\r
- {\r
- this._accessionId = accessionId;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapping'.\r
- * \r
- * @param mapping\r
- * the value of field 'mapping'.\r
- */\r
- public void setMapping(\r
- final jalview.schemabinding.version2.Mapping mapping)\r
- {\r
- this._mapping = mapping;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'source'.\r
- * \r
- * @param source\r
- * the value of field 'source'.\r
- */\r
- public void setSource(final java.lang.String source)\r
- {\r
- this._source = source;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'version'.\r
- * \r
- * @param version\r
- * the value of field 'version'.\r
- */\r
- public void setVersion(final java.lang.String version)\r
- {\r
- this._version = version;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.DBRef\r
- */\r
- public static jalview.schemabinding.version2.DBRef 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.DBRef) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.DBRef.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Feature implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _begin.\r
- */\r
- private int _begin;\r
-\r
- /**\r
- * keeps track of state for field: _begin\r
- */\r
- private boolean _has_begin;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _description.\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _status.\r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Field _featureGroup.\r
- */\r
- private java.lang.String _featureGroup;\r
-\r
- /**\r
- * Field _score.\r
- */\r
- private float _score;\r
-\r
- /**\r
- * keeps track of state for field: _score\r
- */\r
- private boolean _has_score;\r
-\r
- /**\r
- * Field _otherDataList.\r
- */\r
- private java.util.Vector _otherDataList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Feature()\r
- {\r
- super();\r
- this._otherDataList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addOtherData(\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._otherDataList.addElement(vOtherData);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addOtherData(final int index,\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._otherDataList.add(index, vOtherData);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteBegin()\r
- {\r
- this._has_begin = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteScore()\r
- {\r
- this._has_score = false;\r
- }\r
-\r
- /**\r
- * Method enumerateOtherData.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.OtherData\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateOtherData()\r
- {\r
- return this._otherDataList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'begin'.\r
- * \r
- * @return the value of field 'Begin'.\r
- */\r
- public int getBegin()\r
- {\r
- return this._begin;\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 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'featureGroup'.\r
- * \r
- * @return the value of field 'FeatureGroup'.\r
- */\r
- public java.lang.String getFeatureGroup()\r
- {\r
- return this._featureGroup;\r
- }\r
-\r
- /**\r
- * Method getOtherData.\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.OtherData at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.OtherData getOtherData(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._otherDataList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getOtherData: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._otherDataList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.OtherData) _otherDataList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getOtherData.Returns the contents of the collection in an 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.OtherData[] getOtherData()\r
- {\r
- jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];\r
- return (jalview.schemabinding.version2.OtherData[]) this._otherDataList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getOtherDataCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getOtherDataCount()\r
- {\r
- return this._otherDataList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'score'.\r
- * \r
- * @return the value of field 'Score'.\r
- */\r
- public float getScore()\r
- {\r
- return this._score;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'status'.\r
- * \r
- * @return the value of field 'Status'.\r
- */\r
- public java.lang.String getStatus()\r
- {\r
- return this._status;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- }\r
-\r
- /**\r
- * Method hasBegin.\r
- * \r
- * @return true if at least one Begin has been added\r
- */\r
- public boolean hasBegin()\r
- {\r
- return this._has_begin;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\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 isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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 removeAllOtherData()\r
- {\r
- this._otherDataList.clear();\r
- }\r
-\r
- /**\r
- * Method removeOtherData.\r
- * \r
- * @param vOtherData\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeOtherData(\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- {\r
- boolean removed = _otherDataList.remove(vOtherData);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeOtherDataAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.OtherData removeOtherDataAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._otherDataList.remove(index);\r
- return (jalview.schemabinding.version2.OtherData) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'begin'.\r
- * \r
- * @param begin\r
- * the value of field 'begin'.\r
- */\r
- public void setBegin(final int begin)\r
- {\r
- this._begin = begin;\r
- this._has_begin = true;\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 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'featureGroup'.\r
- * \r
- * @param featureGroup\r
- * the value of field 'featureGroup'.\r
- */\r
- public void setFeatureGroup(final java.lang.String featureGroup)\r
- {\r
- this._featureGroup = featureGroup;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setOtherData(final int index,\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._otherDataList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setOtherData: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._otherDataList.size() - 1) + "]");\r
- }\r
-\r
- this._otherDataList.set(index, vOtherData);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vOtherDataArray\r
- */\r
- public void setOtherData(\r
- final jalview.schemabinding.version2.OtherData[] vOtherDataArray)\r
- {\r
- // -- copy array\r
- _otherDataList.clear();\r
-\r
- for (int i = 0; i < vOtherDataArray.length; i++)\r
- {\r
- this._otherDataList.add(vOtherDataArray[i]);\r
- }\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 float score)\r
- {\r
- this._score = score;\r
- this._has_score = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'status'.\r
- * \r
- * @param status\r
- * the value of field 'status'.\r
- */\r
- public void setStatus(final java.lang.String status)\r
- {\r
- this._status = status;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Featur\r
- */\r
- public static jalview.schemabinding.version2.Feature 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.Feature) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Feature.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class Feature implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _begin.\r
+ */\r
+ private int _begin;\r
+\r
+ /**\r
+ * keeps track of state for field: _begin\r
+ */\r
+ private boolean _has_begin;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _type.\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _description.\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _status.\r
+ */\r
+ private java.lang.String _status;\r
+\r
+ /**\r
+ * Field _featureGroup.\r
+ */\r
+ private java.lang.String _featureGroup;\r
+\r
+ /**\r
+ * Field _score.\r
+ */\r
+ private float _score;\r
+\r
+ /**\r
+ * keeps track of state for field: _score\r
+ */\r
+ private boolean _has_score;\r
+\r
+ /**\r
+ * Field _otherDataList.\r
+ */\r
+ private java.util.Vector _otherDataList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Feature() {\r
+ super();\r
+ this._otherDataList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vOtherData\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addOtherData(\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._otherDataList.addElement(vOtherData);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vOtherData\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addOtherData(\r
+ final int index,\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._otherDataList.add(index, vOtherData);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteBegin(\r
+ ) {\r
+ this._has_begin= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScore(\r
+ ) {\r
+ this._has_score= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateOtherData.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.OtherData elements\r
+ */\r
+ public java.util.Enumeration enumerateOtherData(\r
+ ) {\r
+ return this._otherDataList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'begin'.\r
+ * \r
+ * @return the value of field 'Begin'.\r
+ */\r
+ public int getBegin(\r
+ ) {\r
+ return this._begin;\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 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'featureGroup'.\r
+ * \r
+ * @return the value of field 'FeatureGroup'.\r
+ */\r
+ public java.lang.String getFeatureGroup(\r
+ ) {\r
+ return this._featureGroup;\r
+ }\r
+\r
+ /**\r
+ * Method getOtherData.\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.OtherData at the given index\r
+ */\r
+ public jalview.schemabinding.version2.OtherData getOtherData(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._otherDataList.size()) {\r
+ throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getOtherData.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.OtherData[] getOtherData(\r
+ ) {\r
+ jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];\r
+ return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getOtherDataCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getOtherDataCount(\r
+ ) {\r
+ return this._otherDataList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'score'.\r
+ * \r
+ * @return the value of field 'Score'.\r
+ */\r
+ public float getScore(\r
+ ) {\r
+ return this._score;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'status'.\r
+ * \r
+ * @return the value of field 'Status'.\r
+ */\r
+ public java.lang.String getStatus(\r
+ ) {\r
+ return this._status;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return the value of field 'Type'.\r
+ */\r
+ public java.lang.String getType(\r
+ ) {\r
+ return this._type;\r
+ }\r
+\r
+ /**\r
+ * Method hasBegin.\r
+ * \r
+ * @return true if at least one Begin has been added\r
+ */\r
+ public boolean hasBegin(\r
+ ) {\r
+ return this._has_begin;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\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 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
+ * \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 removeAllOtherData(\r
+ ) {\r
+ this._otherDataList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeOtherData.\r
+ * \r
+ * @param vOtherData\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeOtherData(\r
+ final jalview.schemabinding.version2.OtherData vOtherData) {\r
+ boolean removed = _otherDataList.remove(vOtherData);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeOtherDataAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.OtherData removeOtherDataAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._otherDataList.remove(index);\r
+ return (jalview.schemabinding.version2.OtherData) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'begin'.\r
+ * \r
+ * @param begin the value of field 'begin'.\r
+ */\r
+ public void setBegin(\r
+ final int begin) {\r
+ this._begin = begin;\r
+ this._has_begin = true;\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 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'featureGroup'.\r
+ * \r
+ * @param featureGroup the value of field 'featureGroup'.\r
+ */\r
+ public void setFeatureGroup(\r
+ final java.lang.String featureGroup) {\r
+ this._featureGroup = featureGroup;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vOtherData\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setOtherData(\r
+ final int index,\r
+ final jalview.schemabinding.version2.OtherData vOtherData)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._otherDataList.size()) {\r
+ throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._otherDataList.set(index, vOtherData);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vOtherDataArray\r
+ */\r
+ public void setOtherData(\r
+ final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {\r
+ //-- copy array\r
+ _otherDataList.clear();\r
+ \r
+ for (int i = 0; i < vOtherDataArray.length; i++) {\r
+ this._otherDataList.add(vOtherDataArray[i]);\r
+ }\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 float score) {\r
+ this._score = score;\r
+ this._has_score = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'status'.\r
+ * \r
+ * @param status the value of field 'status'.\r
+ */\r
+ public void setStatus(\r
+ final java.lang.String status) {\r
+ this._status = status;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(\r
+ final java.lang.String type) {\r
+ this._type = type;\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 jalview.schemabinding.version2.Featur\r
+ */\r
+ public static jalview.schemabinding.version2.Feature unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class FeatureSettings implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _settingList.\r
- */\r
- private java.util.Vector _settingList;\r
-\r
- /**\r
- * Field _groupList.\r
- */\r
- private java.util.Vector _groupList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public FeatureSettings()\r
- {\r
- super();\r
- this._settingList = new java.util.Vector();\r
- this._groupList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addGroup(final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._groupList.addElement(vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addGroup(final int index,\r
- final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._groupList.add(index, vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSetting(\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._settingList.addElement(vSetting);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSetting(final int index,\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._settingList.add(index, vSetting);\r
- }\r
-\r
- /**\r
- * Method enumerateGroup.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Group\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateGroup()\r
- {\r
- return this._groupList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateSetting.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Setting\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateSetting()\r
- {\r
- return this._settingList.elements();\r
- }\r
-\r
- /**\r
- * Method getGroup.\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.Group at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.Group getGroup(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._groupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getGroup: Index value '" + index\r
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
+public class FeatureSettings implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _settingList.\r
+ */\r
+ private java.util.Vector _settingList;\r
+\r
+ /**\r
+ * Field _groupList.\r
+ */\r
+ private java.util.Vector _groupList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureSettings() {\r
+ super();\r
+ this._settingList = new java.util.Vector();\r
+ this._groupList = new java.util.Vector();\r
}\r
\r
- return (jalview.schemabinding.version2.Group) _groupList.get(index);\r
- }\r
-\r
- /**\r
- * Method getGroup.Returns the contents of the collection in an 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.Group[] getGroup()\r
- {\r
- jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];\r
- return (jalview.schemabinding.version2.Group[]) this._groupList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getGroupCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getGroupCount()\r
- {\r
- return this._groupList.size();\r
- }\r
-\r
- /**\r
- * Method getSetting.\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.Setting at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Setting getSetting(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._settingList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSetting: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._settingList.size() - 1) + "]");\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addGroup(\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._groupList.addElement(vGroup);\r
}\r
\r
- return (jalview.schemabinding.version2.Setting) _settingList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSetting.Returns the contents of the collection in an 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.Setting[] getSetting()\r
- {\r
- jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];\r
- return (jalview.schemabinding.version2.Setting[]) this._settingList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSettingCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSettingCount()\r
- {\r
- return this._settingList.size();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._groupList.add(index, vGroup);\r
}\r
- return true;\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 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 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
+ /**\r
+ * \r
+ * \r
+ * @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllGroup()\r
- {\r
- this._groupList.clear();\r
- }\r
+ public void addSetting(\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._settingList.addElement(vSetting);\r
+ }\r
\r
- /**\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllSetting()\r
- {\r
- this._settingList.clear();\r
- }\r
-\r
- /**\r
- * Method removeGroup.\r
- * \r
- * @param vGroup\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeGroup(\r
- final jalview.schemabinding.version2.Group vGroup)\r
- {\r
- boolean removed = _groupList.remove(vGroup);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeGroupAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Group removeGroupAt(final int index)\r
- {\r
- java.lang.Object obj = this._groupList.remove(index);\r
- return (jalview.schemabinding.version2.Group) obj;\r
- }\r
-\r
- /**\r
- * Method removeSetting.\r
- * \r
- * @param vSetting\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSetting(\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- {\r
- boolean removed = _settingList.remove(vSetting);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSettingAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Setting removeSettingAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._settingList.remove(index);\r
- return (jalview.schemabinding.version2.Setting) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setGroup(final int index,\r
- final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._groupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setGroup: Index value '" + index\r
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
+ public void addSetting(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._settingList.add(index, vSetting);\r
}\r
\r
- this._groupList.set(index, vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vGroupArray\r
- */\r
- public void setGroup(\r
- final jalview.schemabinding.version2.Group[] vGroupArray)\r
- {\r
- // -- copy array\r
- _groupList.clear();\r
-\r
- for (int i = 0; i < vGroupArray.length; i++)\r
- {\r
- this._groupList.add(vGroupArray[i]);\r
+ /**\r
+ * Method enumerateGroup.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Group elements\r
+ */\r
+ public java.util.Enumeration enumerateGroup(\r
+ ) {\r
+ return this._groupList.elements();\r
}\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSetting(final int index,\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._settingList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSetting: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._settingList.size() - 1) + "]");\r
+\r
+ /**\r
+ * Method enumerateSetting.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Setting elements\r
+ */\r
+ public java.util.Enumeration enumerateSetting(\r
+ ) {\r
+ return this._settingList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getGroup.\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.Group at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Group getGroup(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._groupList.size()) {\r
+ throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Group) _groupList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getGroup.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Group[] getGroup(\r
+ ) {\r
+ jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];\r
+ return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getGroupCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getGroupCount(\r
+ ) {\r
+ return this._groupList.size();\r
}\r
\r
- this._settingList.set(index, vSetting);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSettingArray\r
- */\r
- public void setSetting(\r
- final jalview.schemabinding.version2.Setting[] vSettingArray)\r
- {\r
- // -- copy array\r
- _settingList.clear();\r
-\r
- for (int i = 0; i < vSettingArray.length; i++)\r
- {\r
- this._settingList.add(vSettingArray[i]);\r
+ /**\r
+ * Method getSetting.\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.Setting at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Setting getSetting(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._settingList.size()) {\r
+ throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Setting) _settingList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSetting.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Setting[] getSetting(\r
+ ) {\r
+ jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];\r
+ return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSettingCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSettingCount(\r
+ ) {\r
+ return this._settingList.size();\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
+ * \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 removeAllGroup(\r
+ ) {\r
+ this._groupList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllSetting(\r
+ ) {\r
+ this._settingList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeGroup.\r
+ * \r
+ * @param vGroup\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeGroup(\r
+ final jalview.schemabinding.version2.Group vGroup) {\r
+ boolean removed = _groupList.remove(vGroup);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeGroupAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Group removeGroupAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._groupList.remove(index);\r
+ return (jalview.schemabinding.version2.Group) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeSetting.\r
+ * \r
+ * @param vSetting\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSetting(\r
+ final jalview.schemabinding.version2.Setting vSetting) {\r
+ boolean removed = _settingList.remove(vSetting);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSettingAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Setting removeSettingAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._settingList.remove(index);\r
+ return (jalview.schemabinding.version2.Setting) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Group vGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._groupList.size()) {\r
+ throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._groupList.set(index, vGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vGroupArray\r
+ */\r
+ public void setGroup(\r
+ final jalview.schemabinding.version2.Group[] vGroupArray) {\r
+ //-- copy array\r
+ _groupList.clear();\r
+ \r
+ for (int i = 0; i < vGroupArray.length; i++) {\r
+ this._groupList.add(vGroupArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSetting\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSetting(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._settingList.size()) {\r
+ throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._settingList.set(index, vSetting);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSettingArray\r
+ */\r
+ public void setSetting(\r
+ final jalview.schemabinding.version2.Setting[] vSettingArray) {\r
+ //-- copy array\r
+ _settingList.clear();\r
+ \r
+ for (int i = 0; i < vSettingArray.length; i++) {\r
+ this._settingList.add(vSettingArray[i]);\r
+ }\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.FeatureSettings\r
+ */\r
+ public static jalview.schemabinding.version2.FeatureSettings unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.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
- /**\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings\r
- */\r
- public static jalview.schemabinding.version2.FeatureSettings 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.FeatureSettings) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.FeatureSettings.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Features extends Feature implements java.io.Serializable\r
+public class Features extends Feature \r
+implements java.io.Serializable\r
{\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
\r
- public Features()\r
- {\r
- super();\r
- }\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ public Features() {\r
+ super();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //-----------/\r
+ //- Methods -/\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
- return true;\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 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
+ * @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\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 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
+ * @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
- * 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Featur\r
- */\r
- public static jalview.schemabinding.version2.Feature 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.Feature) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Features.class, reader);\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 jalview.schemabinding.version2.Featur\r
+ */\r
+ public static jalview.schemabinding.version2.Feature unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+ * \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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Group implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _display.\r
- */\r
- private boolean _display;\r
-\r
- /**\r
- * keeps track of state for field: _display\r
- */\r
- private boolean _has_display;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Group()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
+public class Group implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _name.\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _display.\r
+ */\r
+ private boolean _display;\r
+\r
+ /**\r
+ * keeps track of state for field: _display\r
+ */\r
+ private boolean _has_display;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Group() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplay(\r
+ ) {\r
+ this._has_display= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'display'.\r
+ * \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean getDisplay(\r
+ ) {\r
+ return this._display;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return the value of field 'Name'.\r
+ */\r
+ public java.lang.String getName(\r
+ ) {\r
+ return this._name;\r
+ }\r
+\r
+ /**\r
+ * Method hasDisplay.\r
+ * \r
+ * @return true if at least one Display has been added\r
+ */\r
+ public boolean hasDisplay(\r
+ ) {\r
+ return this._has_display;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'display'.\r
+ * \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean isDisplay(\r
+ ) {\r
+ return this._display;\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
+ * \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
+ * Sets the value of field 'display'.\r
+ * \r
+ * @param display the value of field 'display'.\r
+ */\r
+ public void setDisplay(\r
+ final boolean display) {\r
+ this._display = display;\r
+ this._has_display = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(\r
+ final java.lang.String name) {\r
+ this._name = name;\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 jalview.schemabinding.version2.Group\r
+ */\r
+ public static jalview.schemabinding.version2.Group unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.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 deleteDisplay()\r
- {\r
- this._has_display = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean getDisplay()\r
- {\r
- return this._display;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Method hasDisplay.\r
- * \r
- * @return true if at least one Display has been added\r
- */\r
- public boolean hasDisplay()\r
- {\r
- return this._has_display;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean isDisplay()\r
- {\r
- return this._display;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
- return true;\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 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 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
- * Sets the value of field 'display'.\r
- * \r
- * @param display\r
- * the value of field 'display'.\r
- */\r
- public void setDisplay(final boolean display)\r
- {\r
- this._display = display;\r
- this._has_display = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Group\r
- */\r
- public static jalview.schemabinding.version2.Group 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.Group) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Group.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class HiddenColumns implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _start.\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public HiddenColumns()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class HiddenColumns implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public HiddenColumns() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\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
+ * \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
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = 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.HiddenColumns\r
+ */\r
+ public static jalview.schemabinding.version2.HiddenColumns unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.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
- return true;\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 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 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
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.HiddenColumns\r
- */\r
- public static jalview.schemabinding.version2.HiddenColumns 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.HiddenColumns) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.HiddenColumns.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JGroup implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _start.\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private java.lang.String _colour;\r
-\r
- /**\r
- * Field _consThreshold.\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold.\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _outlineColour.\r
- */\r
- private int _outlineColour;\r
-\r
- /**\r
- * keeps track of state for field: _outlineColour\r
- */\r
- private boolean _has_outlineColour;\r
-\r
- /**\r
- * Field _displayBoxes.\r
- */\r
- private boolean _displayBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _displayBoxes\r
- */\r
- private boolean _has_displayBoxes;\r
-\r
- /**\r
- * Field _displayText.\r
- */\r
- private boolean _displayText;\r
-\r
- /**\r
- * keeps track of state for field: _displayText\r
- */\r
- private boolean _has_displayText;\r
-\r
- /**\r
- * Field _colourText.\r
- */\r
- private boolean _colourText;\r
-\r
- /**\r
- * keeps track of state for field: _colourText\r
- */\r
- private boolean _has_colourText;\r
-\r
- /**\r
- * Field _textCol1.\r
- */\r
- private int _textCol1;\r
-\r
- /**\r
- * keeps track of state for field: _textCol1\r
- */\r
- private boolean _has_textCol1;\r
-\r
- /**\r
- * Field _textCol2.\r
- */\r
- private int _textCol2;\r
-\r
- /**\r
- * keeps track of state for field: _textCol2\r
- */\r
- private boolean _has_textCol2;\r
-\r
- /**\r
- * Field _textColThreshold.\r
- */\r
- private int _textColThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _textColThreshold\r
- */\r
- private boolean _has_textColThreshold;\r
-\r
- /**\r
- * Field _showUnconserved.\r
- */\r
- private boolean _showUnconserved;\r
-\r
- /**\r
- * keeps track of state for field: _showUnconserved\r
- */\r
- private boolean _has_showUnconserved;\r
-\r
- /**\r
- * Field _ignoreGapsinConsensus.\r
- */\r
- private boolean _ignoreGapsinConsensus = true;\r
-\r
- /**\r
- * keeps track of state for field: _ignoreGapsinConsensus\r
- */\r
- private boolean _has_ignoreGapsinConsensus;\r
-\r
- /**\r
- * Field _showConsensusHistogram.\r
- */\r
- private boolean _showConsensusHistogram = true;\r
-\r
- /**\r
- * keeps track of state for field: _showConsensusHistogram\r
- */\r
- private boolean _has_showConsensusHistogram;\r
-\r
- /**\r
- * Field _showSequenceLogo.\r
- */\r
- private boolean _showSequenceLogo = false;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceLogo\r
- */\r
- private boolean _has_showSequenceLogo;\r
-\r
- /**\r
- * Optional sequence group ID (only needs to be unique for this alignment)\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _seqList.\r
- */\r
- private java.util.Vector _seqList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JGroup()\r
- {\r
- super();\r
- this._seqList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSeq(final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._seqList.addElement(vSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSeq(final int index, final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._seqList.add(index, vSeq);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColourText()\r
- {\r
- this._has_colourText = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayBoxes()\r
- {\r
- this._has_displayBoxes = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayText()\r
- {\r
- this._has_displayText = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteIgnoreGapsinConsensus()\r
- {\r
- this._has_ignoreGapsinConsensus = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteOutlineColour()\r
- {\r
- this._has_outlineColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowConsensusHistogram()\r
- {\r
- this._has_showConsensusHistogram = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowSequenceLogo()\r
- {\r
- this._has_showSequenceLogo = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowUnconserved()\r
- {\r
- this._has_showUnconserved = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol1()\r
- {\r
- this._has_textCol1 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol2()\r
- {\r
- this._has_textCol2 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextColThreshold()\r
- {\r
- this._has_textColThreshold = false;\r
- }\r
-\r
- /**\r
- * Method enumerateSeq.\r
- * \r
- * @return an Enumeration over all java.lang.String elements\r
- */\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
- return this._seqList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public java.lang.String getColour()\r
- {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return the value of field 'ColourText'.\r
- */\r
- public boolean getColourText()\r
- {\r
- return this._colourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return the value of field 'ConsThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return the value of field 'DisplayBoxes'.\r
- */\r
- public boolean getDisplayBoxes()\r
- {\r
- return this._displayBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayText'.\r
- * \r
- * @return the value of field 'DisplayText'.\r
- */\r
- public boolean getDisplayText()\r
- {\r
- return this._displayText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the following\r
- * description: Optional sequence group ID (only needs to be unique for this\r
- * alignment)\r
- * \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 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean getIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'outlineColour'.\r
- * \r
- * @return the value of field 'OutlineColour'.\r
- */\r
- public int getOutlineColour()\r
- {\r
- return this._outlineColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return the value of field 'PidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- }\r
-\r
- /**\r
- * Method getSeq.\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 java.lang.String at the given index\r
- */\r
- public java.lang.String getSeq(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index\r
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
-\r
- return (java.lang.String) _seqList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSeq.Returns the contents of the collection in an 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 java.lang.String[] getSeq()\r
- {\r
- java.lang.String[] array = new java.lang.String[0];\r
- return (java.lang.String[]) this._seqList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSeqCount()\r
- {\r
- return this._seqList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean getShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean getShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean getShowUnconserved()\r
- {\r
- return this._showUnconserved;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return the value of field 'TextCol1'.\r
- */\r
- public int getTextCol1()\r
- {\r
- return this._textCol1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return the value of field 'TextCol2'.\r
- */\r
- public int getTextCol2()\r
- {\r
- return this._textCol2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return the value of field 'TextColThreshold'.\r
- */\r
- public int getTextColThreshold()\r
- {\r
- return this._textColThreshold;\r
- }\r
-\r
- /**\r
- * Method hasColourText.\r
- * \r
- * @return true if at least one ColourText has been added\r
- */\r
- public boolean hasColourText()\r
- {\r
- return this._has_colourText;\r
- }\r
-\r
- /**\r
- * Method hasConsThreshold.\r
- * \r
- * @return true if at least one ConsThreshold has been added\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- }\r
-\r
- /**\r
- * Method hasDisplayBoxes.\r
- * \r
- * @return true if at least one DisplayBoxes has been added\r
- */\r
- public boolean hasDisplayBoxes()\r
- {\r
- return this._has_displayBoxes;\r
- }\r
-\r
- /**\r
- * Method hasDisplayText.\r
- * \r
- * @return true if at least one DisplayText has been added\r
- */\r
- public boolean hasDisplayText()\r
- {\r
- return this._has_displayText;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasIgnoreGapsinConsensus.\r
- * \r
- * @return true if at least one IgnoreGapsinConsensus has been added\r
- */\r
- public boolean hasIgnoreGapsinConsensus()\r
- {\r
- return this._has_ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Method hasOutlineColour.\r
- * \r
- * @return true if at least one OutlineColour has been added\r
- */\r
- public boolean hasOutlineColour()\r
- {\r
- return this._has_outlineColour;\r
- }\r
-\r
- /**\r
- * Method hasPidThreshold.\r
- * \r
- * @return true if at least one PidThreshold has been added\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- }\r
-\r
- /**\r
- * Method hasShowConsensusHistogram.\r
- * \r
- * @return true if at least one ShowConsensusHistogram has been added\r
- */\r
- public boolean hasShowConsensusHistogram()\r
- {\r
- return this._has_showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Method hasShowSequenceLogo.\r
- * \r
- * @return true if at least one ShowSequenceLogo has been added\r
- */\r
- public boolean hasShowSequenceLogo()\r
- {\r
- return this._has_showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Method hasShowUnconserved.\r
- * \r
- * @return true if at least one ShowUnconserved has been added\r
- */\r
- public boolean hasShowUnconserved()\r
- {\r
- return this._has_showUnconserved;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- }\r
-\r
- /**\r
- * Method hasTextCol1.\r
- * \r
- * @return true if at least one TextCol1 has been added\r
- */\r
- public boolean hasTextCol1()\r
- {\r
- return this._has_textCol1;\r
- }\r
-\r
- /**\r
- * Method hasTextCol2.\r
- * \r
- * @return true if at least one TextCol2 has been added\r
- */\r
- public boolean hasTextCol2()\r
- {\r
- return this._has_textCol2;\r
- }\r
-\r
- /**\r
- * Method hasTextColThreshold.\r
- * \r
- * @return true if at least one TextColThreshold has been added\r
- */\r
- public boolean hasTextColThreshold()\r
- {\r
- return this._has_textColThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return the value of field 'ColourText'.\r
- */\r
- public boolean isColourText()\r
- {\r
- return this._colourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return the value of field 'DisplayBoxes'.\r
- */\r
- public boolean isDisplayBoxes()\r
- {\r
- return this._displayBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayText'.\r
- * \r
- * @return the value of field 'DisplayText'.\r
- */\r
- public boolean isDisplayText()\r
- {\r
- return this._displayText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean isIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean isShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean isShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean isShowUnconserved()\r
- {\r
- return this._showUnconserved;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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 removeAllSeq()\r
- {\r
- this._seqList.clear();\r
- }\r
-\r
- /**\r
- * Method removeSeq.\r
- * \r
- * @param vSeq\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSeq(final java.lang.String vSeq)\r
- {\r
- boolean removed = _seqList.remove(vSeq);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public java.lang.String removeSeqAt(final int index)\r
- {\r
- java.lang.Object obj = this._seqList.remove(index);\r
- return (java.lang.String) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final java.lang.String colour)\r
- {\r
- this._colour = colour;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourText'.\r
- * \r
- * @param colourText\r
- * the value of field 'colourText'.\r
- */\r
- public void setColourText(final boolean colourText)\r
- {\r
- this._colourText = colourText;\r
- this._has_colourText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold\r
- * the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(final int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayBoxes'.\r
- * \r
- * @param displayBoxes\r
- * the value of field 'displayBoxes'.\r
- */\r
- public void setDisplayBoxes(final boolean displayBoxes)\r
- {\r
- this._displayBoxes = displayBoxes;\r
- this._has_displayBoxes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayText'.\r
- * \r
- * @param displayText\r
- * the value of field 'displayText'.\r
- */\r
- public void setDisplayText(final boolean displayText)\r
- {\r
- this._displayText = displayText;\r
- this._has_displayText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the following description:\r
- * Optional sequence group ID (only needs to be unique for this alignment)\r
- * \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 'ignoreGapsinConsensus'.\r
- * \r
- * @param ignoreGapsinConsensus\r
- * the value of field 'ignoreGapsinConsensus'.\r
- */\r
- public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
- {\r
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
- this._has_ignoreGapsinConsensus = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'outlineColour'.\r
- * \r
- * @param outlineColour\r
- * the value of field 'outlineColour'.\r
- */\r
- public void setOutlineColour(final int outlineColour)\r
- {\r
- this._outlineColour = outlineColour;\r
- this._has_outlineColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold\r
- * the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(final int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSeq(final int index, final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index\r
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
-\r
- this._seqList.set(index, vSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeqArray\r
- */\r
- public void setSeq(final java.lang.String[] vSeqArray)\r
- {\r
- // -- copy array\r
- _seqList.clear();\r
-\r
- for (int i = 0; i < vSeqArray.length; i++)\r
- {\r
- this._seqList.add(vSeqArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showConsensusHistogram'.\r
- * \r
- * @param showConsensusHistogram\r
- * the value of field 'showConsensusHistogram'.\r
- */\r
- public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
- {\r
- this._showConsensusHistogram = showConsensusHistogram;\r
- this._has_showConsensusHistogram = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showSequenceLogo'.\r
- * \r
- * @param showSequenceLogo\r
- * the value of field 'showSequenceLogo'\r
- */\r
- public void setShowSequenceLogo(final boolean showSequenceLogo)\r
- {\r
- this._showSequenceLogo = showSequenceLogo;\r
- this._has_showSequenceLogo = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showUnconserved'.\r
- * \r
- * @param showUnconserved\r
- * the value of field 'showUnconserved'.\r
- */\r
- public void setShowUnconserved(final boolean showUnconserved)\r
- {\r
- this._showUnconserved = showUnconserved;\r
- this._has_showUnconserved = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1\r
- * the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(final int textCol1)\r
- {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2\r
- * the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(final int textCol2)\r
- {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold\r
- * the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(final int textColThreshold)\r
- {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JGroup\r
- */\r
- public static jalview.schemabinding.version2.JGroup 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.JGroup) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.JGroup.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class JGroup implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _name.\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private java.lang.String _colour;\r
+\r
+ /**\r
+ * Field _consThreshold.\r
+ */\r
+ private int _consThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _consThreshold\r
+ */\r
+ private boolean _has_consThreshold;\r
+\r
+ /**\r
+ * Field _pidThreshold.\r
+ */\r
+ private int _pidThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidThreshold\r
+ */\r
+ private boolean _has_pidThreshold;\r
+\r
+ /**\r
+ * Field _outlineColour.\r
+ */\r
+ private int _outlineColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _outlineColour\r
+ */\r
+ private boolean _has_outlineColour;\r
+\r
+ /**\r
+ * Field _displayBoxes.\r
+ */\r
+ private boolean _displayBoxes;\r
+\r
+ /**\r
+ * keeps track of state for field: _displayBoxes\r
+ */\r
+ private boolean _has_displayBoxes;\r
+\r
+ /**\r
+ * Field _displayText.\r
+ */\r
+ private boolean _displayText;\r
+\r
+ /**\r
+ * keeps track of state for field: _displayText\r
+ */\r
+ private boolean _has_displayText;\r
+\r
+ /**\r
+ * Field _colourText.\r
+ */\r
+ private boolean _colourText;\r
+\r
+ /**\r
+ * keeps track of state for field: _colourText\r
+ */\r
+ private boolean _has_colourText;\r
+\r
+ /**\r
+ * Field _textCol1.\r
+ */\r
+ private int _textCol1;\r
+\r
+ /**\r
+ * keeps track of state for field: _textCol1\r
+ */\r
+ private boolean _has_textCol1;\r
+\r
+ /**\r
+ * Field _textCol2.\r
+ */\r
+ private int _textCol2;\r
+\r
+ /**\r
+ * keeps track of state for field: _textCol2\r
+ */\r
+ private boolean _has_textCol2;\r
+\r
+ /**\r
+ * Field _textColThreshold.\r
+ */\r
+ private int _textColThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _textColThreshold\r
+ */\r
+ private boolean _has_textColThreshold;\r
+\r
+ /**\r
+ * Field _showUnconserved.\r
+ */\r
+ private boolean _showUnconserved;\r
+\r
+ /**\r
+ * keeps track of state for field: _showUnconserved\r
+ */\r
+ private boolean _has_showUnconserved;\r
+\r
+ /**\r
+ * Field _ignoreGapsinConsensus.\r
+ */\r
+ private boolean _ignoreGapsinConsensus = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _ignoreGapsinConsensus\r
+ */\r
+ private boolean _has_ignoreGapsinConsensus;\r
+\r
+ /**\r
+ * Field _showConsensusHistogram.\r
+ */\r
+ private boolean _showConsensusHistogram = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusHistogram\r
+ */\r
+ private boolean _has_showConsensusHistogram;\r
+\r
+ /**\r
+ * Field _showSequenceLogo.\r
+ */\r
+ private boolean _showSequenceLogo = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceLogo\r
+ */\r
+ private boolean _has_showSequenceLogo;\r
+\r
+ /**\r
+ * Optional sequence group ID (only needs to be unique for this\r
+ * alignment)\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _seqList.\r
+ */\r
+ private java.util.Vector _seqList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JGroup() {\r
+ super();\r
+ this._seqList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSeq(\r
+ final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.addElement(vSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSeq(\r
+ final int index,\r
+ final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.add(index, vSeq);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColourText(\r
+ ) {\r
+ this._has_colourText= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteConsThreshold(\r
+ ) {\r
+ this._has_consThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplayBoxes(\r
+ ) {\r
+ this._has_displayBoxes= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplayText(\r
+ ) {\r
+ this._has_displayText= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteIgnoreGapsinConsensus(\r
+ ) {\r
+ this._has_ignoreGapsinConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteOutlineColour(\r
+ ) {\r
+ this._has_outlineColour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePidThreshold(\r
+ ) {\r
+ this._has_pidThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowConsensusHistogram(\r
+ ) {\r
+ this._has_showConsensusHistogram= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowSequenceLogo(\r
+ ) {\r
+ this._has_showSequenceLogo= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowUnconserved(\r
+ ) {\r
+ this._has_showUnconserved= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol1(\r
+ ) {\r
+ this._has_textCol1= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol2(\r
+ ) {\r
+ this._has_textCol2= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextColThreshold(\r
+ ) {\r
+ this._has_textColThreshold= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSeq.\r
+ * \r
+ * @return an Enumeration over all java.lang.String elements\r
+ */\r
+ public java.util.Enumeration enumerateSeq(\r
+ ) {\r
+ return this._seqList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public java.lang.String getColour(\r
+ ) {\r
+ return this._colour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\r
+ * \r
+ * @return the value of field 'ColourText'.\r
+ */\r
+ public boolean getColourText(\r
+ ) {\r
+ return this._colourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\r
+ * \r
+ * @return the value of field 'ConsThreshold'.\r
+ */\r
+ public int getConsThreshold(\r
+ ) {\r
+ return this._consThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayBoxes'.\r
+ * \r
+ * @return the value of field 'DisplayBoxes'.\r
+ */\r
+ public boolean getDisplayBoxes(\r
+ ) {\r
+ return this._displayBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayText'.\r
+ * \r
+ * @return the value of field 'DisplayText'.\r
+ */\r
+ public boolean getDisplayText(\r
+ ) {\r
+ return this._displayText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: Optional sequence group ID (only\r
+ * needs to be unique for this alignment)\r
+ * \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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean getIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return the value of field 'Name'.\r
+ */\r
+ public java.lang.String getName(\r
+ ) {\r
+ return this._name;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'outlineColour'.\r
+ * \r
+ * @return the value of field 'OutlineColour'.\r
+ */\r
+ public int getOutlineColour(\r
+ ) {\r
+ return this._outlineColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\r
+ * \r
+ * @return the value of field 'PidThreshold'.\r
+ */\r
+ public int getPidThreshold(\r
+ ) {\r
+ return this._pidThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method getSeq.\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 java.lang.String at the given index\r
+ */\r
+ public java.lang.String getSeq(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size()) {\r
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (java.lang.String) _seqList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSeq.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public java.lang.String[] getSeq(\r
+ ) {\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._seqList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSeqCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSeqCount(\r
+ ) {\r
+ return this._seqList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean getShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean getShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol1'.\r
+ * \r
+ * @return the value of field 'TextCol1'.\r
+ */\r
+ public int getTextCol1(\r
+ ) {\r
+ return this._textCol1;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol2'.\r
+ * \r
+ * @return the value of field 'TextCol2'.\r
+ */\r
+ public int getTextCol2(\r
+ ) {\r
+ return this._textCol2;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textColThreshold'.\r
+ * \r
+ * @return the value of field 'TextColThreshold'.\r
+ */\r
+ public int getTextColThreshold(\r
+ ) {\r
+ return this._textColThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasColourText.\r
+ * \r
+ * @return true if at least one ColourText has been added\r
+ */\r
+ public boolean hasColourText(\r
+ ) {\r
+ return this._has_colourText;\r
+ }\r
+\r
+ /**\r
+ * Method hasConsThreshold.\r
+ * \r
+ * @return true if at least one ConsThreshold has been added\r
+ */\r
+ public boolean hasConsThreshold(\r
+ ) {\r
+ return this._has_consThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasDisplayBoxes.\r
+ * \r
+ * @return true if at least one DisplayBoxes has been added\r
+ */\r
+ public boolean hasDisplayBoxes(\r
+ ) {\r
+ return this._has_displayBoxes;\r
+ }\r
+\r
+ /**\r
+ * Method hasDisplayText.\r
+ * \r
+ * @return true if at least one DisplayText has been added\r
+ */\r
+ public boolean hasDisplayText(\r
+ ) {\r
+ return this._has_displayText;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been\r
+ * added\r
+ */\r
+ public boolean hasIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._has_ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Method hasOutlineColour.\r
+ * \r
+ * @return true if at least one OutlineColour has been added\r
+ */\r
+ public boolean hasOutlineColour(\r
+ ) {\r
+ return this._has_outlineColour;\r
+ }\r
+\r
+ /**\r
+ * Method hasPidThreshold.\r
+ * \r
+ * @return true if at least one PidThreshold has been added\r
+ */\r
+ public boolean hasPidThreshold(\r
+ ) {\r
+ return this._has_pidThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been\r
+ * added\r
+ */\r
+ public boolean hasShowConsensusHistogram(\r
+ ) {\r
+ return this._has_showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo(\r
+ ) {\r
+ return this._has_showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowUnconserved.\r
+ * \r
+ * @return true if at least one ShowUnconserved has been added\r
+ */\r
+ public boolean hasShowUnconserved(\r
+ ) {\r
+ return this._has_showUnconserved;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextCol1.\r
+ * \r
+ * @return true if at least one TextCol1 has been added\r
+ */\r
+ public boolean hasTextCol1(\r
+ ) {\r
+ return this._has_textCol1;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextCol2.\r
+ * \r
+ * @return true if at least one TextCol2 has been added\r
+ */\r
+ public boolean hasTextCol2(\r
+ ) {\r
+ return this._has_textCol2;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextColThreshold.\r
+ * \r
+ * @return true if at least one TextColThreshold has been added\r
+ */\r
+ public boolean hasTextColThreshold(\r
+ ) {\r
+ return this._has_textColThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\r
+ * \r
+ * @return the value of field 'ColourText'.\r
+ */\r
+ public boolean isColourText(\r
+ ) {\r
+ return this._colourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayBoxes'.\r
+ * \r
+ * @return the value of field 'DisplayBoxes'.\r
+ */\r
+ public boolean isDisplayBoxes(\r
+ ) {\r
+ return this._displayBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayText'.\r
+ * \r
+ * @return the value of field 'DisplayText'.\r
+ */\r
+ public boolean isDisplayText(\r
+ ) {\r
+ return this._displayText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean isIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean isShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean isShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\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
+ * \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 removeAllSeq(\r
+ ) {\r
+ this._seqList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeSeq.\r
+ * \r
+ * @param vSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSeq(\r
+ final java.lang.String vSeq) {\r
+ boolean removed = _seqList.remove(vSeq);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSeqAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public java.lang.String removeSeqAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._seqList.remove(index);\r
+ return (java.lang.String) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final java.lang.String colour) {\r
+ this._colour = colour;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colourText'.\r
+ * \r
+ * @param colourText the value of field 'colourText'.\r
+ */\r
+ public void setColourText(\r
+ final boolean colourText) {\r
+ this._colourText = colourText;\r
+ this._has_colourText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(\r
+ final int consThreshold) {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'displayBoxes'.\r
+ * \r
+ * @param displayBoxes the value of field 'displayBoxes'.\r
+ */\r
+ public void setDisplayBoxes(\r
+ final boolean displayBoxes) {\r
+ this._displayBoxes = displayBoxes;\r
+ this._has_displayBoxes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'displayText'.\r
+ * \r
+ * @param displayText the value of field 'displayText'.\r
+ */\r
+ public void setDisplayText(\r
+ final boolean displayText) {\r
+ this._displayText = displayText;\r
+ this._has_displayText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: Optional sequence group ID (only\r
+ * needs to be unique for this alignment)\r
+ * \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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus the value of field\r
+ * 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(\r
+ final boolean ignoreGapsinConsensus) {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(\r
+ final java.lang.String name) {\r
+ this._name = name;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'outlineColour'.\r
+ * \r
+ * @param outlineColour the value of field 'outlineColour'.\r
+ */\r
+ public void setOutlineColour(\r
+ final int outlineColour) {\r
+ this._outlineColour = outlineColour;\r
+ this._has_outlineColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(\r
+ final int pidThreshold) {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSeq(\r
+ final int index,\r
+ final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size()) {\r
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._seqList.set(index, vSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSeqArray\r
+ */\r
+ public void setSeq(\r
+ final java.lang.String[] vSeqArray) {\r
+ //-- copy array\r
+ _seqList.clear();\r
+ \r
+ for (int i = 0; i < vSeqArray.length; i++) {\r
+ this._seqList.add(vSeqArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram the value of field\r
+ * 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(\r
+ final boolean showConsensusHistogram) {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(\r
+ final boolean showSequenceLogo) {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(\r
+ final boolean showUnconserved) {\r
+ this._showUnconserved = showUnconserved;\r
+ this._has_showUnconserved = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol1'.\r
+ * \r
+ * @param textCol1 the value of field 'textCol1'.\r
+ */\r
+ public void setTextCol1(\r
+ final int textCol1) {\r
+ this._textCol1 = textCol1;\r
+ this._has_textCol1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol2'.\r
+ * \r
+ * @param textCol2 the value of field 'textCol2'.\r
+ */\r
+ public void setTextCol2(\r
+ final int textCol2) {\r
+ this._textCol2 = textCol2;\r
+ this._has_textCol2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textColThreshold'.\r
+ * \r
+ * @param textColThreshold the value of field 'textColThreshold'\r
+ */\r
+ public void setTextColThreshold(\r
+ final int textColThreshold) {\r
+ this._textColThreshold = textColThreshold;\r
+ this._has_textColThreshold = 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 jalview.schemabinding.version2.JGroup\r
+ */\r
+ public static jalview.schemabinding.version2.JGroup unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JSeq implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _start.\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _hidden.\r
- */\r
- private boolean _hidden;\r
-\r
- /**\r
- * keeps track of state for field: _hidden\r
- */\r
- private boolean _has_hidden;\r
-\r
- /**\r
- * Field _featuresList.\r
- */\r
- private java.util.Vector _featuresList;\r
-\r
- /**\r
- * Field _pdbidsList.\r
- */\r
- private java.util.Vector _pdbidsList;\r
-\r
- /**\r
- * Field _hiddenSequencesList.\r
- */\r
- private java.util.Vector _hiddenSequencesList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JSeq()\r
- {\r
- super();\r
- this._featuresList = new java.util.Vector();\r
- this._pdbidsList = new java.util.Vector();\r
- this._hiddenSequencesList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addFeatures(\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._featuresList.addElement(vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addFeatures(final int index,\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._featuresList.add(index, vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenSequences(final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenSequencesList.addElement(new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenSequences(final int index, final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenSequencesList.add(index, new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._pdbidsList.addElement(vPdbids);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbids(final int index,\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._pdbidsList.add(index, vPdbids);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteHidden()\r
- {\r
- this._has_hidden = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- * Method enumerateFeatures.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Features\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return this._featuresList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateHiddenSequences.\r
- * \r
- * @return an Enumeration over all int elements\r
- */\r
- public java.util.Enumeration enumerateHiddenSequences()\r
- {\r
- return this._hiddenSequencesList.elements();\r
- }\r
-\r
- /**\r
- * Method enumeratePdbids.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Pdbids\r
- * elements\r
- */\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return this._pdbidsList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Method getFeatures.\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.Features at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Features getFeatures(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._featuresList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getFeatures: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._featuresList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Features) _featuresList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getFeatures.Returns the contents of the collection in an 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.Features[] getFeatures()\r
- {\r
- jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];\r
- return (jalview.schemabinding.version2.Features[]) this._featuresList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getFeaturesCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getFeaturesCount()\r
- {\r
- return this._featuresList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- * \r
- * @return the value of field 'Hidden'.\r
- */\r
- public boolean getHidden()\r
- {\r
- return this._hidden;\r
- }\r
-\r
- /**\r
- * Method getHiddenSequences.\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 int at the given index\r
- */\r
- public int getHiddenSequences(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenSequencesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "getHiddenSequences: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._hiddenSequencesList.size() - 1) + "]");\r
- }\r
-\r
- return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();\r
- }\r
-\r
- /**\r
- * Method getHiddenSequences.Returns the contents of the collection in an\r
- * Array.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public int[] getHiddenSequences()\r
- {\r
- int size = this._hiddenSequencesList.size();\r
- int[] array = new int[size];\r
- java.util.Iterator iter = _hiddenSequencesList.iterator();\r
- for (int index = 0; index < size; index++)\r
- {\r
- array[index] = ((java.lang.Integer) iter.next()).intValue();\r
- }\r
- return array;\r
- }\r
-\r
- /**\r
- * Method getHiddenSequencesCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getHiddenSequencesCount()\r
- {\r
- return this._hiddenSequencesList.size();\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
- * Method getPdbids.\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.Pdbids at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.Pdbids getPdbids(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._pdbidsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getPdbids: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._pdbidsList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);\r
- }\r
-\r
- /**\r
- * Method getPdbids.Returns the contents of the collection in an 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.Pdbids[] getPdbids()\r
- {\r
- jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];\r
- return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPdbidsCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPdbidsCount()\r
- {\r
- return this._pdbidsList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasHidden.\r
- * \r
- * @return true if at least one Hidden has been added\r
- */\r
- public boolean hasHidden()\r
- {\r
- return this._has_hidden;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- * \r
- * @return the value of field 'Hidden'.\r
- */\r
- public boolean isHidden()\r
- {\r
- return this._hidden;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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 removeAllFeatures()\r
- {\r
- this._featuresList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllHiddenSequences()\r
- {\r
- this._hiddenSequencesList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllPdbids()\r
- {\r
- this._pdbidsList.clear();\r
- }\r
-\r
- /**\r
- * Method removeFeatures.\r
- * \r
- * @param vFeatures\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeFeatures(\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- {\r
- boolean removed = _featuresList.remove(vFeatures);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeFeaturesAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Features removeFeaturesAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._featuresList.remove(index);\r
- return (jalview.schemabinding.version2.Features) obj;\r
- }\r
-\r
- /**\r
- * Method removeHiddenSequences.\r
- * \r
- * @param vHiddenSequences\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeHiddenSequences(final int vHiddenSequences)\r
- {\r
- boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(\r
- vHiddenSequences));\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeHiddenSequencesAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public int removeHiddenSequencesAt(final int index)\r
- {\r
- java.lang.Object obj = this._hiddenSequencesList.remove(index);\r
- return ((java.lang.Integer) obj).intValue();\r
- }\r
-\r
- /**\r
- * Method removePdbids.\r
- * \r
- * @param vPdbids\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removePdbids(\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- {\r
- boolean removed = _pdbidsList.remove(vPdbids);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePdbidsAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Pdbids removePdbidsAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._pdbidsList.remove(index);\r
- return (jalview.schemabinding.version2.Pdbids) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setFeatures(final int index,\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._featuresList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setFeatures: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._featuresList.size() - 1) + "]");\r
- }\r
-\r
- this._featuresList.set(index, vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vFeaturesArray\r
- */\r
- public void setFeatures(\r
- final jalview.schemabinding.version2.Features[] vFeaturesArray)\r
- {\r
- // -- copy array\r
- _featuresList.clear();\r
-\r
- for (int i = 0; i < vFeaturesArray.length; i++)\r
- {\r
- this._featuresList.add(vFeaturesArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'hidden'.\r
- * \r
- * @param hidden\r
- * the value of field 'hidden'.\r
- */\r
- public void setHidden(final boolean hidden)\r
- {\r
- this._hidden = hidden;\r
- this._has_hidden = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setHiddenSequences(final int index, final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenSequencesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setHiddenSequences: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._hiddenSequencesList.size() - 1) + "]");\r
- }\r
-\r
- this._hiddenSequencesList.set(index, new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenSequencesArray\r
- */\r
- public void setHiddenSequences(final int[] vHiddenSequencesArray)\r
- {\r
- // -- copy array\r
- _hiddenSequencesList.clear();\r
-\r
- for (int i = 0; i < vHiddenSequencesArray.length; i++)\r
- {\r
- this._hiddenSequencesList.add(new java.lang.Integer(\r
- vHiddenSequencesArray[i]));\r
- }\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
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setPdbids(final int index,\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._pdbidsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setPdbids: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._pdbidsList.size() - 1) + "]");\r
- }\r
-\r
- this._pdbidsList.set(index, vPdbids);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbidsArray\r
- */\r
- public void setPdbids(\r
- final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)\r
- {\r
- // -- copy array\r
- _pdbidsList.clear();\r
-\r
- for (int i = 0; i < vPdbidsArray.length; i++)\r
- {\r
- this._pdbidsList.add(vPdbidsArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JSeq\r
- */\r
- public static jalview.schemabinding.version2.JSeq 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.JSeq) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.JSeq.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class JSeq implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _hidden.\r
+ */\r
+ private boolean _hidden;\r
+\r
+ /**\r
+ * keeps track of state for field: _hidden\r
+ */\r
+ private boolean _has_hidden;\r
+\r
+ /**\r
+ * Field _featuresList.\r
+ */\r
+ private java.util.Vector _featuresList;\r
+\r
+ /**\r
+ * Field _pdbidsList.\r
+ */\r
+ private java.util.Vector _pdbidsList;\r
+\r
+ /**\r
+ * Field _hiddenSequencesList.\r
+ */\r
+ private java.util.Vector _hiddenSequencesList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JSeq() {\r
+ super();\r
+ this._featuresList = new java.util.Vector();\r
+ this._pdbidsList = new java.util.Vector();\r
+ this._hiddenSequencesList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.addElement(vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.add(index, vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenSequences(\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.addElement(vPdbids);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.add(index, vPdbids);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColour(\r
+ ) {\r
+ this._has_colour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteHidden(\r
+ ) {\r
+ this._has_hidden= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateFeatures.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Features elements\r
+ */\r
+ public java.util.Enumeration enumerateFeatures(\r
+ ) {\r
+ return this._featuresList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateHiddenSequences.\r
+ * \r
+ * @return an Enumeration over all int elements\r
+ */\r
+ public java.util.Enumeration enumerateHiddenSequences(\r
+ ) {\r
+ return this._hiddenSequencesList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumeratePdbids.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Pdbids elements\r
+ */\r
+ public java.util.Enumeration enumeratePdbids(\r
+ ) {\r
+ return this._pdbidsList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour(\r
+ ) {\r
+ return this._colour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Method getFeatures.\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.Features at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Features getFeatures(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Features) _featuresList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getFeatures.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Features[] getFeatures(\r
+ ) {\r
+ jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];\r
+ return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getFeaturesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getFeaturesCount(\r
+ ) {\r
+ return this._featuresList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'hidden'.\r
+ * \r
+ * @return the value of field 'Hidden'.\r
+ */\r
+ public boolean getHidden(\r
+ ) {\r
+ return this._hidden;\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequences.\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 int at the given index\r
+ */\r
+ public int getHiddenSequences(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
+ }\r
+ \r
+ return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequences.Returns the contents of the\r
+ * collection in an Array. \r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public int[] getHiddenSequences(\r
+ ) {\r
+ int size = this._hiddenSequencesList.size();\r
+ int[] array = new int[size];\r
+ java.util.Iterator iter = _hiddenSequencesList.iterator();\r
+ for (int index = 0; index < size; index++) {\r
+ array[index] = ((java.lang.Integer) iter.next()).intValue();\r
+ }\r
+ return array;\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequencesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getHiddenSequencesCount(\r
+ ) {\r
+ return this._hiddenSequencesList.size();\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
+ * Method getPdbids.\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.Pdbids at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids getPdbids(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbids.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids[] getPdbids(\r
+ ) {\r
+ jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];\r
+ return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbidsCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getPdbidsCount(\r
+ ) {\r
+ return this._pdbidsList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour(\r
+ ) {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasHidden.\r
+ * \r
+ * @return true if at least one Hidden has been added\r
+ */\r
+ public boolean hasHidden(\r
+ ) {\r
+ return this._has_hidden;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'hidden'.\r
+ * \r
+ * @return the value of field 'Hidden'.\r
+ */\r
+ public boolean isHidden(\r
+ ) {\r
+ return this._hidden;\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
+ * \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 removeAllFeatures(\r
+ ) {\r
+ this._featuresList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllHiddenSequences(\r
+ ) {\r
+ this._hiddenSequencesList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllPdbids(\r
+ ) {\r
+ this._pdbidsList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeFeatures.\r
+ * \r
+ * @param vFeatures\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures) {\r
+ boolean removed = _featuresList.remove(vFeatures);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeFeaturesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Features removeFeaturesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._featuresList.remove(index);\r
+ return (jalview.schemabinding.version2.Features) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenSequences.\r
+ * \r
+ * @param vHiddenSequences\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeHiddenSequences(\r
+ final int vHiddenSequences) {\r
+ boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenSequencesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public int removeHiddenSequencesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._hiddenSequencesList.remove(index);\r
+ return ((java.lang.Integer) obj).intValue();\r
+ }\r
+\r
+ /**\r
+ * Method removePdbids.\r
+ * \r
+ * @param vPdbids\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removePdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids) {\r
+ boolean removed = _pdbidsList.remove(vPdbids);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePdbidsAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids removePdbidsAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._pdbidsList.remove(index);\r
+ return (jalview.schemabinding.version2.Pdbids) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final int colour) {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._featuresList.set(index, vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vFeaturesArray\r
+ */\r
+ public void setFeatures(\r
+ final jalview.schemabinding.version2.Features[] vFeaturesArray) {\r
+ //-- copy array\r
+ _featuresList.clear();\r
+ \r
+ for (int i = 0; i < vFeaturesArray.length; i++) {\r
+ this._featuresList.add(vFeaturesArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'hidden'.\r
+ * \r
+ * @param hidden the value of field 'hidden'.\r
+ */\r
+ public void setHidden(\r
+ final boolean hidden) {\r
+ this._hidden = hidden;\r
+ this._has_hidden = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenSequencesArray\r
+ */\r
+ public void setHiddenSequences(\r
+ final int[] vHiddenSequencesArray) {\r
+ //-- copy array\r
+ _hiddenSequencesList.clear();\r
+ \r
+ for (int i = 0; i < vHiddenSequencesArray.length; i++) {\r
+ this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));\r
+ }\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
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._pdbidsList.set(index, vPdbids);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbidsArray\r
+ */\r
+ public void setPdbids(\r
+ final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {\r
+ //-- copy array\r
+ _pdbidsList.clear();\r
+ \r
+ for (int i = 0; i < vPdbidsArray.length; i++) {\r
+ this._pdbidsList.add(vPdbidsArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = 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 jalview.schemabinding.version2.JSeq\r
+ */\r
+ public static jalview.schemabinding.version2.JSeq unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModel implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _creationDate.\r
- */\r
- private java.util.Date _creationDate;\r
-\r
- /**\r
- * Field _version.\r
- */\r
- private java.lang.String _version;\r
-\r
- /**\r
- * Field _vamsasModel.\r
- */\r
- private jalview.schemabinding.version2.VamsasModel _vamsasModel;\r
-\r
- /**\r
- * Field _jalviewModelSequence.\r
- */\r
- private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewModel()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'creationDate'.\r
- * \r
- * @return the value of field 'CreationDate'.\r
- */\r
- public java.util.Date getCreationDate()\r
- {\r
- return this._creationDate;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'jalviewModelSequence'.\r
- * \r
- * @return the value of field 'JalviewModelSequence'.\r
- */\r
- public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()\r
- {\r
- return this._jalviewModelSequence;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'vamsasModel'.\r
- * \r
- * @return the value of field 'VamsasModel'.\r
- */\r
- public jalview.schemabinding.version2.VamsasModel getVamsasModel()\r
- {\r
- return this._vamsasModel;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'version'.\r
- * \r
- * @return the value of field 'Version'.\r
- */\r
- public java.lang.String getVersion()\r
- {\r
- return this._version;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class JalviewModel implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _creationDate.\r
+ */\r
+ private java.util.Date _creationDate;\r
+\r
+ /**\r
+ * Field _version.\r
+ */\r
+ private java.lang.String _version;\r
+\r
+ /**\r
+ * Field _vamsasModel.\r
+ */\r
+ private jalview.schemabinding.version2.VamsasModel _vamsasModel;\r
+\r
+ /**\r
+ * Field _jalviewModelSequence.\r
+ */\r
+ private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModel() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'creationDate'.\r
+ * \r
+ * @return the value of field 'CreationDate'.\r
+ */\r
+ public java.util.Date getCreationDate(\r
+ ) {\r
+ return this._creationDate;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'jalviewModelSequence'.\r
+ * \r
+ * @return the value of field 'JalviewModelSequence'.\r
+ */\r
+ public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence(\r
+ ) {\r
+ return this._jalviewModelSequence;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'vamsasModel'.\r
+ * \r
+ * @return the value of field 'VamsasModel'.\r
+ */\r
+ public jalview.schemabinding.version2.VamsasModel getVamsasModel(\r
+ ) {\r
+ return this._vamsasModel;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'version'.\r
+ * \r
+ * @return the value of field 'Version'.\r
+ */\r
+ public java.lang.String getVersion(\r
+ ) {\r
+ return this._version;\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
+ * \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
+ * Sets the value of field 'creationDate'.\r
+ * \r
+ * @param creationDate the value of field 'creationDate'.\r
+ */\r
+ public void setCreationDate(\r
+ final java.util.Date creationDate) {\r
+ this._creationDate = creationDate;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'jalviewModelSequence'.\r
+ * \r
+ * @param jalviewModelSequence the value of field\r
+ * 'jalviewModelSequence'.\r
+ */\r
+ public void setJalviewModelSequence(\r
+ final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) {\r
+ this._jalviewModelSequence = jalviewModelSequence;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'vamsasModel'.\r
+ * \r
+ * @param vamsasModel the value of field 'vamsasModel'.\r
+ */\r
+ public void setVamsasModel(\r
+ final jalview.schemabinding.version2.VamsasModel vamsasModel) {\r
+ this._vamsasModel = vamsasModel;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'version'.\r
+ * \r
+ * @param version the value of field 'version'.\r
+ */\r
+ public void setVersion(\r
+ final java.lang.String version) {\r
+ this._version = version;\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.JalviewModel\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewModel unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.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
- return true;\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 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 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
- * Sets the value of field 'creationDate'.\r
- * \r
- * @param creationDate\r
- * the value of field 'creationDate'.\r
- */\r
- public void setCreationDate(final java.util.Date creationDate)\r
- {\r
- this._creationDate = creationDate;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'jalviewModelSequence'.\r
- * \r
- * @param jalviewModelSequence\r
- * the value of field 'jalviewModelSequence'.\r
- */\r
- public void setJalviewModelSequence(\r
- final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)\r
- {\r
- this._jalviewModelSequence = jalviewModelSequence;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'vamsasModel'.\r
- * \r
- * @param vamsasModel\r
- * the value of field 'vamsasModel'.\r
- */\r
- public void setVamsasModel(\r
- final jalview.schemabinding.version2.VamsasModel vamsasModel)\r
- {\r
- this._vamsasModel = vamsasModel;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'version'.\r
- * \r
- * @param version\r
- * the value of field 'version'.\r
- */\r
- public void setVersion(final java.lang.String version)\r
- {\r
- this._version = version;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JalviewModel\r
- */\r
- public static jalview.schemabinding.version2.JalviewModel 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.JalviewModel) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.JalviewModel.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelSequence implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _JSeqList.\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList.\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList.\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList.\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList.\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _featureSettings.\r
- */\r
- private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewModelSequence()\r
- {\r
- super();\r
- this._JSeqList = new java.util.Vector();\r
- this._JGroupList = new java.util.Vector();\r
- this._viewportList = new java.util.Vector();\r
- this._userColoursList = new java.util.Vector();\r
- this._treeList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._JGroupList.addElement(vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addJGroup(final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._JGroupList.add(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._JSeqList.addElement(vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addJSeq(final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._JSeqList.add(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addTree(final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addTree(final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._userColoursList.addElement(vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addUserColours(final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._userColoursList.add(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._viewportList.addElement(vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addViewport(final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._viewportList.add(index, vViewport);\r
- }\r
-\r
- /**\r
- * Method enumerateJGroup.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.JGroup\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
- return this._JGroupList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateJSeq.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.JSeq\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
- return this._JSeqList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateTree.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Tree\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return this._treeList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateUserColours.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.UserColours\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
- return this._userColoursList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateViewport.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Viewport\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
- return this._viewportList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'featureSettings'.\r
- * \r
- * @return the value of field 'FeatureSettings'.\r
- */\r
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
- {\r
- return this._featureSettings;\r
- }\r
-\r
- /**\r
- * Method getJGroup.\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.JGroup at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.JGroup getJGroup(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getJGroup: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._JGroupList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJGroup.Returns the contents of the collection in an 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.JGroup[] getJGroup()\r
- {\r
- jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
- return (jalview.schemabinding.version2.JGroup[]) this._JGroupList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJGroupCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJGroupCount()\r
- {\r
- return this._JGroupList.size();\r
- }\r
-\r
- /**\r
- * Method getJSeq.\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.JSeq at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.JSeq getJSeq(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index\r
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJSeq.Returns the contents of the collection in an 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.JSeq[] getJSeq()\r
- {\r
- jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
- return (jalview.schemabinding.version2.JSeq[]) this._JSeqList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJSeqCount()\r
- {\r
- return this._JSeqList.size();\r
- }\r
-\r
- /**\r
- * Method getTree.\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.Tree at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.Tree getTree(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getTree: Index value '" + index\r
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getTree.Returns the contents of the collection in an 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.Tree[] getTree()\r
- {\r
- jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
- return (jalview.schemabinding.version2.Tree[]) this._treeList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getTreeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getTreeCount()\r
- {\r
- return this._treeList.size();\r
- }\r
-\r
- /**\r
- * Method getUserColours.\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.UserColours at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.UserColours getUserColours(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getUserColours: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._userColoursList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.UserColours) _userColoursList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getUserColours.Returns the contents of the collection in an 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.UserColours[] getUserColours()\r
- {\r
- jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
- return (jalview.schemabinding.version2.UserColours[]) this._userColoursList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getUserColoursCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getUserColoursCount()\r
- {\r
- return this._userColoursList.size();\r
- }\r
-\r
- /**\r
- * Method getViewport.\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.Viewport at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Viewport getViewport(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getViewport: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._viewportList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Viewport) _viewportList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getViewport.Returns the contents of the collection in an 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.Viewport[] getViewport()\r
- {\r
- jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
- return (jalview.schemabinding.version2.Viewport[]) this._viewportList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getViewportCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getViewportCount()\r
- {\r
- return this._viewportList.size();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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 removeAllJGroup()\r
- {\r
- this._JGroupList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllJSeq()\r
- {\r
- this._JSeqList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllTree()\r
- {\r
- this._treeList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllUserColours()\r
- {\r
- this._userColoursList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllViewport()\r
- {\r
- this._viewportList.clear();\r
- }\r
-\r
- /**\r
- * Method removeJGroup.\r
- * \r
- * @param vJGroup\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJGroup(\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- {\r
- boolean removed = _JGroupList.remove(vJGroup);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJGroupAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._JGroupList.remove(index);\r
- return (jalview.schemabinding.version2.JGroup) obj;\r
- }\r
-\r
- /**\r
- * Method removeJSeq.\r
- * \r
- * @param vJSeq\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)\r
- {\r
- boolean removed = _JSeqList.remove(vJSeq);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)\r
- {\r
- java.lang.Object obj = this._JSeqList.remove(index);\r
- return (jalview.schemabinding.version2.JSeq) obj;\r
- }\r
-\r
- /**\r
- * Method removeTree.\r
- * \r
- * @param vTree\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)\r
- {\r
- boolean removed = _treeList.remove(vTree);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeTreeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Tree removeTreeAt(final int index)\r
- {\r
- java.lang.Object obj = this._treeList.remove(index);\r
- return (jalview.schemabinding.version2.Tree) obj;\r
- }\r
-\r
- /**\r
- * Method removeUserColours.\r
- * \r
- * @param vUserColours\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- {\r
- boolean removed = _userColoursList.remove(vUserColours);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeUserColoursAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._userColoursList.remove(index);\r
- return (jalview.schemabinding.version2.UserColours) obj;\r
- }\r
-\r
- /**\r
- * Method removeViewport.\r
- * \r
- * @param vViewport\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- {\r
- boolean removed = _viewportList.remove(vViewport);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeViewportAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Viewport removeViewportAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._viewportList.remove(index);\r
- return (jalview.schemabinding.version2.Viewport) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'featureSettings'.\r
- * \r
- * @param featureSettings\r
- * the value of field 'featureSettings'.\r
- */\r
- public void setFeatureSettings(\r
- final jalview.schemabinding.version2.FeatureSettings featureSettings)\r
- {\r
- this._featureSettings = featureSettings;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setJGroup(final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setJGroup: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._JGroupList.size() - 1) + "]");\r
- }\r
-\r
- this._JGroupList.set(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroupArray\r
- */\r
- public void setJGroup(\r
- final jalview.schemabinding.version2.JGroup[] vJGroupArray)\r
- {\r
- // -- copy array\r
- _JGroupList.clear();\r
-\r
- for (int i = 0; i < vJGroupArray.length; i++)\r
- {\r
- this._JGroupList.add(vJGroupArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setJSeq(final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index\r
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
-\r
- this._JSeqList.set(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeqArray\r
- */\r
- public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)\r
- {\r
- // -- copy array\r
- _JSeqList.clear();\r
-\r
- for (int i = 0; i < vJSeqArray.length; i++)\r
- {\r
- this._JSeqList.add(vJSeqArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setTree(final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setTree: Index value '" + index\r
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
-\r
- this._treeList.set(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTreeArray\r
- */\r
- public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)\r
- {\r
- // -- copy array\r
- _treeList.clear();\r
-\r
- for (int i = 0; i < vTreeArray.length; i++)\r
- {\r
- this._treeList.add(vTreeArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setUserColours(final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setUserColours: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._userColoursList.size() - 1) + "]");\r
- }\r
-\r
- this._userColoursList.set(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColoursArray\r
- */\r
- public void setUserColours(\r
- final jalview.schemabinding.version2.UserColours[] vUserColoursArray)\r
- {\r
- // -- copy array\r
- _userColoursList.clear();\r
-\r
- for (int i = 0; i < vUserColoursArray.length; i++)\r
- {\r
- this._userColoursList.add(vUserColoursArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setViewport(final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setViewport: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._viewportList.size() - 1) + "]");\r
- }\r
-\r
- this._viewportList.set(index, vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewportArray\r
- */\r
- public void setViewport(\r
- final jalview.schemabinding.version2.Viewport[] vViewportArray)\r
- {\r
- // -- copy array\r
- _viewportList.clear();\r
-\r
- for (int i = 0; i < vViewportArray.length; i++)\r
- {\r
- this._viewportList.add(vViewportArray[i]);\r
- }\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence\r
- */\r
- public static jalview.schemabinding.version2.JalviewModelSequence 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.JalviewModelSequence) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.JalviewModelSequence.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 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
+public class JalviewModelSequence implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _JSeqList.\r
+ */\r
+ private java.util.Vector _JSeqList;\r
+\r
+ /**\r
+ * Field _JGroupList.\r
+ */\r
+ private java.util.Vector _JGroupList;\r
+\r
+ /**\r
+ * Field _viewportList.\r
+ */\r
+ private java.util.Vector _viewportList;\r
+\r
+ /**\r
+ * Field _userColoursList.\r
+ */\r
+ private java.util.Vector _userColoursList;\r
+\r
+ /**\r
+ * Field _treeList.\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _featureSettings.\r
+ */\r
+ private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelSequence() {\r
+ super();\r
+ this._JSeqList = new java.util.Vector();\r
+ this._JGroupList = new java.util.Vector();\r
+ this._viewportList = new java.util.Vector();\r
+ this._userColoursList = new java.util.Vector();\r
+ this._treeList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addJGroup(\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JGroupList.addElement(vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addJGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JGroupList.add(index, vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addJSeq(\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JSeqList.addElement(vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addJSeq(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._JSeqList.add(index, vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addTree(\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.addElement(vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addTree(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.add(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._userColoursList.addElement(vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addUserColours(\r
+ final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._userColoursList.add(index, vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._viewportList.addElement(vViewport);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addViewport(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._viewportList.add(index, vViewport);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateJGroup.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.JGroup elements\r
+ */\r
+ public java.util.Enumeration enumerateJGroup(\r
+ ) {\r
+ return this._JGroupList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateJSeq.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.JSeq elements\r
+ */\r
+ public java.util.Enumeration enumerateJSeq(\r
+ ) {\r
+ return this._JSeqList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateTree.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Tree elements\r
+ */\r
+ public java.util.Enumeration enumerateTree(\r
+ ) {\r
+ return this._treeList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateUserColours.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.UserColours elements\r
+ */\r
+ public java.util.Enumeration enumerateUserColours(\r
+ ) {\r
+ return this._userColoursList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateViewport.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Viewport elements\r
+ */\r
+ public java.util.Enumeration enumerateViewport(\r
+ ) {\r
+ return this._viewportList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'featureSettings'.\r
+ * \r
+ * @return the value of field 'FeatureSettings'.\r
+ */\r
+ public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(\r
+ ) {\r
+ return this._featureSettings;\r
+ }\r
+\r
+ /**\r
+ * Method getJGroup.\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.JGroup at the given index\r
+ */\r
+ public jalview.schemabinding.version2.JGroup getJGroup(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size()) {\r
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getJGroup.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.JGroup[] getJGroup(\r
+ ) {\r
+ jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
+ return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getJGroupCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getJGroupCount(\r
+ ) {\r
+ return this._JGroupList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getJSeq.\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 jalview.schemabinding.version2.JSeq\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.JSeq getJSeq(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size()) {\r
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getJSeq.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.JSeq[] getJSeq(\r
+ ) {\r
+ jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
+ return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getJSeqCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getJSeqCount(\r
+ ) {\r
+ return this._JSeqList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getTree.\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 jalview.schemabinding.version2.Tree\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Tree getTree(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getTree.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Tree[] getTree(\r
+ ) {\r
+ jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
+ return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getTreeCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getTreeCount(\r
+ ) {\r
+ return this._treeList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getUserColours.\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.UserColours at the given index\r
+ */\r
+ public jalview.schemabinding.version2.UserColours getUserColours(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size()) {\r
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getUserColours.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.UserColours[] getUserColours(\r
+ ) {\r
+ jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
+ return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getUserColoursCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getUserColoursCount(\r
+ ) {\r
+ return this._userColoursList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getViewport.\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.Viewport at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Viewport getViewport(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size()) {\r
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getViewport.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Viewport[] getViewport(\r
+ ) {\r
+ jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
+ return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getViewportCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getViewportCount(\r
+ ) {\r
+ return this._viewportList.size();\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
+ * \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 removeAllJGroup(\r
+ ) {\r
+ this._JGroupList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllJSeq(\r
+ ) {\r
+ this._JSeqList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllTree(\r
+ ) {\r
+ this._treeList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllUserColours(\r
+ ) {\r
+ this._userColoursList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllViewport(\r
+ ) {\r
+ this._viewportList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeJGroup.\r
+ * \r
+ * @param vJGroup\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJGroup(\r
+ final jalview.schemabinding.version2.JGroup vJGroup) {\r
+ boolean removed = _JGroupList.remove(vJGroup);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJGroupAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._JGroupList.remove(index);\r
+ return (jalview.schemabinding.version2.JGroup) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeJSeq.\r
+ * \r
+ * @param vJSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJSeq(\r
+ final jalview.schemabinding.version2.JSeq vJSeq) {\r
+ boolean removed = _JSeqList.remove(vJSeq);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJSeqAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.JSeq removeJSeqAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._JSeqList.remove(index);\r
+ return (jalview.schemabinding.version2.JSeq) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeTree.\r
+ * \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(\r
+ final jalview.schemabinding.version2.Tree vTree) {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Tree removeTreeAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
+ return (jalview.schemabinding.version2.Tree) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeUserColours.\r
+ * \r
+ * @param vUserColours\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours) {\r
+ boolean removed = _userColoursList.remove(vUserColours);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeUserColoursAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._userColoursList.remove(index);\r
+ return (jalview.schemabinding.version2.UserColours) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeViewport.\r
+ * \r
+ * @param vViewport\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport) {\r
+ boolean removed = _viewportList.remove(vViewport);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeViewportAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Viewport removeViewportAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._viewportList.remove(index);\r
+ return (jalview.schemabinding.version2.Viewport) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'featureSettings'.\r
+ * \r
+ * @param featureSettings the value of field 'featureSettings'.\r
+ */\r
+ public void setFeatureSettings(\r
+ final jalview.schemabinding.version2.FeatureSettings featureSettings) {\r
+ this._featureSettings = featureSettings;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setJGroup(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size()) {\r
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._JGroupList.set(index, vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJGroupArray\r
+ */\r
+ public void setJGroup(\r
+ final jalview.schemabinding.version2.JGroup[] vJGroupArray) {\r
+ //-- copy array\r
+ _JGroupList.clear();\r
+ \r
+ for (int i = 0; i < vJGroupArray.length; i++) {\r
+ this._JGroupList.add(vJGroupArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setJSeq(\r
+ final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size()) {\r
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._JSeqList.set(index, vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJSeqArray\r
+ */\r
+ public void setJSeq(\r
+ final jalview.schemabinding.version2.JSeq[] vJSeqArray) {\r
+ //-- copy array\r
+ _JSeqList.clear();\r
+ \r
+ for (int i = 0; i < vJSeqArray.length; i++) {\r
+ this._JSeqList.add(vJSeqArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setTree(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._treeList.set(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTreeArray\r
+ */\r
+ public void setTree(\r
+ final jalview.schemabinding.version2.Tree[] vTreeArray) {\r
+ //-- copy array\r
+ _treeList.clear();\r
+ \r
+ for (int i = 0; i < vTreeArray.length; i++) {\r
+ this._treeList.add(vTreeArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setUserColours(\r
+ final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size()) {\r
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._userColoursList.set(index, vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vUserColoursArray\r
+ */\r
+ public void setUserColours(\r
+ final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {\r
+ //-- copy array\r
+ _userColoursList.clear();\r
+ \r
+ for (int i = 0; i < vUserColoursArray.length; i++) {\r
+ this._userColoursList.add(vUserColoursArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setViewport(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size()) {\r
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._viewportList.set(index, vViewport);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vViewportArray\r
+ */\r
+ public void setViewport(\r
+ final jalview.schemabinding.version2.Viewport[] vViewportArray) {\r
+ //-- copy array\r
+ _viewportList.clear();\r
+ \r
+ for (int i = 0; i < vViewportArray.length; i++) {\r
+ this._viewportList.add(vViewportArray[i]);\r
+ }\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.JalviewModelSequence\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewUserColours implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _schemeName.\r
- */\r
- private java.lang.String _schemeName;\r
-\r
- /**\r
- * Jalview colour scheme document version.\r
- * \r
- */\r
- private java.lang.String _version;\r
-\r
- /**\r
- * Field _colourList.\r
- */\r
- private java.util.Vector _colourList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewUserColours()\r
- {\r
- super();\r
- this._colourList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addColour(final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._colourList.addElement(vColour);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addColour(final int index, final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._colourList.add(index, vColour);\r
- }\r
-\r
- /**\r
- * Method enumerateColour.\r
- * \r
- * @return an Enumeration over all Colour elements\r
- */\r
- public java.util.Enumeration enumerateColour()\r
- {\r
- return this._colourList.elements();\r
- }\r
-\r
- /**\r
- * Method getColour.\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 Colour at the given index\r
- */\r
- public Colour getColour(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._colourList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getColour: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._colourList.size() - 1) + "]");\r
+public class JalviewUserColours implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _schemeName.\r
+ */\r
+ private java.lang.String _schemeName;\r
+\r
+ /**\r
+ * Jalview colour scheme document version.\r
+ * \r
+ */\r
+ private java.lang.String _version;\r
+\r
+ /**\r
+ * Field _colourList.\r
+ */\r
+ private java.util.Vector _colourList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewUserColours() {\r
+ super();\r
+ this._colourList = new java.util.Vector();\r
}\r
\r
- return (Colour) _colourList.get(index);\r
- }\r
-\r
- /**\r
- * Method getColour.Returns the contents of the collection in an 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 Colour[] getColour()\r
- {\r
- Colour[] array = new Colour[0];\r
- return (Colour[]) this._colourList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getColourCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getColourCount()\r
- {\r
- return this._colourList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'schemeName'.\r
- * \r
- * @return the value of field 'SchemeName'.\r
- */\r
- public java.lang.String getSchemeName()\r
- {\r
- return this._schemeName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'version'. The field 'version' has the following\r
- * description: Jalview colour scheme document version.\r
- * \r
- * \r
- * @return the value of field 'Version'.\r
- */\r
- public java.lang.String getVersion()\r
- {\r
- return this._version;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addColour(\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._colourList.addElement(vColour);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addColour(\r
+ final int index,\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._colourList.add(index, vColour);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateColour.\r
+ * \r
+ * @return an Enumeration over all Colour elements\r
+ */\r
+ public java.util.Enumeration enumerateColour(\r
+ ) {\r
+ return this._colourList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getColour.\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 Colour at the given index\r
+ */\r
+ public Colour getColour(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._colourList.size()) {\r
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (Colour) _colourList.get(index);\r
}\r
- return true;\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 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 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
+ /**\r
+ * Method getColour.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public Colour[] getColour(\r
+ ) {\r
+ Colour[] array = new Colour[0];\r
+ return (Colour[]) this._colourList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getColourCount.\r
+ * \r
+ * @return the size of this collection\r
*/\r
- public void removeAllColour()\r
- {\r
- this._colourList.clear();\r
- }\r
-\r
- /**\r
- * Method removeColour.\r
- * \r
- * @param vColour\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeColour(final Colour vColour)\r
- {\r
- boolean removed = _colourList.remove(vColour);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeColourAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public Colour removeColourAt(final int index)\r
- {\r
- java.lang.Object obj = this._colourList.remove(index);\r
- return (Colour) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setColour(final int index, final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._colourList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setColour: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._colourList.size() - 1) + "]");\r
+ public int getColourCount(\r
+ ) {\r
+ return this._colourList.size();\r
}\r
\r
- this._colourList.set(index, vColour);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vColourArray\r
- */\r
- public void setColour(final Colour[] vColourArray)\r
- {\r
- // -- copy array\r
- _colourList.clear();\r
-\r
- for (int i = 0; i < vColourArray.length; i++)\r
- {\r
- this._colourList.add(vColourArray[i]);\r
+ /**\r
+ * Returns the value of field 'schemeName'.\r
+ * \r
+ * @return the value of field 'SchemeName'.\r
+ */\r
+ public java.lang.String getSchemeName(\r
+ ) {\r
+ return this._schemeName;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'version'. The field 'version'\r
+ * has the following description: Jalview colour scheme\r
+ * document version.\r
+ * \r
+ * \r
+ * @return the value of field 'Version'.\r
+ */\r
+ public java.lang.String getVersion(\r
+ ) {\r
+ return this._version;\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
+ * \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 removeAllColour(\r
+ ) {\r
+ this._colourList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeColour.\r
+ * \r
+ * @param vColour\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeColour(\r
+ final Colour vColour) {\r
+ boolean removed = _colourList.remove(vColour);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeColourAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public Colour removeColourAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._colourList.remove(index);\r
+ return (Colour) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vColour\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setColour(\r
+ final int index,\r
+ final Colour vColour)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._colourList.size()) {\r
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._colourList.set(index, vColour);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vColourArray\r
+ */\r
+ public void setColour(\r
+ final Colour[] vColourArray) {\r
+ //-- copy array\r
+ _colourList.clear();\r
+ \r
+ for (int i = 0; i < vColourArray.length; i++) {\r
+ this._colourList.add(vColourArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'schemeName'.\r
+ * \r
+ * @param schemeName the value of field 'schemeName'.\r
+ */\r
+ public void setSchemeName(\r
+ final java.lang.String schemeName) {\r
+ this._schemeName = schemeName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'version'. The field 'version' has\r
+ * the following description: Jalview colour scheme document\r
+ * version.\r
+ * \r
+ * \r
+ * @param version the value of field 'version'.\r
+ */\r
+ public void setVersion(\r
+ final java.lang.String version) {\r
+ this._version = version;\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.JalviewUserColours\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.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
- /**\r
- * Sets the value of field 'schemeName'.\r
- * \r
- * @param schemeName\r
- * the value of field 'schemeName'.\r
- */\r
- public void setSchemeName(final java.lang.String schemeName)\r
- {\r
- this._schemeName = schemeName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'version'. The field 'version' has the following\r
- * description: Jalview colour scheme document version.\r
- * \r
- * \r
- * @param version\r
- * the value of field 'version'.\r
- */\r
- public void setVersion(final java.lang.String version)\r
- {\r
- this._version = version;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours\r
- */\r
- public static jalview.schemabinding.version2.JalviewUserColours 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.JalviewUserColours) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.JalviewUserColours.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListFrom implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _start.\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListFrom()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class MapListFrom implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListFrom() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\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
+ * \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
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = 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.MapListFrom\r
+ */\r
+ public static jalview.schemabinding.version2.MapListFrom unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.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
- return true;\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 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 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
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.MapListFrom\r
- */\r
- public static jalview.schemabinding.version2.MapListFrom 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.MapListFrom) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.MapListFrom.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListTo implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _start.\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListTo()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class MapListTo implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListTo() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\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
+ * \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
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = 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.MapListTo\r
+ */\r
+ public static jalview.schemabinding.version2.MapListTo unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.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
- return true;\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 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 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
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.MapListTo\r
- */\r
- public static jalview.schemabinding.version2.MapListTo 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.MapListTo) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.MapListTo.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
/**\r
* developed after mapRangeType from\r
* http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes\r
- * \r
- * This effectively represents a java.util.MapList object\r
- * \r
+ * \r
+ * This effectively represents a java.util.MapList object\r
+ * \r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListType implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * number of dictionary symbol widths involved in each mapped position on this\r
- * sequence (for example, 3 for a dna sequence exon region that is being\r
- * mapped to a protein sequence). This is optional, since the unit can be\r
- * usually be inferred from the dictionary type of each sequence involved in\r
- * the mapping.\r
- */\r
- private long _mapFromUnit;\r
-\r
- /**\r
- * keeps track of state for field: _mapFromUnit\r
- */\r
- private boolean _has_mapFromUnit;\r
-\r
- /**\r
- * number of dictionary symbol widths involved in each mapped position on this\r
- * sequence (for example, 3 for a dna sequence exon region that is being\r
- * mapped to a protein sequence). This is optional, since the unit can be\r
- * usually be inferred from the dictionary type of each sequence involved in\r
- * the mapping.\r
- */\r
- private long _mapToUnit;\r
-\r
- /**\r
- * keeps track of state for field: _mapToUnit\r
- */\r
- private boolean _has_mapToUnit;\r
-\r
- /**\r
- * a region from start to end inclusive\r
- */\r
- private java.util.Vector _mapListFromList;\r
-\r
- /**\r
- * a region from start to end inclusive\r
- */\r
- private java.util.Vector _mapListToList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListType()\r
- {\r
- super();\r
- this._mapListFromList = new java.util.Vector();\r
- this._mapListToList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._mapListFromList.addElement(vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addMapListFrom(final int index,\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._mapListFromList.add(index, vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addMapListTo(\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._mapListToList.addElement(vMapListTo);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addMapListTo(final int index,\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._mapListToList.add(index, vMapListTo);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMapFromUnit()\r
- {\r
- this._has_mapFromUnit = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMapToUnit()\r
- {\r
- this._has_mapToUnit = false;\r
- }\r
-\r
- /**\r
- * Method enumerateMapListFrom.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateMapListFrom()\r
- {\r
- return this._mapListFromList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateMapListTo.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.MapListTo\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateMapListTo()\r
- {\r
- return this._mapListToList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the\r
- * following description: number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna sequence exon\r
- * region that is being mapped to a protein sequence). This is optional, since\r
- * the unit can be usually be inferred from the dictionary type of each\r
- * sequence involved in the mapping.\r
- * \r
- * @return the value of field 'MapFromUnit'.\r
- */\r
- public long getMapFromUnit()\r
- {\r
- return this._mapFromUnit;\r
- }\r
-\r
- /**\r
- * Method getMapListFrom.\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.MapListFrom at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.MapListFrom getMapListFrom(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListFromList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getMapListFrom: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._mapListFromList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.MapListFrom) _mapListFromList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getMapListFrom.Returns the contents of the collection in an 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.MapListFrom[] getMapListFrom()\r
- {\r
- jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];\r
- return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getMapListFromCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getMapListFromCount()\r
- {\r
- return this._mapListFromList.size();\r
- }\r
-\r
- /**\r
- * Method getMapListTo.\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.MapListTo at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.MapListTo getMapListTo(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListToList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getMapListTo: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._mapListToList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.MapListTo) _mapListToList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getMapListTo.Returns the contents of the collection in an 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.MapListTo[] getMapListTo()\r
- {\r
- jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];\r
- return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getMapListToCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getMapListToCount()\r
- {\r
- return this._mapListToList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the\r
- * following description: number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna sequence exon\r
- * region that is being mapped to a protein sequence). This is optional, since\r
- * the unit can be usually be inferred from the dictionary type of each\r
- * sequence involved in the mapping.\r
- * \r
- * @return the value of field 'MapToUnit'.\r
- */\r
- public long getMapToUnit()\r
- {\r
- return this._mapToUnit;\r
- }\r
-\r
- /**\r
- * Method hasMapFromUnit.\r
- * \r
- * @return true if at least one MapFromUnit has been added\r
- */\r
- public boolean hasMapFromUnit()\r
- {\r
- return this._has_mapFromUnit;\r
- }\r
-\r
- /**\r
- * Method hasMapToUnit.\r
- * \r
- * @return true if at least one MapToUnit has been added\r
- */\r
- public boolean hasMapToUnit()\r
- {\r
- return this._has_mapToUnit;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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 removeAllMapListFrom()\r
- {\r
- this._mapListFromList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllMapListTo()\r
- {\r
- this._mapListToList.clear();\r
- }\r
-\r
- /**\r
- * Method removeMapListFrom.\r
- * \r
- * @param vMapListFrom\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- {\r
- boolean removed = _mapListFromList.remove(vMapListFrom);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeMapListFromAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._mapListFromList.remove(index);\r
- return (jalview.schemabinding.version2.MapListFrom) obj;\r
- }\r
-\r
- /**\r
- * Method removeMapListTo.\r
- * \r
- * @param vMapListTo\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeMapListTo(\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- {\r
- boolean removed = _mapListToList.remove(vMapListTo);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeMapListToAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.MapListTo removeMapListToAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._mapListToList.remove(index);\r
- return (jalview.schemabinding.version2.MapListTo) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the\r
- * following description: number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna sequence exon\r
- * region that is being mapped to a protein sequence). This is optional, since\r
- * the unit can be usually be inferred from the dictionary type of each\r
- * sequence involved in the mapping.\r
- * \r
- * @param mapFromUnit\r
- * the value of field 'mapFromUnit'.\r
- */\r
- public void setMapFromUnit(final long mapFromUnit)\r
- {\r
- this._mapFromUnit = mapFromUnit;\r
- this._has_mapFromUnit = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setMapListFrom(final int index,\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListFromList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setMapListFrom: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._mapListFromList.size() - 1) + "]");\r
- }\r
-\r
- this._mapListFromList.set(index, vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListFromArray\r
- */\r
- public void setMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray)\r
- {\r
- // -- copy array\r
- _mapListFromList.clear();\r
-\r
- for (int i = 0; i < vMapListFromArray.length; i++)\r
- {\r
- this._mapListFromList.add(vMapListFromArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setMapListTo(final int index,\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListToList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setMapListTo: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._mapListToList.size() - 1) + "]");\r
- }\r
-\r
- this._mapListToList.set(index, vMapListTo);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListToArray\r
- */\r
- public void setMapListTo(\r
- final jalview.schemabinding.version2.MapListTo[] vMapListToArray)\r
- {\r
- // -- copy array\r
- _mapListToList.clear();\r
-\r
- for (int i = 0; i < vMapListToArray.length; i++)\r
- {\r
- this._mapListToList.add(vMapListToArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the\r
- * following description: number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna sequence exon\r
- * region that is being mapped to a protein sequence). This is optional, since\r
- * the unit can be usually be inferred from the dictionary type of each\r
- * sequence involved in the mapping.\r
- * \r
- * @param mapToUnit\r
- * the value of field 'mapToUnit'.\r
- */\r
- public void setMapToUnit(final long mapToUnit)\r
- {\r
- this._mapToUnit = mapToUnit;\r
- this._has_mapToUnit = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.MapListType\r
- */\r
- public static jalview.schemabinding.version2.MapListType 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.MapListType) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.MapListType.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 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
+public class MapListType implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ */\r
+ private long _mapFromUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapFromUnit\r
+ */\r
+ private boolean _has_mapFromUnit;\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ */\r
+ private long _mapToUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapToUnit\r
+ */\r
+ private boolean _has_mapToUnit;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListFromList;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListToList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListType() {\r
+ super();\r
+ this._mapListFromList = new java.util.Vector();\r
+ this._mapListToList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListFromList.addElement(vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListFromList.add(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListToList.addElement(vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListToList.add(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapFromUnit(\r
+ ) {\r
+ this._has_mapFromUnit= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapToUnit(\r
+ ) {\r
+ this._has_mapToUnit= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListFrom.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.MapListFrom elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListFrom(\r
+ ) {\r
+ return this._mapListFromList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListTo.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.MapListTo elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListTo(\r
+ ) {\r
+ return this._mapListToList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapFromUnit'. The field\r
+ * 'mapFromUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @return the value of field 'MapFromUnit'.\r
+ */\r
+ public long getMapFromUnit(\r
+ ) {\r
+ return this._mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.\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.MapListFrom at the given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom getMapListFrom(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size()) {\r
+ throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(\r
+ ) {\r
+ jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];\r
+ return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFromCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListFromCount(\r
+ ) {\r
+ return this._mapListFromList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.\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.MapListTo at the given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo getMapListTo(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size()) {\r
+ throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo[] getMapListTo(\r
+ ) {\r
+ jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];\r
+ return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListToCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListToCount(\r
+ ) {\r
+ return this._mapListToList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapToUnit'. The field\r
+ * 'mapToUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @return the value of field 'MapToUnit'.\r
+ */\r
+ public long getMapToUnit(\r
+ ) {\r
+ return this._mapToUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapFromUnit.\r
+ * \r
+ * @return true if at least one MapFromUnit has been added\r
+ */\r
+ public boolean hasMapFromUnit(\r
+ ) {\r
+ return this._has_mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapToUnit.\r
+ * \r
+ * @return true if at least one MapToUnit has been added\r
+ */\r
+ public boolean hasMapToUnit(\r
+ ) {\r
+ return this._has_mapToUnit;\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
+ * \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 removeAllMapListFrom(\r
+ ) {\r
+ this._mapListFromList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllMapListTo(\r
+ ) {\r
+ this._mapListToList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFrom.\r
+ * \r
+ * @param vMapListFrom\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom) {\r
+ boolean removed = _mapListFromList.remove(vMapListFrom);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFromAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._mapListFromList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListFrom) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListTo.\r
+ * \r
+ * @param vMapListTo\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo) {\r
+ boolean removed = _mapListToList.remove(vMapListTo);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListToAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo removeMapListToAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._mapListToList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListTo) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapFromUnit'. The field\r
+ * 'mapFromUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @param mapFromUnit the value of field 'mapFromUnit'.\r
+ */\r
+ public void setMapFromUnit(\r
+ final long mapFromUnit) {\r
+ this._mapFromUnit = mapFromUnit;\r
+ this._has_mapFromUnit = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setMapListFrom(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size()) {\r
+ throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._mapListFromList.set(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFromArray\r
+ */\r
+ public void setMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {\r
+ //-- copy array\r
+ _mapListFromList.clear();\r
+ \r
+ for (int i = 0; i < vMapListFromArray.length; i++) {\r
+ this._mapListFromList.add(vMapListFromArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setMapListTo(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size()) {\r
+ throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._mapListToList.set(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListToArray\r
+ */\r
+ public void setMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {\r
+ //-- copy array\r
+ _mapListToList.clear();\r
+ \r
+ for (int i = 0; i < vMapListToArray.length; i++) {\r
+ this._mapListToList.add(vMapListToArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapToUnit'. The field 'mapToUnit'\r
+ * has the following description: number of dictionary symbol\r
+ * widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @param mapToUnit the value of field 'mapToUnit'.\r
+ */\r
+ public void setMapToUnit(\r
+ final long mapToUnit) {\r
+ this._mapToUnit = mapToUnit;\r
+ this._has_mapToUnit = 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.MapListType\r
+ */\r
+ public static jalview.schemabinding.version2.MapListType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Mapping extends jalview.schemabinding.version2.MapListType\r
- implements java.io.Serializable\r
+public class Mapping extends jalview.schemabinding.version2.MapListType \r
+implements java.io.Serializable\r
{\r
\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Internal choice value storage\r
- */\r
- private java.lang.Object _choiceValue;\r
-\r
- /**\r
- * Field _mappingChoice.\r
- */\r
- private jalview.schemabinding.version2.MappingChoice _mappingChoice;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Mapping()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'choiceValue'. The field 'choiceValue' has the\r
- * following description: Internal choice value storage\r
- * \r
- * @return the value of field 'ChoiceValue'.\r
- */\r
- public java.lang.Object getChoiceValue()\r
- {\r
- return this._choiceValue;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mappingChoice'.\r
- * \r
- * @return the value of field 'MappingChoice'.\r
- */\r
- public jalview.schemabinding.version2.MappingChoice getMappingChoice()\r
- {\r
- return this._mappingChoice;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Internal choice value storage\r
+ */\r
+ private java.lang.Object _choiceValue;\r
+\r
+ /**\r
+ * Field _mappingChoice.\r
+ */\r
+ private jalview.schemabinding.version2.MappingChoice _mappingChoice;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Mapping() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'choiceValue'. The field\r
+ * 'choiceValue' has the following description: Internal choice\r
+ * value storage\r
+ * \r
+ * @return the value of field 'ChoiceValue'.\r
+ */\r
+ public java.lang.Object getChoiceValue(\r
+ ) {\r
+ return this._choiceValue;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mappingChoice'.\r
+ * \r
+ * @return the value of field 'MappingChoice'.\r
+ */\r
+ public jalview.schemabinding.version2.MappingChoice getMappingChoice(\r
+ ) {\r
+ return this._mappingChoice;\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
+ * \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
+ * Sets the value of field 'mappingChoice'.\r
+ * \r
+ * @param mappingChoice the value of field 'mappingChoice'.\r
+ */\r
+ public void setMappingChoice(\r
+ final jalview.schemabinding.version2.MappingChoice mappingChoice) {\r
+ this._mappingChoice = mappingChoice;\r
+ this._choiceValue = mappingChoice;\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.MapListType\r
+ */\r
+ public static jalview.schemabinding.version2.MapListType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.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
- return true;\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 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 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
- * Sets the value of field 'mappingChoice'.\r
- * \r
- * @param mappingChoice\r
- * the value of field 'mappingChoice'.\r
- */\r
- public void setMappingChoice(\r
- final jalview.schemabinding.version2.MappingChoice mappingChoice)\r
- {\r
- this._mappingChoice = mappingChoice;\r
- this._choiceValue = mappingChoice;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.MapListType\r
- */\r
- public static jalview.schemabinding.version2.MapListType 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.MapListType) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Mapping.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MappingChoice implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _sequence.\r
- */\r
- private jalview.schemabinding.version2.Sequence _sequence;\r
-\r
- /**\r
- * Field _dseqFor.\r
- */\r
- private java.lang.String _dseqFor;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MappingChoice()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'dseqFor'.\r
- * \r
- * @return the value of field 'DseqFor'.\r
- */\r
- public java.lang.String getDseqFor()\r
- {\r
- return this._dseqFor;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequence'.\r
- * \r
- * @return the value of field 'Sequence'.\r
- */\r
- public jalview.schemabinding.version2.Sequence getSequence()\r
- {\r
- return this._sequence;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class MappingChoice implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _sequence.\r
+ */\r
+ private jalview.schemabinding.version2.Sequence _sequence;\r
+\r
+ /**\r
+ * Field _dseqFor.\r
+ */\r
+ private java.lang.String _dseqFor;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingChoice() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'dseqFor'.\r
+ * \r
+ * @return the value of field 'DseqFor'.\r
+ */\r
+ public java.lang.String getDseqFor(\r
+ ) {\r
+ return this._dseqFor;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequence'.\r
+ * \r
+ * @return the value of field 'Sequence'.\r
+ */\r
+ public jalview.schemabinding.version2.Sequence getSequence(\r
+ ) {\r
+ return this._sequence;\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
+ * \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
+ * Sets the value of field 'dseqFor'.\r
+ * \r
+ * @param dseqFor the value of field 'dseqFor'.\r
+ */\r
+ public void setDseqFor(\r
+ final java.lang.String dseqFor) {\r
+ this._dseqFor = dseqFor;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequence'.\r
+ * \r
+ * @param sequence the value of field 'sequence'.\r
+ */\r
+ public void setSequence(\r
+ final jalview.schemabinding.version2.Sequence sequence) {\r
+ this._sequence = sequence;\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.MappingChoice\r
+ */\r
+ public static jalview.schemabinding.version2.MappingChoice unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.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
- return true;\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 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 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
- * Sets the value of field 'dseqFor'.\r
- * \r
- * @param dseqFor\r
- * the value of field 'dseqFor'.\r
- */\r
- public void setDseqFor(final java.lang.String dseqFor)\r
- {\r
- this._dseqFor = dseqFor;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequence'.\r
- * \r
- * @param sequence\r
- * the value of field 'sequence'.\r
- */\r
- public void setSequence(\r
- final jalview.schemabinding.version2.Sequence sequence)\r
- {\r
- this._sequence = sequence;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.MappingChoice\r
- */\r
- public static jalview.schemabinding.version2.MappingChoice 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.MappingChoice) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.MappingChoice.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class OtherData implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _key.\r
- */\r
- private java.lang.String _key;\r
-\r
- /**\r
- * Field _value.\r
- */\r
- private java.lang.String _value;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public OtherData()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'key'.\r
- * \r
- * @return the value of field 'Key'.\r
- */\r
- public java.lang.String getKey()\r
- {\r
- return this._key;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return the value of field 'Value'.\r
- */\r
- public java.lang.String getValue()\r
- {\r
- return this._value;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class OtherData implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _key.\r
+ */\r
+ private java.lang.String _key;\r
+\r
+ /**\r
+ * Field _value.\r
+ */\r
+ private java.lang.String _value;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public OtherData() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'key'.\r
+ * \r
+ * @return the value of field 'Key'.\r
+ */\r
+ public java.lang.String getKey(\r
+ ) {\r
+ return this._key;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'value'.\r
+ * \r
+ * @return the value of field 'Value'.\r
+ */\r
+ public java.lang.String getValue(\r
+ ) {\r
+ return this._value;\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
+ * \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
+ * Sets the value of field 'key'.\r
+ * \r
+ * @param key the value of field 'key'.\r
+ */\r
+ public void setKey(\r
+ final java.lang.String key) {\r
+ this._key = key;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'value'.\r
+ * \r
+ * @param value the value of field 'value'.\r
+ */\r
+ public void setValue(\r
+ final java.lang.String value) {\r
+ this._value = value;\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.OtherData\r
+ */\r
+ public static jalview.schemabinding.version2.OtherData unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.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
- return true;\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 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 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
- * Sets the value of field 'key'.\r
- * \r
- * @param key\r
- * the value of field 'key'.\r
- */\r
- public void setKey(final java.lang.String key)\r
- {\r
- this._key = key;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value\r
- * the value of field 'value'.\r
- */\r
- public void setValue(final java.lang.String value)\r
- {\r
- this._value = value;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.OtherData\r
- */\r
- public static jalview.schemabinding.version2.OtherData 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.OtherData) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.OtherData.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Pdbentry implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _file.\r
- */\r
- private java.lang.String _file;\r
-\r
- /**\r
- * Field _items.\r
- */\r
- private java.util.Vector _items;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Pdbentry()\r
- {\r
- super();\r
- this._items = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._items.addElement(vPdbentryItem);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbentryItem(final int index,\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._items.add(index, vPdbentryItem);\r
- }\r
-\r
- /**\r
- * Method enumeratePdbentryItem.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem\r
- * elements\r
- */\r
- public java.util.Enumeration enumeratePdbentryItem()\r
- {\r
- return this._items.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'file'.\r
- * \r
- * @return the value of field 'File'.\r
- */\r
- public java.lang.String getFile()\r
- {\r
- return this._file;\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
- * Method getPdbentryItem.\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.PdbentryItem at the\r
- * given inde\r
- */\r
- public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._items.size())\r
- {\r
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"\r
- + index + "' not in range [0.." + (this._items.size() - 1)\r
- + "]");\r
+public class Pdbentry implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _type.\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _file.\r
+ */\r
+ private java.lang.String _file;\r
+\r
+ /**\r
+ * Field _items.\r
+ */\r
+ private java.util.Vector _items;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Pdbentry() {\r
+ super();\r
+ this._items = new java.util.Vector();\r
}\r
\r
- return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);\r
- }\r
-\r
- /**\r
- * Method getPdbentryItem.Returns the contents of the collection in an 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.PdbentryItem[] getPdbentryItem()\r
- {\r
- jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];\r
- return (jalview.schemabinding.version2.PdbentryItem[]) this._items\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPdbentryItemCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPdbentryItemCount()\r
- {\r
- return this._items.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._items.addElement(vPdbentryItem);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbentryItem(\r
+ final int index,\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._items.add(index, vPdbentryItem);\r
+ }\r
+\r
+ /**\r
+ * Method enumeratePdbentryItem.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.PdbentryItem elements\r
+ */\r
+ public java.util.Enumeration enumeratePdbentryItem(\r
+ ) {\r
+ return this._items.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'file'.\r
+ * \r
+ * @return the value of field 'File'.\r
+ */\r
+ public java.lang.String getFile(\r
+ ) {\r
+ return this._file;\r
}\r
- return true;\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 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 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
+ /**\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
+ * Method getPdbentryItem.\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.PdbentryItem at the given inde\r
+ */\r
+ public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._items.size()) {\r
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbentryItem.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.PdbentryItem[] getPdbentryItem(\r
+ ) {\r
+ jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];\r
+ return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbentryItemCount.\r
+ * \r
+ * @return the size of this collection\r
*/\r
- public void removeAllPdbentryItem()\r
- {\r
- this._items.clear();\r
- }\r
-\r
- /**\r
- * Method removePdbentryItem.\r
- * \r
- * @param vPdbentryItem\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removePdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- {\r
- boolean removed = _items.remove(vPdbentryItem);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePdbentryItemAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._items.remove(index);\r
- return (jalview.schemabinding.version2.PdbentryItem) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'file'.\r
- * \r
- * @param file\r
- * the value of field 'file'.\r
- */\r
- public void setFile(final java.lang.String file)\r
- {\r
- this._file = file;\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
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setPdbentryItem(final int index,\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._items.size())\r
- {\r
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"\r
- + index + "' not in range [0.." + (this._items.size() - 1)\r
- + "]");\r
+ public int getPdbentryItemCount(\r
+ ) {\r
+ return this._items.size();\r
}\r
\r
- this._items.set(index, vPdbentryItem);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbentryItemArray\r
- */\r
- public void setPdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)\r
- {\r
- // -- copy array\r
- _items.clear();\r
-\r
- for (int i = 0; i < vPdbentryItemArray.length; i++)\r
- {\r
- this._items.add(vPdbentryItemArray[i]);\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return the value of field 'Type'.\r
+ */\r
+ public java.lang.String getType(\r
+ ) {\r
+ return this._type;\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
+ * \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 removeAllPdbentryItem(\r
+ ) {\r
+ this._items.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removePdbentryItem.\r
+ * \r
+ * @param vPdbentryItem\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removePdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) {\r
+ boolean removed = _items.remove(vPdbentryItem);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePdbentryItemAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._items.remove(index);\r
+ return (jalview.schemabinding.version2.PdbentryItem) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'file'.\r
+ * \r
+ * @param file the value of field 'file'.\r
+ */\r
+ public void setFile(\r
+ final java.lang.String file) {\r
+ this._file = file;\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
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbentryItem\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setPdbentryItem(\r
+ final int index,\r
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._items.size()) {\r
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");\r
+ }\r
+ \r
+ this._items.set(index, vPdbentryItem);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbentryItemArray\r
+ */\r
+ public void setPdbentryItem(\r
+ final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) {\r
+ //-- copy array\r
+ _items.clear();\r
+ \r
+ for (int i = 0; i < vPdbentryItemArray.length; i++) {\r
+ this._items.add(vPdbentryItemArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(\r
+ final java.lang.String type) {\r
+ this._type = type;\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.Pdbentry\r
+ */\r
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.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
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Pdbentry\r
- */\r
- public static jalview.schemabinding.version2.Pdbentry 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.Pdbentry) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Pdbentry.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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
* \r
* @version $Revision$ $Date$\r
*/\r
-public class PdbentryItem implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _propertyList.\r
- */\r
- private java.util.Vector _propertyList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public PdbentryItem()\r
- {\r
- super();\r
- this._propertyList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addProperty(\r
- final jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._propertyList.addElement(vProperty);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addProperty(final int index,\r
- final jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._propertyList.add(index, vProperty);\r
- }\r
-\r
- /**\r
- * Method enumerateProperty.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Property\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return this._propertyList.elements();\r
- }\r
-\r
- /**\r
- * Method getProperty.\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.Property at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Property getProperty(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._propertyList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getProperty: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._propertyList.size() - 1) + "]");\r
+public class PdbentryItem implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _propertyList.\r
+ */\r
+ private java.util.Vector _propertyList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryItem() {\r
+ super();\r
+ this._propertyList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addProperty(\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.addElement(vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addProperty(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._propertyList.add(index, vProperty);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateProperty.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Property elements\r
+ */\r
+ public java.util.Enumeration enumerateProperty(\r
+ ) {\r
+ return this._propertyList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.\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.Property at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Property getProperty(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Property) _propertyList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Property[] getProperty(\r
+ ) {\r
+ jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];\r
+ return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPropertyCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getPropertyCount(\r
+ ) {\r
+ return this._propertyList.size();\r
}\r
\r
- return (jalview.schemabinding.version2.Property) _propertyList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getProperty.Returns the contents of the collection in an 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.Property[] getProperty()\r
- {\r
- jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];\r
- return (jalview.schemabinding.version2.Property[]) this._propertyList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPropertyCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPropertyCount()\r
- {\r
- return this._propertyList.size();\r
- }\r
-\r
- /**\r
+ /**\r
*/\r
- public void removeAllProperty()\r
- {\r
- this._propertyList.clear();\r
- }\r
-\r
- /**\r
- * Method removeProperty.\r
- * \r
- * @param vProperty\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeProperty(\r
- final jalview.schemabinding.version2.Property vProperty)\r
- {\r
- boolean removed = _propertyList.remove(vProperty);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePropertyAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Property removePropertyAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._propertyList.remove(index);\r
- return (jalview.schemabinding.version2.Property) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setProperty(final int index,\r
- final jalview.schemabinding.version2.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._propertyList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setProperty: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._propertyList.size() - 1) + "]");\r
+ public void removeAllProperty(\r
+ ) {\r
+ this._propertyList.clear();\r
}\r
\r
- this._propertyList.set(index, vProperty);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPropertyArray\r
- */\r
- public void setProperty(\r
- final jalview.schemabinding.version2.Property[] vPropertyArray)\r
- {\r
- // -- copy array\r
- _propertyList.clear();\r
-\r
- for (int i = 0; i < vPropertyArray.length; i++)\r
- {\r
- this._propertyList.add(vPropertyArray[i]);\r
+ /**\r
+ * Method removeProperty.\r
+ * \r
+ * @param vProperty\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeProperty(\r
+ final jalview.schemabinding.version2.Property vProperty) {\r
+ boolean removed = _propertyList.remove(vProperty);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePropertyAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Property removePropertyAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._propertyList.remove(index);\r
+ return (jalview.schemabinding.version2.Property) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setProperty(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._propertyList.set(index, vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPropertyArray\r
+ */\r
+ public void setProperty(\r
+ final jalview.schemabinding.version2.Property[] vPropertyArray) {\r
+ //-- copy array\r
+ _propertyList.clear();\r
+ \r
+ for (int i = 0; i < vPropertyArray.length; i++) {\r
+ this._propertyList.add(vPropertyArray[i]);\r
+ }\r
}\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry\r
- implements java.io.Serializable\r
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry \r
+implements java.io.Serializable\r
{\r
\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
\r
- /**\r
- * Field _structureStateList.\r
- */\r
- private java.util.Vector _structureStateList;\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
+ /**\r
+ * Field _structureStateList.\r
+ */\r
+ private java.util.Vector _structureStateList;\r
\r
- public Pdbids()\r
- {\r
- super();\r
- this._structureStateList = new java.util.Vector();\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- /**\r
- * \r
- * \r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addStructureState(\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._structureStateList.addElement(vStructureState);\r
- }\r
+ public Pdbids() {\r
+ super();\r
+ this._structureStateList = new java.util.Vector();\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addStructureState(\r
- final int index,\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._structureStateList.add(index, vStructureState);\r
- }\r
\r
- /**\r
- * Method enumerateStructureState.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.StructureState elements\r
- */\r
- public java.util.Enumeration enumerateStructureState()\r
- {\r
- return this._structureStateList.elements();\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- /**\r
- * Method getStructureState.\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.StructureState at\r
- * the given index\r
- */\r
- public jalview.schemabinding.version2.StructureState getStructureState(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._structureStateList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "getStructureState: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._structureStateList.size() - 1) + "]");\r
+ /**\r
+ * \r
+ * \r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addStructureState(\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._structureStateList.addElement(vStructureState);\r
}\r
\r
- return (jalview.schemabinding.version2.StructureState) _structureStateList\r
- .get(index);\r
- }\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addStructureState(\r
+ final int index,\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._structureStateList.add(index, vStructureState);\r
+ }\r
\r
- /**\r
- * Method getStructureState.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.StructureState[] getStructureState()\r
- {\r
- jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];\r
- return (jalview.schemabinding.version2.StructureState[]) this._structureStateList\r
- .toArray(array);\r
- }\r
+ /**\r
+ * Method enumerateStructureState.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.StructureState elements\r
+ */\r
+ public java.util.Enumeration enumerateStructureState(\r
+ ) {\r
+ return this._structureStateList.elements();\r
+ }\r
\r
- /**\r
- * Method getStructureStateCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getStructureStateCount()\r
- {\r
- return this._structureStateList.size();\r
- }\r
+ /**\r
+ * Method getStructureState.\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.StructureState at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.StructureState getStructureState(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+ /**\r
+ * Method getStructureState.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.StructureState[] getStructureState(\r
+ ) {\r
+ jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];\r
+ return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array);\r
}\r
- return true;\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 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
+ * Method getStructureStateCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getStructureStateCount(\r
+ ) {\r
+ return this._structureStateList.size();\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 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
+ * 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
+ /**\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 removeAllStructureState()\r
- {\r
- this._structureStateList.clear();\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
- * Method removeStructureState.\r
- * \r
- * @param vStructureState\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeStructureState(\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- {\r
- boolean removed = _structureStateList.remove(vStructureState);\r
- return removed;\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
- * Method removeStructureStateAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.StructureState removeStructureStateAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._structureStateList.remove(index);\r
- return (jalview.schemabinding.version2.StructureState) obj;\r
- }\r
+ /**\r
+ */\r
+ public void removeAllStructureState(\r
+ ) {\r
+ this._structureStateList.clear();\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setStructureState(\r
- final int index,\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._structureStateList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setStructureState: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._structureStateList.size() - 1) + "]");\r
+ /**\r
+ * Method removeStructureState.\r
+ * \r
+ * @param vStructureState\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeStructureState(\r
+ final jalview.schemabinding.version2.StructureState vStructureState) {\r
+ boolean removed = _structureStateList.remove(vStructureState);\r
+ return removed;\r
}\r
\r
- this._structureStateList.set(index, vStructureState);\r
- }\r
+ /**\r
+ * Method removeStructureStateAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.StructureState removeStructureStateAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._structureStateList.remove(index);\r
+ return (jalview.schemabinding.version2.StructureState) obj;\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @param vStructureStateArray\r
- */\r
- public void setStructureState(\r
- final jalview.schemabinding.version2.StructureState[] vStructureStateArray)\r
- {\r
- // -- copy array\r
- _structureStateList.clear();\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setStructureState(\r
+ final int index,\r
+ final jalview.schemabinding.version2.StructureState vStructureState)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._structureStateList.set(index, vStructureState);\r
+ }\r
\r
- for (int i = 0; i < vStructureStateArray.length; i++)\r
- {\r
- this._structureStateList.add(vStructureStateArray[i]);\r
+ /**\r
+ * \r
+ * \r
+ * @param vStructureStateArray\r
+ */\r
+ public void setStructureState(\r
+ final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {\r
+ //-- copy array\r
+ _structureStateList.clear();\r
+ \r
+ for (int i = 0; i < vStructureStateArray.length; i++) {\r
+ this._structureStateList.add(vStructureStateArray[i]);\r
+ }\r
}\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Pdbentry\r
- */\r
- public static jalview.schemabinding.version2.Pdbentry 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.Pdbentry) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);\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.Pdbentry\r
+ */\r
+ public static jalview.schemabinding.version2.Pdbentry unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+ * \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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Property implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _value.\r
- */\r
- private java.lang.String _value;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Property()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return the value of field 'Value'.\r
- */\r
- public java.lang.String getValue()\r
- {\r
- return this._value;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class Property implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _name.\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _value.\r
+ */\r
+ private java.lang.String _value;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Property() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return the value of field 'Name'.\r
+ */\r
+ public java.lang.String getName(\r
+ ) {\r
+ return this._name;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'value'.\r
+ * \r
+ * @return the value of field 'Value'.\r
+ */\r
+ public java.lang.String getValue(\r
+ ) {\r
+ return this._value;\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
+ * \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
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(\r
+ final java.lang.String name) {\r
+ this._name = name;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'value'.\r
+ * \r
+ * @param value the value of field 'value'.\r
+ */\r
+ public void setValue(\r
+ final java.lang.String value) {\r
+ this._value = value;\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.Property\r
+ */\r
+ public static jalview.schemabinding.version2.Property unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.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
- return true;\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 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 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
- * Sets the value of field 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value\r
- * the value of field 'value'.\r
- */\r
- public void setValue(final java.lang.String value)\r
- {\r
- this._value = value;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Property\r
- */\r
- public static jalview.schemabinding.version2.Property 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.Property) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Property.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends jalview.schemabinding.version2.SequenceType\r
- implements java.io.Serializable\r
+public class Sequence extends jalview.schemabinding.version2.SequenceType \r
+implements java.io.Serializable\r
{\r
\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * dataset sequence id for this sequence. Will be created as union of\r
- * sequences.\r
- * \r
- */\r
- private java.lang.String _dsseqid;\r
-\r
- /**\r
- * Field _DBRefList.\r
- */\r
- private java.util.Vector _DBRefList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Sequence()\r
- {\r
- super();\r
- this._DBRefList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vDBRef\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._DBRefList.addElement(vDBRef);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vDBRef\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addDBRef(final int index,\r
- final jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._DBRefList.add(index, vDBRef);\r
- }\r
-\r
- /**\r
- * Method enumerateDBRef.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.DBRef\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateDBRef()\r
- {\r
- return this._DBRefList.elements();\r
- }\r
-\r
- /**\r
- * Method getDBRef.\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.DBRef at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.DBRef getDBRef(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._DBRefList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getDBRef: Index value '" + index\r
- + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * dataset sequence id for this sequence. Will be created as\r
+ * union of sequences.\r
+ * \r
+ */\r
+ private java.lang.String _dsseqid;\r
+\r
+ /**\r
+ * Field _DBRefList.\r
+ */\r
+ private java.util.Vector _DBRefList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Sequence() {\r
+ super();\r
+ this._DBRefList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.addElement(vDBRef);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.add(index, vDBRef);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateDBRef.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.DBRef elements\r
+ */\r
+ public java.util.Enumeration enumerateDBRef(\r
+ ) {\r
+ return this._DBRefList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getDBRef.\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.DBRef at the given index\r
+ */\r
+ public jalview.schemabinding.version2.DBRef getDBRef(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getDBRef.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.DBRef[] getDBRef(\r
+ ) {\r
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];\r
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getDBRefCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getDBRefCount(\r
+ ) {\r
+ return this._DBRefList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'dsseqid'. The field 'dsseqid'\r
+ * has the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @return the value of field 'Dsseqid'.\r
+ */\r
+ public java.lang.String getDsseqid(\r
+ ) {\r
+ return this._dsseqid;\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
+ * \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 removeAllDBRef(\r
+ ) {\r
+ this._DBRefList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeDBRef.\r
+ * \r
+ * @param vDBRef\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef) {\r
+ boolean removed = _DBRefList.remove(vDBRef);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeDBRefAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._DBRefList.remove(index);\r
+ return (jalview.schemabinding.version2.DBRef) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._DBRefList.set(index, vDBRef);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vDBRefArray\r
+ */\r
+ public void setDBRef(\r
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray) {\r
+ //-- copy array\r
+ _DBRefList.clear();\r
+ \r
+ for (int i = 0; i < vDBRefArray.length; i++) {\r
+ this._DBRefList.add(vDBRefArray[i]);\r
+ }\r
}\r
\r
- return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);\r
- }\r
-\r
- /**\r
- * Method getDBRef.Returns the contents of the collection in an 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.DBRef[] getDBRef()\r
- {\r
- jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];\r
- return (jalview.schemabinding.version2.DBRef[]) this._DBRefList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getDBRefCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getDBRefCount()\r
- {\r
- return this._DBRefList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following\r
- * description: dataset sequence id for this sequence. Will be created as\r
- * union of sequences.\r
- * \r
- * \r
- * @return the value of field 'Dsseqid'.\r
- */\r
- public java.lang.String getDsseqid()\r
- {\r
- return this._dsseqid;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+ /**\r
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has\r
+ * the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @param dsseqid the value of field 'dsseqid'.\r
+ */\r
+ public void setDsseqid(\r
+ final java.lang.String dsseqid) {\r
+ this._dsseqid = dsseqid;\r
}\r
- return true;\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 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 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
+ /**\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.SequenceType\r
*/\r
- public void removeAllDBRef()\r
- {\r
- this._DBRefList.clear();\r
- }\r
-\r
- /**\r
- * Method removeDBRef.\r
- * \r
- * @param vDBRef\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeDBRef(\r
- final jalview.schemabinding.version2.DBRef vDBRef)\r
- {\r
- boolean removed = _DBRefList.remove(vDBRef);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeDBRefAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)\r
- {\r
- java.lang.Object obj = this._DBRefList.remove(index);\r
- return (jalview.schemabinding.version2.DBRef) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vDBRef\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setDBRef(final int index,\r
- final jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._DBRefList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setDBRef: Index value '" + index\r
- + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+ public static jalview.schemabinding.version2.SequenceType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);\r
}\r
\r
- this._DBRefList.set(index, vDBRef);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vDBRefArray\r
- */\r
- public void setDBRef(\r
- final jalview.schemabinding.version2.DBRef[] vDBRefArray)\r
- {\r
- // -- copy array\r
- _DBRefList.clear();\r
-\r
- for (int i = 0; i < vDBRefArray.length; i++)\r
- {\r
- this._DBRefList.add(vDBRefArray[i]);\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
- /**\r
- * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following\r
- * description: dataset sequence id for this sequence. Will be created as\r
- * union of sequences.\r
- * \r
- * \r
- * @param dsseqid\r
- * the value of field 'dsseqid'.\r
- */\r
- public void setDsseqid(final java.lang.String dsseqid)\r
- {\r
- this._dsseqid = dsseqid;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.SequenceType\r
- */\r
- public static jalview.schemabinding.version2.SequenceType 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.SequenceType) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Sequence.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceSet implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _gapChar.\r
- */\r
- private java.lang.String _gapChar;\r
-\r
- /**\r
- * reference to set where jalview will gather the dataset sequences for all\r
- * sequences in the set.\r
- * \r
- */\r
- private java.lang.String _datasetId;\r
-\r
- /**\r
- * Field _sequenceList.\r
- */\r
- private java.util.Vector _sequenceList;\r
-\r
- /**\r
- * Field _annotationList.\r
- */\r
- private java.util.Vector _annotationList;\r
-\r
- /**\r
- * Field _sequenceSetPropertiesList.\r
- */\r
- private java.util.Vector _sequenceSetPropertiesList;\r
-\r
- /**\r
- * Field _alcodonFrameList.\r
- */\r
- private java.util.Vector _alcodonFrameList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceSet()\r
- {\r
- super();\r
- this._sequenceList = new java.util.Vector();\r
- this._annotationList = new java.util.Vector();\r
- this._sequenceSetPropertiesList = new java.util.Vector();\r
- this._alcodonFrameList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodonFrame\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodonFrame(\r
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonFrameList.addElement(vAlcodonFrame);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodonFrame\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodonFrame(final int index,\r
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonFrameList.add(index, vAlcodonFrame);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotation\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAnnotation(\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._annotationList.addElement(vAnnotation);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotation\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAnnotation(final int index,\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._annotationList.add(index, vAnnotation);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequence\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequence(\r
- final jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceList.addElement(vSequence);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequence\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequence(final int index,\r
- final jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceList.add(index, vSequence);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSetProperties\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequenceSetProperties(\r
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSetProperties\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequenceSetProperties(\r
- final int index,\r
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);\r
- }\r
-\r
- /**\r
- * Method enumerateAlcodonFrame.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAlcodonFrame()\r
- {\r
- return this._alcodonFrameList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateAnnotation.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Annotation\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAnnotation()\r
- {\r
- return this._annotationList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateSequence.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Sequence\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateSequence()\r
- {\r
- return this._sequenceList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateSequenceSetProperties.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.SequenceSetProperties elements\r
- */\r
- public java.util.Enumeration enumerateSequenceSetProperties()\r
- {\r
- return this._sequenceSetPropertiesList.elements();\r
- }\r
-\r
- /**\r
- * Method getAlcodonFrame.\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.AlcodonFrame at the\r
- * given inde\r
- */\r
- public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonFrameList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonFrameList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodonFrame.Returns the contents of the collection in an 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.AlcodonFrame[] getAlcodonFrame()\r
- {\r
- jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];\r
- return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAlcodonFrameCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAlcodonFrameCount()\r
- {\r
- return this._alcodonFrameList.size();\r
- }\r
-\r
- /**\r
- * Method getAnnotation.\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.Annotation at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Annotation getAnnotation(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._annotationList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Annotation) _annotationList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getAnnotation.Returns the contents of the collection in an 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.Annotation[] getAnnotation()\r
- {\r
- jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];\r
- return (jalview.schemabinding.version2.Annotation[]) this._annotationList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAnnotationCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAnnotationCount()\r
- {\r
- return this._annotationList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'datasetId'. The field 'datasetId' has the\r
- * following description: reference to set where jalview will gather the\r
- * dataset sequences for all sequences in the set.\r
- * \r
- * \r
- * @return the value of field 'DatasetId'.\r
- */\r
- public java.lang.String getDatasetId()\r
- {\r
- return this._datasetId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'gapChar'.\r
- * \r
- * @return the value of field 'GapChar'.\r
- */\r
- public java.lang.String getGapChar()\r
- {\r
- return this._gapChar;\r
- }\r
-\r
- /**\r
- * Method getSequence.\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.Sequence at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Sequence getSequence(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSequence: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._sequenceList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Sequence) _sequenceList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getSequence.Returns the contents of the collection in an 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.Sequence[] getSequence()\r
- {\r
- jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];\r
- return (jalview.schemabinding.version2.Sequence[]) this._sequenceList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSequenceCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSequenceCount()\r
- {\r
- return this._sequenceList.size();\r
- }\r
-\r
- /**\r
- * Method getSequenceSetProperties.\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\r
- * jalview.schemabinding.version2.SequenceSetProperties at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetPropertiesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "getSequenceSetProperties: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getSequenceSetProperties.Returns the contents of the collection in\r
- * an 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.SequenceSetProperties[] getSequenceSetProperties()\r
- {\r
- jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];\r
- return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSequenceSetPropertiesCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSequenceSetPropertiesCount()\r
- {\r
- return this._sequenceSetPropertiesList.size();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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
- * Method removeAlcodonFrame.\r
- * \r
- * @param vAlcodonFrame\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodonFrame(\r
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
- {\r
- boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAlcodonFrameAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._alcodonFrameList.remove(index);\r
- return (jalview.schemabinding.version2.AlcodonFrame) obj;\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllAlcodonFrame()\r
- {\r
- this._alcodonFrameList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllAnnotation()\r
- {\r
- this._annotationList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllSequence()\r
- {\r
- this._sequenceList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllSequenceSetProperties()\r
- {\r
- this._sequenceSetPropertiesList.clear();\r
- }\r
-\r
- /**\r
- * Method removeAnnotation.\r
- * \r
- * @param vAnnotation\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAnnotation(\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- {\r
- boolean removed = _annotationList.remove(vAnnotation);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAnnotationAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Annotation removeAnnotationAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._annotationList.remove(index);\r
- return (jalview.schemabinding.version2.Annotation) obj;\r
- }\r
-\r
- /**\r
- * Method removeSequence.\r
- * \r
- * @param vSequence\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSequence(\r
- final jalview.schemabinding.version2.Sequence vSequence)\r
- {\r
- boolean removed = _sequenceList.remove(vSequence);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSequenceAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Sequence removeSequenceAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._sequenceList.remove(index);\r
- return (jalview.schemabinding.version2.Sequence) obj;\r
- }\r
-\r
- /**\r
- * Method removeSequenceSetProperties.\r
- * \r
- * @param vSequenceSetProperties\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSequenceSetProperties(\r
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- {\r
- boolean removed = _sequenceSetPropertiesList\r
- .remove(vSequenceSetProperties);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSequenceSetPropertiesAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);\r
- return (jalview.schemabinding.version2.SequenceSetProperties) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodonFrame\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAlcodonFrame(final int index,\r
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonFrameList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonFrameList.size() - 1) + "]");\r
- }\r
-\r
- this._alcodonFrameList.set(index, vAlcodonFrame);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodonFrameArray\r
- */\r
- public void setAlcodonFrame(\r
- final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)\r
- {\r
- // -- copy array\r
- _alcodonFrameList.clear();\r
-\r
- for (int i = 0; i < vAlcodonFrameArray.length; i++)\r
- {\r
- this._alcodonFrameList.add(vAlcodonFrameArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotation\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAnnotation(final int index,\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._annotationList.size() - 1) + "]");\r
- }\r
-\r
- this._annotationList.set(index, vAnnotation);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationArray\r
- */\r
- public void setAnnotation(\r
- final jalview.schemabinding.version2.Annotation[] vAnnotationArray)\r
- {\r
- // -- copy array\r
- _annotationList.clear();\r
-\r
- for (int i = 0; i < vAnnotationArray.length; i++)\r
- {\r
- this._annotationList.add(vAnnotationArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'datasetId'. The field 'datasetId' has the\r
- * following description: reference to set where jalview will gather the\r
- * dataset sequences for all sequences in the set.\r
- * \r
- * \r
- * @param datasetId\r
- * the value of field 'datasetId'.\r
- */\r
- public void setDatasetId(final java.lang.String datasetId)\r
- {\r
- this._datasetId = datasetId;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'gapChar'.\r
- * \r
- * @param gapChar\r
- * the value of field 'gapChar'.\r
- */\r
- public void setGapChar(final java.lang.String gapChar)\r
- {\r
- this._gapChar = gapChar;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequence\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSequence(final int index,\r
- final jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSequence: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._sequenceList.size() - 1) + "]");\r
- }\r
-\r
- this._sequenceList.set(index, vSequence);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceArray\r
- */\r
- public void setSequence(\r
- final jalview.schemabinding.version2.Sequence[] vSequenceArray)\r
- {\r
- // -- copy array\r
- _sequenceList.clear();\r
-\r
- for (int i = 0; i < vSequenceArray.length; i++)\r
- {\r
- this._sequenceList.add(vSequenceArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSetProperties\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSequenceSetProperties(\r
- final int index,\r
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetPropertiesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setSequenceSetProperties: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
- }\r
-\r
- this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSetPropertiesArray\r
- */\r
- public void setSequenceSetProperties(\r
- final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)\r
- {\r
- // -- copy array\r
- _sequenceSetPropertiesList.clear();\r
-\r
- for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)\r
- {\r
- this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);\r
- }\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.SequenceSet\r
- */\r
- public static jalview.schemabinding.version2.SequenceSet 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.SequenceSet) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.SequenceSet.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 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
+public class SequenceSet implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _gapChar.\r
+ */\r
+ private java.lang.String _gapChar;\r
+\r
+ /**\r
+ * reference to set where jalview will gather the dataset\r
+ * sequences for all sequences in the set. \r
+ * \r
+ */\r
+ private java.lang.String _datasetId;\r
+\r
+ /**\r
+ * Field _sequenceList.\r
+ */\r
+ private java.util.Vector _sequenceList;\r
+\r
+ /**\r
+ * Field _annotationList.\r
+ */\r
+ private java.util.Vector _annotationList;\r
+\r
+ /**\r
+ * Field _sequenceSetPropertiesList.\r
+ */\r
+ private java.util.Vector _sequenceSetPropertiesList;\r
+\r
+ /**\r
+ * Field _alcodonFrameList.\r
+ */\r
+ private java.util.Vector _alcodonFrameList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSet() {\r
+ super();\r
+ this._sequenceList = new java.util.Vector();\r
+ this._annotationList = new java.util.Vector();\r
+ this._sequenceSetPropertiesList = new java.util.Vector();\r
+ this._alcodonFrameList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonFrameList.addElement(vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonFrameList.add(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationList.addElement(vAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotation(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._annotationList.add(index, vAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceList.addElement(vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequence(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceList.add(index, vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAlcodonFrame.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AlcodonFrame elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodonFrame(\r
+ ) {\r
+ return this._alcodonFrameList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAnnotation.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Annotation elements\r
+ */\r
+ public java.util.Enumeration enumerateAnnotation(\r
+ ) {\r
+ return this._annotationList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequence.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Sequence elements\r
+ */\r
+ public java.util.Enumeration enumerateSequence(\r
+ ) {\r
+ return this._sequenceList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequenceSetProperties.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSetProperties elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSetProperties(\r
+ ) {\r
+ return this._sequenceSetPropertiesList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrame.\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.AlcodonFrame at the given inde\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrame.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.AlcodonFrame[] getAlcodonFrame(\r
+ ) {\r
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];\r
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrameCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonFrameCount(\r
+ ) {\r
+ return this._alcodonFrameList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotation.\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.Annotation at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Annotation getAnnotation(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Annotation) _annotationList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotation.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Annotation[] getAnnotation(\r
+ ) {\r
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];\r
+ return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAnnotationCount(\r
+ ) {\r
+ return this._annotationList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'datasetId'. The field\r
+ * 'datasetId' has the following description: reference to set\r
+ * where jalview will gather the dataset sequences for all\r
+ * sequences in the set. \r
+ * \r
+ * \r
+ * @return the value of field 'DatasetId'.\r
+ */\r
+ public java.lang.String getDatasetId(\r
+ ) {\r
+ return this._datasetId;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'gapChar'.\r
+ * \r
+ * @return the value of field 'GapChar'.\r
+ */\r
+ public java.lang.String getGapChar(\r
+ ) {\r
+ return this._gapChar;\r
+ }\r
+\r
+ /**\r
+ * Method getSequence.\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.Sequence at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Sequence getSequence(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSequence.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Sequence[] getSequence(\r
+ ) {\r
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];\r
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceCount(\r
+ ) {\r
+ return this._sequenceList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetProperties.\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.SequenceSetProperties at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetProperties.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.SequenceSetProperties[] getSequenceSetProperties(\r
+ ) {\r
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];\r
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetPropertiesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceSetPropertiesCount(\r
+ ) {\r
+ return this._sequenceSetPropertiesList.size();\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
+ * \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
+ * Method removeAlcodonFrame.\r
+ * \r
+ * @param vAlcodonFrame\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {\r
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodonFrameAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodonFrameList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodonFrame(\r
+ ) {\r
+ this._alcodonFrameList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAnnotation(\r
+ ) {\r
+ this._annotationList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllSequence(\r
+ ) {\r
+ this._sequenceList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllSequenceSetProperties(\r
+ ) {\r
+ this._sequenceSetPropertiesList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotation.\r
+ * \r
+ * @param vAnnotation\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation) {\r
+ boolean removed = _annotationList.remove(vAnnotation);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationList.remove(index);\r
+ return (jalview.schemabinding.version2.Annotation) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequence.\r
+ * \r
+ * @param vSequence\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence) {\r
+ boolean removed = _sequenceList.remove(vSequence);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceList.remove(index);\r
+ return (jalview.schemabinding.version2.Sequence) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetProperties.\r
+ * \r
+ * @param vSequenceSetProperties\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {\r
+ boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetPropertiesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);\r
+ return (jalview.schemabinding.version2.SequenceSetProperties) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodonFrameList.set(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrameArray\r
+ */\r
+ public void setAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {\r
+ //-- copy array\r
+ _alcodonFrameList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodonFrameArray.length; i++) {\r
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotation(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._annotationList.set(index, vAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationArray\r
+ */\r
+ public void setAnnotation(\r
+ final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {\r
+ //-- copy array\r
+ _annotationList.clear();\r
+ \r
+ for (int i = 0; i < vAnnotationArray.length; i++) {\r
+ this._annotationList.add(vAnnotationArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'datasetId'. The field 'datasetId'\r
+ * has the following description: reference to set where\r
+ * jalview will gather the dataset sequences for all sequences\r
+ * in the set. \r
+ * \r
+ * \r
+ * @param datasetId the value of field 'datasetId'.\r
+ */\r
+ public void setDatasetId(\r
+ final java.lang.String datasetId) {\r
+ this._datasetId = datasetId;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'gapChar'.\r
+ * \r
+ * @param gapChar the value of field 'gapChar'.\r
+ */\r
+ public void setGapChar(\r
+ final java.lang.String gapChar) {\r
+ this._gapChar = gapChar;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSequence(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._sequenceList.set(index, vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceArray\r
+ */\r
+ public void setSequence(\r
+ final jalview.schemabinding.version2.Sequence[] vSequenceArray) {\r
+ //-- copy array\r
+ _sequenceList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceArray.length; i++) {\r
+ this._sequenceList.add(vSequenceArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetPropertiesArray\r
+ */\r
+ public void setSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {\r
+ //-- copy array\r
+ _sequenceSetPropertiesList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {\r
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);\r
+ }\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.SequenceSet\r
+ */\r
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.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
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * 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 -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSetProperties implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _key.
- */
- private java.lang.String _key;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceSetProperties()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'key'.
- *
- * @return the value of field 'Key'.
- */
- public java.lang.String getKey()
- {
- return this._key;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue()
- {
- return this._value;
- }
-
- /**
- * 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;
+public class SequenceSetProperties implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _key.
+ */
+ private java.lang.String _key;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSetProperties() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'key'.
+ *
+ * @return the value of field 'Key'.
+ */
+ public java.lang.String getKey(
+ ) {
+ return this._key;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'key'.
+ *
+ * @param key the value of field 'key'.
+ */
+ public void setKey(
+ final java.lang.String key) {
+ this._key = key;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final java.lang.String value) {
+ this._value = value;
+ }
+
+ /**
+ * 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.SequenceSetProperties
+ */
+ public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.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);
}
- return true;
- }
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Sets the value of field 'key'.
- *
- * @param key
- * the value of field 'key'.
- */
- public void setKey(final java.lang.String key)
- {
- this._key = key;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value
- * the value of field 'value'.
- */
- public void setValue(final java.lang.String value)
- {
- this._value = value;
- }
-
- /**
- * 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.SequenceSetProperties
- */
- public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller
- .unmarshal(
- jalview.schemabinding.version2.SequenceSetProperties.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);
- }
}
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceType implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _description.\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _sequence.\r
- */\r
- private java.lang.String _sequence;\r
-\r
- /**\r
- * Field _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceType()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\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 '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 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequence'.\r
- * \r
- * @return the value of field 'Sequence'.\r
- */\r
- public java.lang.String getSequence()\r
- {\r
- return this._sequence;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class SequenceType implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _description.\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _sequence.\r
+ */\r
+ private java.lang.String _sequence;\r
+\r
+ /**\r
+ * Field _name.\r
+ */\r
+ private java.lang.String _name;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceType() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\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 '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 'name'.\r
+ * \r
+ * @return the value of field 'Name'.\r
+ */\r
+ public java.lang.String getName(\r
+ ) {\r
+ return this._name;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequence'.\r
+ * \r
+ * @return the value of field 'Sequence'.\r
+ */\r
+ public java.lang.String getSequence(\r
+ ) {\r
+ return this._sequence;\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
+ * \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
+ * 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 '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 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(\r
+ final java.lang.String name) {\r
+ this._name = name;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequence'.\r
+ * \r
+ * @param sequence the value of field 'sequence'.\r
+ */\r
+ public void setSequence(\r
+ final java.lang.String sequence) {\r
+ this._sequence = sequence;\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.SequenceType\r
+ */\r
+ public static jalview.schemabinding.version2.SequenceType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.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
- return true;\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 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 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
- * 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 '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 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequence'.\r
- * \r
- * @param sequence\r
- * the value of field 'sequence'.\r
- */\r
- public void setSequence(final java.lang.String sequence)\r
- {\r
- this._sequence = sequence;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.SequenceType\r
- */\r
- public static jalview.schemabinding.version2.SequenceType 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.SequenceType) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.SequenceType.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Setting implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _display.\r
- */\r
- private boolean _display;\r
-\r
- /**\r
- * keeps track of state for field: _display\r
- */\r
- private boolean _has_display;\r
-\r
- /**\r
- * Field _order.\r
- */\r
- private float _order;\r
-\r
- /**\r
- * keeps track of state for field: _order\r
- */\r
- private boolean _has_order;\r
-\r
- /**\r
- * Optional minimum colour for graduated feature colour\r
- */\r
- private int _mincolour;\r
-\r
- /**\r
- * keeps track of state for field: _mincolour\r
- */\r
- private boolean _has_mincolour;\r
-\r
- /**\r
- * threshold value for graduated feature colour\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- /**\r
- * threshold type for graduated feature colour\r
- */\r
- private int _threshstate;\r
-\r
- /**\r
- * keeps track of state for field: _threshstate\r
- */\r
- private boolean _has_threshstate;\r
-\r
- /**\r
- * Field _max.\r
- */\r
- private float _max;\r
-\r
- /**\r
- * keeps track of state for field: _max\r
- */\r
- private boolean _has_max;\r
-\r
- /**\r
- * Field _min.\r
- */\r
- private float _min;\r
-\r
- /**\r
- * keeps track of state for field: _min\r
- */\r
- private boolean _has_min;\r
-\r
- /**\r
- * Field _colourByLabel.\r
- */\r
- private boolean _colourByLabel;\r
-\r
- /**\r
- * keeps track of state for field: _colourByLabel\r
- */\r
- private boolean _has_colourByLabel;\r
-\r
- /**\r
- * Field _autoScale.\r
- */\r
- private boolean _autoScale;\r
-\r
- /**\r
- * keeps track of state for field: _autoScale\r
- */\r
- private boolean _has_autoScale;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Setting()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteAutoScale()\r
- {\r
- this._has_autoScale = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColourByLabel()\r
- {\r
- this._has_colourByLabel = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplay()\r
- {\r
- this._has_display = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMax()\r
- {\r
- this._has_max = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMin()\r
- {\r
- this._has_min = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMincolour()\r
- {\r
- this._has_mincolour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteOrder()\r
- {\r
- this._has_order = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshstate()\r
- {\r
- this._has_threshstate = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoScale'.\r
- * \r
- * @return the value of field 'AutoScale'.\r
- */\r
- public boolean getAutoScale()\r
- {\r
- return this._autoScale;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourByLabel'.\r
- * \r
- * @return the value of field 'ColourByLabel'.\r
- */\r
- public boolean getColourByLabel()\r
- {\r
- return this._colourByLabel;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean getDisplay()\r
- {\r
- return this._display;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'max'.\r
- * \r
- * @return the value of field 'Max'.\r
- */\r
- public float getMax()\r
- {\r
- return this._max;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'min'.\r
- * \r
- * @return the value of field 'Min'.\r
- */\r
- public float getMin()\r
- {\r
- return this._min;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mincolour'. The field 'mincolour' has the\r
- * following description: Optional minimum colour for graduated feature colour\r
- * \r
- * @return the value of field 'Mincolour'.\r
- */\r
- public int getMincolour()\r
- {\r
- return this._mincolour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'order'.\r
- * \r
- * @return the value of field 'Order'.\r
- */\r
- public float getOrder()\r
- {\r
- return this._order;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'. The field 'threshold' has the\r
- * following description: threshold value for graduated feature colour\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshstate'. The field 'threshstate' has the\r
- * following description: threshold type for graduated feature colour\r
- * \r
- * @return the value of field 'Threshstate'.\r
- */\r
- public int getThreshstate()\r
- {\r
- return this._threshstate;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- }\r
-\r
- /**\r
- * Method hasAutoScale.\r
- * \r
- * @return true if at least one AutoScale has been added\r
- */\r
- public boolean hasAutoScale()\r
- {\r
- return this._has_autoScale;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasColourByLabel.\r
- * \r
- * @return true if at least one ColourByLabel has been added\r
- */\r
- public boolean hasColourByLabel()\r
- {\r
- return this._has_colourByLabel;\r
- }\r
-\r
- /**\r
- * Method hasDisplay.\r
- * \r
- * @return true if at least one Display has been added\r
- */\r
- public boolean hasDisplay()\r
- {\r
- return this._has_display;\r
- }\r
-\r
- /**\r
- * Method hasMax.\r
- * \r
- * @return true if at least one Max has been added\r
- */\r
- public boolean hasMax()\r
- {\r
- return this._has_max;\r
- }\r
-\r
- /**\r
- * Method hasMin.\r
- * \r
- * @return true if at least one Min has been added\r
- */\r
- public boolean hasMin()\r
- {\r
- return this._has_min;\r
- }\r
-\r
- /**\r
- * Method hasMincolour.\r
- * \r
- * @return true if at least one Mincolour has been added\r
- */\r
- public boolean hasMincolour()\r
- {\r
- return this._has_mincolour;\r
- }\r
-\r
- /**\r
- * Method hasOrder.\r
- * \r
- * @return true if at least one Order has been added\r
- */\r
- public boolean hasOrder()\r
- {\r
- return this._has_order;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\r
- }\r
-\r
- /**\r
- * Method hasThreshstate.\r
- * \r
- * @return true if at least one Threshstate has been added\r
- */\r
- public boolean hasThreshstate()\r
- {\r
- return this._has_threshstate;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoScale'.\r
- * \r
- * @return the value of field 'AutoScale'.\r
- */\r
- public boolean isAutoScale()\r
- {\r
- return this._autoScale;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourByLabel'.\r
- * \r
- * @return the value of field 'ColourByLabel'.\r
- */\r
- public boolean isColourByLabel()\r
- {\r
- return this._colourByLabel;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean isDisplay()\r
- {\r
- return this._display;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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
- * Sets the value of field 'autoScale'.\r
- * \r
- * @param autoScale\r
- * the value of field 'autoScale'.\r
- */\r
- public void setAutoScale(final boolean autoScale)\r
- {\r
- this._autoScale = autoScale;\r
- this._has_autoScale = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourByLabel'.\r
- * \r
- * @param colourByLabel\r
- * the value of field 'colourByLabel'.\r
- */\r
- public void setColourByLabel(final boolean colourByLabel)\r
- {\r
- this._colourByLabel = colourByLabel;\r
- this._has_colourByLabel = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'display'.\r
- * \r
- * @param display\r
- * the value of field 'display'.\r
- */\r
- public void setDisplay(final boolean display)\r
- {\r
- this._display = display;\r
- this._has_display = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'max'.\r
- * \r
- * @param max\r
- * the value of field 'max'.\r
- */\r
- public void setMax(final float max)\r
- {\r
- this._max = max;\r
- this._has_max = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'min'.\r
- * \r
- * @param min\r
- * the value of field 'min'.\r
- */\r
- public void setMin(final float min)\r
- {\r
- this._min = min;\r
- this._has_min = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mincolour'. The field 'mincolour' has the\r
- * following description: Optional minimum colour for graduated feature colour\r
- * \r
- * @param mincolour\r
- * the value of field 'mincolour'.\r
- */\r
- public void setMincolour(final int mincolour)\r
- {\r
- this._mincolour = mincolour;\r
- this._has_mincolour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'order'.\r
- * \r
- * @param order\r
- * the value of field 'order'.\r
- */\r
- public void setOrder(final float order)\r
- {\r
- this._order = order;\r
- this._has_order = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'. The field 'threshold' has the\r
- * following description: threshold value for graduated feature colour\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshstate'. The field 'threshstate' has the\r
- * following description: threshold type for graduated feature colour\r
- * \r
- * @param threshstate\r
- * the value of field 'threshstate'.\r
- */\r
- public void setThreshstate(final int threshstate)\r
- {\r
- this._threshstate = threshstate;\r
- this._has_threshstate = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Settin\r
- */\r
- public static jalview.schemabinding.version2.Setting 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.Setting) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Setting.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class Setting implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _type.\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
+ * Field _display.\r
+ */\r
+ private boolean _display;\r
+\r
+ /**\r
+ * keeps track of state for field: _display\r
+ */\r
+ private boolean _has_display;\r
+\r
+ /**\r
+ * Field _order.\r
+ */\r
+ private float _order;\r
+\r
+ /**\r
+ * keeps track of state for field: _order\r
+ */\r
+ private boolean _has_order;\r
+\r
+ /**\r
+ * Optional minimum colour for graduated feature colour\r
+ */\r
+ private int _mincolour;\r
+\r
+ /**\r
+ * keeps track of state for field: _mincolour\r
+ */\r
+ private boolean _has_mincolour;\r
+\r
+ /**\r
+ * threshold value for graduated feature colour\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+ /**\r
+ * threshold type for graduated feature colour\r
+ */\r
+ private int _threshstate;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshstate\r
+ */\r
+ private boolean _has_threshstate;\r
+\r
+ /**\r
+ * Field _max.\r
+ */\r
+ private float _max;\r
+\r
+ /**\r
+ * keeps track of state for field: _max\r
+ */\r
+ private boolean _has_max;\r
+\r
+ /**\r
+ * Field _min.\r
+ */\r
+ private float _min;\r
+\r
+ /**\r
+ * keeps track of state for field: _min\r
+ */\r
+ private boolean _has_min;\r
+\r
+ /**\r
+ * Field _colourByLabel.\r
+ */\r
+ private boolean _colourByLabel;\r
+\r
+ /**\r
+ * keeps track of state for field: _colourByLabel\r
+ */\r
+ private boolean _has_colourByLabel;\r
+\r
+ /**\r
+ * Field _autoScale.\r
+ */\r
+ private boolean _autoScale;\r
+\r
+ /**\r
+ * keeps track of state for field: _autoScale\r
+ */\r
+ private boolean _has_autoScale;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Setting() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteAutoScale(\r
+ ) {\r
+ this._has_autoScale= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColour(\r
+ ) {\r
+ this._has_colour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColourByLabel(\r
+ ) {\r
+ this._has_colourByLabel= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplay(\r
+ ) {\r
+ this._has_display= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMax(\r
+ ) {\r
+ this._has_max= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMin(\r
+ ) {\r
+ this._has_min= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMincolour(\r
+ ) {\r
+ this._has_mincolour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteOrder(\r
+ ) {\r
+ this._has_order= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshstate(\r
+ ) {\r
+ this._has_threshstate= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean getAutoScale(\r
+ ) {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour(\r
+ ) {\r
+ return this._colour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean getColourByLabel(\r
+ ) {\r
+ return this._colourByLabel;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'display'.\r
+ * \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean getDisplay(\r
+ ) {\r
+ return this._display;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'max'.\r
+ * \r
+ * @return the value of field 'Max'.\r
+ */\r
+ public float getMax(\r
+ ) {\r
+ return this._max;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'min'.\r
+ * \r
+ * @return the value of field 'Min'.\r
+ */\r
+ public float getMin(\r
+ ) {\r
+ return this._min;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mincolour'. The field\r
+ * 'mincolour' has the following description: Optional minimum\r
+ * colour for graduated feature colour\r
+ * \r
+ * @return the value of field 'Mincolour'.\r
+ */\r
+ public int getMincolour(\r
+ ) {\r
+ return this._mincolour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'order'.\r
+ * \r
+ * @return the value of field 'Order'.\r
+ */\r
+ public float getOrder(\r
+ ) {\r
+ return this._order;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshold'. The field\r
+ * 'threshold' has the following description: threshold value\r
+ * for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshstate'. The field\r
+ * 'threshstate' has the following description: threshold type\r
+ * for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshstate'.\r
+ */\r
+ public int getThreshstate(\r
+ ) {\r
+ return this._threshstate;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return the value of field 'Type'.\r
+ */\r
+ public java.lang.String getType(\r
+ ) {\r
+ return this._type;\r
+ }\r
+\r
+ /**\r
+ * Method hasAutoScale.\r
+ * \r
+ * @return true if at least one AutoScale has been added\r
+ */\r
+ public boolean hasAutoScale(\r
+ ) {\r
+ return this._has_autoScale;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour(\r
+ ) {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasColourByLabel.\r
+ * \r
+ * @return true if at least one ColourByLabel has been added\r
+ */\r
+ public boolean hasColourByLabel(\r
+ ) {\r
+ return this._has_colourByLabel;\r
+ }\r
+\r
+ /**\r
+ * Method hasDisplay.\r
+ * \r
+ * @return true if at least one Display has been added\r
+ */\r
+ public boolean hasDisplay(\r
+ ) {\r
+ return this._has_display;\r
+ }\r
+\r
+ /**\r
+ * Method hasMax.\r
+ * \r
+ * @return true if at least one Max has been added\r
+ */\r
+ public boolean hasMax(\r
+ ) {\r
+ return this._has_max;\r
+ }\r
+\r
+ /**\r
+ * Method hasMin.\r
+ * \r
+ * @return true if at least one Min has been added\r
+ */\r
+ public boolean hasMin(\r
+ ) {\r
+ return this._has_min;\r
+ }\r
+\r
+ /**\r
+ * Method hasMincolour.\r
+ * \r
+ * @return true if at least one Mincolour has been added\r
+ */\r
+ public boolean hasMincolour(\r
+ ) {\r
+ return this._has_mincolour;\r
+ }\r
+\r
+ /**\r
+ * Method hasOrder.\r
+ * \r
+ * @return true if at least one Order has been added\r
+ */\r
+ public boolean hasOrder(\r
+ ) {\r
+ return this._has_order;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshstate.\r
+ * \r
+ * @return true if at least one Threshstate has been added\r
+ */\r
+ public boolean hasThreshstate(\r
+ ) {\r
+ return this._has_threshstate;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean isAutoScale(\r
+ ) {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean isColourByLabel(\r
+ ) {\r
+ return this._colourByLabel;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'display'.\r
+ * \r
+ * @return the value of field 'Display'.\r
+ */\r
+ public boolean isDisplay(\r
+ ) {\r
+ return this._display;\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
+ * \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
+ * Sets the value of field 'autoScale'.\r
+ * \r
+ * @param autoScale the value of field 'autoScale'.\r
+ */\r
+ public void setAutoScale(\r
+ final boolean autoScale) {\r
+ this._autoScale = autoScale;\r
+ this._has_autoScale = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final int colour) {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colourByLabel'.\r
+ * \r
+ * @param colourByLabel the value of field 'colourByLabel'.\r
+ */\r
+ public void setColourByLabel(\r
+ final boolean colourByLabel) {\r
+ this._colourByLabel = colourByLabel;\r
+ this._has_colourByLabel = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'display'.\r
+ * \r
+ * @param display the value of field 'display'.\r
+ */\r
+ public void setDisplay(\r
+ final boolean display) {\r
+ this._display = display;\r
+ this._has_display = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'max'.\r
+ * \r
+ * @param max the value of field 'max'.\r
+ */\r
+ public void setMax(\r
+ final float max) {\r
+ this._max = max;\r
+ this._has_max = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'min'.\r
+ * \r
+ * @param min the value of field 'min'.\r
+ */\r
+ public void setMin(\r
+ final float min) {\r
+ this._min = min;\r
+ this._has_min = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mincolour'. The field 'mincolour'\r
+ * has the following description: Optional minimum colour for\r
+ * graduated feature colour\r
+ * \r
+ * @param mincolour the value of field 'mincolour'.\r
+ */\r
+ public void setMincolour(\r
+ final int mincolour) {\r
+ this._mincolour = mincolour;\r
+ this._has_mincolour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'order'.\r
+ * \r
+ * @param order the value of field 'order'.\r
+ */\r
+ public void setOrder(\r
+ final float order) {\r
+ this._order = order;\r
+ this._has_order = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshold'. The field 'threshold'\r
+ * has the following description: threshold value for graduated\r
+ * feature colour\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshstate'. The field\r
+ * 'threshstate' has the following description: threshold type\r
+ * for graduated feature colour\r
+ * \r
+ * @param threshstate the value of field 'threshstate'.\r
+ */\r
+ public void setThreshstate(\r
+ final int threshstate) {\r
+ this._threshstate = threshstate;\r
+ this._has_threshstate = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(\r
+ final java.lang.String type) {\r
+ this._type = type;\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 jalview.schemabinding.version2.Settin\r
+ */\r
+ public static jalview.schemabinding.version2.Setting unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.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
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * 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 -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class StructureState implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
- /**
- * Field _visible.
- */
- private boolean _visible;
-
- /**
- * keeps track of state for field: _visible
- */
- private boolean _has_visible;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * additional identifier which properly disambiguates the structure view from
- * any other view with the same attributes. This is not an ID, because it is
- * possible to have many references to the same physical structure view from
- * different sequences in an alignment. A structureState element citing the
- * same viewId will appear for each instance.
- */
- private java.lang.String _viewId;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public StructureState()
- {
- super();
- setContent("");
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
-
- /**
- */
- public void deleteVisible()
- {
- this._has_visible = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'content'. The field 'content' has the following
- * description: internal content storage
- *
- * @return the value of field 'Content'.
- */
- public java.lang.String getContent()
- {
- return this._content;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'viewId'. The field 'viewId' has the following
- * description: additional identifier which properly disambiguates the
- * structure view from any other view with the same attributes. This is not an
- * ID, because it is possible to have many references to the same physical
- * structure view from different sequences in an alignment. A structureState
- * element citing the same viewId will appear for each instance.
- *
- * @return the value of field 'ViewId'.
- */
- public java.lang.String getViewId()
- {
- return this._viewId;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean getVisible()
- {
- return this._visible;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasVisible.
- *
- * @return true if at least one Visible has been added
- */
- public boolean hasVisible()
- {
- return this._has_visible;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * 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);
- }
-
- /**
- * Sets the value of field 'content'. The field 'content' has the following
- * description: internal content storage
- *
- * @param content
- * the value of field 'content'.
- */
- public void setContent(final java.lang.String content)
- {
- this._content = content;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'viewId'. The field 'viewId' has the following
- * description: additional identifier which properly disambiguates the
- * structure view from any other view with the same attributes. This is not an
- * ID, because it is possible to have many references to the same physical
- * structure view from different sequences in an alignment. A structureState
- * element citing the same viewId will appear for each instance.
- *
- * @param viewId
- * the value of field 'viewId'.
- */
- public void setViewId(final java.lang.String viewId)
- {
- this._viewId = viewId;
- }
-
- /**
- * 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;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = 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.StructureState
- */
- public static jalview.schemabinding.version2.StructureState unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.StructureState) Unmarshaller
- .unmarshal(jalview.schemabinding.version2.StructureState.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);
- }
+public class StructureState implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * additional identifier which properly disambiguates
+ * the structure view from any other view with the same
+ * attributes. This is not an ID,
+ * because it is possible to have many references to the same
+ * physical structure view
+ * from different sequences in an alignment. A structureState
+ * element citing the same
+ * viewId will appear for each instance.
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should
+ * be explicitly linked to the Jmol view referred to/created by
+ * this structureState (since Jalview 2.7).
+ *
+ */
+ private boolean _linkAlignPanel = true;
+
+ /**
+ * keeps track of state for field: _linkAlignPanel
+ */
+ private boolean _has_linkAlignPanel;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should
+ * be included in those used to perform a structure
+ * superposition (since Jalview 2.7).
+ *
+ */
+ private boolean _alignwithAlignPanel = true;
+
+ /**
+ * keeps track of state for field: _alignwithAlignPanel
+ */
+ private boolean _has_alignwithAlignPanel;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public StructureState() {
+ super();
+ setContent("");
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAlignwithAlignPanel(
+ ) {
+ this._has_alignwithAlignPanel= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteLinkAlignPanel(
+ ) {
+ this._has_linkAlignPanel= false;
+ }
+
+ /**
+ */
+ public void deleteVisible(
+ ) {
+ this._has_visible= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to perform a structure superposition
+ * (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean getAlignwithAlignPanel(
+ ) {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return the value of field 'Content'.
+ */
+ public java.lang.String getContent(
+ ) {
+ return this._content;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'linkAlignPanel'. The field
+ * 'linkAlignPanel' has the following description: Flag set if
+ * the alignment panel containing this JSeq should be
+ * explicitly linked to the Jmol view referred to/created by
+ * this structureState (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'LinkAlignPanel'.
+ */
+ public boolean getLinkAlignPanel(
+ ) {
+ return this._linkAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'viewId'. The field 'viewId' has
+ * the following description: additional identifier which
+ * properly disambiguates
+ * the structure view from any other view with the same
+ * attributes. This is not an ID,
+ * because it is possible to have many references to the same
+ * physical structure view
+ * from different sequences in an alignment. A structureState
+ * element citing the same
+ * viewId will appear for each instance.
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId(
+ ) {
+ return this._viewId;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible(
+ ) {
+ return this._visible;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasAlignwithAlignPanel.
+ *
+ * @return true if at least one AlignwithAlignPanel has been
+ * added
+ */
+ public boolean hasAlignwithAlignPanel(
+ ) {
+ return this._has_alignwithAlignPanel;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasLinkAlignPanel.
+ *
+ * @return true if at least one LinkAlignPanel has been added
+ */
+ public boolean hasLinkAlignPanel(
+ ) {
+ return this._has_linkAlignPanel;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible(
+ ) {
+ return this._has_visible;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to perform a structure superposition
+ * (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean isAlignwithAlignPanel(
+ ) {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'linkAlignPanel'. The field
+ * 'linkAlignPanel' has the following description: Flag set if
+ * the alignment panel containing this JSeq should be
+ * explicitly linked to the Jmol view referred to/created by
+ * this structureState (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'LinkAlignPanel'.
+ */
+ public boolean isLinkAlignPanel(
+ ) {
+ return this._linkAlignPanel;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Sets the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to perform a structure superposition
+ * (since Jalview 2.7).
+ *
+ *
+ * @param alignwithAlignPanel the value of field
+ * 'alignwithAlignPanel'.
+ */
+ public void setAlignwithAlignPanel(
+ final boolean alignwithAlignPanel) {
+ this._alignwithAlignPanel = alignwithAlignPanel;
+ this._has_alignwithAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(
+ final java.lang.String content) {
+ this._content = content;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'linkAlignPanel'. The field
+ * 'linkAlignPanel' has the following description: Flag set if
+ * the alignment panel containing this JSeq should be
+ * explicitly linked to the Jmol view referred to/created by
+ * this structureState (since Jalview 2.7).
+ *
+ *
+ * @param linkAlignPanel the value of field 'linkAlignPanel'.
+ */
+ public void setLinkAlignPanel(
+ final boolean linkAlignPanel) {
+ this._linkAlignPanel = linkAlignPanel;
+ this._has_linkAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'viewId'. The field 'viewId' has the
+ * following description: additional identifier which properly
+ * disambiguates
+ * the structure view from any other view with the same
+ * attributes. This is not an ID,
+ * because it is possible to have many references to the same
+ * physical structure view
+ * from different sequences in an alignment. A structureState
+ * element citing the same
+ * viewId will appear for each instance.
+ *
+ * @param viewId the value of field 'viewId'.
+ */
+ public void setViewId(
+ final java.lang.String viewId) {
+ this._viewId = viewId;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = 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.StructureState
+ */
+ public static jalview.schemabinding.version2.StructureState unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.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);
+ }
}
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class ThresholdLine implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _label.\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _value.\r
- */\r
- private float _value;\r
-\r
- /**\r
- * keeps track of state for field: _value\r
- */\r
- private boolean _has_value;\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public ThresholdLine()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
+public class ThresholdLine implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _label.\r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Field _value.\r
+ */\r
+ private float _value;\r
+\r
+ /**\r
+ * keeps track of state for field: _value\r
+ */\r
+ private boolean _has_value;\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
*/\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- }\r
+ private boolean _has_colour;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ThresholdLine() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteColour(\r
+ ) {\r
+ this._has_colour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteValue(\r
+ ) {\r
+ this._has_value= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour(\r
+ ) {\r
+ return this._colour;\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 'value'.\r
+ * \r
+ * @return the value of field 'Value'.\r
+ */\r
+ public float getValue(\r
+ ) {\r
+ return this._value;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour(\r
+ ) {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasValue.\r
+ * \r
+ * @return true if at least one Value has been added\r
+ */\r
+ public boolean hasValue(\r
+ ) {\r
+ return this._has_value;\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
+ * \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
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final int colour) {\r
+ this._colour = colour;\r
+ this._has_colour = true;\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 'value'.\r
+ * \r
+ * @param value the value of field 'value'.\r
+ */\r
+ public void setValue(\r
+ final float value) {\r
+ this._value = value;\r
+ this._has_value = 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.ThresholdLine\r
+ */\r
+ public static jalview.schemabinding.version2.ThresholdLine unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);\r
+ }\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 deleteValue()\r
- {\r
- this._has_value = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\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 'value'.\r
- * \r
- * @return the value of field 'Value'.\r
- */\r
- public float getValue()\r
- {\r
- return this._value;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasValue.\r
- * \r
- * @return true if at least one Value has been added\r
- */\r
- public boolean hasValue()\r
- {\r
- return this._has_value;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
- return true;\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 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 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
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\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 'value'.\r
- * \r
- * @param value\r
- * the value of field 'value'.\r
- */\r
- public void setValue(final float value)\r
- {\r
- this._value = value;\r
- this._has_value = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.ThresholdLine\r
- */\r
- public static jalview.schemabinding.version2.ThresholdLine 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.ThresholdLine) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.ThresholdLine.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Tree implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _width.\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height.\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _xpos.\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos.\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _fontName.\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize.\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle.\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
- /**\r
- * Field _threshold.\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- /**\r
- * Field _showBootstrap.\r
- */\r
- private boolean _showBootstrap;\r
-\r
- /**\r
- * keeps track of state for field: _showBootstrap\r
- */\r
- private boolean _has_showBootstrap;\r
-\r
- /**\r
- * Field _showDistances.\r
- */\r
- private boolean _showDistances;\r
-\r
- /**\r
- * keeps track of state for field: _showDistances\r
- */\r
- private boolean _has_showDistances;\r
-\r
- /**\r
- * Field _markUnlinked.\r
- */\r
- private boolean _markUnlinked;\r
-\r
- /**\r
- * keeps track of state for field: _markUnlinked\r
- */\r
- private boolean _has_markUnlinked;\r
-\r
- /**\r
- * Field _fitToWindow.\r
- */\r
- private boolean _fitToWindow;\r
-\r
- /**\r
- * keeps track of state for field: _fitToWindow\r
- */\r
- private boolean _has_fitToWindow;\r
-\r
- /**\r
- * Field _currentTree.\r
- */\r
- private boolean _currentTree;\r
-\r
- /**\r
- * keeps track of state for field: _currentTree\r
- */\r
- private boolean _has_currentTree;\r
-\r
- /**\r
- * Tree ID added for binding tree visualization settings to vamsas document\r
- * trees in jalview 2.4.1\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _title.\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _newick.\r
- */\r
- private java.lang.String _newick;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Tree()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteCurrentTree()\r
- {\r
- this._has_currentTree = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFitToWindow()\r
- {\r
- this._has_fitToWindow = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMarkUnlinked()\r
- {\r
- this._has_markUnlinked = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowBootstrap()\r
- {\r
- this._has_showBootstrap = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowDistances()\r
- {\r
- this._has_showDistances = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'currentTree'.\r
- * \r
- * @return the value of field 'CurrentTree'.\r
- */\r
- public boolean getCurrentTree()\r
- {\r
- return this._currentTree;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- * \r
- * @return the value of field 'FitToWindow'.\r
- */\r
- public boolean getFitToWindow()\r
- {\r
- return this._fitToWindow;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return the value of field 'FontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return the value of field 'FontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return the value of field 'FontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return the value of field 'Height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the following\r
- * description: Tree ID added for binding tree visualization settings to\r
- * vamsas document trees in jalview 2.4.1\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 'markUnlinked'.\r
- * \r
- * @return the value of field 'MarkUnlinked'.\r
- */\r
- public boolean getMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'newick'.\r
- * \r
- * @return the value of field 'Newick'.\r
- */\r
- public java.lang.String getNewick()\r
- {\r
- return this._newick;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- * \r
- * @return the value of field 'ShowBootstrap'.\r
- */\r
- public boolean getShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- * \r
- * @return the value of field 'ShowDistances'.\r
- */\r
- public boolean getShowDistances()\r
- {\r
- return this._showDistances;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return the value of field 'Title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return the value of field 'Width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return the value of field 'Xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return the value of field 'Ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- }\r
-\r
- /**\r
- * Method hasCurrentTree.\r
- * \r
- * @return true if at least one CurrentTree has been added\r
- */\r
- public boolean hasCurrentTree()\r
- {\r
- return this._has_currentTree;\r
- }\r
-\r
- /**\r
- * Method hasFitToWindow.\r
- * \r
- * @return true if at least one FitToWindow has been added\r
- */\r
- public boolean hasFitToWindow()\r
- {\r
- return this._has_fitToWindow;\r
- }\r
-\r
- /**\r
- * Method hasFontSize.\r
- * \r
- * @return true if at least one FontSize has been added\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- }\r
-\r
- /**\r
- * Method hasFontStyle.\r
- * \r
- * @return true if at least one FontStyle has been added\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- }\r
-\r
- /**\r
- * Method hasHeight.\r
- * \r
- * @return true if at least one Height has been added\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- }\r
-\r
- /**\r
- * Method hasMarkUnlinked.\r
- * \r
- * @return true if at least one MarkUnlinked has been added\r
- */\r
- public boolean hasMarkUnlinked()\r
- {\r
- return this._has_markUnlinked;\r
- }\r
-\r
- /**\r
- * Method hasShowBootstrap.\r
- * \r
- * @return true if at least one ShowBootstrap has been added\r
- */\r
- public boolean hasShowBootstrap()\r
- {\r
- return this._has_showBootstrap;\r
- }\r
-\r
- /**\r
- * Method hasShowDistances.\r
- * \r
- * @return true if at least one ShowDistances has been added\r
- */\r
- public boolean hasShowDistances()\r
- {\r
- return this._has_showDistances;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\r
- }\r
-\r
- /**\r
- * Method hasWidth.\r
- * \r
- * @return true if at least one Width has been added\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- }\r
-\r
- /**\r
- * Method hasXpos.\r
- * \r
- * @return true if at least one Xpos has been added\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- }\r
-\r
- /**\r
- * Method hasYpos.\r
- * \r
- * @return true if at least one Ypos has been added\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'currentTree'.\r
- * \r
- * @return the value of field 'CurrentTree'.\r
- */\r
- public boolean isCurrentTree()\r
- {\r
- return this._currentTree;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- * \r
- * @return the value of field 'FitToWindow'.\r
- */\r
- public boolean isFitToWindow()\r
- {\r
- return this._fitToWindow;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'markUnlinked'.\r
- * \r
- * @return the value of field 'MarkUnlinked'.\r
- */\r
- public boolean isMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- * \r
- * @return the value of field 'ShowBootstrap'.\r
- */\r
- public boolean isShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- * \r
- * @return the value of field 'ShowDistances'.\r
- */\r
- public boolean isShowDistances()\r
- {\r
- return this._showDistances;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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 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 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
- * Sets the value of field 'currentTree'.\r
- * \r
- * @param currentTree\r
- * the value of field 'currentTree'.\r
- */\r
- public void setCurrentTree(final boolean currentTree)\r
- {\r
- this._currentTree = currentTree;\r
- this._has_currentTree = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fitToWindow'.\r
- * \r
- * @param fitToWindow\r
- * the value of field 'fitToWindow'.\r
- */\r
- public void setFitToWindow(final boolean fitToWindow)\r
- {\r
- this._fitToWindow = fitToWindow;\r
- this._has_fitToWindow = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName\r
- * the value of field 'fontName'.\r
- */\r
- public void setFontName(final java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize\r
- * the value of field 'fontSize'.\r
- */\r
- public void setFontSize(final int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle\r
- * the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(final int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height\r
- * the value of field 'height'.\r
- */\r
- public void setHeight(final int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the following description:\r
- * Tree ID added for binding tree visualization settings to vamsas document\r
- * trees in jalview 2.4.1\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 'markUnlinked'.\r
- * \r
- * @param markUnlinked\r
- * the value of field 'markUnlinked'.\r
- */\r
- public void setMarkUnlinked(final boolean markUnlinked)\r
- {\r
- this._markUnlinked = markUnlinked;\r
- this._has_markUnlinked = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'newick'.\r
- * \r
- * @param newick\r
- * the value of field 'newick'.\r
- */\r
- public void setNewick(final java.lang.String newick)\r
- {\r
- this._newick = newick;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showBootstrap'.\r
- * \r
- * @param showBootstrap\r
- * the value of field 'showBootstrap'.\r
- */\r
- public void setShowBootstrap(final boolean showBootstrap)\r
- {\r
- this._showBootstrap = showBootstrap;\r
- this._has_showBootstrap = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showDistances'.\r
- * \r
- * @param showDistances\r
- * the value of field 'showDistances'.\r
- */\r
- public void setShowDistances(final boolean showDistances)\r
- {\r
- this._showDistances = showDistances;\r
- this._has_showDistances = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title\r
- * the value of field 'title'.\r
- */\r
- public void setTitle(final java.lang.String title)\r
- {\r
- this._title = title;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width\r
- * the value of field 'width'.\r
- */\r
- public void setWidth(final int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos\r
- * the value of field 'xpos'.\r
- */\r
- public void setXpos(final int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos\r
- * the value of field 'ypos'.\r
- */\r
- public void setYpos(final int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Tree\r
- */\r
- public static jalview.schemabinding.version2.Tree 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.Tree) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Tree.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+public class Tree implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _width.\r
+ */\r
+ private int _width;\r
+\r
+ /**\r
+ * keeps track of state for field: _width\r
+ */\r
+ private boolean _has_width;\r
+\r
+ /**\r
+ * Field _height.\r
+ */\r
+ private int _height;\r
+\r
+ /**\r
+ * keeps track of state for field: _height\r
+ */\r
+ private boolean _has_height;\r
+\r
+ /**\r
+ * Field _xpos.\r
+ */\r
+ private int _xpos;\r
+\r
+ /**\r
+ * keeps track of state for field: _xpos\r
+ */\r
+ private boolean _has_xpos;\r
+\r
+ /**\r
+ * Field _ypos.\r
+ */\r
+ private int _ypos;\r
+\r
+ /**\r
+ * keeps track of state for field: _ypos\r
+ */\r
+ private boolean _has_ypos;\r
+\r
+ /**\r
+ * Field _fontName.\r
+ */\r
+ private java.lang.String _fontName;\r
+\r
+ /**\r
+ * Field _fontSize.\r
+ */\r
+ private int _fontSize;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontSize\r
+ */\r
+ private boolean _has_fontSize;\r
+\r
+ /**\r
+ * Field _fontStyle.\r
+ */\r
+ private int _fontStyle;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontStyle\r
+ */\r
+ private boolean _has_fontStyle;\r
+\r
+ /**\r
+ * Field _threshold.\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+ /**\r
+ * Field _showBootstrap.\r
+ */\r
+ private boolean _showBootstrap;\r
+\r
+ /**\r
+ * keeps track of state for field: _showBootstrap\r
+ */\r
+ private boolean _has_showBootstrap;\r
+\r
+ /**\r
+ * Field _showDistances.\r
+ */\r
+ private boolean _showDistances;\r
+\r
+ /**\r
+ * keeps track of state for field: _showDistances\r
+ */\r
+ private boolean _has_showDistances;\r
+\r
+ /**\r
+ * Field _markUnlinked.\r
+ */\r
+ private boolean _markUnlinked;\r
+\r
+ /**\r
+ * keeps track of state for field: _markUnlinked\r
+ */\r
+ private boolean _has_markUnlinked;\r
+\r
+ /**\r
+ * Field _fitToWindow.\r
+ */\r
+ private boolean _fitToWindow;\r
+\r
+ /**\r
+ * keeps track of state for field: _fitToWindow\r
+ */\r
+ private boolean _has_fitToWindow;\r
+\r
+ /**\r
+ * Field _currentTree.\r
+ */\r
+ private boolean _currentTree;\r
+\r
+ /**\r
+ * keeps track of state for field: _currentTree\r
+ */\r
+ private boolean _has_currentTree;\r
+\r
+ /**\r
+ * Tree ID added for binding tree visualization settings to\r
+ * vamsas document trees in jalview 2.4.1\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _title.\r
+ */\r
+ private java.lang.String _title;\r
+\r
+ /**\r
+ * Field _newick.\r
+ */\r
+ private java.lang.String _newick;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Tree() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteCurrentTree(\r
+ ) {\r
+ this._has_currentTree= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFitToWindow(\r
+ ) {\r
+ this._has_fitToWindow= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFontSize(\r
+ ) {\r
+ this._has_fontSize= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFontStyle(\r
+ ) {\r
+ this._has_fontStyle= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteHeight(\r
+ ) {\r
+ this._has_height= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMarkUnlinked(\r
+ ) {\r
+ this._has_markUnlinked= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowBootstrap(\r
+ ) {\r
+ this._has_showBootstrap= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowDistances(\r
+ ) {\r
+ this._has_showDistances= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteWidth(\r
+ ) {\r
+ this._has_width= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteXpos(\r
+ ) {\r
+ this._has_xpos= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteYpos(\r
+ ) {\r
+ this._has_ypos= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'currentTree'.\r
+ * \r
+ * @return the value of field 'CurrentTree'.\r
+ */\r
+ public boolean getCurrentTree(\r
+ ) {\r
+ return this._currentTree;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
+ * \r
+ * @return the value of field 'FitToWindow'.\r
+ */\r
+ public boolean getFitToWindow(\r
+ ) {\r
+ return this._fitToWindow;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontName'.\r
+ * \r
+ * @return the value of field 'FontName'.\r
+ */\r
+ public java.lang.String getFontName(\r
+ ) {\r
+ return this._fontName;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontSize'.\r
+ * \r
+ * @return the value of field 'FontSize'.\r
+ */\r
+ public int getFontSize(\r
+ ) {\r
+ return this._fontSize;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontStyle'.\r
+ * \r
+ * @return the value of field 'FontStyle'.\r
+ */\r
+ public int getFontStyle(\r
+ ) {\r
+ return this._fontStyle;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'height'.\r
+ * \r
+ * @return the value of field 'Height'.\r
+ */\r
+ public int getHeight(\r
+ ) {\r
+ return this._height;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: Tree ID added for binding tree\r
+ * visualization settings to vamsas document trees in jalview\r
+ * 2.4.1\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 'markUnlinked'.\r
+ * \r
+ * @return the value of field 'MarkUnlinked'.\r
+ */\r
+ public boolean getMarkUnlinked(\r
+ ) {\r
+ return this._markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'newick'.\r
+ * \r
+ * @return the value of field 'Newick'.\r
+ */\r
+ public java.lang.String getNewick(\r
+ ) {\r
+ return this._newick;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
+ * \r
+ * @return the value of field 'ShowBootstrap'.\r
+ */\r
+ public boolean getShowBootstrap(\r
+ ) {\r
+ return this._showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
+ * \r
+ * @return the value of field 'ShowDistances'.\r
+ */\r
+ public boolean getShowDistances(\r
+ ) {\r
+ return this._showDistances;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshold'.\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'title'.\r
+ * \r
+ * @return the value of field 'Title'.\r
+ */\r
+ public java.lang.String getTitle(\r
+ ) {\r
+ return this._title;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'width'.\r
+ * \r
+ * @return the value of field 'Width'.\r
+ */\r
+ public int getWidth(\r
+ ) {\r
+ return this._width;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'xpos'.\r
+ * \r
+ * @return the value of field 'Xpos'.\r
+ */\r
+ public int getXpos(\r
+ ) {\r
+ return this._xpos;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'ypos'.\r
+ * \r
+ * @return the value of field 'Ypos'.\r
+ */\r
+ public int getYpos(\r
+ ) {\r
+ return this._ypos;\r
+ }\r
+\r
+ /**\r
+ * Method hasCurrentTree.\r
+ * \r
+ * @return true if at least one CurrentTree has been added\r
+ */\r
+ public boolean hasCurrentTree(\r
+ ) {\r
+ return this._has_currentTree;\r
+ }\r
+\r
+ /**\r
+ * Method hasFitToWindow.\r
+ * \r
+ * @return true if at least one FitToWindow has been added\r
+ */\r
+ public boolean hasFitToWindow(\r
+ ) {\r
+ return this._has_fitToWindow;\r
+ }\r
+\r
+ /**\r
+ * Method hasFontSize.\r
+ * \r
+ * @return true if at least one FontSize has been added\r
+ */\r
+ public boolean hasFontSize(\r
+ ) {\r
+ return this._has_fontSize;\r
+ }\r
+\r
+ /**\r
+ * Method hasFontStyle.\r
+ * \r
+ * @return true if at least one FontStyle has been added\r
+ */\r
+ public boolean hasFontStyle(\r
+ ) {\r
+ return this._has_fontStyle;\r
+ }\r
+\r
+ /**\r
+ * Method hasHeight.\r
+ * \r
+ * @return true if at least one Height has been added\r
+ */\r
+ public boolean hasHeight(\r
+ ) {\r
+ return this._has_height;\r
+ }\r
+\r
+ /**\r
+ * Method hasMarkUnlinked.\r
+ * \r
+ * @return true if at least one MarkUnlinked has been added\r
+ */\r
+ public boolean hasMarkUnlinked(\r
+ ) {\r
+ return this._has_markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowBootstrap.\r
+ * \r
+ * @return true if at least one ShowBootstrap has been added\r
+ */\r
+ public boolean hasShowBootstrap(\r
+ ) {\r
+ return this._has_showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowDistances.\r
+ * \r
+ * @return true if at least one ShowDistances has been added\r
+ */\r
+ public boolean hasShowDistances(\r
+ ) {\r
+ return this._has_showDistances;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasWidth.\r
+ * \r
+ * @return true if at least one Width has been added\r
+ */\r
+ public boolean hasWidth(\r
+ ) {\r
+ return this._has_width;\r
+ }\r
+\r
+ /**\r
+ * Method hasXpos.\r
+ * \r
+ * @return true if at least one Xpos has been added\r
+ */\r
+ public boolean hasXpos(\r
+ ) {\r
+ return this._has_xpos;\r
+ }\r
+\r
+ /**\r
+ * Method hasYpos.\r
+ * \r
+ * @return true if at least one Ypos has been added\r
+ */\r
+ public boolean hasYpos(\r
+ ) {\r
+ return this._has_ypos;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'currentTree'.\r
+ * \r
+ * @return the value of field 'CurrentTree'.\r
+ */\r
+ public boolean isCurrentTree(\r
+ ) {\r
+ return this._currentTree;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
+ * \r
+ * @return the value of field 'FitToWindow'.\r
+ */\r
+ public boolean isFitToWindow(\r
+ ) {\r
+ return this._fitToWindow;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'markUnlinked'.\r
+ * \r
+ * @return the value of field 'MarkUnlinked'.\r
+ */\r
+ public boolean isMarkUnlinked(\r
+ ) {\r
+ return this._markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
+ * \r
+ * @return the value of field 'ShowBootstrap'.\r
+ */\r
+ public boolean isShowBootstrap(\r
+ ) {\r
+ return this._showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
+ * \r
+ * @return the value of field 'ShowDistances'.\r
+ */\r
+ public boolean isShowDistances(\r
+ ) {\r
+ return this._showDistances;\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
+ * \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
+ * Sets the value of field 'currentTree'.\r
+ * \r
+ * @param currentTree the value of field 'currentTree'.\r
+ */\r
+ public void setCurrentTree(\r
+ final boolean currentTree) {\r
+ this._currentTree = currentTree;\r
+ this._has_currentTree = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fitToWindow'.\r
+ * \r
+ * @param fitToWindow the value of field 'fitToWindow'.\r
+ */\r
+ public void setFitToWindow(\r
+ final boolean fitToWindow) {\r
+ this._fitToWindow = fitToWindow;\r
+ this._has_fitToWindow = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName the value of field 'fontName'.\r
+ */\r
+ public void setFontName(\r
+ final java.lang.String fontName) {\r
+ this._fontName = fontName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(\r
+ final int fontSize) {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(\r
+ final int fontStyle) {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height the value of field 'height'.\r
+ */\r
+ public void setHeight(\r
+ final int height) {\r
+ this._height = height;\r
+ this._has_height = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: Tree ID added for binding tree\r
+ * visualization settings to vamsas document trees in jalview\r
+ * 2.4.1\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 'markUnlinked'.\r
+ * \r
+ * @param markUnlinked the value of field 'markUnlinked'.\r
+ */\r
+ public void setMarkUnlinked(\r
+ final boolean markUnlinked) {\r
+ this._markUnlinked = markUnlinked;\r
+ this._has_markUnlinked = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'newick'.\r
+ * \r
+ * @param newick the value of field 'newick'.\r
+ */\r
+ public void setNewick(\r
+ final java.lang.String newick) {\r
+ this._newick = newick;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showBootstrap'.\r
+ * \r
+ * @param showBootstrap the value of field 'showBootstrap'.\r
+ */\r
+ public void setShowBootstrap(\r
+ final boolean showBootstrap) {\r
+ this._showBootstrap = showBootstrap;\r
+ this._has_showBootstrap = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDistances'.\r
+ * \r
+ * @param showDistances the value of field 'showDistances'.\r
+ */\r
+ public void setShowDistances(\r
+ final boolean showDistances) {\r
+ this._showDistances = showDistances;\r
+ this._has_showDistances = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshold'.\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title the value of field 'title'.\r
+ */\r
+ public void setTitle(\r
+ final java.lang.String title) {\r
+ this._title = title;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width the value of field 'width'.\r
+ */\r
+ public void setWidth(\r
+ final int width) {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos the value of field 'xpos'.\r
+ */\r
+ public void setXpos(\r
+ final int xpos) {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos the value of field 'ypos'.\r
+ */\r
+ public void setYpos(\r
+ final int ypos) {\r
+ this._ypos = ypos;\r
+ this._has_ypos = 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 jalview.schemabinding.version2.Tree\r
+ */\r
+ public static jalview.schemabinding.version2.Tree unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColourScheme extends JalviewUserColours implements\r
- java.io.Serializable\r
+public class UserColourScheme extends JalviewUserColours \r
+implements java.io.Serializable\r
{\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
\r
- public UserColourScheme()\r
- {\r
- super();\r
- }\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ public UserColourScheme() {\r
+ super();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //-----------/\r
+ //- Methods -/\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
- return true;\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 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
+ * @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\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 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
+ * @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
- * 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours\r
- */\r
- public static jalview.schemabinding.version2.JalviewUserColours 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.JalviewUserColours) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.UserColourScheme.class,\r
- reader);\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.JalviewUserColours\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+ * \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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColours implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _userColourScheme.\r
- */\r
- private jalview.schemabinding.version2.UserColourScheme _userColourScheme;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public UserColours()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\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 'userColourScheme'.\r
- * \r
- * @return the value of field 'UserColourScheme'.\r
- */\r
- public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()\r
- {\r
- return this._userColourScheme;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+public class UserColours implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _userColourScheme.\r
+ */\r
+ private jalview.schemabinding.version2.UserColourScheme _userColourScheme;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColours() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\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 'userColourScheme'.\r
+ * \r
+ * @return the value of field 'UserColourScheme'.\r
+ */\r
+ public jalview.schemabinding.version2.UserColourScheme getUserColourScheme(\r
+ ) {\r
+ return this._userColourScheme;\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
+ * \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
+ * 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 'userColourScheme'.\r
+ * \r
+ * @param userColourScheme the value of field 'userColourScheme'\r
+ */\r
+ public void setUserColourScheme(\r
+ final jalview.schemabinding.version2.UserColourScheme userColourScheme) {\r
+ this._userColourScheme = userColourScheme;\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.UserColours\r
+ */\r
+ public static jalview.schemabinding.version2.UserColours unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.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
- return true;\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 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 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
- * 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 'userColourScheme'.\r
- * \r
- * @param userColourScheme\r
- * the value of field 'userColourScheme'\r
- */\r
- public void setUserColourScheme(\r
- final jalview.schemabinding.version2.UserColourScheme userColourScheme)\r
- {\r
- this._userColourScheme = userColourScheme;\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.UserColours\r
- */\r
- public static jalview.schemabinding.version2.UserColours 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.UserColours) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.UserColours.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 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class VAMSAS implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _treeList.\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _sequenceSetList.\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public VAMSAS()\r
- {\r
- super();\r
- this._treeList = new java.util.Vector();\r
- this._sequenceSetList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceSetList.addElement(vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSequenceSet(final int index,\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceSetList.add(index, vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addTree(final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addTree(final int index, final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * Method enumerateSequenceSet.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return this._sequenceSetList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateTree.\r
- * \r
- * @return an Enumeration over all java.lang.String elements\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return this._treeList.elements();\r
- }\r
-\r
- /**\r
- * Method getSequenceSet.\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.SequenceSet at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._sequenceSetList.size() - 1) + "]");\r
+public class VAMSAS implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _treeList.\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _sequenceSetList.\r
+ */\r
+ private java.util.Vector _sequenceSetList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VAMSAS() {\r
+ super();\r
+ this._treeList = new java.util.Vector();\r
+ this._sequenceSetList = new java.util.Vector();\r
}\r
\r
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getSequenceSet.Returns the contents of the collection in an 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.SequenceSet[] getSequenceSet()\r
- {\r
- jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
- return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSequenceSetCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSequenceSetCount()\r
- {\r
- return this._sequenceSetList.size();\r
- }\r
-\r
- /**\r
- * Method getTree.\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 java.lang.String at the given index\r
- */\r
- public java.lang.String getTree(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getTree: Index value '" + index\r
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetList.addElement(vSequenceSet);\r
}\r
\r
- return (java.lang.String) _treeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getTree.Returns the contents of the collection in an 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 java.lang.String[] getTree()\r
- {\r
- java.lang.String[] array = new java.lang.String[0];\r
- return (java.lang.String[]) this._treeList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getTreeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getTreeCount()\r
- {\r
- return this._treeList.size();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._sequenceSetList.add(index, vSequenceSet);\r
}\r
- return true;\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 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 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
+ /**\r
+ * \r
+ * \r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllSequenceSet()\r
- {\r
- this._sequenceSetList.clear();\r
- }\r
+ public void addTree(\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.addElement(vTree);\r
+ }\r
\r
- /**\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void removeAllTree()\r
- {\r
- this._treeList.clear();\r
- }\r
-\r
- /**\r
- * Method removeSequenceSet.\r
- * \r
- * @param vSequenceSet\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- {\r
- boolean removed = _sequenceSetList.remove(vSequenceSet);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSequenceSetAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._sequenceSetList.remove(index);\r
- return (jalview.schemabinding.version2.SequenceSet) obj;\r
- }\r
-\r
- /**\r
- * Method removeTree.\r
- * \r
- * @param vTree\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeTree(final java.lang.String vTree)\r
- {\r
- boolean removed = _treeList.remove(vTree);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeTreeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public java.lang.String removeTreeAt(final int index)\r
- {\r
- java.lang.Object obj = this._treeList.remove(index);\r
- return (java.lang.String) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSequenceSet(final int index,\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._sequenceSetList.size() - 1) + "]");\r
+ public void addTree(\r
+ final int index,\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.add(index, vTree);\r
}\r
\r
- this._sequenceSetList.set(index, vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSetArray\r
- */\r
- public void setSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)\r
- {\r
- // -- copy array\r
- _sequenceSetList.clear();\r
-\r
- for (int i = 0; i < vSequenceSetArray.length; i++)\r
- {\r
- this._sequenceSetList.add(vSequenceSetArray[i]);\r
+ /**\r
+ * Method enumerateSequenceSet.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSet elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSet(\r
+ ) {\r
+ return this._sequenceSetList.elements();\r
}\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setTree(final int index, final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setTree: Index value '" + index\r
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+\r
+ /**\r
+ * Method enumerateTree.\r
+ * \r
+ * @return an Enumeration over all java.lang.String elements\r
+ */\r
+ public java.util.Enumeration enumerateTree(\r
+ ) {\r
+ return this._treeList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSet.\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.SequenceSet at the given index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size()) {\r
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSet.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(\r
+ ) {\r
+ jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
+ return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceSetCount(\r
+ ) {\r
+ return this._sequenceSetList.size();\r
}\r
\r
- this._treeList.set(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTreeArray\r
- */\r
- public void setTree(final java.lang.String[] vTreeArray)\r
- {\r
- // -- copy array\r
- _treeList.clear();\r
-\r
- for (int i = 0; i < vTreeArray.length; i++)\r
- {\r
- this._treeList.add(vTreeArray[i]);\r
+ /**\r
+ * Method getTree.\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 java.lang.String at the given index\r
+ */\r
+ public java.lang.String getTree(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (java.lang.String) _treeList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getTree.Returns the contents of the collection in an\r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public java.lang.String[] getTree(\r
+ ) {\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._treeList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getTreeCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getTreeCount(\r
+ ) {\r
+ return this._treeList.size();\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
+ * \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 removeAllSequenceSet(\r
+ ) {\r
+ this._sequenceSetList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllTree(\r
+ ) {\r
+ this._treeList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSet.\r
+ * \r
+ * @param vSequenceSet\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet) {\r
+ boolean removed = _sequenceSetList.remove(vSequenceSet);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._sequenceSetList.remove(index);\r
+ return (jalview.schemabinding.version2.SequenceSet) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeTree.\r
+ * \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(\r
+ final java.lang.String vTree) {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public java.lang.String removeTreeAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
+ return (java.lang.String) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSequenceSet(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size()) {\r
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._sequenceSetList.set(index, vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetArray\r
+ */\r
+ public void setSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {\r
+ //-- copy array\r
+ _sequenceSetList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceSetArray.length; i++) {\r
+ this._sequenceSetList.add(vSequenceSetArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setTree(\r
+ final int index,\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size()) {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._treeList.set(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTreeArray\r
+ */\r
+ public void setTree(\r
+ final java.lang.String[] vTreeArray) {\r
+ //-- copy array\r
+ _treeList.clear();\r
+ \r
+ for (int i = 0; i < vTreeArray.length; i++) {\r
+ this._treeList.add(vTreeArray[i]);\r
+ }\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 jalview.schemabinding.version2.VAMSAS\r
+ */\r
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.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
- /**\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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
- */\r
- public static jalview.schemabinding.version2.VAMSAS 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.VAMSAS) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.VAMSAS.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class VamsasModel extends VAMSAS implements java.io.Serializable\r
+public class VamsasModel extends VAMSAS \r
+implements java.io.Serializable\r
{\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
\r
- public VamsasModel()\r
- {\r
- super();\r
- }\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ public VamsasModel() {\r
+ super();\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ //-----------/\r
+ //- Methods -/\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
- return true;\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 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
+ * @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\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 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
+ * @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
- * 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
- */\r
- public static jalview.schemabinding.version2.VAMSAS 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.VAMSAS) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.VamsasModel.class, reader);\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 jalview.schemabinding.version2.VAMSAS\r
+ */\r
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);\r
+ }\r
\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the 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
+ * \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
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Viewport implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _conservationSelected.\r
- */\r
- private boolean _conservationSelected;\r
-\r
- /**\r
- * keeps track of state for field: _conservationSelected\r
- */\r
- private boolean _has_conservationSelected;\r
-\r
- /**\r
- * Field _pidSelected.\r
- */\r
- private boolean _pidSelected;\r
-\r
- /**\r
- * keeps track of state for field: _pidSelected\r
- */\r
- private boolean _has_pidSelected;\r
-\r
- /**\r
- * Field _bgColour.\r
- */\r
- private java.lang.String _bgColour;\r
-\r
- /**\r
- * Field _consThreshold.\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold.\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _title.\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _showFullId.\r
- */\r
- private boolean _showFullId;\r
-\r
- /**\r
- * keeps track of state for field: _showFullId\r
- */\r
- private boolean _has_showFullId;\r
-\r
- /**\r
- * Field _rightAlignIds.\r
- */\r
- private boolean _rightAlignIds;\r
-\r
- /**\r
- * keeps track of state for field: _rightAlignIds\r
- */\r
- private boolean _has_rightAlignIds;\r
-\r
- /**\r
- * Field _showText.\r
- */\r
- private boolean _showText;\r
-\r
- /**\r
- * keeps track of state for field: _showText\r
- */\r
- private boolean _has_showText;\r
-\r
- /**\r
- * Field _showColourText.\r
- */\r
- private boolean _showColourText;\r
-\r
- /**\r
- * keeps track of state for field: _showColourText\r
- */\r
- private boolean _has_showColourText;\r
-\r
- /**\r
- * Field _showUnconserved.\r
- */\r
- private boolean _showUnconserved = false;\r
-\r
- /**\r
- * keeps track of state for field: _showUnconserved\r
- */\r
- private boolean _has_showUnconserved;\r
-\r
- /**\r
- * Field _showBoxes.\r
- */\r
- private boolean _showBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _showBoxes\r
- */\r
- private boolean _has_showBoxes;\r
-\r
- /**\r
- * Field _wrapAlignment.\r
- */\r
- private boolean _wrapAlignment;\r
-\r
- /**\r
- * keeps track of state for field: _wrapAlignment\r
- */\r
- private boolean _has_wrapAlignment;\r
-\r
- /**\r
- * Field _renderGaps.\r
- */\r
- private boolean _renderGaps;\r
-\r
- /**\r
- * keeps track of state for field: _renderGaps\r
- */\r
- private boolean _has_renderGaps;\r
-\r
- /**\r
- * Field _showSequenceFeatures.\r
- */\r
- private boolean _showSequenceFeatures;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceFeatures\r
- */\r
- private boolean _has_showSequenceFeatures;\r
-\r
- /**\r
- * Field _showNPfeatureTooltip.\r
- */\r
- private boolean _showNPfeatureTooltip;\r
-\r
- /**\r
- * keeps track of state for field: _showNPfeatureTooltip\r
- */\r
- private boolean _has_showNPfeatureTooltip;\r
-\r
- /**\r
- * Field _showDbRefTooltip.\r
- */\r
- private boolean _showDbRefTooltip;\r
-\r
- /**\r
- * keeps track of state for field: _showDbRefTooltip\r
- */\r
- private boolean _has_showDbRefTooltip;\r
-\r
- /**\r
- * Field _followHighlight.\r
- */\r
- private boolean _followHighlight = true;\r
-\r
- /**\r
- * keeps track of state for field: _followHighlight\r
- */\r
- private boolean _has_followHighlight;\r
-\r
- /**\r
- * Field _followSelection.\r
- */\r
- private boolean _followSelection = true;\r
-\r
- /**\r
- * keeps track of state for field: _followSelection\r
- */\r
- private boolean _has_followSelection;\r
-\r
- /**\r
- * Field _showAnnotation.\r
- */\r
- private boolean _showAnnotation;\r
-\r
- /**\r
- * keeps track of state for field: _showAnnotation\r
- */\r
- private boolean _has_showAnnotation;\r
-\r
- /**\r
- * Field _centreColumnLabels.\r
- */\r
- private boolean _centreColumnLabels = false;\r
-\r
- /**\r
- * keeps track of state for field: _centreColumnLabels\r
- */\r
- private boolean _has_centreColumnLabels;\r
-\r
- /**\r
- * Field _showGroupConservation.\r
- */\r
- private boolean _showGroupConservation = false;\r
-\r
- /**\r
- * keeps track of state for field: _showGroupConservation\r
- */\r
- private boolean _has_showGroupConservation;\r
-\r
- /**\r
- * Field _showGroupConsensus.\r
- */\r
- private boolean _showGroupConsensus = false;\r
-\r
- /**\r
- * keeps track of state for field: _showGroupConsensus\r
- */\r
- private boolean _has_showGroupConsensus;\r
-\r
- /**\r
- * Field _showConsensusHistogram.\r
- */\r
- private boolean _showConsensusHistogram = true;\r
-\r
- /**\r
- * keeps track of state for field: _showConsensusHistogram\r
- */\r
- private boolean _has_showConsensusHistogram;\r
-\r
- /**\r
- * Field _showSequenceLogo.\r
- */\r
- private boolean _showSequenceLogo = false;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceLogo\r
- */\r
- private boolean _has_showSequenceLogo;\r
-\r
- /**\r
- * Field _ignoreGapsinConsensus.\r
- */\r
- private boolean _ignoreGapsinConsensus = true;\r
-\r
- /**\r
- * keeps track of state for field: _ignoreGapsinConsensus\r
- */\r
- private boolean _has_ignoreGapsinConsensus;\r
-\r
- /**\r
- * Field _xpos.\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos.\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width.\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height.\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _startRes.\r
- */\r
- private int _startRes;\r
-\r
- /**\r
- * keeps track of state for field: _startRes\r
- */\r
- private boolean _has_startRes;\r
-\r
- /**\r
- * Field _startSeq.\r
- */\r
- private int _startSeq;\r
-\r
- /**\r
- * keeps track of state for field: _startSeq\r
- */\r
- private boolean _has_startSeq;\r
-\r
- /**\r
- * Field _fontName.\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize.\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle.\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
- /**\r
- * Field _viewName.\r
- */\r
- private java.lang.String _viewName;\r
-\r
- /**\r
- * Field _sequenceSetId.\r
- */\r
- private java.lang.String _sequenceSetId;\r
-\r
- /**\r
- * Field _gatheredViews.\r
- */\r
- private boolean _gatheredViews;\r
-\r
- /**\r
- * keeps track of state for field: _gatheredViews\r
- */\r
- private boolean _has_gatheredViews;\r
-\r
- /**\r
- * Field _textCol1.\r
- */\r
- private int _textCol1;\r
-\r
- /**\r
- * keeps track of state for field: _textCol1\r
- */\r
- private boolean _has_textCol1;\r
-\r
- /**\r
- * Field _textCol2.\r
- */\r
- private int _textCol2;\r
-\r
- /**\r
- * keeps track of state for field: _textCol2\r
- */\r
- private boolean _has_textCol2;\r
-\r
- /**\r
- * Field _textColThreshold.\r
- */\r
- private int _textColThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _textColThreshold\r
- */\r
- private boolean _has_textColThreshold;\r
-\r
- /**\r
- * unique id used by jalview to synchronize between stored and instantiated\r
- * views\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _annotationColours.\r
- */\r
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
-\r
- /**\r
- * Field _hiddenColumnsList.\r
- */\r
- private java.util.Vector _hiddenColumnsList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Viewport()\r
- {\r
- super();\r
- this._hiddenColumnsList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenColumnsList.addElement(vHiddenColumns);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenColumns(final int index,\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenColumnsList.add(index, vHiddenColumns);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteCentreColumnLabels()\r
- {\r
- this._has_centreColumnLabels = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConservationSelected()\r
- {\r
- this._has_conservationSelected = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFollowHighlight()\r
- {\r
- this._has_followHighlight = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFollowSelection()\r
- {\r
- this._has_followSelection = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle = false;\r
- }\r
+public class Viewport implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _conservationSelected.\r
+ */\r
+ private boolean _conservationSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _conservationSelected\r
+ */\r
+ private boolean _has_conservationSelected;\r
+\r
+ /**\r
+ * Field _pidSelected.\r
+ */\r
+ private boolean _pidSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidSelected\r
+ */\r
+ private boolean _has_pidSelected;\r
+\r
+ /**\r
+ * Field _bgColour.\r
+ */\r
+ private java.lang.String _bgColour;\r
+\r
+ /**\r
+ * Field _consThreshold.\r
+ */\r
+ private int _consThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _consThreshold\r
+ */\r
+ private boolean _has_consThreshold;\r
+\r
+ /**\r
+ * Field _pidThreshold.\r
+ */\r
+ private int _pidThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidThreshold\r
+ */\r
+ private boolean _has_pidThreshold;\r
+\r
+ /**\r
+ * Field _title.\r
+ */\r
+ private java.lang.String _title;\r
+\r
+ /**\r
+ * Field _showFullId.\r
+ */\r
+ private boolean _showFullId;\r
+\r
+ /**\r
+ * keeps track of state for field: _showFullId\r
+ */\r
+ private boolean _has_showFullId;\r
+\r
+ /**\r
+ * Field _rightAlignIds.\r
+ */\r
+ private boolean _rightAlignIds;\r
+\r
+ /**\r
+ * keeps track of state for field: _rightAlignIds\r
+ */\r
+ private boolean _has_rightAlignIds;\r
+\r
+ /**\r
+ * Field _showText.\r
+ */\r
+ private boolean _showText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showText\r
+ */\r
+ private boolean _has_showText;\r
+\r
+ /**\r
+ * Field _showColourText.\r
+ */\r
+ private boolean _showColourText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showColourText\r
+ */\r
+ private boolean _has_showColourText;\r
+\r
+ /**\r
+ * Field _showUnconserved.\r
+ */\r
+ private boolean _showUnconserved = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showUnconserved\r
+ */\r
+ private boolean _has_showUnconserved;\r
+\r
+ /**\r
+ * Field _showBoxes.\r
+ */\r
+ private boolean _showBoxes;\r
+\r
+ /**\r
+ * keeps track of state for field: _showBoxes\r
+ */\r
+ private boolean _has_showBoxes;\r
+\r
+ /**\r
+ * Field _wrapAlignment.\r
+ */\r
+ private boolean _wrapAlignment;\r
+\r
+ /**\r
+ * keeps track of state for field: _wrapAlignment\r
+ */\r
+ private boolean _has_wrapAlignment;\r
+\r
+ /**\r
+ * Field _renderGaps.\r
+ */\r
+ private boolean _renderGaps;\r
+\r
+ /**\r
+ * keeps track of state for field: _renderGaps\r
+ */\r
+ private boolean _has_renderGaps;\r
+\r
+ /**\r
+ * Field _showSequenceFeatures.\r
+ */\r
+ private boolean _showSequenceFeatures;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceFeatures\r
+ */\r
+ private boolean _has_showSequenceFeatures;\r
+\r
+ /**\r
+ * Field _showNPfeatureTooltip.\r
+ */\r
+ private boolean _showNPfeatureTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showNPfeatureTooltip\r
+ */\r
+ private boolean _has_showNPfeatureTooltip;\r
+\r
+ /**\r
+ * Field _showDbRefTooltip.\r
+ */\r
+ private boolean _showDbRefTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showDbRefTooltip\r
+ */\r
+ private boolean _has_showDbRefTooltip;\r
+\r
+ /**\r
+ * Field _followHighlight.\r
+ */\r
+ private boolean _followHighlight = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followHighlight\r
+ */\r
+ private boolean _has_followHighlight;\r
+\r
+ /**\r
+ * Field _followSelection.\r
+ */\r
+ private boolean _followSelection = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followSelection\r
+ */\r
+ private boolean _has_followSelection;\r
+\r
+ /**\r
+ * Field _showAnnotation.\r
+ */\r
+ private boolean _showAnnotation;\r
+\r
+ /**\r
+ * keeps track of state for field: _showAnnotation\r
+ */\r
+ private boolean _has_showAnnotation;\r
+\r
+ /**\r
+ * Field _centreColumnLabels.\r
+ */\r
+ private boolean _centreColumnLabels = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _centreColumnLabels\r
+ */\r
+ private boolean _has_centreColumnLabels;\r
+\r
+ /**\r
+ * Field _showGroupConservation.\r
+ */\r
+ private boolean _showGroupConservation = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConservation\r
+ */\r
+ private boolean _has_showGroupConservation;\r
+\r
+ /**\r
+ * Field _showGroupConsensus.\r
+ */\r
+ private boolean _showGroupConsensus = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConsensus\r
+ */\r
+ private boolean _has_showGroupConsensus;\r
+\r
+ /**\r
+ * Field _showConsensusHistogram.\r
+ */\r
+ private boolean _showConsensusHistogram = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusHistogram\r
+ */\r
+ private boolean _has_showConsensusHistogram;\r
+\r
+ /**\r
+ * Field _showSequenceLogo.\r
+ */\r
+ private boolean _showSequenceLogo = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceLogo\r
+ */\r
+ private boolean _has_showSequenceLogo;\r
+\r
+ /**\r
+ * Field _ignoreGapsinConsensus.\r
+ */\r
+ private boolean _ignoreGapsinConsensus = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _ignoreGapsinConsensus\r
+ */\r
+ private boolean _has_ignoreGapsinConsensus;\r
+\r
+ /**\r
+ * Field _xpos.\r
+ */\r
+ private int _xpos;\r
+\r
+ /**\r
+ * keeps track of state for field: _xpos\r
+ */\r
+ private boolean _has_xpos;\r
+\r
+ /**\r
+ * Field _ypos.\r
+ */\r
+ private int _ypos;\r
+\r
+ /**\r
+ * keeps track of state for field: _ypos\r
+ */\r
+ private boolean _has_ypos;\r
+\r
+ /**\r
+ * Field _width.\r
+ */\r
+ private int _width;\r
+\r
+ /**\r
+ * keeps track of state for field: _width\r
+ */\r
+ private boolean _has_width;\r
+\r
+ /**\r
+ * Field _height.\r
+ */\r
+ private int _height;\r
+\r
+ /**\r
+ * keeps track of state for field: _height\r
+ */\r
+ private boolean _has_height;\r
+\r
+ /**\r
+ * Field _startRes.\r
+ */\r
+ private int _startRes;\r
+\r
+ /**\r
+ * keeps track of state for field: _startRes\r
+ */\r
+ private boolean _has_startRes;\r
\r
- /**\r
+ /**\r
+ * Field _startSeq.\r
*/\r
- public void deleteGatheredViews()\r
- {\r
- this._has_gatheredViews = false;\r
- }\r
+ private int _startSeq;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _startSeq\r
*/\r
- public void deleteHeight()\r
- {\r
- this._has_height = false;\r
- }\r
+ private boolean _has_startSeq;\r
\r
- /**\r
+ /**\r
+ * Field _fontName.\r
*/\r
- public void deleteIgnoreGapsinConsensus()\r
- {\r
- this._has_ignoreGapsinConsensus = false;\r
- }\r
+ private java.lang.String _fontName;\r
\r
- /**\r
+ /**\r
+ * Field _fontSize.\r
*/\r
- public void deletePidSelected()\r
- {\r
- this._has_pidSelected = false;\r
- }\r
+ private int _fontSize;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _fontSize\r
*/\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold = false;\r
- }\r
+ private boolean _has_fontSize;\r
\r
- /**\r
+ /**\r
+ * Field _fontStyle.\r
*/\r
- public void deleteRenderGaps()\r
- {\r
- this._has_renderGaps = false;\r
- }\r
+ private int _fontStyle;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _fontStyle\r
*/\r
- public void deleteRightAlignIds()\r
- {\r
- this._has_rightAlignIds = false;\r
- }\r
+ private boolean _has_fontStyle;\r
\r
- /**\r
+ /**\r
+ * Field _viewName.\r
*/\r
- public void deleteShowAnnotation()\r
- {\r
- this._has_showAnnotation = false;\r
- }\r
+ private java.lang.String _viewName;\r
\r
- /**\r
+ /**\r
+ * Field _sequenceSetId.\r
*/\r
- public void deleteShowBoxes()\r
- {\r
- this._has_showBoxes = false;\r
- }\r
+ private java.lang.String _sequenceSetId;\r
\r
- /**\r
+ /**\r
+ * Field _gatheredViews.\r
*/\r
- public void deleteShowColourText()\r
- {\r
- this._has_showColourText = false;\r
- }\r
+ private boolean _gatheredViews;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _gatheredViews\r
*/\r
- public void deleteShowConsensusHistogram()\r
- {\r
- this._has_showConsensusHistogram = false;\r
- }\r
+ private boolean _has_gatheredViews;\r
\r
- /**\r
+ /**\r
+ * Field _textCol1.\r
*/\r
- public void deleteShowDbRefTooltip()\r
- {\r
- this._has_showDbRefTooltip = false;\r
- }\r
+ private int _textCol1;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _textCol1\r
*/\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId = false;\r
- }\r
+ private boolean _has_textCol1;\r
\r
- /**\r
+ /**\r
+ * Field _textCol2.\r
*/\r
- public void deleteShowGroupConsensus()\r
- {\r
- this._has_showGroupConsensus = false;\r
- }\r
+ private int _textCol2;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _textCol2\r
*/\r
- public void deleteShowGroupConservation()\r
- {\r
- this._has_showGroupConservation = false;\r
- }\r
+ private boolean _has_textCol2;\r
\r
- /**\r
+ /**\r
+ * Field _textColThreshold.\r
*/\r
- public void deleteShowNPfeatureTooltip()\r
- {\r
- this._has_showNPfeatureTooltip = false;\r
- }\r
+ private int _textColThreshold;\r
\r
- /**\r
+ /**\r
+ * keeps track of state for field: _textColThreshold\r
*/\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures = false;\r
- }\r
+ private boolean _has_textColThreshold;\r
\r
- /**\r
+ /**\r
+ * unique id used by jalview to synchronize between stored and\r
+ * instantiated views\r
+ * \r
*/\r
- public void deleteShowSequenceLogo()\r
- {\r
- this._has_showSequenceLogo = false;\r
- }\r
+ private java.lang.String _id;\r
\r
- /**\r
+ /**\r
+ * Field _annotationColours.\r
*/\r
- public void deleteShowText()\r
- {\r
- this._has_showText = false;\r
- }\r
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
\r
- /**\r
+ /**\r
+ * Field _hiddenColumnsList.\r
*/\r
- public void deleteShowUnconserved()\r
- {\r
- this._has_showUnconserved = false;\r
- }\r
+ private java.util.Vector _hiddenColumnsList;\r
\r
- /**\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Viewport() {\r
+ super();\r
+ this._hiddenColumnsList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenColumnsList.addElement(vHiddenColumns);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenColumns(\r
+ final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenColumnsList.add(index, vHiddenColumns);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteCentreColumnLabels(\r
+ ) {\r
+ this._has_centreColumnLabels= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteConsThreshold(\r
+ ) {\r
+ this._has_consThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteConservationSelected(\r
+ ) {\r
+ this._has_conservationSelected= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFollowHighlight(\r
+ ) {\r
+ this._has_followHighlight= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFollowSelection(\r
+ ) {\r
+ this._has_followSelection= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFontSize(\r
+ ) {\r
+ this._has_fontSize= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFontStyle(\r
+ ) {\r
+ this._has_fontStyle= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGatheredViews(\r
+ ) {\r
+ this._has_gatheredViews= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteHeight(\r
+ ) {\r
+ this._has_height= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteIgnoreGapsinConsensus(\r
+ ) {\r
+ this._has_ignoreGapsinConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePidSelected(\r
+ ) {\r
+ this._has_pidSelected= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePidThreshold(\r
+ ) {\r
+ this._has_pidThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteRenderGaps(\r
+ ) {\r
+ this._has_renderGaps= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteRightAlignIds(\r
+ ) {\r
+ this._has_rightAlignIds= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowAnnotation(\r
+ ) {\r
+ this._has_showAnnotation= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowBoxes(\r
+ ) {\r
+ this._has_showBoxes= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowColourText(\r
+ ) {\r
+ this._has_showColourText= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowConsensusHistogram(\r
+ ) {\r
+ this._has_showConsensusHistogram= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowDbRefTooltip(\r
+ ) {\r
+ this._has_showDbRefTooltip= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowFullId(\r
+ ) {\r
+ this._has_showFullId= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowGroupConsensus(\r
+ ) {\r
+ this._has_showGroupConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowGroupConservation(\r
+ ) {\r
+ this._has_showGroupConservation= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowNPfeatureTooltip(\r
+ ) {\r
+ this._has_showNPfeatureTooltip= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowSequenceFeatures(\r
+ ) {\r
+ this._has_showSequenceFeatures= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowSequenceLogo(\r
+ ) {\r
+ this._has_showSequenceLogo= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowText(\r
+ ) {\r
+ this._has_showText= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowUnconserved(\r
+ ) {\r
+ this._has_showUnconserved= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStartRes(\r
+ ) {\r
+ this._has_startRes= false;\r
+ }\r
+\r
+ /**\r
*/\r
- public void deleteStartRes()\r
- {\r
- this._has_startRes = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStartSeq()\r
- {\r
- this._has_startSeq = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol1()\r
- {\r
- this._has_textCol1 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol2()\r
- {\r
- this._has_textCol2 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextColThreshold()\r
- {\r
- this._has_textColThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWrapAlignment()\r
- {\r
- this._has_wrapAlignment = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos = false;\r
- }\r
-\r
- /**\r
- * Method enumerateHiddenColumns.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.HiddenColumns elements\r
- */\r
- public java.util.Enumeration enumerateHiddenColumns()\r
- {\r
- return this._hiddenColumnsList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'annotationColours'.\r
- * \r
- * @return the value of field 'AnnotationColours'.\r
- */\r
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
- {\r
- return this._annotationColours;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'bgColour'.\r
- * \r
- * @return the value of field 'BgColour'.\r
- */\r
- public java.lang.String getBgColour()\r
- {\r
- return this._bgColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColumnLabels'.\r
- * \r
- * @return the value of field 'CentreColumnLabels'.\r
- */\r
- public boolean getCentreColumnLabels()\r
- {\r
- return this._centreColumnLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return the value of field 'ConsThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return the value of field 'ConservationSelected'.\r
- */\r
- public boolean getConservationSelected()\r
- {\r
- return this._conservationSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'followHighlight'.\r
- * \r
- * @return the value of field 'FollowHighlight'.\r
- */\r
- public boolean getFollowHighlight()\r
- {\r
- return this._followHighlight;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'followSelection'.\r
- * \r
- * @return the value of field 'FollowSelection'.\r
- */\r
- public boolean getFollowSelection()\r
- {\r
- return this._followSelection;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return the value of field 'FontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return the value of field 'FontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return the value of field 'FontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'gatheredViews'.\r
- * \r
- * @return the value of field 'GatheredViews'.\r
- */\r
- public boolean getGatheredViews()\r
- {\r
- return this._gatheredViews;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return the value of field 'Height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- }\r
-\r
- /**\r
- * Method getHiddenColumns.\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.HiddenColumns at\r
- * the given index\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenColumnsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._hiddenColumnsList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getHiddenColumns.Returns the contents of the collection in an 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.HiddenColumns[] getHiddenColumns()\r
- {\r
- jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];\r
- return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getHiddenColumnsCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getHiddenColumnsCount()\r
- {\r
- return this._hiddenColumnsList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the following\r
- * description: unique id used by jalview to synchronize between stored and\r
- * instantiated views\r
- * \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 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean getIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return the value of field 'PidSelected'.\r
- */\r
- public boolean getPidSelected()\r
- {\r
- return this._pidSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return the value of field 'PidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return the value of field 'RenderGaps'.\r
- */\r
- public boolean getRenderGaps()\r
- {\r
- return this._renderGaps;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'rightAlignIds'.\r
- * \r
- * @return the value of field 'RightAlignIds'.\r
- */\r
- public boolean getRightAlignIds()\r
- {\r
- return this._rightAlignIds;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceSetId'.\r
- * \r
- * @return the value of field 'SequenceSetId'.\r
- */\r
- public java.lang.String getSequenceSetId()\r
- {\r
- return this._sequenceSetId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return the value of field 'ShowAnnotation'.\r
- */\r
- public boolean getShowAnnotation()\r
- {\r
- return this._showAnnotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return the value of field 'ShowBoxes'.\r
- */\r
- public boolean getShowBoxes()\r
- {\r
- return this._showBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return the value of field 'ShowColourText'.\r
- */\r
- public boolean getShowColourText()\r
- {\r
- return this._showColourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean getShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDbRefTooltip'.\r
- * \r
- * @return the value of field 'ShowDbRefTooltip'.\r
- */\r
- public boolean getShowDbRefTooltip()\r
- {\r
- return this._showDbRefTooltip;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return the value of field 'ShowFullId'.\r
- */\r
- public boolean getShowFullId()\r
- {\r
- return this._showFullId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showGroupConsensus'.\r
- * \r
- * @return the value of field 'ShowGroupConsensus'.\r
- */\r
- public boolean getShowGroupConsensus()\r
- {\r
- return this._showGroupConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showGroupConservation'.\r
- * \r
- * @return the value of field 'ShowGroupConservation'.\r
- */\r
- public boolean getShowGroupConservation()\r
- {\r
- return this._showGroupConservation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showNPfeatureTooltip'.\r
- * \r
- * @return the value of field 'ShowNPfeatureTooltip'.\r
- */\r
- public boolean getShowNPfeatureTooltip()\r
- {\r
- return this._showNPfeatureTooltip;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return the value of field 'ShowSequenceFeatures'.\r
- */\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return this._showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean getShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return the value of field 'ShowText'.\r
- */\r
- public boolean getShowText()\r
- {\r
- return this._showText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean getShowUnconserved()\r
- {\r
- return this._showUnconserved;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'startRes'.\r
- * \r
- * @return the value of field 'StartRes'.\r
- */\r
- public int getStartRes()\r
- {\r
- return this._startRes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'startSeq'.\r
- * \r
- * @return the value of field 'StartSeq'.\r
- */\r
- public int getStartSeq()\r
- {\r
- return this._startSeq;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return the value of field 'TextCol1'.\r
- */\r
- public int getTextCol1()\r
- {\r
- return this._textCol1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return the value of field 'TextCol2'.\r
- */\r
- public int getTextCol2()\r
- {\r
- return this._textCol2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return the value of field 'TextColThreshold'.\r
- */\r
- public int getTextColThreshold()\r
- {\r
- return this._textColThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return the value of field 'Title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'viewName'.\r
- * \r
- * @return the value of field 'ViewName'.\r
- */\r
- public java.lang.String getViewName()\r
- {\r
- return this._viewName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return the value of field 'Width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return the value of field 'WrapAlignment'.\r
- */\r
- public boolean getWrapAlignment()\r
- {\r
- return this._wrapAlignment;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return the value of field 'Xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return the value of field 'Ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- }\r
-\r
- /**\r
- * Method hasCentreColumnLabels.\r
- * \r
- * @return true if at least one CentreColumnLabels has been adde\r
- */\r
- public boolean hasCentreColumnLabels()\r
- {\r
- return this._has_centreColumnLabels;\r
- }\r
-\r
- /**\r
- * Method hasConsThreshold.\r
- * \r
- * @return true if at least one ConsThreshold has been added\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- }\r
-\r
- /**\r
- * Method hasConservationSelected.\r
- * \r
- * @return true if at least one ConservationSelected has been added\r
- */\r
- public boolean hasConservationSelected()\r
- {\r
- return this._has_conservationSelected;\r
- }\r
-\r
- /**\r
- * Method hasFollowHighlight.\r
- * \r
- * @return true if at least one FollowHighlight has been added\r
- */\r
- public boolean hasFollowHighlight()\r
- {\r
- return this._has_followHighlight;\r
- }\r
-\r
- /**\r
- * Method hasFollowSelection.\r
- * \r
- * @return true if at least one FollowSelection has been added\r
- */\r
- public boolean hasFollowSelection()\r
- {\r
- return this._has_followSelection;\r
- }\r
-\r
- /**\r
- * Method hasFontSize.\r
- * \r
- * @return true if at least one FontSize has been added\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- }\r
-\r
- /**\r
- * Method hasFontStyle.\r
- * \r
- * @return true if at least one FontStyle has been added\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- }\r
-\r
- /**\r
- * Method hasGatheredViews.\r
- * \r
- * @return true if at least one GatheredViews has been added\r
- */\r
- public boolean hasGatheredViews()\r
- {\r
- return this._has_gatheredViews;\r
- }\r
-\r
- /**\r
- * Method hasHeight.\r
- * \r
- * @return true if at least one Height has been added\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- }\r
-\r
- /**\r
- * Method hasIgnoreGapsinConsensus.\r
- * \r
- * @return true if at least one IgnoreGapsinConsensus has been added\r
- */\r
- public boolean hasIgnoreGapsinConsensus()\r
- {\r
- return this._has_ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Method hasPidSelected.\r
- * \r
- * @return true if at least one PidSelected has been added\r
- */\r
- public boolean hasPidSelected()\r
- {\r
- return this._has_pidSelected;\r
- }\r
-\r
- /**\r
- * Method hasPidThreshold.\r
- * \r
- * @return true if at least one PidThreshold has been added\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- }\r
-\r
- /**\r
- * Method hasRenderGaps.\r
- * \r
- * @return true if at least one RenderGaps has been added\r
- */\r
- public boolean hasRenderGaps()\r
- {\r
- return this._has_renderGaps;\r
- }\r
-\r
- /**\r
- * Method hasRightAlignIds.\r
- * \r
- * @return true if at least one RightAlignIds has been added\r
- */\r
- public boolean hasRightAlignIds()\r
- {\r
- return this._has_rightAlignIds;\r
- }\r
-\r
- /**\r
- * Method hasShowAnnotation.\r
- * \r
- * @return true if at least one ShowAnnotation has been added\r
- */\r
- public boolean hasShowAnnotation()\r
- {\r
- return this._has_showAnnotation;\r
- }\r
-\r
- /**\r
- * Method hasShowBoxes.\r
- * \r
- * @return true if at least one ShowBoxes has been added\r
- */\r
- public boolean hasShowBoxes()\r
- {\r
- return this._has_showBoxes;\r
- }\r
-\r
- /**\r
- * Method hasShowColourText.\r
- * \r
- * @return true if at least one ShowColourText has been added\r
- */\r
- public boolean hasShowColourText()\r
- {\r
- return this._has_showColourText;\r
- }\r
-\r
- /**\r
- * Method hasShowConsensusHistogram.\r
- * \r
- * @return true if at least one ShowConsensusHistogram has been added\r
- */\r
- public boolean hasShowConsensusHistogram()\r
- {\r
- return this._has_showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Method hasShowDbRefTooltip.\r
- * \r
- * @return true if at least one ShowDbRefTooltip has been added\r
- */\r
- public boolean hasShowDbRefTooltip()\r
- {\r
- return this._has_showDbRefTooltip;\r
- }\r
-\r
- /**\r
- * Method hasShowFullId.\r
- * \r
- * @return true if at least one ShowFullId has been added\r
- */\r
- public boolean hasShowFullId()\r
- {\r
- return this._has_showFullId;\r
- }\r
-\r
- /**\r
- * Method hasShowGroupConsensus.\r
- * \r
- * @return true if at least one ShowGroupConsensus has been adde\r
- */\r
- public boolean hasShowGroupConsensus()\r
- {\r
- return this._has_showGroupConsensus;\r
- }\r
-\r
- /**\r
- * Method hasShowGroupConservation.\r
- * \r
- * @return true if at least one ShowGroupConservation has been added\r
- */\r
- public boolean hasShowGroupConservation()\r
- {\r
- return this._has_showGroupConservation;\r
- }\r
-\r
- /**\r
- * Method hasShowNPfeatureTooltip.\r
- * \r
- * @return true if at least one ShowNPfeatureTooltip has been added\r
- */\r
- public boolean hasShowNPfeatureTooltip()\r
- {\r
- return this._has_showNPfeatureTooltip;\r
- }\r
-\r
- /**\r
- * Method hasShowSequenceFeatures.\r
- * \r
- * @return true if at least one ShowSequenceFeatures has been added\r
- */\r
- public boolean hasShowSequenceFeatures()\r
- {\r
- return this._has_showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Method hasShowSequenceLogo.\r
- * \r
- * @return true if at least one ShowSequenceLogo has been added\r
- */\r
- public boolean hasShowSequenceLogo()\r
- {\r
- return this._has_showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Method hasShowText.\r
- * \r
- * @return true if at least one ShowText has been added\r
- */\r
- public boolean hasShowText()\r
- {\r
- return this._has_showText;\r
- }\r
-\r
- /**\r
- * Method hasShowUnconserved.\r
- * \r
- * @return true if at least one ShowUnconserved has been added\r
- */\r
- public boolean hasShowUnconserved()\r
- {\r
- return this._has_showUnconserved;\r
- }\r
-\r
- /**\r
- * Method hasStartRes.\r
- * \r
- * @return true if at least one StartRes has been added\r
- */\r
- public boolean hasStartRes()\r
- {\r
- return this._has_startRes;\r
- }\r
-\r
- /**\r
- * Method hasStartSeq.\r
- * \r
- * @return true if at least one StartSeq has been added\r
- */\r
- public boolean hasStartSeq()\r
- {\r
- return this._has_startSeq;\r
- }\r
-\r
- /**\r
- * Method hasTextCol1.\r
- * \r
- * @return true if at least one TextCol1 has been added\r
- */\r
- public boolean hasTextCol1()\r
- {\r
- return this._has_textCol1;\r
- }\r
-\r
- /**\r
- * Method hasTextCol2.\r
- * \r
- * @return true if at least one TextCol2 has been added\r
- */\r
- public boolean hasTextCol2()\r
- {\r
- return this._has_textCol2;\r
- }\r
-\r
- /**\r
- * Method hasTextColThreshold.\r
- * \r
- * @return true if at least one TextColThreshold has been added\r
- */\r
- public boolean hasTextColThreshold()\r
- {\r
- return this._has_textColThreshold;\r
- }\r
-\r
- /**\r
- * Method hasWidth.\r
- * \r
- * @return true if at least one Width has been added\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- }\r
-\r
- /**\r
- * Method hasWrapAlignment.\r
- * \r
- * @return true if at least one WrapAlignment has been added\r
- */\r
- public boolean hasWrapAlignment()\r
- {\r
- return this._has_wrapAlignment;\r
- }\r
-\r
- /**\r
- * Method hasXpos.\r
- * \r
- * @return true if at least one Xpos has been added\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- }\r
-\r
- /**\r
- * Method hasYpos.\r
- * \r
- * @return true if at least one Ypos has been added\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColumnLabels'.\r
- * \r
- * @return the value of field 'CentreColumnLabels'.\r
- */\r
- public boolean isCentreColumnLabels()\r
- {\r
- return this._centreColumnLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return the value of field 'ConservationSelected'.\r
- */\r
- public boolean isConservationSelected()\r
- {\r
- return this._conservationSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'followHighlight'.\r
- * \r
- * @return the value of field 'FollowHighlight'.\r
- */\r
- public boolean isFollowHighlight()\r
- {\r
- return this._followHighlight;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'followSelection'.\r
- * \r
- * @return the value of field 'FollowSelection'.\r
- */\r
- public boolean isFollowSelection()\r
- {\r
- return this._followSelection;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'gatheredViews'.\r
- * \r
- * @return the value of field 'GatheredViews'.\r
- */\r
- public boolean isGatheredViews()\r
- {\r
- return this._gatheredViews;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean isIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return the value of field 'PidSelected'.\r
- */\r
- public boolean isPidSelected()\r
- {\r
- return this._pidSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return the value of field 'RenderGaps'.\r
- */\r
- public boolean isRenderGaps()\r
- {\r
- return this._renderGaps;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'rightAlignIds'.\r
- * \r
- * @return the value of field 'RightAlignIds'.\r
- */\r
- public boolean isRightAlignIds()\r
- {\r
- return this._rightAlignIds;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return the value of field 'ShowAnnotation'.\r
- */\r
- public boolean isShowAnnotation()\r
- {\r
- return this._showAnnotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return the value of field 'ShowBoxes'.\r
- */\r
- public boolean isShowBoxes()\r
- {\r
- return this._showBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return the value of field 'ShowColourText'.\r
- */\r
- public boolean isShowColourText()\r
- {\r
- return this._showColourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean isShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDbRefTooltip'.\r
- * \r
- * @return the value of field 'ShowDbRefTooltip'.\r
- */\r
- public boolean isShowDbRefTooltip()\r
- {\r
- return this._showDbRefTooltip;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return the value of field 'ShowFullId'.\r
- */\r
- public boolean isShowFullId()\r
- {\r
- return this._showFullId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showGroupConsensus'.\r
- * \r
- * @return the value of field 'ShowGroupConsensus'.\r
- */\r
- public boolean isShowGroupConsensus()\r
- {\r
- return this._showGroupConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showGroupConservation'.\r
- * \r
- * @return the value of field 'ShowGroupConservation'.\r
- */\r
- public boolean isShowGroupConservation()\r
- {\r
- return this._showGroupConservation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showNPfeatureTooltip'.\r
- * \r
- * @return the value of field 'ShowNPfeatureTooltip'.\r
- */\r
- public boolean isShowNPfeatureTooltip()\r
- {\r
- return this._showNPfeatureTooltip;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return the value of field 'ShowSequenceFeatures'.\r
- */\r
- public boolean isShowSequenceFeatures()\r
- {\r
- return this._showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean isShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return the value of field 'ShowText'.\r
- */\r
- public boolean isShowText()\r
- {\r
- return this._showText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean isShowUnconserved()\r
- {\r
- return this._showUnconserved;\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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return the value of field 'WrapAlignment'.\r
- */\r
- public boolean isWrapAlignment()\r
- {\r
- return this._wrapAlignment;\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 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 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 removeAllHiddenColumns()\r
- {\r
- this._hiddenColumnsList.clear();\r
- }\r
-\r
- /**\r
- * Method removeHiddenColumns.\r
- * \r
- * @param vHiddenColumns\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- {\r
- boolean removed = _hiddenColumnsList.remove(vHiddenColumns);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeHiddenColumnsAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._hiddenColumnsList.remove(index);\r
- return (jalview.schemabinding.version2.HiddenColumns) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'annotationColours'.\r
- * \r
- * @param annotationColours\r
- * the value of field 'annotationColours'.\r
- */\r
- public void setAnnotationColours(\r
- final jalview.schemabinding.version2.AnnotationColours annotationColours)\r
- {\r
- this._annotationColours = annotationColours;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'bgColour'.\r
- * \r
- * @param bgColour\r
- * the value of field 'bgColour'.\r
- */\r
- public void setBgColour(final java.lang.String bgColour)\r
- {\r
- this._bgColour = bgColour;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'centreColumnLabels'.\r
- * \r
- * @param centreColumnLabels\r
- * the value of field 'centreColumnLabels'.\r
- */\r
- public void setCentreColumnLabels(final boolean centreColumnLabels)\r
- {\r
- this._centreColumnLabels = centreColumnLabels;\r
- this._has_centreColumnLabels = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold\r
- * the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(final int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'conservationSelected'.\r
- * \r
- * @param conservationSelected\r
- * the value of field 'conservationSelected'.\r
- */\r
- public void setConservationSelected(final boolean conservationSelected)\r
- {\r
- this._conservationSelected = conservationSelected;\r
- this._has_conservationSelected = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'followHighlight'.\r
- * \r
- * @param followHighlight\r
- * the value of field 'followHighlight'.\r
- */\r
- public void setFollowHighlight(final boolean followHighlight)\r
- {\r
- this._followHighlight = followHighlight;\r
- this._has_followHighlight = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'followSelection'.\r
- * \r
- * @param followSelection\r
- * the value of field 'followSelection'.\r
- */\r
- public void setFollowSelection(final boolean followSelection)\r
- {\r
- this._followSelection = followSelection;\r
- this._has_followSelection = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName\r
- * the value of field 'fontName'.\r
- */\r
- public void setFontName(final java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize\r
- * the value of field 'fontSize'.\r
- */\r
- public void setFontSize(final int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle\r
- * the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(final int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'gatheredViews'.\r
- * \r
- * @param gatheredViews\r
- * the value of field 'gatheredViews'.\r
- */\r
- public void setGatheredViews(final boolean gatheredViews)\r
- {\r
- this._gatheredViews = gatheredViews;\r
- this._has_gatheredViews = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height\r
- * the value of field 'height'.\r
- */\r
- public void setHeight(final int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setHiddenColumns(final int index,\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenColumnsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._hiddenColumnsList.size() - 1) + "]");\r
- }\r
-\r
- this._hiddenColumnsList.set(index, vHiddenColumns);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenColumnsArray\r
- */\r
- public void setHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)\r
- {\r
- // -- copy array\r
- _hiddenColumnsList.clear();\r
-\r
- for (int i = 0; i < vHiddenColumnsArray.length; i++)\r
- {\r
- this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the following description:\r
- * unique id used by jalview to synchronize between stored and instantiated\r
- * views\r
- * \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 'ignoreGapsinConsensus'.\r
- * \r
- * @param ignoreGapsinConsensus\r
- * the value of field 'ignoreGapsinConsensus'.\r
- */\r
- public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
- {\r
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
- this._has_ignoreGapsinConsensus = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidSelected'.\r
- * \r
- * @param pidSelected\r
- * the value of field 'pidSelected'.\r
- */\r
- public void setPidSelected(final boolean pidSelected)\r
- {\r
- this._pidSelected = pidSelected;\r
- this._has_pidSelected = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold\r
- * the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(final int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'renderGaps'.\r
- * \r
- * @param renderGaps\r
- * the value of field 'renderGaps'.\r
- */\r
- public void setRenderGaps(final boolean renderGaps)\r
- {\r
- this._renderGaps = renderGaps;\r
- this._has_renderGaps = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'rightAlignIds'.\r
- * \r
- * @param rightAlignIds\r
- * the value of field 'rightAlignIds'.\r
- */\r
- public void setRightAlignIds(final boolean rightAlignIds)\r
- {\r
- this._rightAlignIds = rightAlignIds;\r
- this._has_rightAlignIds = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequenceSetId'.\r
- * \r
- * @param sequenceSetId\r
- * the value of field 'sequenceSetId'.\r
- */\r
- public void setSequenceSetId(final java.lang.String sequenceSetId)\r
- {\r
- this._sequenceSetId = sequenceSetId;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showAnnotation'.\r
- * \r
- * @param showAnnotation\r
- * the value of field 'showAnnotation'.\r
- */\r
- public void setShowAnnotation(final boolean showAnnotation)\r
- {\r
- this._showAnnotation = showAnnotation;\r
- this._has_showAnnotation = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showBoxes'.\r
- * \r
- * @param showBoxes\r
- * the value of field 'showBoxes'.\r
- */\r
- public void setShowBoxes(final boolean showBoxes)\r
- {\r
- this._showBoxes = showBoxes;\r
- this._has_showBoxes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showColourText'.\r
- * \r
- * @param showColourText\r
- * the value of field 'showColourText'.\r
- */\r
- public void setShowColourText(final boolean showColourText)\r
- {\r
- this._showColourText = showColourText;\r
- this._has_showColourText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showConsensusHistogram'.\r
- * \r
- * @param showConsensusHistogram\r
- * the value of field 'showConsensusHistogram'.\r
- */\r
- public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
- {\r
- this._showConsensusHistogram = showConsensusHistogram;\r
- this._has_showConsensusHistogram = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showDbRefTooltip'.\r
- * \r
- * @param showDbRefTooltip\r
- * the value of field 'showDbRefTooltip'\r
- */\r
- public void setShowDbRefTooltip(final boolean showDbRefTooltip)\r
- {\r
- this._showDbRefTooltip = showDbRefTooltip;\r
- this._has_showDbRefTooltip = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showFullId'.\r
- * \r
- * @param showFullId\r
- * the value of field 'showFullId'.\r
- */\r
- public void setShowFullId(final boolean showFullId)\r
- {\r
- this._showFullId = showFullId;\r
- this._has_showFullId = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showGroupConsensus'.\r
- * \r
- * @param showGroupConsensus\r
- * the value of field 'showGroupConsensus'.\r
- */\r
- public void setShowGroupConsensus(final boolean showGroupConsensus)\r
- {\r
- this._showGroupConsensus = showGroupConsensus;\r
- this._has_showGroupConsensus = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showGroupConservation'.\r
- * \r
- * @param showGroupConservation\r
- * the value of field 'showGroupConservation'.\r
- */\r
- public void setShowGroupConservation(final boolean showGroupConservation)\r
- {\r
- this._showGroupConservation = showGroupConservation;\r
- this._has_showGroupConservation = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showNPfeatureTooltip'.\r
- * \r
- * @param showNPfeatureTooltip\r
- * the value of field 'showNPfeatureTooltip'.\r
- */\r
- public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)\r
- {\r
- this._showNPfeatureTooltip = showNPfeatureTooltip;\r
- this._has_showNPfeatureTooltip = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showSequenceFeatures'.\r
- * \r
- * @param showSequenceFeatures\r
- * the value of field 'showSequenceFeatures'.\r
- */\r
- public void setShowSequenceFeatures(final boolean showSequenceFeatures)\r
- {\r
- this._showSequenceFeatures = showSequenceFeatures;\r
- this._has_showSequenceFeatures = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showSequenceLogo'.\r
- * \r
- * @param showSequenceLogo\r
- * the value of field 'showSequenceLogo'\r
- */\r
- public void setShowSequenceLogo(final boolean showSequenceLogo)\r
- {\r
- this._showSequenceLogo = showSequenceLogo;\r
- this._has_showSequenceLogo = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showText'.\r
- * \r
- * @param showText\r
- * the value of field 'showText'.\r
- */\r
- public void setShowText(final boolean showText)\r
- {\r
- this._showText = showText;\r
- this._has_showText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showUnconserved'.\r
- * \r
- * @param showUnconserved\r
- * the value of field 'showUnconserved'.\r
- */\r
- public void setShowUnconserved(final boolean showUnconserved)\r
- {\r
- this._showUnconserved = showUnconserved;\r
- this._has_showUnconserved = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'startRes'.\r
- * \r
- * @param startRes\r
- * the value of field 'startRes'.\r
- */\r
- public void setStartRes(final int startRes)\r
- {\r
- this._startRes = startRes;\r
- this._has_startRes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'startSeq'.\r
- * \r
- * @param startSeq\r
- * the value of field 'startSeq'.\r
- */\r
- public void setStartSeq(final int startSeq)\r
- {\r
- this._startSeq = startSeq;\r
- this._has_startSeq = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1\r
- * the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(final int textCol1)\r
- {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2\r
- * the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(final int textCol2)\r
- {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold\r
- * the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(final int textColThreshold)\r
- {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title\r
- * the value of field 'title'.\r
- */\r
- public void setTitle(final java.lang.String title)\r
- {\r
- this._title = title;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'viewName'.\r
- * \r
- * @param viewName\r
- * the value of field 'viewName'.\r
- */\r
- public void setViewName(final java.lang.String viewName)\r
- {\r
- this._viewName = viewName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width\r
- * the value of field 'width'.\r
- */\r
- public void setWidth(final int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'wrapAlignment'.\r
- * \r
- * @param wrapAlignment\r
- * the value of field 'wrapAlignment'.\r
- */\r
- public void setWrapAlignment(final boolean wrapAlignment)\r
- {\r
- this._wrapAlignment = wrapAlignment;\r
- this._has_wrapAlignment = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos\r
- * the value of field 'xpos'.\r
- */\r
- public void setXpos(final int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos\r
- * the value of field 'ypos'.\r
- */\r
- public void setYpos(final int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = 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 schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Viewport\r
- */\r
- public static jalview.schemabinding.version2.Viewport 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.Viewport) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Viewport.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 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
+ public void deleteStartSeq(\r
+ ) {\r
+ this._has_startSeq= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol1(\r
+ ) {\r
+ this._has_textCol1= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol2(\r
+ ) {\r
+ this._has_textCol2= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextColThreshold(\r
+ ) {\r
+ this._has_textColThreshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteWidth(\r
+ ) {\r
+ this._has_width= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteWrapAlignment(\r
+ ) {\r
+ this._has_wrapAlignment= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteXpos(\r
+ ) {\r
+ this._has_xpos= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteYpos(\r
+ ) {\r
+ this._has_ypos= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateHiddenColumns.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.HiddenColumns elements\r
+ */\r
+ public java.util.Enumeration enumerateHiddenColumns(\r
+ ) {\r
+ return this._hiddenColumnsList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'annotationColours'.\r
+ * \r
+ * @return the value of field 'AnnotationColours'.\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(\r
+ ) {\r
+ return this._annotationColours;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'bgColour'.\r
+ * \r
+ * @return the value of field 'BgColour'.\r
+ */\r
+ public java.lang.String getBgColour(\r
+ ) {\r
+ return this._bgColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean getCentreColumnLabels(\r
+ ) {\r
+ return this._centreColumnLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\r
+ * \r
+ * @return the value of field 'ConsThreshold'.\r
+ */\r
+ public int getConsThreshold(\r
+ ) {\r
+ return this._consThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'conservationSelected'.\r
+ * \r
+ * @return the value of field 'ConservationSelected'.\r
+ */\r
+ public boolean getConservationSelected(\r
+ ) {\r
+ return this._conservationSelected;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean getFollowHighlight(\r
+ ) {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean getFollowSelection(\r
+ ) {\r
+ return this._followSelection;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontName'.\r
+ * \r
+ * @return the value of field 'FontName'.\r
+ */\r
+ public java.lang.String getFontName(\r
+ ) {\r
+ return this._fontName;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontSize'.\r
+ * \r
+ * @return the value of field 'FontSize'.\r
+ */\r
+ public int getFontSize(\r
+ ) {\r
+ return this._fontSize;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fontStyle'.\r
+ * \r
+ * @return the value of field 'FontStyle'.\r
+ */\r
+ public int getFontStyle(\r
+ ) {\r
+ return this._fontStyle;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'gatheredViews'.\r
+ * \r
+ * @return the value of field 'GatheredViews'.\r
+ */\r
+ public boolean getGatheredViews(\r
+ ) {\r
+ return this._gatheredViews;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'height'.\r
+ * \r
+ * @return the value of field 'Height'.\r
+ */\r
+ public int getHeight(\r
+ ) {\r
+ return this._height;\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenColumns.\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.HiddenColumns at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenColumns.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.HiddenColumns[] getHiddenColumns(\r
+ ) {\r
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];\r
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenColumnsCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getHiddenColumnsCount(\r
+ ) {\r
+ return this._hiddenColumnsList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: unique id used by jalview to\r
+ * synchronize between stored and instantiated views\r
+ * \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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean getIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidSelected'.\r
+ * \r
+ * @return the value of field 'PidSelected'.\r
+ */\r
+ public boolean getPidSelected(\r
+ ) {\r
+ return this._pidSelected;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\r
+ * \r
+ * @return the value of field 'PidThreshold'.\r
+ */\r
+ public int getPidThreshold(\r
+ ) {\r
+ return this._pidThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'renderGaps'.\r
+ * \r
+ * @return the value of field 'RenderGaps'.\r
+ */\r
+ public boolean getRenderGaps(\r
+ ) {\r
+ return this._renderGaps;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'rightAlignIds'.\r
+ * \r
+ * @return the value of field 'RightAlignIds'.\r
+ */\r
+ public boolean getRightAlignIds(\r
+ ) {\r
+ return this._rightAlignIds;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequenceSetId'.\r
+ * \r
+ * @return the value of field 'SequenceSetId'.\r
+ */\r
+ public java.lang.String getSequenceSetId(\r
+ ) {\r
+ return this._sequenceSetId;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showAnnotation'.\r
+ * \r
+ * @return the value of field 'ShowAnnotation'.\r
+ */\r
+ public boolean getShowAnnotation(\r
+ ) {\r
+ return this._showAnnotation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBoxes'.\r
+ * \r
+ * @return the value of field 'ShowBoxes'.\r
+ */\r
+ public boolean getShowBoxes(\r
+ ) {\r
+ return this._showBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showColourText'.\r
+ * \r
+ * @return the value of field 'ShowColourText'.\r
+ */\r
+ public boolean getShowColourText(\r
+ ) {\r
+ return this._showColourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean getShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean getShowDbRefTooltip(\r
+ ) {\r
+ return this._showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showFullId'.\r
+ * \r
+ * @return the value of field 'ShowFullId'.\r
+ */\r
+ public boolean getShowFullId(\r
+ ) {\r
+ return this._showFullId;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean getShowGroupConsensus(\r
+ ) {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean getShowGroupConservation(\r
+ ) {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean getShowNPfeatureTooltip(\r
+ ) {\r
+ return this._showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @return the value of field 'ShowSequenceFeatures'.\r
+ */\r
+ public boolean getShowSequenceFeatures(\r
+ ) {\r
+ return this._showSequenceFeatures;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showText'.\r
+ * \r
+ * @return the value of field 'ShowText'.\r
+ */\r
+ public boolean getShowText(\r
+ ) {\r
+ return this._showText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean getShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'startRes'.\r
+ * \r
+ * @return the value of field 'StartRes'.\r
+ */\r
+ public int getStartRes(\r
+ ) {\r
+ return this._startRes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'startSeq'.\r
+ * \r
+ * @return the value of field 'StartSeq'.\r
+ */\r
+ public int getStartSeq(\r
+ ) {\r
+ return this._startSeq;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol1'.\r
+ * \r
+ * @return the value of field 'TextCol1'.\r
+ */\r
+ public int getTextCol1(\r
+ ) {\r
+ return this._textCol1;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol2'.\r
+ * \r
+ * @return the value of field 'TextCol2'.\r
+ */\r
+ public int getTextCol2(\r
+ ) {\r
+ return this._textCol2;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textColThreshold'.\r
+ * \r
+ * @return the value of field 'TextColThreshold'.\r
+ */\r
+ public int getTextColThreshold(\r
+ ) {\r
+ return this._textColThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'title'.\r
+ * \r
+ * @return the value of field 'Title'.\r
+ */\r
+ public java.lang.String getTitle(\r
+ ) {\r
+ return this._title;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'viewName'.\r
+ * \r
+ * @return the value of field 'ViewName'.\r
+ */\r
+ public java.lang.String getViewName(\r
+ ) {\r
+ return this._viewName;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'width'.\r
+ * \r
+ * @return the value of field 'Width'.\r
+ */\r
+ public int getWidth(\r
+ ) {\r
+ return this._width;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'wrapAlignment'.\r
+ * \r
+ * @return the value of field 'WrapAlignment'.\r
+ */\r
+ public boolean getWrapAlignment(\r
+ ) {\r
+ return this._wrapAlignment;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'xpos'.\r
+ * \r
+ * @return the value of field 'Xpos'.\r
+ */\r
+ public int getXpos(\r
+ ) {\r
+ return this._xpos;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'ypos'.\r
+ * \r
+ * @return the value of field 'Ypos'.\r
+ */\r
+ public int getYpos(\r
+ ) {\r
+ return this._ypos;\r
+ }\r
+\r
+ /**\r
+ * Method hasCentreColumnLabels.\r
+ * \r
+ * @return true if at least one CentreColumnLabels has been adde\r
+ */\r
+ public boolean hasCentreColumnLabels(\r
+ ) {\r
+ return this._has_centreColumnLabels;\r
+ }\r
+\r
+ /**\r
+ * Method hasConsThreshold.\r
+ * \r
+ * @return true if at least one ConsThreshold has been added\r
+ */\r
+ public boolean hasConsThreshold(\r
+ ) {\r
+ return this._has_consThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasConservationSelected.\r
+ * \r
+ * @return true if at least one ConservationSelected has been\r
+ * added\r
+ */\r
+ public boolean hasConservationSelected(\r
+ ) {\r
+ return this._has_conservationSelected;\r
+ }\r
+\r
+ /**\r
+ * Method hasFollowHighlight.\r
+ * \r
+ * @return true if at least one FollowHighlight has been added\r
+ */\r
+ public boolean hasFollowHighlight(\r
+ ) {\r
+ return this._has_followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Method hasFollowSelection.\r
+ * \r
+ * @return true if at least one FollowSelection has been added\r
+ */\r
+ public boolean hasFollowSelection(\r
+ ) {\r
+ return this._has_followSelection;\r
+ }\r
+\r
+ /**\r
+ * Method hasFontSize.\r
+ * \r
+ * @return true if at least one FontSize has been added\r
+ */\r
+ public boolean hasFontSize(\r
+ ) {\r
+ return this._has_fontSize;\r
+ }\r
+\r
+ /**\r
+ * Method hasFontStyle.\r
+ * \r
+ * @return true if at least one FontStyle has been added\r
+ */\r
+ public boolean hasFontStyle(\r
+ ) {\r
+ return this._has_fontStyle;\r
+ }\r
+\r
+ /**\r
+ * Method hasGatheredViews.\r
+ * \r
+ * @return true if at least one GatheredViews has been added\r
+ */\r
+ public boolean hasGatheredViews(\r
+ ) {\r
+ return this._has_gatheredViews;\r
+ }\r
+\r
+ /**\r
+ * Method hasHeight.\r
+ * \r
+ * @return true if at least one Height has been added\r
+ */\r
+ public boolean hasHeight(\r
+ ) {\r
+ return this._has_height;\r
+ }\r
+\r
+ /**\r
+ * Method hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been\r
+ * added\r
+ */\r
+ public boolean hasIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._has_ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Method hasPidSelected.\r
+ * \r
+ * @return true if at least one PidSelected has been added\r
+ */\r
+ public boolean hasPidSelected(\r
+ ) {\r
+ return this._has_pidSelected;\r
+ }\r
+\r
+ /**\r
+ * Method hasPidThreshold.\r
+ * \r
+ * @return true if at least one PidThreshold has been added\r
+ */\r
+ public boolean hasPidThreshold(\r
+ ) {\r
+ return this._has_pidThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasRenderGaps.\r
+ * \r
+ * @return true if at least one RenderGaps has been added\r
+ */\r
+ public boolean hasRenderGaps(\r
+ ) {\r
+ return this._has_renderGaps;\r
+ }\r
+\r
+ /**\r
+ * Method hasRightAlignIds.\r
+ * \r
+ * @return true if at least one RightAlignIds has been added\r
+ */\r
+ public boolean hasRightAlignIds(\r
+ ) {\r
+ return this._has_rightAlignIds;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowAnnotation.\r
+ * \r
+ * @return true if at least one ShowAnnotation has been added\r
+ */\r
+ public boolean hasShowAnnotation(\r
+ ) {\r
+ return this._has_showAnnotation;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowBoxes.\r
+ * \r
+ * @return true if at least one ShowBoxes has been added\r
+ */\r
+ public boolean hasShowBoxes(\r
+ ) {\r
+ return this._has_showBoxes;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowColourText.\r
+ * \r
+ * @return true if at least one ShowColourText has been added\r
+ */\r
+ public boolean hasShowColourText(\r
+ ) {\r
+ return this._has_showColourText;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been\r
+ * added\r
+ */\r
+ public boolean hasShowConsensusHistogram(\r
+ ) {\r
+ return this._has_showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowDbRefTooltip.\r
+ * \r
+ * @return true if at least one ShowDbRefTooltip has been added\r
+ */\r
+ public boolean hasShowDbRefTooltip(\r
+ ) {\r
+ return this._has_showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowFullId.\r
+ * \r
+ * @return true if at least one ShowFullId has been added\r
+ */\r
+ public boolean hasShowFullId(\r
+ ) {\r
+ return this._has_showFullId;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowGroupConsensus.\r
+ * \r
+ * @return true if at least one ShowGroupConsensus has been adde\r
+ */\r
+ public boolean hasShowGroupConsensus(\r
+ ) {\r
+ return this._has_showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowGroupConservation.\r
+ * \r
+ * @return true if at least one ShowGroupConservation has been\r
+ * added\r
+ */\r
+ public boolean hasShowGroupConservation(\r
+ ) {\r
+ return this._has_showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowNPfeatureTooltip.\r
+ * \r
+ * @return true if at least one ShowNPfeatureTooltip has been\r
+ * added\r
+ */\r
+ public boolean hasShowNPfeatureTooltip(\r
+ ) {\r
+ return this._has_showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceFeatures.\r
+ * \r
+ * @return true if at least one ShowSequenceFeatures has been\r
+ * added\r
+ */\r
+ public boolean hasShowSequenceFeatures(\r
+ ) {\r
+ return this._has_showSequenceFeatures;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo(\r
+ ) {\r
+ return this._has_showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowText.\r
+ * \r
+ * @return true if at least one ShowText has been added\r
+ */\r
+ public boolean hasShowText(\r
+ ) {\r
+ return this._has_showText;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowUnconserved.\r
+ * \r
+ * @return true if at least one ShowUnconserved has been added\r
+ */\r
+ public boolean hasShowUnconserved(\r
+ ) {\r
+ return this._has_showUnconserved;\r
+ }\r
+\r
+ /**\r
+ * Method hasStartRes.\r
+ * \r
+ * @return true if at least one StartRes has been added\r
+ */\r
+ public boolean hasStartRes(\r
+ ) {\r
+ return this._has_startRes;\r
+ }\r
+\r
+ /**\r
+ * Method hasStartSeq.\r
+ * \r
+ * @return true if at least one StartSeq has been added\r
+ */\r
+ public boolean hasStartSeq(\r
+ ) {\r
+ return this._has_startSeq;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextCol1.\r
+ * \r
+ * @return true if at least one TextCol1 has been added\r
+ */\r
+ public boolean hasTextCol1(\r
+ ) {\r
+ return this._has_textCol1;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextCol2.\r
+ * \r
+ * @return true if at least one TextCol2 has been added\r
+ */\r
+ public boolean hasTextCol2(\r
+ ) {\r
+ return this._has_textCol2;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextColThreshold.\r
+ * \r
+ * @return true if at least one TextColThreshold has been added\r
+ */\r
+ public boolean hasTextColThreshold(\r
+ ) {\r
+ return this._has_textColThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasWidth.\r
+ * \r
+ * @return true if at least one Width has been added\r
+ */\r
+ public boolean hasWidth(\r
+ ) {\r
+ return this._has_width;\r
+ }\r
+\r
+ /**\r
+ * Method hasWrapAlignment.\r
+ * \r
+ * @return true if at least one WrapAlignment has been added\r
+ */\r
+ public boolean hasWrapAlignment(\r
+ ) {\r
+ return this._has_wrapAlignment;\r
+ }\r
+\r
+ /**\r
+ * Method hasXpos.\r
+ * \r
+ * @return true if at least one Xpos has been added\r
+ */\r
+ public boolean hasXpos(\r
+ ) {\r
+ return this._has_xpos;\r
+ }\r
+\r
+ /**\r
+ * Method hasYpos.\r
+ * \r
+ * @return true if at least one Ypos has been added\r
+ */\r
+ public boolean hasYpos(\r
+ ) {\r
+ return this._has_ypos;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean isCentreColumnLabels(\r
+ ) {\r
+ return this._centreColumnLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'conservationSelected'.\r
+ * \r
+ * @return the value of field 'ConservationSelected'.\r
+ */\r
+ public boolean isConservationSelected(\r
+ ) {\r
+ return this._conservationSelected;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean isFollowHighlight(\r
+ ) {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean isFollowSelection(\r
+ ) {\r
+ return this._followSelection;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'gatheredViews'.\r
+ * \r
+ * @return the value of field 'GatheredViews'.\r
+ */\r
+ public boolean isGatheredViews(\r
+ ) {\r
+ return this._gatheredViews;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean isIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidSelected'.\r
+ * \r
+ * @return the value of field 'PidSelected'.\r
+ */\r
+ public boolean isPidSelected(\r
+ ) {\r
+ return this._pidSelected;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'renderGaps'.\r
+ * \r
+ * @return the value of field 'RenderGaps'.\r
+ */\r
+ public boolean isRenderGaps(\r
+ ) {\r
+ return this._renderGaps;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'rightAlignIds'.\r
+ * \r
+ * @return the value of field 'RightAlignIds'.\r
+ */\r
+ public boolean isRightAlignIds(\r
+ ) {\r
+ return this._rightAlignIds;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showAnnotation'.\r
+ * \r
+ * @return the value of field 'ShowAnnotation'.\r
+ */\r
+ public boolean isShowAnnotation(\r
+ ) {\r
+ return this._showAnnotation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBoxes'.\r
+ * \r
+ * @return the value of field 'ShowBoxes'.\r
+ */\r
+ public boolean isShowBoxes(\r
+ ) {\r
+ return this._showBoxes;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showColourText'.\r
+ * \r
+ * @return the value of field 'ShowColourText'.\r
+ */\r
+ public boolean isShowColourText(\r
+ ) {\r
+ return this._showColourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean isShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean isShowDbRefTooltip(\r
+ ) {\r
+ return this._showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showFullId'.\r
+ * \r
+ * @return the value of field 'ShowFullId'.\r
+ */\r
+ public boolean isShowFullId(\r
+ ) {\r
+ return this._showFullId;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean isShowGroupConsensus(\r
+ ) {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean isShowGroupConservation(\r
+ ) {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean isShowNPfeatureTooltip(\r
+ ) {\r
+ return this._showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @return the value of field 'ShowSequenceFeatures'.\r
+ */\r
+ public boolean isShowSequenceFeatures(\r
+ ) {\r
+ return this._showSequenceFeatures;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showText'.\r
+ * \r
+ * @return the value of field 'ShowText'.\r
+ */\r
+ public boolean isShowText(\r
+ ) {\r
+ return this._showText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean isShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\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 'wrapAlignment'.\r
+ * \r
+ * @return the value of field 'WrapAlignment'.\r
+ */\r
+ public boolean isWrapAlignment(\r
+ ) {\r
+ return this._wrapAlignment;\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 removeAllHiddenColumns(\r
+ ) {\r
+ this._hiddenColumnsList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenColumns.\r
+ * \r
+ * @param vHiddenColumns\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {\r
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenColumnsAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);\r
+ return (jalview.schemabinding.version2.HiddenColumns) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'annotationColours'.\r
+ * \r
+ * @param annotationColours the value of field\r
+ * 'annotationColours'.\r
+ */\r
+ public void setAnnotationColours(\r
+ final jalview.schemabinding.version2.AnnotationColours annotationColours) {\r
+ this._annotationColours = annotationColours;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'bgColour'.\r
+ * \r
+ * @param bgColour the value of field 'bgColour'.\r
+ */\r
+ public void setBgColour(\r
+ final java.lang.String bgColour) {\r
+ this._bgColour = bgColour;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'centreColumnLabels'.\r
+ * \r
+ * @param centreColumnLabels the value of field\r
+ * 'centreColumnLabels'.\r
+ */\r
+ public void setCentreColumnLabels(\r
+ final boolean centreColumnLabels) {\r
+ this._centreColumnLabels = centreColumnLabels;\r
+ this._has_centreColumnLabels = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(\r
+ final int consThreshold) {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'conservationSelected'.\r
+ * \r
+ * @param conservationSelected the value of field\r
+ * 'conservationSelected'.\r
+ */\r
+ public void setConservationSelected(\r
+ final boolean conservationSelected) {\r
+ this._conservationSelected = conservationSelected;\r
+ this._has_conservationSelected = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followHighlight'.\r
+ * \r
+ * @param followHighlight the value of field 'followHighlight'.\r
+ */\r
+ public void setFollowHighlight(\r
+ final boolean followHighlight) {\r
+ this._followHighlight = followHighlight;\r
+ this._has_followHighlight = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followSelection'.\r
+ * \r
+ * @param followSelection the value of field 'followSelection'.\r
+ */\r
+ public void setFollowSelection(\r
+ final boolean followSelection) {\r
+ this._followSelection = followSelection;\r
+ this._has_followSelection = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName the value of field 'fontName'.\r
+ */\r
+ public void setFontName(\r
+ final java.lang.String fontName) {\r
+ this._fontName = fontName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(\r
+ final int fontSize) {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(\r
+ final int fontStyle) {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'gatheredViews'.\r
+ * \r
+ * @param gatheredViews the value of field 'gatheredViews'.\r
+ */\r
+ public void setGatheredViews(\r
+ final boolean gatheredViews) {\r
+ this._gatheredViews = gatheredViews;\r
+ this._has_gatheredViews = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height the value of field 'height'.\r
+ */\r
+ public void setHeight(\r
+ final int height) {\r
+ this._height = height;\r
+ this._has_height = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenColumns(\r
+ final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._hiddenColumnsList.set(index, vHiddenColumns);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenColumnsArray\r
+ */\r
+ public void setHiddenColumns(\r
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {\r
+ //-- copy array\r
+ _hiddenColumnsList.clear();\r
+ \r
+ for (int i = 0; i < vHiddenColumnsArray.length; i++) {\r
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: unique id used by jalview to\r
+ * synchronize between stored and instantiated views\r
+ * \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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus the value of field\r
+ * 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(\r
+ final boolean ignoreGapsinConsensus) {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidSelected'.\r
+ * \r
+ * @param pidSelected the value of field 'pidSelected'.\r
+ */\r
+ public void setPidSelected(\r
+ final boolean pidSelected) {\r
+ this._pidSelected = pidSelected;\r
+ this._has_pidSelected = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(\r
+ final int pidThreshold) {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'renderGaps'.\r
+ * \r
+ * @param renderGaps the value of field 'renderGaps'.\r
+ */\r
+ public void setRenderGaps(\r
+ final boolean renderGaps) {\r
+ this._renderGaps = renderGaps;\r
+ this._has_renderGaps = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'rightAlignIds'.\r
+ * \r
+ * @param rightAlignIds the value of field 'rightAlignIds'.\r
+ */\r
+ public void setRightAlignIds(\r
+ final boolean rightAlignIds) {\r
+ this._rightAlignIds = rightAlignIds;\r
+ this._has_rightAlignIds = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequenceSetId'.\r
+ * \r
+ * @param sequenceSetId the value of field 'sequenceSetId'.\r
+ */\r
+ public void setSequenceSetId(\r
+ final java.lang.String sequenceSetId) {\r
+ this._sequenceSetId = sequenceSetId;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showAnnotation'.\r
+ * \r
+ * @param showAnnotation the value of field 'showAnnotation'.\r
+ */\r
+ public void setShowAnnotation(\r
+ final boolean showAnnotation) {\r
+ this._showAnnotation = showAnnotation;\r
+ this._has_showAnnotation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showBoxes'.\r
+ * \r
+ * @param showBoxes the value of field 'showBoxes'.\r
+ */\r
+ public void setShowBoxes(\r
+ final boolean showBoxes) {\r
+ this._showBoxes = showBoxes;\r
+ this._has_showBoxes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showColourText'.\r
+ * \r
+ * @param showColourText the value of field 'showColourText'.\r
+ */\r
+ public void setShowColourText(\r
+ final boolean showColourText) {\r
+ this._showColourText = showColourText;\r
+ this._has_showColourText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram the value of field\r
+ * 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(\r
+ final boolean showConsensusHistogram) {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @param showDbRefTooltip the value of field 'showDbRefTooltip'\r
+ */\r
+ public void setShowDbRefTooltip(\r
+ final boolean showDbRefTooltip) {\r
+ this._showDbRefTooltip = showDbRefTooltip;\r
+ this._has_showDbRefTooltip = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showFullId'.\r
+ * \r
+ * @param showFullId the value of field 'showFullId'.\r
+ */\r
+ public void setShowFullId(\r
+ final boolean showFullId) {\r
+ this._showFullId = showFullId;\r
+ this._has_showFullId = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConsensus'.\r
+ * \r
+ * @param showGroupConsensus the value of field\r
+ * 'showGroupConsensus'.\r
+ */\r
+ public void setShowGroupConsensus(\r
+ final boolean showGroupConsensus) {\r
+ this._showGroupConsensus = showGroupConsensus;\r
+ this._has_showGroupConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConservation'.\r
+ * \r
+ * @param showGroupConservation the value of field\r
+ * 'showGroupConservation'.\r
+ */\r
+ public void setShowGroupConservation(\r
+ final boolean showGroupConservation) {\r
+ this._showGroupConservation = showGroupConservation;\r
+ this._has_showGroupConservation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @param showNPfeatureTooltip the value of field\r
+ * 'showNPfeatureTooltip'.\r
+ */\r
+ public void setShowNPfeatureTooltip(\r
+ final boolean showNPfeatureTooltip) {\r
+ this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+ this._has_showNPfeatureTooltip = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @param showSequenceFeatures the value of field\r
+ * 'showSequenceFeatures'.\r
+ */\r
+ public void setShowSequenceFeatures(\r
+ final boolean showSequenceFeatures) {\r
+ this._showSequenceFeatures = showSequenceFeatures;\r
+ this._has_showSequenceFeatures = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(\r
+ final boolean showSequenceLogo) {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showText'.\r
+ * \r
+ * @param showText the value of field 'showText'.\r
+ */\r
+ public void setShowText(\r
+ final boolean showText) {\r
+ this._showText = showText;\r
+ this._has_showText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(\r
+ final boolean showUnconserved) {\r
+ this._showUnconserved = showUnconserved;\r
+ this._has_showUnconserved = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'startRes'.\r
+ * \r
+ * @param startRes the value of field 'startRes'.\r
+ */\r
+ public void setStartRes(\r
+ final int startRes) {\r
+ this._startRes = startRes;\r
+ this._has_startRes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'startSeq'.\r
+ * \r
+ * @param startSeq the value of field 'startSeq'.\r
+ */\r
+ public void setStartSeq(\r
+ final int startSeq) {\r
+ this._startSeq = startSeq;\r
+ this._has_startSeq = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol1'.\r
+ * \r
+ * @param textCol1 the value of field 'textCol1'.\r
+ */\r
+ public void setTextCol1(\r
+ final int textCol1) {\r
+ this._textCol1 = textCol1;\r
+ this._has_textCol1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol2'.\r
+ * \r
+ * @param textCol2 the value of field 'textCol2'.\r
+ */\r
+ public void setTextCol2(\r
+ final int textCol2) {\r
+ this._textCol2 = textCol2;\r
+ this._has_textCol2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textColThreshold'.\r
+ * \r
+ * @param textColThreshold the value of field 'textColThreshold'\r
+ */\r
+ public void setTextColThreshold(\r
+ final int textColThreshold) {\r
+ this._textColThreshold = textColThreshold;\r
+ this._has_textColThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title the value of field 'title'.\r
+ */\r
+ public void setTitle(\r
+ final java.lang.String title) {\r
+ this._title = title;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'viewName'.\r
+ * \r
+ * @param viewName the value of field 'viewName'.\r
+ */\r
+ public void setViewName(\r
+ final java.lang.String viewName) {\r
+ this._viewName = viewName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width the value of field 'width'.\r
+ */\r
+ public void setWidth(\r
+ final int width) {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'wrapAlignment'.\r
+ * \r
+ * @param wrapAlignment the value of field 'wrapAlignment'.\r
+ */\r
+ public void setWrapAlignment(\r
+ final boolean wrapAlignment) {\r
+ this._wrapAlignment = wrapAlignment;\r
+ this._has_wrapAlignment = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos the value of field 'xpos'.\r
+ */\r
+ public void setXpos(\r
+ final int xpos) {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos the value of field 'ypos'.\r
+ */\r
+ public void setYpos(\r
+ final int ypos) {\r
+ this._ypos = ypos;\r
+ this._has_ypos = 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.Viewport\r
+ */\r
+ public static jalview.schemabinding.version2.Viewport unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.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
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * 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 -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class WebServiceParameterSet implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * The short name for the parameter set. This will be shown amongst the other
- * presets for the web service.
- *
- */
- private java.lang.String _name;
-
- /**
- * A Jalview Web Service Parameter Set container version number. Version 1
- * created for storing Jaba user presets.
- *
- */
- private java.lang.String _version;
-
- /**
- * Short description - as utf8 encoded text. This is usually displayed in the
- * body of an HTML capable tooltip, so HTML tags may be embedded using
- * standard UTF8 encoding.
- *
- */
- private java.lang.String _description;
-
- /**
- * URL for which the parameter set is valid. Jalview will use it to match up
- * parameter sets to service instances that can parse the parameter set
- * payload.
- *
- */
- private java.util.Vector _serviceURLList;
-
- /**
- * UTF8 encoded string to be processed into a specific web services' parameter
- * set. Note - newlines may be important to the structure of this file.
- *
- */
- private java.lang.String _parameters;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public WebServiceParameterSet()
- {
- super();
- this._serviceURLList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addServiceURL(final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException
- {
- this._serviceURLList.addElement(vServiceURL);
- }
-
- /**
- *
- *
- * @param index
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addServiceURL(final int index,
- final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException
- {
- this._serviceURLList.add(index, vServiceURL);
- }
-
- /**
- * Method enumerateServiceURL.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateServiceURL()
- {
- return this._serviceURLList.elements();
- }
-
- /**
- * Returns the value of field 'description'. The field 'description' has the
- * following description: Short description - as utf8 encoded text. This is
- * usually displayed in the body of an HTML capable tooltip, so HTML tags may
- * be embedded using standard UTF8 encoding.
- *
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- }
-
- /**
- * Returns the value of field 'name'. The field 'name' has the following
- * description: The short name for the parameter set. This will be shown
- * amongst the other presets for the web service.
- *
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'parameters'. The field 'parameters' has the
- * following description: UTF8 encoded string to be processed into a specific
- * web services' parameter set. Note - newlines may be important to the
- * structure of this file.
- *
- *
- * @return the value of field 'Parameters'.
- */
- public java.lang.String getParameters()
- {
- return this._parameters;
- }
-
- /**
- * Method getServiceURL.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getServiceURL(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._serviceURLList.size())
- {
- throw new IndexOutOfBoundsException("getServiceURL: Index value '"
- + index + "' not in range [0.."
- + (this._serviceURLList.size() - 1) + "]");
+public class WebServiceParameterSet implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * The short name for the parameter set. This will be shown
+ * amongst the
+ * other presets for the web service.
+ *
+ */
+ private java.lang.String _name;
+
+ /**
+ * A Jalview Web Service Parameter Set container
+ * version number.
+ * Version 1 created for storing Jaba user presets.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Short description - as utf8 encoded text. This is
+ * usually displayed
+ * in the body of an HTML capable tooltip, so HTML tags may be
+ * embedded
+ * using standard UTF8 encoding.
+ *
+ */
+ private java.lang.String _description;
+
+ /**
+ * URL for which the parameter set is valid. Jalview will use
+ * it to
+ * match up parameter sets to service instances that can parse
+ * the
+ * parameter set payload.
+ *
+ */
+ private java.util.Vector _serviceURLList;
+
+ /**
+ * UTF8 encoded string to be processed into a specific web
+ * services'
+ * parameter set. Note - newlines may be important to the
+ * structure
+ * of this file.
+ *
+ */
+ private java.lang.String _parameters;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public WebServiceParameterSet() {
+ super();
+ this._serviceURLList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addServiceURL(
+ final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException {
+ this._serviceURLList.addElement(vServiceURL);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addServiceURL(
+ final int index,
+ final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException {
+ this._serviceURLList.add(index, vServiceURL);
+ }
+
+ /**
+ * Method enumerateServiceURL.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateServiceURL(
+ ) {
+ return this._serviceURLList.elements();
+ }
+
+ /**
+ * Returns the value of field 'description'. The field
+ * 'description' has the following description: Short
+ * description - as utf8 encoded text. This is
+ * usually displayed
+ * in the body of an HTML capable tooltip, so HTML tags may be
+ * embedded
+ * using standard UTF8 encoding.
+ *
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'name'. The field 'name' has the
+ * following description: The short name for the parameter set.
+ * This will be shown amongst the
+ * other presets for the web service.
+ *
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'parameters'. The field
+ * 'parameters' has the following description: UTF8 encoded
+ * string to be processed into a specific web services'
+ * parameter set. Note - newlines may be important to the
+ * structure
+ * of this file.
+ *
+ *
+ * @return the value of field 'Parameters'.
+ */
+ public java.lang.String getParameters(
+ ) {
+ return this._parameters;
+ }
+
+ /**
+ * Method getServiceURL.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getServiceURL(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._serviceURLList.size()) {
+ throw new IndexOutOfBoundsException("getServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _serviceURLList.get(index);
+ }
+
+ /**
+ * Method getServiceURL.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 java.lang.String[] getServiceURL(
+ ) {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._serviceURLList.toArray(array);
+ }
+
+ /**
+ * Method getServiceURLCount.
+ *
+ * @return the size of this collection
+ */
+ public int getServiceURLCount(
+ ) {
+ return this._serviceURLList.size();
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: A Jalview Web Service
+ * Parameter Set container
+ * version number.
+ * Version 1 created for storing Jaba user presets.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
}
- return (java.lang.String) _serviceURLList.get(index);
- }
-
- /**
- * Method getServiceURL.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 java.lang.String[] getServiceURL()
- {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._serviceURLList.toArray(array);
- }
-
- /**
- * Method getServiceURLCount.
- *
- * @return the size of this collection
- */
- public int getServiceURLCount()
- {
- return this._serviceURLList.size();
- }
-
- /**
- * Returns the value of field 'version'. The field 'version' has the following
- * description: A Jalview Web Service Parameter Set container version number.
- * Version 1 created for storing Jaba user presets.
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- }
-
- /**
- * 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;
+ /**
+ *
+ *
+ * @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);
}
- return true;
- }
-
- /**
- *
- *
- * @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 removeAllServiceURL()
- {
- this._serviceURLList.clear();
- }
-
- /**
- * Method removeServiceURL.
- *
- * @param vServiceURL
- * @return true if the object was removed from the collection.
- */
- public boolean removeServiceURL(final java.lang.String vServiceURL)
- {
- boolean removed = _serviceURLList.remove(vServiceURL);
- return removed;
- }
-
- /**
- * Method removeServiceURLAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeServiceURLAt(final int index)
- {
- java.lang.Object obj = this._serviceURLList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- * Sets the value of field 'description'. The field 'description' has the
- * following description: Short description - as utf8 encoded text. This is
- * usually displayed in the body of an HTML capable tooltip, so HTML tags may
- * be embedded using standard UTF8 encoding.
- *
- *
- * @param description
- * the value of field 'description'.
- */
- public void setDescription(final java.lang.String description)
- {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'name'. The field 'name' has the following
- * description: The short name for the parameter set. This will be shown
- * amongst the other presets for the web service.
- *
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'parameters'. The field 'parameters' has the
- * following description: UTF8 encoded string to be processed into a specific
- * web services' parameter set. Note - newlines may be important to the
- * structure of this file.
- *
- *
- * @param parameters
- * the value of field 'parameters'.
- */
- public void setParameters(final java.lang.String parameters)
- {
- this._parameters = parameters;
- }
-
- /**
- *
- *
- * @param index
- * @param vServiceURL
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setServiceURL(final int index,
- final java.lang.String vServiceURL)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._serviceURLList.size())
- {
- throw new IndexOutOfBoundsException("setServiceURL: Index value '"
- + index + "' not in range [0.."
- + (this._serviceURLList.size() - 1) + "]");
+ public void removeAllServiceURL(
+ ) {
+ this._serviceURLList.clear();
}
- this._serviceURLList.set(index, vServiceURL);
- }
-
- /**
- *
- *
- * @param vServiceURLArray
- */
- public void setServiceURL(final java.lang.String[] vServiceURLArray)
- {
- // -- copy array
- _serviceURLList.clear();
-
- for (int i = 0; i < vServiceURLArray.length; i++)
- {
- this._serviceURLList.add(vServiceURLArray[i]);
+ /**
+ * Method removeServiceURL.
+ *
+ * @param vServiceURL
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeServiceURL(
+ final java.lang.String vServiceURL) {
+ boolean removed = _serviceURLList.remove(vServiceURL);
+ return removed;
+ }
+
+ /**
+ * Method removeServiceURLAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeServiceURLAt(
+ final int index) {
+ java.lang.Object obj = this._serviceURLList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ * Sets the value of field 'description'. The field
+ * 'description' has the following description: Short
+ * description - as utf8 encoded text. This is
+ * usually displayed
+ * in the body of an HTML capable tooltip, so HTML tags may be
+ * embedded
+ * using standard UTF8 encoding.
+ *
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'name'. The field 'name' has the
+ * following description: The short name for the parameter set.
+ * This will be shown amongst the
+ * other presets for the web service.
+ *
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'parameters'. The field 'parameters'
+ * has the following description: UTF8 encoded string to be
+ * processed into a specific web services'
+ * parameter set. Note - newlines may be important to the
+ * structure
+ * of this file.
+ *
+ *
+ * @param parameters the value of field 'parameters'.
+ */
+ public void setParameters(
+ final java.lang.String parameters) {
+ this._parameters = parameters;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vServiceURL
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setServiceURL(
+ final int index,
+ final java.lang.String vServiceURL)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._serviceURLList.size()) {
+ throw new IndexOutOfBoundsException("setServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
+ }
+
+ this._serviceURLList.set(index, vServiceURL);
+ }
+
+ /**
+ *
+ *
+ * @param vServiceURLArray
+ */
+ public void setServiceURL(
+ final java.lang.String[] vServiceURLArray) {
+ //-- copy array
+ _serviceURLList.clear();
+
+ for (int i = 0; i < vServiceURLArray.length; i++) {
+ this._serviceURLList.add(vServiceURLArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: A Jalview Web Service Parameter
+ * Set container
+ * version number.
+ * Version 1 created for storing Jaba user presets.
+ *
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * 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.WebServiceParameterSet
+ */
+ public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.WebServiceParameterSet.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);
}
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has the following
- * description: A Jalview Web Service Parameter Set container version number.
- * Version 1 created for storing Jaba user presets.
- *
- *
- * @param version
- * the value of field 'version'.
- */
- public void setVersion(final java.lang.String version)
- {
- this._version = version;
- }
-
- /**
- * 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.WebServiceParameterSet
- */
- public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller
- .unmarshal(
- jalview.schemabinding.version2.WebServiceParameterSet.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);
- }
}
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.AlcodMap;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlcodMapDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AlcodMapDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "alcodMap";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _dnasq\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_dnasq", "dnasq",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AlcodMap target = (AlcodMap) object;\r
- return target.getDnasq();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodMap target = (AlcodMap) object;\r
- target.setDnasq((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodMapDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "alcodMap";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _dnasq\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodMap target = (AlcodMap) object;\r
+ return target.getDnasq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodMap target = (AlcodMap) object;\r
+ target.setDnasq( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dnasq\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _dnasq\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mapping\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodMap target = (AlcodMap) object;\r
+ return target.getMapping();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodMap target = (AlcodMap) object;\r
+ target.setMapping( (jalview.schemabinding.version2.Mapping) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Mapping();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapping\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _mapping\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Mapping.class, "_mapping",\r
- "Mapping", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AlcodMap target = (AlcodMap) object;\r
- return target.getMapping();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodMap target = (AlcodMap) object;\r
- target.setMapping((jalview.schemabinding.version2.Mapping) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Mapping();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _mapping\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.AlcodMap.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AlcodMap.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Alcodon;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlcodonDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
+public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
\r
- public AlcodonDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "alcodon";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
\r
- // -- _pos1\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Long.TYPE, "_pos1", "pos1",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Alcodon target = (Alcodon) object;\r
- if (!target.hasPos1())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Long(target.getPos1());\r
- }\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Alcodon target = (Alcodon) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePos1();\r
- return;\r
- }\r
- target.setPos1(((java.lang.Long) value).longValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ public AlcodonDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "alcodon";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _pos1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos1()) { return null; }\r
+ return new java.lang.Long(target.getPos1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos1();\r
+ return;\r
+ }\r
+ target.setPos1( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pos1\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.LongValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _pos2\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Long.TYPE, "_pos2", "pos2",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Alcodon target = (Alcodon) object;\r
- if (!target.hasPos2())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pos2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos2()) { return null; }\r
+ return new java.lang.Long(target.getPos2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos2();\r
+ return;\r
+ }\r
+ target.setPos2( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Long(target.getPos2());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Alcodon target = (Alcodon) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePos2();\r
- return;\r
- }\r
- target.setPos2(((java.lang.Long) value).longValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pos3\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos3()) { return null; }\r
+ return new java.lang.Long(target.getPos3());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos3();\r
+ return;\r
+ }\r
+ target.setPos3( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos3\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pos2\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.LongValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _pos3\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Long.TYPE, "_pos3", "pos3",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Alcodon target = (Alcodon) object;\r
- if (!target.hasPos3())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Long(target.getPos3());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Alcodon target = (Alcodon) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePos3();\r
- return;\r
- }\r
- target.setPos3(((java.lang.Long) value).longValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _pos3\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.LongValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Alcodon.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Alcodon.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.AlcodonFrame;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlcodonFrameDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AlcodonFrameDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "AlcodonFrame";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _alcodonList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Alcodon.class, "_alcodonList",\r
- "alcodon", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- return target.getAlcodon();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- target.addAlcodon((jalview.schemabinding.version2.Alcodon) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodonFrameDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "AlcodonFrame";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _alcodonList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ return target.getAlcodon();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.removeAllAlcodon();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Alcodon();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodonList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- target.removeAllAlcodon();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _alcodMapList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ return target.getAlcodMap();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.removeAllAlcodMap();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AlcodMap();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodMapList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Alcodon();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _alcodonList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _alcodMapList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList",\r
- "alcodMap", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- return target.getAlcodMap();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- target.addAlcodMap((jalview.schemabinding.version2.AlcodMap) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- AlcodonFrame target = (AlcodonFrame) object;\r
- target.removeAllAlcodMap();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.AlcodMap();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _alcodMapList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.AlcodonFrame.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AlcodonFrame.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.AnnotationColours;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationColoursDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationColoursDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "AnnotationColours";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _aboveThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- if (!target.hasAboveThreshold())\r
- {\r
- return null;\r
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "AnnotationColours";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _aboveThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasAboveThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getAboveThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAboveThreshold();\r
+ return;\r
+ }\r
+ target.setAboveThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _aboveThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getAboveThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteAboveThreshold();\r
- return;\r
- }\r
- target.setAboveThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _annotation\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ return target.getAnnotation();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ target.setAnnotation( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotation\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _aboveThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _annotation\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_annotation", "annotation",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- return target.getAnnotation();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- target.setAnnotation((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _minColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasMinColour()) { return null; }\r
+ return new java.lang.Integer(target.getMinColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMinColour();\r
+ return;\r
+ }\r
+ target.setMinColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _minColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _annotation\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _minColour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_minColour", "minColour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- if (!target.hasMinColour())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getMinColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMinColour();\r
- return;\r
- }\r
- target.setMinColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _maxColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasMaxColour()) { return null; }\r
+ return new java.lang.Integer(target.getMaxColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMaxColour();\r
+ return;\r
+ }\r
+ target.setMaxColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _maxColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _minColour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _maxColour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_maxColour", "maxColour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- if (!target.hasMaxColour())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourScheme\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ return target.getColourScheme();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ target.setColourScheme( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourScheme\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getMaxColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMaxColour();\r
- return;\r
- }\r
- target.setMaxColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationColours target = (AnnotationColours) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _maxColour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _colourScheme\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_colourScheme", "colourScheme",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- return target.getColourScheme();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- target.setColourScheme((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colourScheme\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _threshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_threshold", "threshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- if (!target.hasThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Float(target.getThreshold());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationColours target = (AnnotationColours) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteThreshold();\r
- return;\r
- }\r
- target.setThreshold(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _threshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.AnnotationColours.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AnnotationColours.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Annotation;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "Annotation";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _graph\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_graph", "graph",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasGraph())\r
- {\r
- return null;\r
+public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Annotation";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _graph\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraph()) { return null; }\r
+ return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setGraph( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graph\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return (target.getGraph() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setGraph(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphType\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphType()) { return null; }\r
+ return new java.lang.Integer(target.getGraphType());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphType();\r
+ return;\r
+ }\r
+ target.setGraphType( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphType\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _graph\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _graphType\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_graphType", "graphType",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasGraphType())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceRef\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getSequenceRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setSequenceRef( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceRef\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getGraphType());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteGraphType();\r
- return;\r
- }\r
- target.setGraphType(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _groupRef\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getGroupRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setGroupRef( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _groupRef\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _graphType\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _sequenceRef\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_sequenceRef", "sequenceRef",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getSequenceRef();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setSequenceRef((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphColour()) { return null; }\r
+ return new java.lang.Integer(target.getGraphColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphColour();\r
+ return;\r
+ }\r
+ target.setGraphColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _sequenceRef\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _groupRef\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_groupRef", "groupRef",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getGroupRef();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setGroupRef((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphGroup\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasGraphGroup()) { return null; }\r
+ return new java.lang.Integer(target.getGraphGroup());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphGroup();\r
+ return;\r
+ }\r
+ target.setGraphGroup( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphGroup\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _groupRef\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _graphColour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_graphColour", "graphColour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasGraphColour())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getGraphColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteGraphColour();\r
- return;\r
- }\r
- target.setGraphColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _scoreOnly\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasScoreOnly()) { return null; }\r
+ return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScoreOnly();\r
+ return;\r
+ }\r
+ target.setScoreOnly( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _scoreOnly\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _graphColour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _graphGroup\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_graphGroup", "graphGroup",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasGraphGroup())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _score\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasScore()) { return null; }\r
+ return new java.lang.Double(target.getScore());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScore();\r
+ return;\r
+ }\r
+ target.setScore( ((java.lang.Double) value).doubleValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _score\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.DoubleValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-1.7976931348623157E308);\r
+ typeValidator.setMaxInclusive(1.7976931348623157E308);\r
}\r
- return new java.lang.Integer(target.getGraphGroup());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteGraphGroup();\r
- return;\r
- }\r
- target.setGraphGroup(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _visible\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasVisible()) { return null; }\r
+ return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteVisible();\r
+ return;\r
+ }\r
+ target.setVisible( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _visible\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _graphGroup\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _centreColLabels\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasCentreColLabels()) { return null; }\r
+ return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteCentreColLabels();\r
+ return;\r
+ }\r
+ target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _centreColLabels\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _scoreOnly\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasScoreOnly())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _scaleColLabels\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasScaleColLabels()) { return null; }\r
+ return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScaleColLabels();\r
+ return;\r
+ }\r
+ target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _scaleColLabels\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return (target.getScoreOnly() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteScoreOnly();\r
- return;\r
- }\r
- target.setScoreOnly(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showAllColLabels\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasShowAllColLabels()) { return null; }\r
+ return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowAllColLabels();\r
+ return;\r
+ }\r
+ target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showAllColLabels\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _scoreOnly\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _score\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Double.TYPE, "_score", "score",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasScore())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _autoCalculated\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if (!target.hasAutoCalculated()) { return null; }\r
+ return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAutoCalculated();\r
+ return;\r
+ }\r
+ target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _autoCalculated\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Double(target.getScore());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteScore();\r
- return;\r
- }\r
- target.setScore(((java.lang.Double) value).doubleValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _annotationElementList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getAnnotationElement();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.removeAllAnnotationElement();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AnnotationElement();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationElementList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _score\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.DoubleValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-1.7976931348623157E308);\r
- typeValidator.setMaxInclusive(1.7976931348623157E308);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _visible\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_visible", "visible",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasVisible())\r
- {\r
- return null;\r
- }\r
- return (target.getVisible() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteVisible();\r
- return;\r
- }\r
- target.setVisible(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _label\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getLabel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setLabel( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _label\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _visible\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _centreColLabels\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasCentreColLabels())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return (target.getCentreColLabels() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteCentreColLabels();\r
- return;\r
- }\r
- target.setCentreColLabels(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _thresholdLine\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ return target.getThresholdLine();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.ThresholdLine();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _thresholdLine\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _centreColLabels\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _scaleColLabels\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasScaleColLabels())\r
- {\r
- return null;\r
- }\r
- return (target.getScaleColLabels() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteScaleColLabels();\r
- return;\r
- }\r
- target.setScaleColLabels(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _scaleColLabels\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showAllColLabels\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showAllColLabels",\r
- "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasShowAllColLabels())\r
- {\r
- return null;\r
- }\r
- return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowAllColLabels();\r
- return;\r
- }\r
- target.setShowAllColLabels(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showAllColLabels\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _autoCalculated\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- if (!target.hasAutoCalculated())\r
- {\r
- return null;\r
- }\r
- return (target.getAutoCalculated() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteAutoCalculated();\r
- return;\r
- }\r
- target.setAutoCalculated(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _autoCalculated\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _annotationElementList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.AnnotationElement.class,\r
- "_annotationElementList", "annotationElement",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getAnnotationElement();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.removeAllAnnotationElement();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.AnnotationElement();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _annotationElementList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Annotation.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _label\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_label", "label",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getLabel();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setLabel((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _label\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_description", "description",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getDescription();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setDescription((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _thresholdLine\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.ThresholdLine.class,\r
- "_thresholdLine", "thresholdLine",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Annotation target = (Annotation) object;\r
- return target.getThresholdLine();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Annotation target = (Annotation) object;\r
- target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.ThresholdLine();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _thresholdLine\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Annotation.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.AnnotationElement;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationElementDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationElementDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "annotationElement";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _position\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_position", "position",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- if (!target.hasPosition())\r
- {\r
- return null;\r
+public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AnnotationElementDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "annotationElement";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _position\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasPosition()) { return null; }\r
+ return new java.lang.Integer(target.getPosition());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setPosition( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _position\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getPosition());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setPosition(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _position\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _colour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_colour", "colour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- if (!target.hasColour())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _displayCharacter\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getDisplayCharacter();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setDisplayCharacter( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayCharacter\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColour();\r
- return;\r
- }\r
- target.setColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- _secondaryStructure\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ return target.getSecondaryStructure();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ target.setSecondaryStructure( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _secondaryStructure\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ typeValidator.setLength(1);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if (!target.hasValue()) { return null; }\r
+ return new java.lang.Float(target.getValue());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteValue();\r
+ return;\r
+ }\r
+ target.setValue( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _displayCharacter\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_displayCharacter",\r
- "displayCharacter", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- return target.getDisplayCharacter();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- target.setDisplayCharacter((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _displayCharacter\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_description", "description",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- return target.getDescription();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- target.setDescription((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _secondaryStructure\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_secondaryStructure",\r
- "secondaryStructure", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- return target.getSecondaryStructure();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- target.setSecondaryStructure((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _secondaryStructure\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- typeValidator.setLength(1);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AnnotationElement.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _value\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_value", "value",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- if (!target.hasValue())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Float(target.getValue());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- AnnotationElement target = (AnnotationElement) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteValue();\r
- return;\r
- }\r
- target.setValue(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _value\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.AnnotationElement.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Colour;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class ColourDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public ColourDescriptor()\r
- {\r
- super();\r
- _xmlName = "colour";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_name", "Name",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- return target.getName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- target.setName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _RGB\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_RGB", "RGB",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- return target.getRGB();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- target.setRGB((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ColourDescriptor() {\r
+ super();\r
+ _xmlName = "colour";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _RGB\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _minRGB\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_minRGB", "minRGB",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- return target.getMinRGB();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- target.setMinRGB((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _RGB\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getRGB();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setRGB( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _RGB\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _minRGB\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _threshType\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_threshType", "threshType",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- return target.getThreshType();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- target.setThreshType((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _minRGB\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getMinRGB();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setMinRGB( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _minRGB\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _threshType\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _threshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_threshold", "threshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- if (!target.hasThreshold())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshType\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ return target.getThreshType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ target.setThreshType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshType\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Float(target.getThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteThreshold();\r
- return;\r
- }\r
- target.setThreshold(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _threshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _max\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_max", "max",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- if (!target.hasMax())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _max\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ if (!target.hasMax()) { return null; }\r
+ return new java.lang.Float(target.getMax());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMax();\r
+ return;\r
+ }\r
+ target.setMax( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _max\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- return new java.lang.Float(target.getMax());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMax();\r
- return;\r
- }\r
- target.setMax(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _min\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ if (!target.hasMin()) { return null; }\r
+ return new java.lang.Float(target.getMin());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMin();\r
+ return;\r
+ }\r
+ target.setMin( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _min\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _max\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _min\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_min", "min",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- if (!target.hasMin())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourByLabel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ if (!target.hasColourByLabel()) { return null; }\r
+ return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColourByLabel();\r
+ return;\r
+ }\r
+ target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourByLabel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Float(target.getMin());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMin();\r
- return;\r
- }\r
- target.setMin(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _autoScale\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Colour target = (Colour) object;\r
+ if (!target.hasAutoScale()) { return null; }\r
+ return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Colour target = (Colour) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAutoScale();\r
+ return;\r
+ }\r
+ target.setAutoScale( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _autoScale\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _min\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _colourByLabel\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- if (!target.hasColourByLabel())\r
- {\r
- return null;\r
- }\r
- return (target.getColourByLabel() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColourByLabel();\r
- return;\r
- }\r
- target.setColourByLabel(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _colourByLabel\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _autoScale\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_autoScale", "autoScale",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Colour target = (Colour) object;\r
- if (!target.hasAutoScale())\r
- {\r
- return null;\r
- }\r
- return (target.getAutoScale() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Colour target = (Colour) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteAutoScale();\r
- return;\r
- }\r
- target.setAutoScale(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _autoScale\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Colour.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Colour.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.DBRef;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class DBRefDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public DBRefDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "DBRef";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _source\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_source", "source",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- DBRef target = (DBRef) object;\r
- return target.getSource();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- DBRef target = (DBRef) object;\r
- target.setSource((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public DBRefDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "DBRef";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _source\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getSource();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setSource( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _source\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _source\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _version\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_version", "version",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- DBRef target = (DBRef) object;\r
- return target.getVersion();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- DBRef target = (DBRef) object;\r
- target.setVersion((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _version\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _accessionId\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_accessionId", "accessionId",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- DBRef target = (DBRef) object;\r
- return target.getAccessionId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- DBRef target = (DBRef) object;\r
- target.setAccessionId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _accessionId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getAccessionId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setAccessionId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _accessionId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _accessionId\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mapping\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getMapping();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setMapping( (jalview.schemabinding.version2.Mapping) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Mapping();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapping\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _mapping\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Mapping.class, "_mapping",\r
- "Mapping", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- DBRef target = (DBRef) object;\r
- return target.getMapping();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- DBRef target = (DBRef) object;\r
- target.setMapping((jalview.schemabinding.version2.Mapping) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Mapping();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _mapping\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.DBRef.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.DBRef.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Feature;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class FeatureDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public FeatureDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "feature";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _begin\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_begin", "begin",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- if (!target.hasBegin())\r
- {\r
- return null;\r
+public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "feature";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _begin\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasBegin()) { return null; }\r
+ return new java.lang.Integer(target.getBegin());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setBegin( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _begin\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getBegin());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setBegin(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _begin\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_type", "type",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- return target.getType();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.setType((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _status\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getStatus();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setStatus( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _status\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_description", "description",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- return target.getDescription();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.setDescription((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _featureGroup\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getFeatureGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.setFeatureGroup( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featureGroup\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _status\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_status", "status",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- return target.getStatus();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.setStatus((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _score\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ if (!target.hasScore()) { return null; }\r
+ return new java.lang.Float(target.getScore());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScore();\r
+ return;\r
+ }\r
+ target.setScore( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _score\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _status\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _featureGroup\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_featureGroup", "featureGroup",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- return target.getFeatureGroup();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.setFeatureGroup((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _otherDataList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Feature target = (Feature) object;\r
+ return target.getOtherData();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.addOtherData( (jalview.schemabinding.version2.OtherData) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Feature target = (Feature) object;\r
+ target.removeAllOtherData();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.OtherData();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _otherDataList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _featureGroup\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _score\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_score", "score",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- if (!target.hasScore())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Float(target.getScore());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteScore();\r
- return;\r
- }\r
- target.setScore(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _score\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _otherDataList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.OtherData.class,\r
- "_otherDataList", "otherData",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Feature target = (Feature) object;\r
- return target.getOtherData();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.addOtherData((jalview.schemabinding.version2.OtherData) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Feature target = (Feature) object;\r
- target.removeAllOtherData();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.OtherData();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _otherDataList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Feature.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Feature.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.FeatureSettings;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class FeatureSettingsDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public FeatureSettingsDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "FeatureSettings";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _settingList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Setting.class, "_settingList",\r
- "setting", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- return target.getSetting();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- target.addSetting((jalview.schemabinding.version2.Setting) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureSettingsDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "FeatureSettings";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _settingList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ return target.getSetting();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.addSetting( (jalview.schemabinding.version2.Setting) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.removeAllSetting();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Setting();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _settingList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- target.removeAllSetting();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _groupList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ return target.getGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.addGroup( (jalview.schemabinding.version2.Group) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ FeatureSettings target = (FeatureSettings) object;\r
+ target.removeAllGroup();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Group();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _groupList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Setting();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _settingList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _groupList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Group.class, "_groupList",\r
- "group", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- return target.getGroup();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- target.addGroup((jalview.schemabinding.version2.Group) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- FeatureSettings target = (FeatureSettings) object;\r
- target.removeAllGroup();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Group();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _groupList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.FeatureSettings.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.FeatureSettings.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Features;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class FeaturesDescriptor extends\r
- jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public FeaturesDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "features";\r
- _elementDefinition = true;\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Features.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeaturesDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "features";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Features.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Group;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class GroupDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public GroupDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "group";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_name", "name",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Group target = (Group) object;\r
- return target.getName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Group target = (Group) object;\r
- target.setName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public GroupDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "group";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Group target = (Group) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Group target = (Group) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _display\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_display", "display",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Group target = (Group) object;\r
- if (!target.hasDisplay())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _display\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Group target = (Group) object;\r
+ if (!target.hasDisplay()) { return null; }\r
+ return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Group target = (Group) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setDisplay( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _display\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return (target.getDisplay() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Group target = (Group) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
\r
- target.setDisplay(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _display\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Group.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Group.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.HiddenColumns;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class HiddenColumnsDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public HiddenColumnsDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "hiddenColumns";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_start", "start",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- HiddenColumns target = (HiddenColumns) object;\r
- if (!target.hasStart())\r
- {\r
- return null;\r
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public HiddenColumnsDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "hiddenColumns";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStart();\r
+ return;\r
+ }\r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getStart());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- HiddenColumns target = (HiddenColumns) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteStart();\r
- return;\r
- }\r
- target.setStart(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteEnd();\r
+ return;\r
+ }\r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- HiddenColumns target = (HiddenColumns) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- HiddenColumns target = (HiddenColumns) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteEnd();\r
- return;\r
- }\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.HiddenColumns.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.HiddenColumns.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.JGroup;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JGroupDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JGroupDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "JGroup";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_start", "start",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasStart())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getStart());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteStart();\r
- return;\r
- }\r
- target.setStart(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteEnd();\r
- return;\r
- }\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_name", "name",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- return target.getName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- target.setName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _colour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_colour", "colour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- return target.getColour();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- target.setColour((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _consThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_consThreshold", "consThreshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasConsThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getConsThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteConsThreshold();\r
- return;\r
- }\r
- target.setConsThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _consThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _pidThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasPidThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getPidThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePidThreshold();\r
- return;\r
- }\r
- target.setPidThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pidThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _outlineColour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_outlineColour", "outlineColour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasOutlineColour())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getOutlineColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteOutlineColour();\r
- return;\r
- }\r
- target.setOutlineColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _outlineColour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _displayBoxes\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasDisplayBoxes())\r
- {\r
- return null;\r
- }\r
- return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteDisplayBoxes();\r
- return;\r
- }\r
- target.setDisplayBoxes(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _displayBoxes\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JGroupDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JGroup";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStart();\r
+ return;\r
+ }\r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteEnd();\r
+ return;\r
+ }\r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.setColour( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _consThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasConsThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getConsThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConsThreshold();\r
+ return;\r
+ }\r
+ target.setConsThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _consThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasPidThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getPidThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidThreshold();\r
+ return;\r
+ }\r
+ target.setPidThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _outlineColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasOutlineColour()) { return null; }\r
+ return new java.lang.Integer(target.getOutlineColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteOutlineColour();\r
+ return;\r
+ }\r
+ target.setOutlineColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _outlineColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _displayBoxes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasDisplayBoxes()) { return null; }\r
+ return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteDisplayBoxes();\r
+ return;\r
+ }\r
+ target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayBoxes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _displayText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasDisplayText()) { return null; }\r
+ return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteDisplayText();\r
+ return;\r
+ }\r
+ target.setDisplayText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _displayText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasColourText()) { return null; }\r
+ return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColourText();\r
+ return;\r
+ }\r
+ target.setColourText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextCol1()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol1();\r
+ return;\r
+ }\r
+ target.setTextCol1( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextCol2()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol2();\r
+ return;\r
+ }\r
+ target.setTextCol2( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textColThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasTextColThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getTextColThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextColThreshold();\r
+ return;\r
+ }\r
+ target.setTextColThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textColThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showUnconserved\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasShowUnconserved()) { return null; }\r
+ return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowUnconserved();\r
+ return;\r
+ }\r
+ target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showUnconserved\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ignoreGapsinConsensus\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasIgnoreGapsinConsensus()) { return null; }\r
+ return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteIgnoreGapsinConsensus();\r
+ return;\r
+ }\r
+ target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ignoreGapsinConsensus\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showConsensusHistogram\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasShowConsensusHistogram()) { return null; }\r
+ return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowConsensusHistogram();\r
+ return;\r
+ }\r
+ target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showConsensusHistogram\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showSequenceLogo\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ if (!target.hasShowSequenceLogo()) { return null; }\r
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowSequenceLogo();\r
+ return;\r
+ }\r
+ target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showSequenceLogo\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _seqList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JGroup target = (JGroup) object;\r
+ return target.getSeq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.addSeq( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JGroup target = (JGroup) object;\r
+ target.removeAllSeq();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _seqList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _displayText\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_displayText", "displayText",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasDisplayText())\r
- {\r
- return null;\r
- }\r
- return (target.getDisplayText() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteDisplayText();\r
- return;\r
- }\r
- target.setDisplayText(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _displayText\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _colourText\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_colourText", "colourText",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasColourText())\r
- {\r
- return null;\r
- }\r
- return (target.getColourText() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColourText();\r
- return;\r
- }\r
- target.setColourText(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colourText\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _textCol1\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textCol1", "textCol1",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasTextCol1())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextCol1());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextCol1();\r
- return;\r
- }\r
- target.setTextCol1(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _textCol1\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _textCol2\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textCol2", "textCol2",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasTextCol2())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextCol2());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextCol2();\r
- return;\r
- }\r
- target.setTextCol2(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _textCol2\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _textColThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textColThreshold",\r
- "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasTextColThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextColThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextColThreshold();\r
- return;\r
- }\r
- target.setTextColThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _textColThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _showUnconserved\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasShowUnconserved())\r
- {\r
- return null;\r
- }\r
- return (target.getShowUnconserved() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowUnconserved();\r
- return;\r
- }\r
- target.setShowUnconserved(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _showUnconserved\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JGroup.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _ignoreGapsinConsensus\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",\r
- "ignoreGapsinConsensus",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasIgnoreGapsinConsensus())\r
- {\r
- return null;\r
- }\r
- return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteIgnoreGapsinConsensus();\r
- return;\r
- }\r
- target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _ignoreGapsinConsensus\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _showConsensusHistogram\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showConsensusHistogram",\r
- "showConsensusHistogram",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasShowConsensusHistogram())\r
- {\r
- return null;\r
- }\r
- return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowConsensusHistogram();\r
- return;\r
- }\r
- target.setShowConsensusHistogram(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _showConsensusHistogram\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _showSequenceLogo\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showSequenceLogo",\r
- "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- if (!target.hasShowSequenceLogo())\r
- {\r
- return null;\r
- }\r
- return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowSequenceLogo();\r
- return;\r
- }\r
- target.setShowSequenceLogo(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _showSequenceLogo\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _seqList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_seqList", "seq",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JGroup target = (JGroup) object;\r
- return target.getSeq();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- target.addSeq((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JGroup target = (JGroup) object;\r
- target.removeAllSeq();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _seqList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.JGroup.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.JSeq;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JSeqDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JSeqDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "JSeq";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _colour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_colour", "colour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- if (!target.hasColour())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColour();\r
- return;\r
- }\r
- target.setColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JSeqDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JSeq";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_start", "start",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- if (!target.hasStart())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getStart());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setStart(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hidden\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if (!target.hasHidden()) { return null; }\r
+ return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHidden();\r
+ return;\r
+ }\r
+ target.setHidden( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hidden\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _featuresList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getFeatures();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.addFeatures( (jalview.schemabinding.version2.Features) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllFeatures();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Features();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featuresList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _hidden\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_hidden", "hidden",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- if (!target.hasHidden())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pdbidsList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getPdbids();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllPdbids();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Pdbids();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pdbidsList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- return (target.getHidden() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteHidden();\r
- return;\r
- }\r
- target.setHidden(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hiddenSequencesList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getHiddenSequences();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.addHiddenSequences( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ target.removeAllHiddenSequences();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenSequencesList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _hidden\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _featuresList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Features.class, "_featuresList",\r
- "features", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- return target.getFeatures();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.addFeatures((jalview.schemabinding.version2.Features) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.removeAllFeatures();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Features();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _featuresList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _pdbidsList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",\r
- "pdbids", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- return target.getPdbids();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.addPdbids((jalview.schemabinding.version2.Pdbids) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.removeAllPdbids();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Pdbids();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pdbidsList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _hiddenSequencesList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_hiddenSequencesList",\r
- "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JSeq target = (JSeq) object;\r
- return target.getHiddenSequences();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
\r
- target.addHiddenSequences(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JSeq target = (JSeq) object;\r
- target.removeAllHiddenSequences();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _hiddenSequencesList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JSeq.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.JSeq.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.JalviewModel;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewModelDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "JalviewModel";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _creationDate\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.util.Date.class, "_creationDate", "creationDate",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- return target.getCreationDate();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- target.setCreationDate((java.util.Date) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "JalviewModel";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _creationDate\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getCreationDate();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setCreationDate( (java.util.Date) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new java.util.Date();\r
+ }\r
+ };\r
+ handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);\r
+ desc.setImmutable(true);\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _creationDate\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.DateTimeValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new java.util.Date();\r
- }\r
- };\r
- handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);\r
- desc.setImmutable(true);\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _creationDate\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.DateTimeValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _version\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_version", "version",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- return target.getVersion();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- target.setVersion((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _version\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _vamsasModel\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.VamsasModel.class,\r
- "_vamsasModel", "vamsasModel",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- return target.getVamsasModel();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- target.setVamsasModel((jalview.schemabinding.version2.VamsasModel) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _vamsasModel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getVamsasModel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.VamsasModel();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _vamsasModel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.VamsasModel();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _vamsasModel\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
+ //-- _jalviewModelSequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModel target = (JalviewModel) object;\r
+ return target.getJalviewModelSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModel target = (JalviewModel) object;\r
+ target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JalviewModelSequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _jalviewModelSequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _jalviewModelSequence\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.JalviewModelSequence.class,\r
- "_jalviewModelSequence", "-error-if-this-is-used-",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- return target.getJalviewModelSequence();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModel target = (JalviewModel) object;\r
- target.setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.JalviewModelSequence();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setContainer(true);\r
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _jalviewModelSequence\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.JalviewModel.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewModel.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.JalviewModelSequence;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelSequenceDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewModelSequenceDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _JSeqList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getJSeq();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.addJSeq((jalview.schemabinding.version2.JSeq) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelSequenceDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _JSeqList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getJSeq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addJSeq( (jalview.schemabinding.version2.JSeq) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllJSeq();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JSeq();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _JSeqList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.removeAllJSeq();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _JGroupList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getJGroup();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addJGroup( (jalview.schemabinding.version2.JGroup) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllJGroup();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.JGroup();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _JGroupList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.JSeq();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _JSeqList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _JGroupList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.JGroup.class, "_JGroupList",\r
- "JGroup", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getJGroup();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.addJGroup((jalview.schemabinding.version2.JGroup) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _viewportList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getViewport();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addViewport( (jalview.schemabinding.version2.Viewport) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllViewport();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Viewport();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _viewportList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.removeAllJGroup();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _userColoursList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getUserColours();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addUserColours( (jalview.schemabinding.version2.UserColours) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllUserColours();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.UserColours();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _userColoursList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.JGroup();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _JGroupList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _viewportList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Viewport.class, "_viewportList",\r
- "Viewport", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getViewport();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.addViewport((jalview.schemabinding.version2.Viewport) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _treeList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getTree();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.addTree( (jalview.schemabinding.version2.Tree) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.removeAllTree();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Tree();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _treeList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.removeAllViewport();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _featureSettings\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ return target.getFeatureSettings();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewModelSequence target = (JalviewModelSequence) object;\r
+ target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.FeatureSettings();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _featureSettings\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Viewport();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _viewportList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _userColoursList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.UserColours.class,\r
- "_userColoursList", "UserColours",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getUserColours();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.addUserColours((jalview.schemabinding.version2.UserColours) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.removeAllUserColours();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.UserColours();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _userColoursList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _treeList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Tree.class, "_treeList", "tree",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getTree();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.addTree((jalview.schemabinding.version2.Tree) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.removeAllTree();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Tree();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _treeList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _featureSettings\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.FeatureSettings.class,\r
- "_featureSettings", "FeatureSettings",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- return target.getFeatureSettings();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewModelSequence target = (JalviewModelSequence) object;\r
- target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.FeatureSettings();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _featureSettings\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewModelSequence.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.JalviewModelSequence.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import jalview.schemabinding.version2.JalviewUserColours;\r
import jalview.schemabinding.version2.Colour;\r
+import jalview.schemabinding.version2.JalviewUserColours;\r
\r
/**\r
* Class JalviewUserColoursDescriptor.\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewUserColoursDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewUserColoursDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org/colours";\r
- _xmlName = "JalviewUserColours";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _schemeName\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_schemeName", "schemeName",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- return target.getSchemeName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- target.setSchemeName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewUserColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org/colours";\r
+ _xmlName = "JalviewUserColours";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _schemeName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ return target.getSchemeName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.setSchemeName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _schemeName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _schemeName\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ return target.getColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.addColour( (Colour) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ JalviewUserColours target = (JalviewUserColours) object;\r
+ target.removeAllColour();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new Colour();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _version\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_version", "Version",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- return target.getVersion();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- target.setVersion((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _version\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _colourList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- Colour.class, "_colourList", "colour",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- return target.getColour();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- target.addColour((Colour) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- JalviewUserColours target = (JalviewUserColours) object;\r
- target.removeAllColour();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new Colour();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _colourList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.JalviewUserColours.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.JalviewUserColours.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.MapListFrom;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListFromDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListFromDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "mapListFrom";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_start", "start",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListFrom target = (MapListFrom) object;\r
- if (!target.hasStart())\r
- {\r
- return null;\r
+public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListFromDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListFrom";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListFrom target = (MapListFrom) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListFrom target = (MapListFrom) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getStart());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListFrom target = (MapListFrom) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setStart(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListFrom target = (MapListFrom) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListFrom target = (MapListFrom) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListFrom target = (MapListFrom) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListFrom target = (MapListFrom) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.MapListFrom.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListFrom.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.MapListTo;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListToDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListToDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "mapListTo";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_start", "start",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListTo target = (MapListTo) object;\r
- if (!target.hasStart())\r
- {\r
- return null;\r
+public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListToDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListTo";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListTo target = (MapListTo) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListTo target = (MapListTo) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getStart());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListTo target = (MapListTo) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setStart(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListTo target = (MapListTo) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListTo target = (MapListTo) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_end", "end",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListTo target = (MapListTo) object;\r
- if (!target.hasEnd())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListTo target = (MapListTo) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
\r
- target.setEnd(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.MapListTo.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListTo.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.MapListType;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListTypeDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MapListTypeDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "mapListType";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _mapFromUnit\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListType target = (MapListType) object;\r
- if (!target.hasMapFromUnit())\r
- {\r
- return null;\r
+public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListTypeDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListType";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _mapFromUnit\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ if (!target.hasMapFromUnit()) { return null; }\r
+ return new java.lang.Long(target.getMapFromUnit());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setMapFromUnit( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapFromUnit\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(1L);\r
}\r
- return new java.lang.Long(target.getMapFromUnit());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setMapFromUnit(((java.lang.Long) value).longValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _mapToUnit\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ if (!target.hasMapToUnit()) { return null; }\r
+ return new java.lang.Long(target.getMapToUnit());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setMapToUnit( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapToUnit\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(1L);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _mapFromUnit\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.LongValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(1L);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _mapToUnit\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Long.TYPE, "_mapToUnit", "mapToUnit",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListType target = (MapListType) object;\r
- if (!target.hasMapToUnit())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mapListFromList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ return target.getMapListFrom();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.removeAllMapListFrom();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MapListFrom();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapListFromList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- return new java.lang.Long(target.getMapToUnit());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setMapToUnit(((java.lang.Long) value).longValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _mapListToList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ return target.getMapListTo();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.removeAllMapListTo();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MapListTo();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapListToList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _mapToUnit\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.LongValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(1L);\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _mapListFromList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.MapListFrom.class,\r
- "_mapListFromList", "mapListFrom",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListType target = (MapListType) object;\r
- return target.getMapListFrom();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- target.addMapListFrom((jalview.schemabinding.version2.MapListFrom) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- target.removeAllMapListFrom();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.MapListFrom();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _mapListFromList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _mapListToList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.MapListTo.class,\r
- "_mapListToList", "mapListTo",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MapListType target = (MapListType) object;\r
- return target.getMapListTo();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- target.addMapListTo((jalview.schemabinding.version2.MapListTo) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- MapListType target = (MapListType) object;\r
- target.removeAllMapListTo();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.MapListTo();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _mapListToList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.MapListType.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListType.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.MappingChoice;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MappingChoiceDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MappingChoiceDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _sequence\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Sequence.class, "_sequence",\r
- "Sequence", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MappingChoice target = (MappingChoice) object;\r
- return target.getSequence();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MappingChoice target = (MappingChoice) object;\r
- target.setSequence((jalview.schemabinding.version2.Sequence) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingChoiceDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsChoice();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MappingChoice target = (MappingChoice) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MappingChoice target = (MappingChoice) object;\r
+ target.setSequence( (jalview.schemabinding.version2.Sequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Sequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Sequence();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _sequence\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _dseqFor\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_dseqFor", "dseqFor",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- MappingChoice target = (MappingChoice) object;\r
- return target.getDseqFor();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- MappingChoice target = (MappingChoice) object;\r
- target.setDseqFor((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _dseqFor\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MappingChoice target = (MappingChoice) object;\r
+ return target.getDseqFor();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MappingChoice target = (MappingChoice) object;\r
+ target.setDseqFor( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dseqFor\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _dseqFor\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.MappingChoice.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MappingChoice.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Mapping;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MappingDescriptor extends\r
- jalview.schemabinding.version2.descriptors.MapListTypeDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public MappingDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "Mapping";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _mappingChoice\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.MappingChoice.class,\r
- "_mappingChoice", "-error-if-this-is-used-",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Mapping target = (Mapping) object;\r
- return target.getMappingChoice();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Mapping target = (Mapping) object;\r
- target.setMappingChoice((jalview.schemabinding.version2.MappingChoice) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Mapping";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsChoice();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mappingChoice\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Mapping target = (Mapping) object;\r
+ return target.getMappingChoice();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Mapping target = (Mapping) object;\r
+ target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MappingChoice();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mappingChoice\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.MappingChoice();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setContainer(true);\r
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _mappingChoice\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Mapping.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Mapping.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.OtherData;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class OtherDataDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public OtherDataDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "otherData";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _key\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_key", "key",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- OtherData target = (OtherData) object;\r
- return target.getKey();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- OtherData target = (OtherData) object;\r
- target.setKey((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public OtherDataDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "otherData";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _key\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ OtherData target = (OtherData) object;\r
+ return target.getKey();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ OtherData target = (OtherData) object;\r
+ target.setKey( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _key\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _key\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _value\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_value", "value",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- OtherData target = (OtherData) object;\r
- return target.getValue();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- OtherData target = (OtherData) object;\r
- target.setValue((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ OtherData target = (OtherData) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ OtherData target = (OtherData) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _value\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.OtherData.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.OtherData.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Pdbentry;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class PdbentryDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public PdbentryDescriptor()\r
- {\r
- super();\r
- _xmlName = "pdbentry";\r
- _elementDefinition = false;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryDescriptor() {\r
+ super();\r
+ _xmlName = "pdbentry";\r
+ _elementDefinition = false;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_type", "type",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- return target.getType();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- target.setType((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _file\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_file", "file",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- return target.getFile();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- target.setFile((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _file\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getFile();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.setFile( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _file\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _file\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _items\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.PdbentryItem.class, "_items",\r
- (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- return target.getPdbentryItem();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- target.addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _items\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbentry target = (Pdbentry) object;\r
+ return target.getPdbentryItem();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Pdbentry target = (Pdbentry) object;\r
+ target.removeAllPdbentryItem();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.PdbentryItem();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _items\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbentry target = (Pdbentry) object;\r
- target.removeAllPdbentryItem();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.PdbentryItem();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setContainer(true);\r
- desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _items\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Pdbentry.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Pdbentry.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.PdbentryItem;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class PdbentryItemDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public PdbentryItemDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "pdbentry";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _propertyList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Property.class, "_propertyList",\r
- "property", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- PdbentryItem target = (PdbentryItem) object;\r
- return target.getProperty();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- PdbentryItem target = (PdbentryItem) object;\r
- target.addProperty((jalview.schemabinding.version2.Property) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- PdbentryItem target = (PdbentryItem) object;\r
- target.removeAllProperty();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryItemDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "pdbentry";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _propertyList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ return target.getProperty();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ target.addProperty( (jalview.schemabinding.version2.Property) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ PdbentryItem target = (PdbentryItem) object;\r
+ target.removeAllProperty();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Property();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _propertyList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Property();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _propertyList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.PdbentryItem.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.PdbentryItem.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Pdbids;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class PdbidsDescriptor extends\r
- jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public PdbidsDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "pdbids";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _structureStateList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.StructureState.class,\r
- "_structureStateList", "structureState",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Pdbids target = (Pdbids) object;\r
- return target.getStructureState();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbids target = (Pdbids) object;\r
- target.addStructureState((jalview.schemabinding.version2.StructureState) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Pdbids target = (Pdbids) object;\r
- target.removeAllStructureState();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbidsDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "pdbids";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _structureStateList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Pdbids target = (Pdbids) object;\r
+ return target.getStructureState();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Pdbids target = (Pdbids) object;\r
+ target.addStructureState( (jalview.schemabinding.version2.StructureState) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Pdbids target = (Pdbids) object;\r
+ target.removeAllStructureState();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.StructureState();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _structureStateList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.StructureState();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _structureStateList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Pdbids.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Pdbids.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Property;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class PropertyDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public PropertyDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "property";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_name", "name",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Property target = (Property) object;\r
- target.setName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PropertyDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "property";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Property target = (Property) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Property target = (Property) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _value\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_value", "value",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getValue();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Property target = (Property) object;\r
- target.setValue((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Property target = (Property) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Property target = (Property) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _value\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Property.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Property.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Sequence;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceDescriptor extends\r
- jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "Sequence";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _dsseqid\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_dsseqid", "dsseqid",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Sequence target = (Sequence) object;\r
- return target.getDsseqid();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Sequence target = (Sequence) object;\r
- target.setDsseqid((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Sequence";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _dsseqid\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Sequence target = (Sequence) object;\r
+ return target.getDsseqid();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.setDsseqid( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dsseqid\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _dsseqid\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _DBRefList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.DBRef.class, "_DBRefList",\r
- "DBRef", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Sequence target = (Sequence) object;\r
- return target.getDBRef();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Sequence target = (Sequence) object;\r
- target.addDBRef((jalview.schemabinding.version2.DBRef) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _DBRefList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Sequence target = (Sequence) object;\r
+ return target.getDBRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.removeAllDBRef();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.DBRef();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _DBRefList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Sequence target = (Sequence) object;\r
- target.removeAllDBRef();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.DBRef();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _DBRefList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Sequence.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Sequence.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.SequenceSet;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceSetDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceSetDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "SequenceSet";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _gapChar\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_gapChar", "gapChar",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getGapChar();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.setGapChar((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSetDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "SequenceSet";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _gapChar\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getGapChar();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.setGapChar( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _gapChar\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _gapChar\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _datasetId\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_datasetId", "datasetId",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getDatasetId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.setDatasetId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _datasetId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getDatasetId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.setDatasetId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _datasetId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _datasetId\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _sequenceList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Sequence.class, "_sequenceList",\r
- "Sequence", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getSequence();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.addSequence((jalview.schemabinding.version2.Sequence) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequenceList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllSequence();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Sequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.removeAllSequence();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _annotationList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getAnnotation();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllAnnotation();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Annotation();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Sequence();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _sequenceList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _annotationList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.Annotation.class,\r
- "_annotationList", "Annotation",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getAnnotation();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.addAnnotation((jalview.schemabinding.version2.Annotation) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetPropertiesList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getSequenceSetProperties();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllSequenceSetProperties();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.SequenceSetProperties();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetPropertiesList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.removeAllAnnotation();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _alcodonFrameList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getAlcodonFrame();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllAlcodonFrame();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AlcodonFrame();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodonFrameList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.Annotation();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _annotationList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _sequenceSetPropertiesList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.SequenceSetProperties.class,\r
- "_sequenceSetPropertiesList", "sequenceSetProperties",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getSequenceSetProperties();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.removeAllSequenceSetProperties();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.SequenceSetProperties();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _sequenceSetPropertiesList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _alcodonFrameList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.AlcodonFrame.class,\r
- "_alcodonFrameList", "AlcodonFrame",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- return target.getAlcodonFrame();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSet target = (SequenceSet) object;\r
- target.removeAllAlcodonFrame();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.AlcodonFrame();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _alcodonFrameList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.SequenceSet.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceSet.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.SequenceSetProperties;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceSetPropertiesDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceSetPropertiesDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "sequenceSetProperties";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _key\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_key", "key",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSetProperties target = (SequenceSetProperties) object;\r
- return target.getKey();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSetProperties target = (SequenceSetProperties) object;\r
- target.setKey((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSetPropertiesDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "sequenceSetProperties";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _key\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ return target.getKey();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ target.setKey( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _key\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ return target.getValue();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSetProperties target = (SequenceSetProperties) object;\r
+ target.setValue( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _key\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _value\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_value", "value",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceSetProperties target = (SequenceSetProperties) object;\r
- return target.getValue();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceSetProperties target = (SequenceSetProperties) object;\r
- target.setValue((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _value\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceSetProperties.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.SequenceSetProperties.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.SequenceType;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceTypeDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SequenceTypeDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "SequenceType";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceType target = (SequenceType) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceType target = (SequenceType) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceTypeDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "SequenceType";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_description", "description",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceType target = (SequenceType) object;\r
- return target.getDescription();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceType target = (SequenceType) object;\r
- target.setDescription((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _description\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getDescription();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setDescription( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _description\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setSequence( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _name\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceType target = (SequenceType) object;\r
+ return target.getName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceType target = (SequenceType) object;\r
+ target.setName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _name\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _sequence\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_sequence", "sequence",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceType target = (SequenceType) object;\r
- return target.getSequence();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceType target = (SequenceType) object;\r
- target.setSequence((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _sequence\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_name", "name",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- SequenceType target = (SequenceType) object;\r
- return target.getName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- SequenceType target = (SequenceType) object;\r
- target.setName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.SequenceType.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.SequenceType.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Setting;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SettingDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public SettingDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "setting";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_type", "type",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- return target.getType();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- target.setType((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SettingDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "setting";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _type\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ return target.getType();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ target.setType( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _type\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _colour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_colour", "colour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasColour())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getColour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _display\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasDisplay()) { return null; }\r
+ return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setDisplay( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _display\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _display\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_display", "display",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasDisplay())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _order\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasOrder()) { return null; }\r
+ return new java.lang.Float(target.getOrder());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteOrder();\r
+ return;\r
+ }\r
+ target.setOrder( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _order\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- return (target.getDisplay() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // ignore null values for non optional primitives\r
- if (value == null)\r
- {\r
- return;\r
- }\r
-\r
- target.setDisplay(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _mincolour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasMincolour()) { return null; }\r
+ return new java.lang.Integer(target.getMincolour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMincolour();\r
+ return;\r
+ }\r
+ target.setMincolour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mincolour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _display\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _order\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_order", "order",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasOrder())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- return new java.lang.Float(target.getOrder());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteOrder();\r
- return;\r
- }\r
- target.setOrder(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshstate\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasThreshstate()) { return null; }\r
+ return new java.lang.Integer(target.getThreshstate());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshstate();\r
+ return;\r
+ }\r
+ target.setThreshstate( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshstate\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _order\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _mincolour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_mincolour", "mincolour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasMincolour())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _max\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasMax()) { return null; }\r
+ return new java.lang.Float(target.getMax());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMax();\r
+ return;\r
+ }\r
+ target.setMax( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _max\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- return new java.lang.Integer(target.getMincolour());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMincolour();\r
- return;\r
- }\r
- target.setMincolour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _min\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasMin()) { return null; }\r
+ return new java.lang.Float(target.getMin());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMin();\r
+ return;\r
+ }\r
+ target.setMin( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _min\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _mincolour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _threshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_threshold", "threshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasThreshold())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colourByLabel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasColourByLabel()) { return null; }\r
+ return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColourByLabel();\r
+ return;\r
+ }\r
+ target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colourByLabel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Float(target.getThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteThreshold();\r
- return;\r
- }\r
- target.setThreshold(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _autoScale\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Setting target = (Setting) object;\r
+ if (!target.hasAutoScale()) { return null; }\r
+ return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAutoScale();\r
+ return;\r
+ }\r
+ target.setAutoScale( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _autoScale\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _threshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _threshstate\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_threshstate", "threshstate",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasThreshstate())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getThreshstate());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteThreshstate();\r
- return;\r
- }\r
- target.setThreshstate(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _threshstate\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _max\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_max", "max",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasMax())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Float(target.getMax());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMax();\r
- return;\r
- }\r
- target.setMax(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _max\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _min\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_min", "min",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasMin())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Float(target.getMin());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMin();\r
- return;\r
- }\r
- target.setMin(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _min\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _colourByLabel\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasColourByLabel())\r
- {\r
- return null;\r
- }\r
- return (target.getColourByLabel() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColourByLabel();\r
- return;\r
- }\r
- target.setColourByLabel(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _colourByLabel\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Setting.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _autoScale\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_autoScale", "autoScale",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Setting target = (Setting) object;\r
- if (!target.hasAutoScale())\r
- {\r
- return null;\r
- }\r
- return (target.getAutoScale() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Setting target = (Setting) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteAutoScale();\r
- return;\r
- }\r
- target.setAutoScale(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _autoScale\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Setting.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.StructureState;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class StructureStateDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public StructureStateDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "structureState";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_content", "PCDATA",\r
- org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- return target.getContent();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- target.setContent((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public StructureStateDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "structureState";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- _content\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ return target.getContent();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ target.setContent( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _content\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- initialize attribute descriptors\r
-\r
- // -- _visible\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_visible", "visible",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if (!target.hasVisible())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _visible\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasVisible()) { return null; }\r
+ return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteVisible();\r
+ return;\r
+ }\r
+ target.setVisible( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _visible\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return (target.getVisible() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteVisible();\r
- return;\r
- }\r
- target.setVisible(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _visible\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _xpos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_xpos", "xpos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if (!target.hasXpos())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getXpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteXpos();\r
- return;\r
- }\r
- target.setXpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _xpos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _ypos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_ypos", "ypos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if (!target.hasYpos())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getYpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteYpos();\r
- return;\r
- }\r
- target.setYpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _viewId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ return target.getViewId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ target.setViewId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _viewId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _ypos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _width\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_width", "width",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if (!target.hasWidth())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _linkAlignPanel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_linkAlignPanel", "linkAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasLinkAlignPanel()) { return null; }\r
+ return (target.getLinkAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteLinkAlignPanel();\r
+ return;\r
+ }\r
+ target.setLinkAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _linkAlignPanel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Integer(target.getWidth());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteWidth();\r
- return;\r
- }\r
- target.setWidth(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _alignwithAlignPanel\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ StructureState target = (StructureState) object;\r
+ if (!target.hasAlignwithAlignPanel()) { return null; }\r
+ return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ StructureState target = (StructureState) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteAlignwithAlignPanel();\r
+ return;\r
+ }\r
+ target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alignwithAlignPanel\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _width\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _height\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_height", "height",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if (!target.hasHeight())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getHeight());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteHeight();\r
- return;\r
- }\r
- target.setHeight(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _height\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _viewId\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_viewId", "viewId",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- return target.getViewId();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- StructureState target = (StructureState) object;\r
- target.setViewId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _viewId\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.StructureState.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.StructureState.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.ThresholdLine;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class ThresholdLineDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
+public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
\r
- public ThresholdLineDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "thresholdLine";\r
- _elementDefinition = true;\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
\r
- // -- _label\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_label", "label",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- return target.getLabel();\r
- }\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- target.setLabel((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ public ThresholdLineDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "thresholdLine";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _label\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ return target.getLabel();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ target.setLabel( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _label\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _label\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _value\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_value", "value",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- if (!target.hasValue())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _value\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ if (!target.hasValue()) { return null; }\r
+ return new java.lang.Float(target.getValue());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteValue();\r
+ return;\r
+ }\r
+ target.setValue( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _value\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- return new java.lang.Float(target.getValue());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteValue();\r
- return;\r
- }\r
- target.setValue(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ if (!target.hasColour()) { return null; }\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ ThresholdLine target = (ThresholdLine) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _value\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _colour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_colour", "colour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- if (!target.hasColour())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getColour());\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- ThresholdLine target = (ThresholdLine) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteColour();\r
- return;\r
- }\r
- target.setColour(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _colour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.ThresholdLine.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.ThresholdLine.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Tree;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class TreeDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public TreeDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "tree";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _width\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_width", "width",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasWidth())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getWidth());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteWidth();\r
- return;\r
- }\r
- target.setWidth(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public TreeDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "tree";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _width\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _height\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_height", "height",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasHeight())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getHeight());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteHeight();\r
- return;\r
- }\r
- target.setHeight(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _height\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _xpos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_xpos", "xpos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasXpos())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getXpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteXpos();\r
- return;\r
- }\r
- target.setXpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getFontName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setFontName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _xpos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _ypos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_ypos", "ypos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasYpos())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontSize\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFontSize()) { return null; }\r
+ return new java.lang.Integer(target.getFontSize());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontSize();\r
+ return;\r
+ }\r
+ target.setFontSize( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontSize\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- return new java.lang.Integer(target.getYpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteYpos();\r
- return;\r
- }\r
- target.setYpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontStyle\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFontStyle()) { return null; }\r
+ return new java.lang.Integer(target.getFontStyle());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontStyle();\r
+ return;\r
+ }\r
+ target.setFontStyle( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontStyle\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _ypos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontName\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_fontName", "fontName",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- return target.getFontName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- target.setFontName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _fontName\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontSize\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_fontSize", "fontSize",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasFontSize())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showBootstrap\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasShowBootstrap()) { return null; }\r
+ return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowBootstrap();\r
+ return;\r
+ }\r
+ target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showBootstrap\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Integer(target.getFontSize());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFontSize();\r
- return;\r
- }\r
- target.setFontSize(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showDistances\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasShowDistances()) { return null; }\r
+ return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowDistances();\r
+ return;\r
+ }\r
+ target.setShowDistances( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showDistances\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _fontSize\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontStyle\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_fontStyle", "fontStyle",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasFontStyle())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _markUnlinked\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasMarkUnlinked()) { return null; }\r
+ return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMarkUnlinked();\r
+ return;\r
+ }\r
+ target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _markUnlinked\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Integer(target.getFontStyle());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFontStyle();\r
- return;\r
- }\r
- target.setFontStyle(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fitToWindow\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasFitToWindow()) { return null; }\r
+ return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFitToWindow();\r
+ return;\r
+ }\r
+ target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fitToWindow\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _fontStyle\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _threshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Float.TYPE, "_threshold", "threshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasThreshold())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- _currentTree\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ if (!target.hasCurrentTree()) { return null; }\r
+ return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteCurrentTree();\r
+ return;\r
+ }\r
+ target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _currentTree\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- return new java.lang.Float(target.getThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteThreshold();\r
- return;\r
- }\r
- target.setThreshold(((java.lang.Float) value).floatValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ super.setIdentity(desc);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new java.lang.String();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IdValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _threshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive((float) -3.4028235E38);\r
- typeValidator.setMaxInclusive((float) 3.4028235E38);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showBootstrap\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasShowBootstrap())\r
- {\r
- return null;\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _title\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getTitle();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setTitle( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _title\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- return (target.getShowBootstrap() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowBootstrap();\r
- return;\r
- }\r
- target.setShowBootstrap(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _newick\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Tree target = (Tree) object;\r
+ return target.getNewick();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Tree target = (Tree) object;\r
+ target.setNewick( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _newick\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showBootstrap\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _showDistances\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showDistances", "showDistances",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasShowDistances())\r
- {\r
- return null;\r
- }\r
- return (target.getShowDistances() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowDistances();\r
- return;\r
- }\r
- target.setShowDistances(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _showDistances\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _markUnlinked\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasMarkUnlinked())\r
- {\r
- return null;\r
- }\r
- return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteMarkUnlinked();\r
- return;\r
- }\r
- target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _markUnlinked\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _fitToWindow\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasFitToWindow())\r
- {\r
- return null;\r
- }\r
- return (target.getFitToWindow() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFitToWindow();\r
- return;\r
- }\r
- target.setFitToWindow(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _fitToWindow\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _currentTree\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_currentTree", "currentTree",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- if (!target.hasCurrentTree())\r
- {\r
- return null;\r
- }\r
- return (target.getCurrentTree() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteCurrentTree();\r
- return;\r
- }\r
- target.setCurrentTree(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _currentTree\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Tree.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- super.setIdentity(desc);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IdValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _title\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_title", "title",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- return target.getTitle();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- target.setTitle((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _title\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _newick\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_newick", "newick",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Tree target = (Tree) object;\r
- return target.getNewick();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Tree target = (Tree) object;\r
- target.setNewick((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _newick\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Tree.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.UserColourScheme;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColourSchemeDescriptor\r
- extends\r
- jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public UserColourSchemeDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "UserColourScheme";\r
- _elementDefinition = true;\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.UserColourScheme.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColourSchemeDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "UserColourScheme";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.UserColourScheme.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.UserColours;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColoursDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public UserColoursDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "UserColours";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- UserColours target = (UserColours) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- UserColours target = (UserColours) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColoursDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "UserColours";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ UserColours target = (UserColours) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ UserColours target = (UserColours) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _userColourScheme\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ UserColours target = (UserColours) object;\r
+ return target.getUserColourScheme();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ UserColours target = (UserColours) object;\r
+ target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.UserColourScheme();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _userColourScheme\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
\r
- // -- _userColourScheme\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.UserColourScheme.class,\r
- "_userColourScheme", "UserColourScheme",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- UserColours target = (UserColours) object;\r
- return target.getUserColourScheme();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- UserColours target = (UserColours) object;\r
- target.setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.UserColourScheme();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _userColourScheme\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.UserColours.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.UserColours.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.VAMSAS;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class VAMSASDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public VAMSASDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
- _xmlName = "VAMSAS";\r
- _elementDefinition = false;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- initialize element descriptors\r
-\r
- // -- _treeList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_treeList", "Tree",\r
- org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- return target.getTree();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- target.addTree((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VAMSASDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "VAMSAS";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _treeList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ VAMSAS target = (VAMSAS) object;\r
+ return target.getTree();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.addTree( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.removeAllTree();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _treeList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
}\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- target.removeAllTree();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ VAMSAS target = (VAMSAS) object;\r
+ return target.getSequenceSet();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ VAMSAS target = (VAMSAS) object;\r
+ target.removeAllSequenceSet();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.SequenceSet();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
}\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _treeList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _sequenceSetList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.SequenceSet.class,\r
- "_sequenceSetList", "SequenceSet",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- return target.getSequenceSet();\r
- }\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- target.addSequenceSet((jalview.schemabinding.version2.SequenceSet) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- VAMSAS target = (VAMSAS) object;\r
- target.removeAllSequenceSet();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.SequenceSet();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- // -- validation code for: _sequenceSetList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.VAMSAS.class;\r
- }\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.VAMSAS.class;\r
+ }\r
\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.VamsasModel;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class VamsasModelDescriptor extends\r
- jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public VamsasModelDescriptor()\r
- {\r
- super();\r
- setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "vamsasModel";\r
- _elementDefinition = true;\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.VamsasModel.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
+public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VamsasModelDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "vamsasModel";\r
+ _elementDefinition = true;\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.VamsasModel.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
\r
}\r
/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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.descriptors;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import jalview.schemabinding.version2.Viewport;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class ViewportDescriptor extends\r
- org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _elementDefinition.\r
- */\r
- private boolean _elementDefinition;\r
-\r
- /**\r
- * Field _nsPrefix.\r
- */\r
- private java.lang.String _nsPrefix;\r
-\r
- /**\r
- * Field _nsURI.\r
- */\r
- private java.lang.String _nsURI;\r
-\r
- /**\r
- * Field _xmlName.\r
- */\r
- private java.lang.String _xmlName;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public ViewportDescriptor()\r
- {\r
- super();\r
- _nsURI = "www.jalview.org";\r
- _xmlName = "Viewport";\r
- _elementDefinition = true;\r
-\r
- // -- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- // -- initialize attribute descriptors\r
-\r
- // -- _conservationSelected\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_conservationSelected",\r
- "conservationSelected",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasConservationSelected())\r
- {\r
- return null;\r
- }\r
- return (target.getConservationSelected() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteConservationSelected();\r
- return;\r
- }\r
- target.setConservationSelected(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _conservationSelected\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _pidSelected\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_pidSelected", "pidSelected",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasPidSelected())\r
- {\r
- return null;\r
- }\r
- return (target.getPidSelected() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePidSelected();\r
- return;\r
- }\r
- target.setPidSelected(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pidSelected\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _bgColour\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_bgColour", "bgColour",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getBgColour();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setBgColour((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _bgColour\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _consThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_consThreshold", "consThreshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasConsThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getConsThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteConsThreshold();\r
- return;\r
- }\r
- target.setConsThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _consThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _pidThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasPidThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getPidThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deletePidThreshold();\r
- return;\r
- }\r
- target.setPidThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _pidThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _title\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_title", "title",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getTitle();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setTitle((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _title\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showFullId\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showFullId", "showFullId",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowFullId())\r
- {\r
- return null;\r
- }\r
- return (target.getShowFullId() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowFullId();\r
- return;\r
- }\r
- target.setShowFullId(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showFullId\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _rightAlignIds\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasRightAlignIds())\r
- {\r
- return null;\r
- }\r
- return (target.getRightAlignIds() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteRightAlignIds();\r
- return;\r
- }\r
- target.setRightAlignIds(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _rightAlignIds\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showText\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showText", "showText",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowText())\r
- {\r
- return null;\r
- }\r
- return (target.getShowText() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowText();\r
- return;\r
- }\r
- target.setShowText(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showText\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showColourText\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showColourText", "showColourText",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowColourText())\r
- {\r
- return null;\r
- }\r
- return (target.getShowColourText() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowColourText();\r
- return;\r
- }\r
- target.setShowColourText(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showColourText\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showUnconserved\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowUnconserved())\r
- {\r
- return null;\r
- }\r
- return (target.getShowUnconserved() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowUnconserved();\r
- return;\r
- }\r
- target.setShowUnconserved(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showUnconserved\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showBoxes\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showBoxes", "showBoxes",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowBoxes())\r
- {\r
- return null;\r
- }\r
- return (target.getShowBoxes() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowBoxes();\r
- return;\r
- }\r
- target.setShowBoxes(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showBoxes\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _wrapAlignment\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasWrapAlignment())\r
- {\r
- return null;\r
- }\r
- return (target.getWrapAlignment() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteWrapAlignment();\r
- return;\r
- }\r
- target.setWrapAlignment(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _wrapAlignment\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _renderGaps\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_renderGaps", "renderGaps",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasRenderGaps())\r
- {\r
- return null;\r
- }\r
- return (target.getRenderGaps() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteRenderGaps();\r
- return;\r
- }\r
- target.setRenderGaps(((java.lang.Boolean) value).booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _renderGaps\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showSequenceFeatures\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showSequenceFeatures",\r
- "showSequenceFeatures",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowSequenceFeatures())\r
- {\r
- return null;\r
- }\r
- return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowSequenceFeatures();\r
- return;\r
- }\r
- target.setShowSequenceFeatures(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showSequenceFeatures\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showNPfeatureTooltip\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showNPfeatureTooltip",\r
- "showNPfeatureTooltip",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowNPfeatureTooltip())\r
- {\r
- return null;\r
- }\r
- return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowNPfeatureTooltip();\r
- return;\r
- }\r
- target.setShowNPfeatureTooltip(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showNPfeatureTooltip\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showDbRefTooltip\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showDbRefTooltip",\r
- "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowDbRefTooltip())\r
- {\r
- return null;\r
- }\r
- return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowDbRefTooltip();\r
- return;\r
- }\r
- target.setShowDbRefTooltip(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showDbRefTooltip\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _followHighlight\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_followHighlight", "followHighlight",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasFollowHighlight())\r
- {\r
- return null;\r
- }\r
- return (target.getFollowHighlight() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFollowHighlight();\r
- return;\r
- }\r
- target.setFollowHighlight(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _followHighlight\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _followSelection\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_followSelection", "followSelection",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasFollowSelection())\r
- {\r
- return null;\r
- }\r
- return (target.getFollowSelection() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFollowSelection();\r
- return;\r
- }\r
- target.setFollowSelection(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _followSelection\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showAnnotation\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowAnnotation())\r
- {\r
- return null;\r
- }\r
- return (target.getShowAnnotation() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowAnnotation();\r
- return;\r
- }\r
- target.setShowAnnotation(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showAnnotation\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public ViewportDescriptor() {\r
+ super();\r
+ _nsURI = "www.jalview.org";\r
+ _xmlName = "Viewport";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _conservationSelected\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasConservationSelected()) { return null; }\r
+ return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConservationSelected();\r
+ return;\r
+ }\r
+ target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _conservationSelected\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidSelected\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasPidSelected()) { return null; }\r
+ return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidSelected();\r
+ return;\r
+ }\r
+ target.setPidSelected( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidSelected\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _bgColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getBgColour();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setBgColour( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _bgColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _consThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasConsThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getConsThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteConsThreshold();\r
+ return;\r
+ }\r
+ target.setConsThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _consThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pidThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasPidThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getPidThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePidThreshold();\r
+ return;\r
+ }\r
+ target.setPidThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pidThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _title\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getTitle();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setTitle( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _title\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showFullId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowFullId()) { return null; }\r
+ return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowFullId();\r
+ return;\r
+ }\r
+ target.setShowFullId( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showFullId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _rightAlignIds\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasRightAlignIds()) { return null; }\r
+ return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteRightAlignIds();\r
+ return;\r
+ }\r
+ target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _rightAlignIds\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowText()) { return null; }\r
+ return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowText();\r
+ return;\r
+ }\r
+ target.setShowText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showColourText\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowColourText()) { return null; }\r
+ return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowColourText();\r
+ return;\r
+ }\r
+ target.setShowColourText( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showColourText\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showUnconserved\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowUnconserved()) { return null; }\r
+ return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowUnconserved();\r
+ return;\r
+ }\r
+ target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showUnconserved\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showBoxes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowBoxes()) { return null; }\r
+ return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowBoxes();\r
+ return;\r
+ }\r
+ target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showBoxes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _wrapAlignment\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasWrapAlignment()) { return null; }\r
+ return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWrapAlignment();\r
+ return;\r
+ }\r
+ target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _wrapAlignment\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _renderGaps\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasRenderGaps()) { return null; }\r
+ return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteRenderGaps();\r
+ return;\r
+ }\r
+ target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _renderGaps\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showSequenceFeatures\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowSequenceFeatures()) { return null; }\r
+ return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowSequenceFeatures();\r
+ return;\r
+ }\r
+ target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showSequenceFeatures\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showNPfeatureTooltip\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowNPfeatureTooltip()) { return null; }\r
+ return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowNPfeatureTooltip();\r
+ return;\r
+ }\r
+ target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showNPfeatureTooltip\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showDbRefTooltip\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowDbRefTooltip()) { return null; }\r
+ return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowDbRefTooltip();\r
+ return;\r
+ }\r
+ target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showDbRefTooltip\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _followHighlight\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFollowHighlight()) { return null; }\r
+ return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFollowHighlight();\r
+ return;\r
+ }\r
+ target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _followHighlight\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _followSelection\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFollowSelection()) { return null; }\r
+ return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFollowSelection();\r
+ return;\r
+ }\r
+ target.setFollowSelection( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _followSelection\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showAnnotation\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowAnnotation()) { return null; }\r
+ return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowAnnotation();\r
+ return;\r
+ }\r
+ target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showAnnotation\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _centreColumnLabels\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasCentreColumnLabels()) { return null; }\r
+ return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteCentreColumnLabels();\r
+ return;\r
+ }\r
+ target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _centreColumnLabels\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showGroupConservation\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowGroupConservation()) { return null; }\r
+ return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowGroupConservation();\r
+ return;\r
+ }\r
+ target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showGroupConservation\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showGroupConsensus\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowGroupConsensus()) { return null; }\r
+ return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowGroupConsensus();\r
+ return;\r
+ }\r
+ target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showGroupConsensus\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showConsensusHistogram\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowConsensusHistogram()) { return null; }\r
+ return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowConsensusHistogram();\r
+ return;\r
+ }\r
+ target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showConsensusHistogram\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _showSequenceLogo\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasShowSequenceLogo()) { return null; }\r
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteShowSequenceLogo();\r
+ return;\r
+ }\r
+ target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _showSequenceLogo\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ignoreGapsinConsensus\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasIgnoreGapsinConsensus()) { return null; }\r
+ return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteIgnoreGapsinConsensus();\r
+ return;\r
+ }\r
+ target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ignoreGapsinConsensus\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _xpos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasXpos()) { return null; }\r
+ return new java.lang.Integer(target.getXpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteXpos();\r
+ return;\r
+ }\r
+ target.setXpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _xpos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _ypos\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasYpos()) { return null; }\r
+ return new java.lang.Integer(target.getYpos());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteYpos();\r
+ return;\r
+ }\r
+ target.setYpos( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _ypos\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _width\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasWidth()) { return null; }\r
+ return new java.lang.Integer(target.getWidth());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteWidth();\r
+ return;\r
+ }\r
+ target.setWidth( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _width\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _height\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasHeight()) { return null; }\r
+ return new java.lang.Integer(target.getHeight());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHeight();\r
+ return;\r
+ }\r
+ target.setHeight( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _height\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _startRes\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasStartRes()) { return null; }\r
+ return new java.lang.Integer(target.getStartRes());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStartRes();\r
+ return;\r
+ }\r
+ target.setStartRes( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _startRes\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _startSeq\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasStartSeq()) { return null; }\r
+ return new java.lang.Integer(target.getStartSeq());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStartSeq();\r
+ return;\r
+ }\r
+ target.setStartSeq( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _startSeq\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getFontName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setFontName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontSize\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFontSize()) { return null; }\r
+ return new java.lang.Integer(target.getFontSize());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontSize();\r
+ return;\r
+ }\r
+ target.setFontSize( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontSize\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _fontStyle\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasFontStyle()) { return null; }\r
+ return new java.lang.Integer(target.getFontStyle());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteFontStyle();\r
+ return;\r
+ }\r
+ target.setFontStyle( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _fontStyle\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _viewName\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getViewName();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setViewName( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _viewName\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _sequenceSetId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getSequenceSetId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setSequenceSetId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequenceSetId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _gatheredViews\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasGatheredViews()) { return null; }\r
+ return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGatheredViews();\r
+ return;\r
+ }\r
+ target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _gatheredViews\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextCol1()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol1();\r
+ return;\r
+ }\r
+ target.setTextCol1( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textCol2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextCol2()) { return null; }\r
+ return new java.lang.Integer(target.getTextCol2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextCol2();\r
+ return;\r
+ }\r
+ target.setTextCol2( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textCol2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _textColThreshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ if (!target.hasTextColThreshold()) { return null; }\r
+ return new java.lang.Integer(target.getTextColThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteTextColThreshold();\r
+ return;\r
+ }\r
+ target.setTextColThreshold( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _textColThreshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _id\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+ super.setIdentity(desc);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new java.lang.String();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _id\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IdValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _annotationColours\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getAnnotationColours();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AnnotationColours();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _annotationColours\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _hiddenColumnsList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getHiddenColumns();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.removeAllHiddenColumns();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.HiddenColumns();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenColumnsList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _centreColumnLabels\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_centreColumnLabels",\r
- "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasCentreColumnLabels())\r
- {\r
- return null;\r
- }\r
- return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteCentreColumnLabels();\r
- return;\r
- }\r
- target.setCentreColumnLabels(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _centreColumnLabels\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showGroupConservation\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showGroupConservation",\r
- "showGroupConservation",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowGroupConservation())\r
- {\r
- return null;\r
- }\r
- return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowGroupConservation();\r
- return;\r
- }\r
- target.setShowGroupConservation(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showGroupConservation\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showGroupConsensus\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showGroupConsensus",\r
- "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowGroupConsensus())\r
- {\r
- return null;\r
- }\r
- return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowGroupConsensus();\r
- return;\r
- }\r
- target.setShowGroupConsensus(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showGroupConsensus\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showConsensusHistogram\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showConsensusHistogram",\r
- "showConsensusHistogram",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowConsensusHistogram())\r
- {\r
- return null;\r
- }\r
- return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowConsensusHistogram();\r
- return;\r
- }\r
- target.setShowConsensusHistogram(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showConsensusHistogram\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _showSequenceLogo\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_showSequenceLogo",\r
- "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasShowSequenceLogo())\r
- {\r
- return null;\r
- }\r
- return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteShowSequenceLogo();\r
- return;\r
- }\r
- target.setShowSequenceLogo(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _showSequenceLogo\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _ignoreGapsinConsensus\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",\r
- "ignoreGapsinConsensus",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasIgnoreGapsinConsensus())\r
- {\r
- return null;\r
- }\r
- return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteIgnoreGapsinConsensus();\r
- return;\r
- }\r
- target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _ignoreGapsinConsensus\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _xpos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_xpos", "xpos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasXpos())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getXpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteXpos();\r
- return;\r
- }\r
- target.setXpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _xpos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _ypos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_ypos", "ypos",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasYpos())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getYpos());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteYpos();\r
- return;\r
- }\r
- target.setYpos(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _ypos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _width\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_width", "width",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasWidth())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getWidth());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteWidth();\r
- return;\r
- }\r
- target.setWidth(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _width\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _height\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_height", "height",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasHeight())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getHeight());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteHeight();\r
- return;\r
- }\r
- target.setHeight(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _height\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _startRes\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_startRes", "startRes",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasStartRes())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getStartRes());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteStartRes();\r
- return;\r
- }\r
- target.setStartRes(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _startRes\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _startSeq\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_startSeq", "startSeq",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasStartSeq())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getStartSeq());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteStartSeq();\r
- return;\r
- }\r
- target.setStartSeq(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _startSeq\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontName\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_fontName", "fontName",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getFontName();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setFontName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _fontName\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontSize\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_fontSize", "fontSize",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasFontSize())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getFontSize());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFontSize();\r
- return;\r
- }\r
- target.setFontSize(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _fontSize\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _fontStyle\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_fontStyle", "fontStyle",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasFontStyle())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getFontStyle());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteFontStyle();\r
- return;\r
- }\r
- target.setFontStyle(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _fontStyle\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _viewName\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_viewName", "viewName",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getViewName();\r
- }\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setViewName((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _viewName\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _sequenceSetId\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_sequenceSetId", "sequenceSetId",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getSequenceSetId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setSequenceSetId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _sequenceSetId\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.StringValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setWhiteSpace("preserve");\r
- }\r
- desc.setValidator(fieldValidator);\r
- // -- _gatheredViews\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasGatheredViews())\r
- {\r
- return null;\r
- }\r
- return (target.getGatheredViews() ? java.lang.Boolean.TRUE\r
- : java.lang.Boolean.FALSE);\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteGatheredViews();\r
- return;\r
- }\r
- target.setGatheredViews(((java.lang.Boolean) value)\r
- .booleanValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _gatheredViews\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _textCol1\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textCol1", "textCol1",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasTextCol1())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextCol1());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextCol1();\r
- return;\r
- }\r
- target.setTextCol1(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _textCol1\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Viewport.class;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _textCol2\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textCol2", "textCol2",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasTextCol2())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextCol2());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextCol2();\r
- return;\r
- }\r
- target.setTextCol2(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _textCol2\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _textColThreshold\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.Integer.TYPE, "_textColThreshold",\r
- "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- if (!target.hasTextColThreshold())\r
- {\r
- return null;\r
- }\r
- return new java.lang.Integer(target.getTextColThreshold());\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- // if null, use delete method for optional primitives\r
- if (value == null)\r
- {\r
- target.deleteTextColThreshold();\r
- return;\r
- }\r
- target.setTextColThreshold(((java.lang.Integer) value).intValue());\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _textColThreshold\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IntValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- typeValidator.setMinInclusive(-2147483648);\r
- typeValidator.setMaxInclusive(2147483647);\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- java.lang.String.class, "_id", "id",\r
- org.exolab.castor.xml.NodeType.Attribute);\r
- super.setIdentity(desc);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getId();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setId((java.lang.String) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
-\r
- // -- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
- org.exolab.castor.xml.validators.IdValidator typeValidator;\r
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();\r
- fieldValidator.setValidator(typeValidator);\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- initialize element descriptors\r
-\r
- // -- _annotationColours\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.AnnotationColours.class,\r
- "_annotationColours", "AnnotationColours",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getAnnotationColours();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.AnnotationColours();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _annotationColours\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { // -- local scope\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
}\r
- desc.setValidator(fieldValidator);\r
- // -- _hiddenColumnsList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(\r
- jalview.schemabinding.version2.HiddenColumns.class,\r
- "_hiddenColumnsList", "hiddenColumns",\r
- org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler()\r
- {\r
- public java.lang.Object getValue(java.lang.Object object)\r
- throws IllegalStateException\r
- {\r
- Viewport target = (Viewport) object;\r
- return target.getHiddenColumns();\r
- }\r
-\r
- public void setValue(java.lang.Object object, java.lang.Object value)\r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value);\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public void resetValue(Object object) throws IllegalStateException,\r
- IllegalArgumentException\r
- {\r
- try\r
- {\r
- Viewport target = (Viewport) object;\r
- target.removeAllHiddenColumns();\r
- } catch (java.lang.Exception ex)\r
- {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
-\r
- public java.lang.Object newInstance(java.lang.Object parent)\r
- {\r
- return new jalview.schemabinding.version2.HiddenColumns();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("www.jalview.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
\r
- // -- validation code for: _hiddenColumnsList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { // -- local scope\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
}\r
- desc.setValidator(fieldValidator);\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * Method getAccessMode.\r
- * \r
- * @return the access mode specified for this class.\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- }\r
-\r
- /**\r
- * Method getIdentity.\r
- * \r
- * @return the identity field, null if this class has no identity.\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return super.getIdentity();\r
- }\r
-\r
- /**\r
- * Method getJavaClass.\r
- * \r
- * @return the Java class represented by this descriptor.\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.Viewport.class;\r
- }\r
-\r
- /**\r
- * Method getNameSpacePrefix.\r
- * \r
- * @return the namespace prefix to use when marshaling as XML.\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return _nsPrefix;\r
- }\r
-\r
- /**\r
- * Method getNameSpaceURI.\r
- * \r
- * @return the namespace URI used when marshaling and unmarshaling as XML.\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return _nsURI;\r
- }\r
-\r
- /**\r
- * Method getValidator.\r
- * \r
- * @return a specific validator for the class described by this\r
- * ClassDescriptor.\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- }\r
-\r
- /**\r
- * Method getXMLName.\r
- * \r
- * @return the XML Name for the Class being described.\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return _xmlName;\r
- }\r
-\r
- /**\r
- * Method isElementDefinition.\r
- * \r
- * @return true if XML schema definition of this Class is that of a global\r
- * element or element with anonymous type definition.\r
- */\r
- public boolean isElementDefinition()\r
- {\r
- return _elementDefinition;\r
- }\r
\r
}\r
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * 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.descriptors;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.WebServiceParameterSet;
*
* @version $Revision$ $Date$
*/
-public class WebServiceParameterSetDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public WebServiceParameterSetDescriptor()
- {
- super();
- _nsURI = "www.jalview.org/xml/wsparamset";
- _xmlName = "WebServiceParameterSet";
- _elementDefinition = false;
-
- // -- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- // -- initialize attribute descriptors
-
- // -- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_name", "name",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getName();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setName((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+public class WebServiceParameterSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public WebServiceParameterSetDescriptor() {
+ super();
+ _nsURI = "www.jalview.org/xml/wsparamset";
+ _xmlName = "WebServiceParameterSet";
+ _elementDefinition = false;
+
+ //-- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setName( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
-
- // -- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_version", "Version",
- org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getVersion();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setVersion((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ //-- _version
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getVersion();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setVersion( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _version
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_description", "description",
- org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getDescription();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setDescription((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _description
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getDescription();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setDescription( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _description
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _serviceURLList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_serviceURLList", "serviceURL",
- org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getServiceURL();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.addServiceURL((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _serviceURLList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_serviceURLList", "serviceURL", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getServiceURL();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.addServiceURL( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.removeAllServiceURL();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _serviceURLList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
}
- }
-
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.removeAllServiceURL();
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _parameters
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_parameters", "parameters", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ return target.getParameters();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ WebServiceParameterSet target = (WebServiceParameterSet) object;
+ target.setParameters( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _parameters
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- // -- validation code for: _serviceURLList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { // -- local scope
+ desc.setValidator(fieldValidator);
}
- desc.setValidator(fieldValidator);
- // -- _parameters
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_parameters", "parameters",
- org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- return target.getParameters();
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- WebServiceParameterSet target = (WebServiceParameterSet) object;
- target.setParameters((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
+ //-----------/
+ //- Methods -/
+ //-----------/
- // -- validation code for: _parameters
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
+ return null;
}
- desc.setValidator(fieldValidator);
- }
-
- // -----------/
- // - Methods -/
- // -----------/
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return super.getIdentity();
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass()
- {
- return jalview.schemabinding.version2.WebServiceParameterSet.class;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.WebServiceParameterSet.class;
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix()
- {
- return _nsPrefix;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI()
- {
- return _nsURI;
- }
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator()
- {
- return this;
- }
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName()
- {
- return _xmlName;
- }
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName(
+ ) {
+ return _xmlName;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition()
- {
- return _elementDefinition;
- }
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that
+ * of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition(
+ ) {
+ return _elementDefinition;
+ }
}
git://source.jalview.org / jalview.git / commitdiff