<classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
<classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
<classpathentry kind="lib" path="lib/java-json.jar"/>
+ <classpathentry kind="lib" path="lib/Jmol-14.2.14_2015.06.11.jar"/>
+ <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
<classpathentry kind="output" path="classes"/>
</classpath>
public SequenceStructureBinding addStructureViewInstance(
Object jmolviewer, String[] sequenceIds)
{
- // TODO method never called - remove?
- org.jmol.api.JmolViewer viewer = null;
+ Viewer viewer = null;
try
{
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
System.err.println("Unsupported viewer object :"
/*
-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--//- Imported classes and packages -/
--//---------------------------------/
--
--import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getAnnotationElement",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
-- }));
++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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setAnnotationElement",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
-- }));
++
++ /**
++ *
++ *
++ * @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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
--//---------------------------------/
--//- Imported classes and packages -/
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--import jalview.util.MessageManager;
--
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getSetting",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._settingList.size() - 1)).toString()
-- }));
++ /**
++ *
++ *
++ * @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setSetting",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._settingList.size() - 1)).toString()
-- }));
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 -/
++ //----------------/
++
++ public Features() {
++ super();
++ }
++
-- // -----------/
-- // - Methods -/
-- // -----------/
++ //-----------/
++ //- 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;
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--//- Imported classes and packages -/
--//---------------------------------/
--
--import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getSeq",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._seqList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setSeq",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._seqList.size() - 1)).toString()
-- }));
-- }
--
-- 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--//- Imported classes and packages -/
--//---------------------------------/
--
--import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getFeatures",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._featuresList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getPdbids",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setFeatures",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._featuresList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setPdbids",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
-- }));
-- }
--
-- 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--//- Imported classes and packages -/
--//---------------------------------/
--
--import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getJGroup",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._JGroupList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getJSeq",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._JSeqList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getJgetTreeSeq",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._treeList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getUserColours",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._userColoursList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getViewport",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._viewportList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setJGroup",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._JGroupList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setJSeq",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._JSeqList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setTree",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._treeList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setUserColours",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._userColoursList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setViewport",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._viewportList.size() - 1)).toString()
-- }));
-- }
--
-- 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
--//---------------------------------/
--//- Imported classes and packages -/
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--import jalview.util.MessageManager;
--
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getColour",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._colourList.size() - 1)).toString()
-- }));
++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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setColour",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._colourList.size() - 1)).toString()
-- }));
++ 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
--//---------------------------------/
--//- Imported classes and packages -/
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--import jalview.util.MessageManager;
--
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getPdbentryItem",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._items.size() - 1)).toString()
-- }));
++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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setPdbentryItem",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._items.size() - 1)).toString()
-- }));
++ 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
--package jalview.binding;
--import jalview.util.MessageManager;
++package jalview.binding;
/**
* Class PdbentryItem.
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getProperty",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._propertyList.size() - 1)).toString()
-- }));
++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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setProperty",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._propertyList.size() - 1)).toString()
-- }));
++ 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 -/
++ //----------------/
++
++ public Pdbids() {
++ super();
++ }
++
-- // -----------/
-- // - Methods -/
-- // -----------/
++ //-----------/
++ //- 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;
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 -/
++ //----------------/
++
++ public Sequence() {
++ super();
++ }
++
-- // -----------/
-- // - Methods -/
-- // -----------/
++ //-----------/
++ //- 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;
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--//- Imported classes and packages -/
--//---------------------------------/
--
--import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getAnnotation",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._annotationList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getSequence",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._sequenceList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setAnnotation",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._annotationList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setSequence",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._sequenceList.size() - 1)).toString()
-- }));
-- }
--
-- 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 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 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 -/
++ //----------------/
++
++ public UserColourScheme() {
++ super();
++ }
++
-- // -----------/
-- // - Methods -/
-- // -----------/
++ //-----------/
++ //- 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;
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.binding;
--//---------------------------------/
--//- Imported classes and packages -/
++ //---------------------------------/
++ //- Imported classes and packages -/
//---------------------------------/
--import jalview.util.MessageManager;
--
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getAlignment",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._alignmentList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getSequenceSet",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "getTree",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._treeList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setAlignment",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._alignmentList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setSequenceSet",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
-- }));
-- }
--
-- 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-- "setTree",
-- Integer.valueOf(index).toString(),
-- Integer.valueOf((this._treeList.size() - 1)).toString()
-- }));
-- }
--
-- 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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 -/
++ //----------------/
++
++ public VamsasModel() {
++ super();
++ }
++
-- // -----------/
-- // - Methods -/
-- // -----------/
++ //-----------/
++ //- 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;
++ /**
++ * 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 ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
++ * This class was automatically generated with
++ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
++ * Schema.
++ * $Id$
*/
++
package jalview.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
*/
-- public void deleteConsThreshold()
-- {
-- this._has_consThreshold = false;
-- }
++ private boolean _has_width;
-- /**
++ /**
++ * Field _height.
*/
-- public void deleteConservationSelected()
-- {
-- this._has_conservationSelected = false;
-- }
++ private int _height;
-- /**
++ /**
++ * keeps track of state for field: _height
*/
-- public void deleteFontSize()
-- {
-- this._has_fontSize = false;
-- }
++ private boolean _has_height;
-- /**
++ /**
++ * Field _startRes.
*/
-- public void deleteFontStyle()
-- {
-- this._has_fontStyle = false;
-- }
++ private int _startRes;
-- /**
++ /**
++ * keeps track of state for field: _startRes
*/
-- public void deleteHeight()
-- {
-- this._has_height = false;
-- }
++ private boolean _has_startRes;
-- /**
++ /**
++ * Field _startSeq.
*/
-- public void deletePidSelected()
-- {
-- this._has_pidSelected = false;
-- }
++ private int _startSeq;
-- /**
++ /**
++ * keeps track of state for field: _startSeq
*/
-- public void deletePidThreshold()
-- {
-- this._has_pidThreshold = false;
-- }
++ private boolean _has_startSeq;
-- /**
++ /**
++ * Field _fontName.
*/
-- public void deleteRenderGaps()
-- {
-- this._has_renderGaps = false;
-- }
++ private java.lang.String _fontName;
-- /**
++ /**
++ * Field _fontSize.
*/
-- public void deleteShowAnnotation()
-- {
-- this._has_showAnnotation = false;
-- }
++ private int _fontSize;
-- /**
++ /**
++ * keeps track of state for field: _fontSize
*/
-- public void deleteShowBoxes()
-- {
-- this._has_showBoxes = false;
-- }
++ private boolean _has_fontSize;
-- /**
++ /**
++ * Field _fontStyle.
*/
-- public void deleteShowColourText()
-- {
-- this._has_showColourText = false;
-- }
++ private int _fontStyle;
-- /**
++ /**
++ * keeps track of state for field: _fontStyle
*/
-- public void deleteShowConservation()
-- {
-- this._has_showConservation = false;
-- }
++ private boolean _has_fontStyle;
-- /**
++
++ //----------------/
++ //- Constructors -/
++ //----------------/
++
++ public Viewport() {
++ super();
++ }
++
++
++ //-----------/
++ //- Methods -/
++ //-----------/
++
++ /**
++ */
++ public void deleteConsThreshold(
++ ) {
++ this._has_consThreshold= false;
++ }
++
++ /**
*/
-- public void deleteShowFullId()
-- {
-- this._has_showFullId = false;
-- }
++ public void deleteConservationSelected(
++ ) {
++ this._has_conservationSelected= false;
++ }
-- /**
++ /**
*/
-- public void deleteShowIdentity()
-- {
-- this._has_showIdentity = 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 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 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);
++ }
}
- #Wed Jun 17 15:04:02 BST 2015
-#Wed Jun 10 11:15:53 BST 2015
++#Fri Jun 26 14:22:47 BST 2015
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
//--------------------------/
/**
-- * handle for the calculation which uses this parameter set
++ * handle for the calculation which uses
++ * this parameter set
++ *
*/
private java.lang.String _calcId;
/**
-- * should the calculation be performed immediately after
-- * loading in order to refresh results
++ * should the calculation be performed
++ * immediately after loading in order to refresh results
++ *
*/
private boolean _needsUpdate = false;
private boolean _has_needsUpdate;
/**
-- * should the calculation be automatically performed on edits
++ * should the calculation be automatically
++ * performed on edits
++ *
*/
private boolean _autoUpdate;
/**
* Returns the value of field 'autoUpdate'. The field
* 'autoUpdate' has the following description: should the
-- * calculation be automatically performed on edits
++ * calculation be automatically
++ * performed on edits
++ *
*
* @return the value of field 'AutoUpdate'.
*/
/**
* Returns the value of field 'calcId'. The field 'calcId' has
* the following description: handle for the calculation which
-- * uses this parameter set
++ * uses
++ * this parameter set
++ *
*
* @return the value of field 'CalcId'.
*/
/**
* Returns the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
-- * calculation be performed immediately after loading in order
-- * to refresh results
++ * calculation be performed
++ * immediately after loading in order to refresh results
++ *
*
* @return the value of field 'NeedsUpdate'.
*/
/**
* Returns the value of field 'autoUpdate'. The field
* 'autoUpdate' has the following description: should the
-- * calculation be automatically performed on edits
++ * calculation be automatically
++ * performed on edits
++ *
*
* @return the value of field 'AutoUpdate'.
*/
/**
* Returns the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
-- * calculation be performed immediately after loading in order
-- * to refresh results
++ * calculation be performed
++ * immediately after loading in order to refresh results
++ *
*
* @return the value of field 'NeedsUpdate'.
*/
/**
* Sets the value of field 'autoUpdate'. The field 'autoUpdate'
* has the following description: should the calculation be
-- * automatically performed on edits
++ * automatically
++ * performed on edits
++ *
*
* @param autoUpdate the value of field 'autoUpdate'.
*/
/**
* Sets the value of field 'calcId'. The field 'calcId' has the
* following description: handle for the calculation which uses
-- * this parameter set
++ * this parameter set
++ *
*
* @param calcId the value of field 'calcId'.
*/
/**
* Sets the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
-- * calculation be performed immediately after loading in order
-- * to refresh results
++ * calculation be performed
++ * immediately after loading in order to refresh results
++ *
*
* @param needsUpdate the value of field 'needsUpdate'.
*/
/**
* Optional sequence group ID (only
-- * needs to be unique for this
++ * needs to be
++ * unique for this
* alignment)
*
*/
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
-- * needs to be unique for this
++ * needs to be
++ * unique for this
* alignment)
*
*
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
-- * needs to be unique for this
++ * needs to be
++ * unique for this
* alignment)
*
*
/**
* Optional minimum colour
-- * for graduated feature
++ * for graduated
++ * feature
* colour
*
*/
* Returns the value of field 'mincolour'. The field
* 'mincolour' has the following description: Optional minimum
* colour
-- * for graduated feature
++ * for graduated
++ * feature
* colour
*
*
/**
* Sets the value of field 'mincolour'. The field 'mincolour'
* has the following description: Optional minimum colour
-- * for graduated feature
++ * for graduated
++ * feature
* colour
*
*
private boolean _has_colourByJmol;
/**
-- * An identifier for the viewer type, currently either
-- * JMOL or CHIMERA
++ * An
++ * identifier
++ * for
++ * the
++ * viewer
++ * type,
++ * currently
++ * either
++ * JMOL
++ * or
++ * CHIMERA
*
*/
private java.lang.String _type;
/**
* Returns the value of field 'type'. The field 'type' has the
-- * following description: An identifier for the viewer type,
-- * currently either
-- * JMOL or CHIMERA
++ * following description: An
++ * identifier
++ * for
++ * the
++ * viewer
++ * type,
++ * currently
++ * either
++ * JMOL
++ * or
++ * CHIMERA
*
*
* @return the value of field 'Type'.
/**
* Sets the value of field 'type'. The field 'type' has the
-- * following description: An identifier for the viewer type,
-- * currently either
-- * JMOL or CHIMERA
++ * following description: An
++ * identifier
++ * for
++ * the
++ * viewer
++ * type,
++ * currently
++ * either
++ * JMOL
++ * or
++ * CHIMERA
*
*
* @param type the value of field 'type'.
/**
* Tree ID added for binding tree
-- * visualization settings to vamsas
++ * visualization
++ * settings to vamsas
* document trees in jalview 2.4.1
*
*/
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: Tree ID added for binding tree
-- * visualization settings to vamsas
++ * visualization
++ * settings to vamsas
* document trees in jalview 2.4.1
*
*
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: Tree ID added for binding tree
-- * visualization settings to vamsas
++ * visualization
++ * settings to vamsas
* document trees in jalview 2.4.1
*
*
/**
* unique id used by jalview to
-- * synchronize between stored and
++ * synchronize
++ * between stored and
* instantiated views
*
*/
private java.lang.String _id;
/**
-- * The viewport id of this viewport's (cdna/protein) coding
-- * complement, if any
++ * The viewport id of this viewport's
++ * (cdna/protein) coding complement, if any
*
*/
private java.lang.String _complementId;
/**
* Returns the value of field 'complementId'. The field
* 'complementId' has the following description: The viewport
-- * id of this viewport's (cdna/protein) coding complement, if
-- * any
++ * id of this viewport's
++ * (cdna/protein) coding complement, if any
*
*
* @return the value of field 'ComplementId'.
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
-- * synchronize between stored and
++ * synchronize
++ * between stored and
* instantiated views
*
*
/**
* Sets the value of field 'complementId'. The field
* 'complementId' has the following description: The viewport
-- * id of this viewport's (cdna/protein) coding complement, if
-- * any
++ * id of this viewport's
++ * (cdna/protein) coding complement, if any
*
*
* @param complementId the value of field 'complementId'.
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
-- * synchronize between stored and
++ * synchronize
++ * between stored and
* instantiated views
*
*
git://source.jalview.org / jalview.git / commitdiff