/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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/>.
*/
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Annotation implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _graph.
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _graphType.
- */
- private int _graphType;
-
- /**
- * keeps track of state for field: _graphType
- */
- private boolean _has_graphType;
-
- /**
- * Field _annotationElementList.
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Annotation() {
- super();
- this._annotationElementList = new java.util.Vector();
+public class Annotation implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Annotation()
+ {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph()
+ {
+ this._has_graph = false;
+ }
+
+ /**
+ */
+ public void deleteGraphType()
+ {
+ this._has_graphType = false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all jalview.binding.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.AnnotationElement at the given
+ * index
+ */
+ public jalview.binding.AnnotationElement getAnnotationElement(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
}
-
- //-----------/
- //- 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);
+ 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;
}
-
- /**
- */
- 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);
- }
-
- /**
- * 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;
+ 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) + "]");
}
- /**
- * 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);
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff