/*
- * 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.schemabinding.version2;
+ //---------------------------------/
+ //- 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;
-
- /**
- * reference to set where jalview will gather the dataset sequences for all
- * sequences in the set.
- *
- */
- private java.lang.String _datasetId;
-
- /**
- * Field _sequenceList.
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList.
- */
- private java.util.Vector _annotationList;
-
- /**
- * Field _sequenceSetPropertiesList.
- */
- private java.util.Vector _sequenceSetPropertiesList;
-
- /**
- * Field _alcodonFrameList.
- */
- private java.util.Vector _alcodonFrameList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceSet()
- {
- super();
- this._sequenceList = new java.util.Vector();
- this._annotationList = new java.util.Vector();
- this._sequenceSetPropertiesList = new java.util.Vector();
- this._alcodonFrameList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alcodonFrameList.addElement(vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlcodonFrame(final int index,
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alcodonFrameList.add(index, vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotation(
- final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceList.add(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSetProperties(
- final int index,
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
- }
-
- /**
- * Method enumerateAlcodonFrame.
- *
- * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame
- * elements
- */
- public java.util.Enumeration enumerateAlcodonFrame()
- {
- return this._alcodonFrameList.elements();
- }
-
- /**
- * Method enumerateAnnotation.
- *
- * @return an Enumeration over all jalview.schemabinding.version2.Annotation
- * elements
- */
- public java.util.Enumeration enumerateAnnotation()
- {
- return this._annotationList.elements();
- }
-
- /**
- * Method enumerateSequence.
- *
- * @return an Enumeration over all jalview.schemabinding.version2.Sequence
- * elements
- */
- public java.util.Enumeration enumerateSequence()
- {
- return this._sequenceList.elements();
- }
-
- /**
- * Method enumerateSequenceSetProperties.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.SequenceSetProperties elements
- */
- public java.util.Enumeration enumerateSequenceSetProperties()
- {
- return this._sequenceSetPropertiesList.elements();
- }
-
- /**
- * Method getAlcodonFrame.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the
- * given inde
- */
- public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
- final int index) throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alcodonFrameList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getAlcodonFrame",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
- }));
- }
-
- return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
- .get(index);
- }
-
- /**
- * Method getAlcodonFrame.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()
- {
- jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
- return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList
- .toArray(array);
- }
-
- /**
- * Method getAlcodonFrameCount.
- *
- * @return the size of this collection
- */
- public int getAlcodonFrameCount()
- {
- return this._alcodonFrameList.size();
- }
-
- /**
- * 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.schemabinding.version2.Annotation at the
- * given index
- */
- public jalview.schemabinding.version2.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._alcodonFrameList.size() - 1)).toString()
- }));
- }
-
- return (jalview.schemabinding.version2.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.schemabinding.version2.Annotation[] getAnnotation()
- {
- jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
- return (jalview.schemabinding.version2.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 'datasetId'. The field 'datasetId' has the
- * following description: reference to set where jalview will gather the
- * dataset sequences for all sequences in the set.
- *
- *
- * @return the value of field 'DatasetId'.
- */
- public java.lang.String getDatasetId()
- {
- return this._datasetId;
- }
-
- /**
- * 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.schemabinding.version2.Sequence at the
- * given index
- */
- public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence[] getSequence()
- {
- jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
- return (jalview.schemabinding.version2.Sequence[]) this._sequenceList
- .toArray(array);
- }
-
- /**
- * Method getSequenceCount.
- *
- * @return the size of this collection
- */
- public int getSequenceCount()
- {
- return this._sequenceList.size();
- }
-
- /**
- * Method getSequenceSetProperties.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.SequenceSetProperties at the given
- * index
- */
- public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
- final int index) throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetPropertiesList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getSequenceSetProperties",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
- }));
- }
-
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
- .get(index);
- }
-
- /**
- * Method getSequenceSetProperties.Returns the contents of the collection in
- * an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
- {
- jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
- return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList
- .toArray(array);
- }
-
- /**
- * Method getSequenceSetPropertiesCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetPropertiesCount()
- {
- return this._sequenceSetPropertiesList.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 removeAlcodonFrame.
- *
- * @param vAlcodonFrame
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- {
- boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
- return removed;
- }
-
- /**
- * Method removeAlcodonFrameAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
- final int index)
- {
- java.lang.Object obj = this._alcodonFrameList.remove(index);
- return (jalview.schemabinding.version2.AlcodonFrame) obj;
- }
-
- /**
- */
- public void removeAllAlcodonFrame()
- {
- this._alcodonFrameList.clear();
- }
-
- /**
- */
- public void removeAllAnnotation()
- {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence()
- {
- this._sequenceList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSetProperties()
- {
- this._sequenceSetPropertiesList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.schemabinding.version2.Annotation vAnnotation)
- {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Annotation removeAnnotationAt(
- final int index)
- {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.schemabinding.version2.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(
- final jalview.schemabinding.version2.Sequence vSequence)
- {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Sequence removeSequenceAt(
- final int index)
- {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.schemabinding.version2.Sequence) obj;
- }
-
- /**
- * Method removeSequenceSetProperties.
- *
- * @param vSequenceSetProperties
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- {
- boolean removed = _sequenceSetPropertiesList
- .remove(vSequenceSetProperties);
- return removed;
- }
-
- /**
- * Method removeSequenceSetPropertiesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
- final int index)
- {
- java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
- return (jalview.schemabinding.version2.SequenceSetProperties) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlcodonFrame(final int index,
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alcodonFrameList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setAlcodonFrame",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
- }));
- }
-
- this._alcodonFrameList.set(index, vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param vAlcodonFrameArray
- */
- public void setAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)
- {
- // -- copy array
- _alcodonFrameList.clear();
-
- for (int i = 0; i < vAlcodonFrameArray.length; i++)
- {
- this._alcodonFrameList.add(vAlcodonFrameArray[i]);
- }
- }
-
- /**
- *
- *
- * @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.schemabinding.version2.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.schemabinding.version2.Annotation[] vAnnotationArray)
- {
- // -- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++)
- {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'datasetId'. The field 'datasetId' has the
- * following description: reference to set where jalview will gather the
- * dataset sequences for all sequences in the set.
- *
- *
- * @param datasetId
- * the value of field 'datasetId'.
- */
- public void setDatasetId(final java.lang.String datasetId)
- {
- this._datasetId = datasetId;
- }
-
- /**
- * 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.schemabinding.version2.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.schemabinding.version2.Sequence[] vSequenceArray)
- {
- // -- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++)
- {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequenceSetProperties(
- final int index,
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetPropertiesList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setSequenceSetProperties",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
- }));
- }
-
- this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
- }
-
- /**
- *
- *
- * @param vSequenceSetPropertiesArray
- */
- public void setSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)
- {
- // -- copy array
- _sequenceSetPropertiesList.clear();
-
- for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)
- {
- this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[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.schemabinding.version2.SequenceSet
- */
- public static jalview.schemabinding.version2.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.SequenceSet) Unmarshaller
- .unmarshal(jalview.schemabinding.version2.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;
+
+ /**
+ * reference to set where jalview will gather the dataset
+ * sequences for all sequences in the set.
+ *
+ */
+ private java.lang.String _datasetId;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+ /**
+ * Field _sequenceSetPropertiesList.
+ */
+ private java.util.Vector _sequenceSetPropertiesList;
+
+ /**
+ * Field _alcodonFrameList.
+ */
+ private java.util.Vector _alcodonFrameList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet() {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ this._sequenceSetPropertiesList = new java.util.Vector();
+ this._alcodonFrameList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodonFrameList.addElement(vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(
+ final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodonFrameList.add(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
+ }
+
+ /**
+ * Method enumerateAlcodonFrame.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.AlcodonFrame elements
+ */
+ public java.util.Enumeration enumerateAlcodonFrame(
+ ) {
+ return this._alcodonFrameList.elements();
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.Annotation elements
+ */
+ public java.util.Enumeration enumerateAnnotation(
+ ) {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.Sequence elements
+ */
+ public java.util.Enumeration enumerateSequence(
+ ) {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSetProperties.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SequenceSetProperties elements
+ */
+ public java.util.Enumeration enumerateSequenceSetProperties(
+ ) {
+ return this._sequenceSetPropertiesList.elements();
+ }
+
+ /**
+ * Method getAlcodonFrame.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.AlcodonFrame at the given inde
+ */
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size()) {
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);
+ }
+
+ /**
+ * Method getAlcodonFrame.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(
+ ) {
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);
+ }
+
+ /**
+ * Method getAlcodonFrameCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonFrameCount(
+ ) {
+ return this._alcodonFrameList.size();
+ }
+
+ /**
+ * 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.schemabinding.version2.Annotation at the given index
+ */
+ public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Annotation[] getAnnotation(
+ ) {
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
+ return (jalview.schemabinding.version2.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 'datasetId'. The field
+ * 'datasetId' has the following description: reference to set
+ * where jalview will gather the dataset sequences for all
+ * sequences in the set.
+ *
+ *
+ * @return the value of field 'DatasetId'.
+ */
+ public java.lang.String getDatasetId(
+ ) {
+ return this._datasetId;
+ }
+
+ /**
+ * 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.schemabinding.version2.Sequence at the given index
+ */
+ public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence[] getSequence(
+ ) {
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount(
+ ) {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method getSequenceSetProperties.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.SequenceSetProperties at the
+ * given index
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
+ throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);
+ }
+
+ /**
+ * Method getSequenceSetProperties.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(
+ ) {
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetPropertiesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetPropertiesCount(
+ ) {
+ return this._sequenceSetPropertiesList.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 removeAlcodonFrame.
+ *
+ * @param vAlcodonFrame
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonFrameAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+ final int index) {
+ java.lang.Object obj = this._alcodonFrameList.remove(index);
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlcodonFrame(
+ ) {
+ this._alcodonFrameList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAnnotation(
+ ) {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence(
+ ) {
+ this._sequenceList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSetProperties(
+ ) {
+ this._sequenceSetPropertiesList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.schemabinding.version2.Annotation vAnnotation) {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.schemabinding.version2.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.schemabinding.version2.Sequence vSequence) {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.schemabinding.version2.Sequence) obj;
+ }
+
+ /**
+ * Method removeSequenceSetProperties.
+ *
+ * @param vSequenceSetProperties
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {
+ boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetPropertiesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
+ return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlcodonFrame(
+ final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size()) {
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ this._alcodonFrameList.set(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonFrameArray
+ */
+ public void setAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
+ //-- copy array
+ _alcodonFrameList.clear();
+
+ for (int i = 0; i < vAlcodonFrameArray.length; i++) {
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @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.schemabinding.version2.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.schemabinding.version2.Annotation[] vAnnotationArray) {
+ //-- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++) {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'datasetId'. The field 'datasetId'
+ * has the following description: reference to set where
+ * jalview will gather the dataset sequences for all sequences
+ * in the set.
+ *
+ *
+ * @param datasetId the value of field 'datasetId'.
+ */
+ public void setDatasetId(
+ final java.lang.String datasetId) {
+ this._datasetId = datasetId;
+ }
+
+ /**
+ * 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.schemabinding.version2.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.schemabinding.version2.Sequence[] vSequenceArray) {
+ //-- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++) {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
+ throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetPropertiesArray
+ */
+ public void setSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {
+ //-- copy array
+ _sequenceSetPropertiesList.clear();
+
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[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.schemabinding.version2.SequenceSet
+ */
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff