/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- *******************************************************************************/
+ *
+ * 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
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VAMSAS implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList.
- */
- private java.util.Vector _sequenceSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS() {
- super();
- this._treeList = new java.util.Vector();
- this._sequenceSetList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSequenceSet(
- final jalview.schemabinding.version2.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 jalview.schemabinding.version2.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException {
- this._sequenceSetList.add(index, vSequenceSet);
+public class VAMSAS implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VAMSAS()
+ {
+ super();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final jalview.schemabinding.version2.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 jalview.schemabinding.version2.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 enumerateSequenceSet.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.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 getSequenceSet.
+ *
+ * @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.SequenceSet at the
+ * given index
+ */
+ public jalview.schemabinding.version2.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) + "]");
}
- /**
- *
- *
- * @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);
+ return (jalview.schemabinding.version2.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 jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+ {
+ jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+ return (jalview.schemabinding.version2.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) + "]");
}
- /**
- *
- *
- * @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);
+ 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;
}
-
- /**
- * Method enumerateSequenceSet.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.SequenceSet elements
+ 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 java.util.Enumeration enumerateSequenceSet(
- ) {
- return this._sequenceSetList.elements();
- }
+ public void removeAllSequenceSet()
+ {
+ this._sequenceSetList.clear();
+ }
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all java.lang.String elements
+ /**
*/
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+ {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (jalview.schemabinding.version2.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 vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceSet(final int index,
+ final jalview.schemabinding.version2.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) + "]");
}
- /**
- * Method getSequenceSet.
- *
- * @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.SequenceSet at the given index
- */
- public jalview.schemabinding.version2.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 (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)
+ {
+ // -- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++)
+ {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
}
-
- /**
- * 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 jalview.schemabinding.version2.SequenceSet[] getSequenceSet(
- ) {
- jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
- return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);
+ }
+
+ /**
+ *
+ *
+ * @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) + "]");
}
- /**
- * 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);
- }
-
- /**
- */
- 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 jalview.schemabinding.version2.SequenceSet vSequenceSet) {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
- final int index) {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (jalview.schemabinding.version2.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 vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequenceSet(
- final int index,
- final jalview.schemabinding.version2.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 jalview.schemabinding.version2.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.schemabinding.version2.VAMSAS
- */
- public static jalview.schemabinding.version2.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.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);
+ 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.schemabinding.version2.VAMSAS
+ */
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff