/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+// ---------------------------------/\r
+// - Imported classes and packages -/\r
+// ---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class VAMSAS implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _treeList.\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _sequenceSetList.\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VAMSAS() {\r
- super();\r
- this._treeList = new java.util.Vector();\r
- this._sequenceSetList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._sequenceSetList.addElement(vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSequenceSet(\r
- final int index,\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._sequenceSetList.add(index, vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final int index,\r
- final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * Method enumerateSequenceSet.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.SequenceSet elements\r
- */\r
- public java.util.Enumeration enumerateSequenceSet(\r
- ) {\r
- return this._sequenceSetList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateTree.\r
- * \r
- * @return an Enumeration over all java.lang.String elements\r
- */\r
- public java.util.Enumeration enumerateTree(\r
- ) {\r
- return this._treeList.elements();\r
- }\r
-\r
- /**\r
- * Method getSequenceSet.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.SequenceSet at the given index\r
- */\r
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetList.size()) {\r
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSequenceSet.Returns the contents of the collection\r
- * in an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(\r
- ) {\r
- jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
- return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);\r
+public class VAMSAS implements java.io.Serializable\r
+{\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * Field _treeList.\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _sequenceSetList.\r
+ */\r
+ private java.util.Vector _sequenceSetList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public VAMSAS()\r
+ {\r
+ super();\r
+ this._treeList = new java.util.Vector();\r
+ this._sequenceSetList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetList.addElement(vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetList.add(index, vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.addElement(vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final int index, final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.add(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequenceSet.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSet()\r
+ {\r
+ return this._sequenceSetList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateTree.\r
+ * \r
+ * @return an Enumeration over all java.lang.String elements\r
+ */\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
+ return this._treeList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSet.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.SequenceSet at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._sequenceSetList.size() - 1) + "]");\r
}\r
\r
- /**\r
- * Method getSequenceSetCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSequenceSetCount(\r
- ) {\r
- return this._sequenceSetList.size();\r
+ return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSet.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
+ {\r
+ jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
+ return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceSetCount()\r
+ {\r
+ return this._sequenceSetList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getTree.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the java.lang.String at the given index\r
+ */\r
+ public java.lang.String getTree(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index\r
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
\r
- /**\r
- * Method getTree.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the java.lang.String at the given index\r
- */\r
- public java.lang.String getTree(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- return (java.lang.String) _treeList.get(index);\r
+ return (java.lang.String) _treeList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getTree.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public java.lang.String[] getTree()\r
+ {\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._treeList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getTreeCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getTreeCount()\r
+ {\r
+ return this._treeList.size();\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try\r
+ {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
}\r
-\r
- /**\r
- * Method getTree.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public java.lang.String[] getTree(\r
- ) {\r
- java.lang.String[] array = new java.lang.String[0];\r
- return (java.lang.String[]) this._treeList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getTreeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getTreeCount(\r
- ) {\r
- return this._treeList.size();\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllSequenceSet(\r
- ) {\r
- this._sequenceSetList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllTree(\r
- ) {\r
- this._treeList.clear();\r
- }\r
-\r
- /**\r
- * Method removeSequenceSet.\r
- * \r
- * @param vSequenceSet\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet) {\r
- boolean removed = _sequenceSetList.remove(vSequenceSet);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSequenceSetAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(\r
- final int index) {\r
- java.lang.Object obj = this._sequenceSetList.remove(index);\r
- return (jalview.schemabinding.version2.SequenceSet) obj;\r
- }\r
-\r
- /**\r
- * Method removeTree.\r
- * \r
- * @param vTree\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeTree(\r
- final java.lang.String vTree) {\r
- boolean removed = _treeList.remove(vTree);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeTreeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public java.lang.String removeTreeAt(\r
- final int index) {\r
- java.lang.Object obj = this._treeList.remove(index);\r
- return (java.lang.String) obj;\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllSequenceSet()\r
+ {\r
+ this._sequenceSetList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ this._treeList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSet.\r
+ * \r
+ * @param vSequenceSet\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ {\r
+ boolean removed = _sequenceSetList.remove(vSequenceSet);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._sequenceSetList.remove(index);\r
+ return (jalview.schemabinding.version2.SequenceSet) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeTree.\r
+ * \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(final java.lang.String vTree)\r
+ {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public java.lang.String removeTreeAt(final int index)\r
+ {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
+ return (java.lang.String) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setSequenceSet(final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._sequenceSetList.size() - 1) + "]");\r
}\r
\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setSequenceSet(\r
- final int index,\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetList.size()) {\r
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
- }\r
- \r
- this._sequenceSetList.set(index, vSequenceSet);\r
+ this._sequenceSetList.set(index, vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetArray\r
+ */\r
+ public void setSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)\r
+ {\r
+ // -- copy array\r
+ _sequenceSetList.clear();\r
+\r
+ for (int i = 0; i < vSequenceSetArray.length; i++)\r
+ {\r
+ this._sequenceSetList.add(vSequenceSetArray[i]);\r
}\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSetArray\r
- */\r
- public void setSequenceSet(\r
- final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {\r
- //-- copy array\r
- _sequenceSetList.clear();\r
- \r
- for (int i = 0; i < vSequenceSetArray.length; i++) {\r
- this._sequenceSetList.add(vSequenceSetArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setTree(\r
- final int index,\r
- final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- this._treeList.set(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTreeArray\r
- */\r
- public void setTree(\r
- final java.lang.String[] vTreeArray) {\r
- //-- copy array\r
- _treeList.clear();\r
- \r
- for (int i = 0; i < vTreeArray.length; i++) {\r
- this._treeList.add(vTreeArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
- */\r
- public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setTree(final int index, final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index\r
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
}\r
\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
+ this._treeList.set(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTreeArray\r
+ */\r
+ public void setTree(final java.lang.String[] vTreeArray)\r
+ {\r
+ // -- copy array\r
+ _treeList.clear();\r
+\r
+ for (int i = 0; i < vTreeArray.length; i++)\r
+ {\r
+ this._treeList.add(vTreeArray[i]);\r
}\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.VAMSAS\r
+ */\r
+ public static jalview.schemabinding.version2.VAMSAS unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(\r
+ jalview.schemabinding.version2.VAMSAS.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ */\r
+ public void validate() throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff