/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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
*/\r
+\r
package jalview.schemabinding.version2;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\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
- // - 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
+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
- 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
+ //- 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
- 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
+ * @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
- 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 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 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
+ /**\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 removeAllSequenceSet()\r
- {\r
- this._sequenceSetList.clear();\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
+ * \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 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
+ 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
- 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
+ * 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
- /**\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
+ * 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
+ }\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
- 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
+ * 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
+ }\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
+ }\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
+ }\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
+ * @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
}\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 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 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