+\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