- /**\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