/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 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
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class VAMSAS.\r
//--------------------------/\r
\r
/**\r
- * Field _treeList\r
+ * Field _treeList.\r
*/\r
private java.util.Vector _treeList;\r
\r
/**\r
- * Field _sequenceSetList\r
+ * Field _sequenceSetList.\r
*/\r
private java.util.Vector _sequenceSetList;\r
\r
\r
public VAMSAS() {\r
super();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.schemabinding.version2.VAMSAS()\r
+ this._treeList = new java.util.Vector();\r
+ this._sequenceSetList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addSequenceSet\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(jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) \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
- * Method addSequenceSet\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(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \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
- * Method addTree\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(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String) \r
+ public void addTree(\r
+ final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._treeList.addElement(vTree);\r
+ }\r
\r
/**\r
- * Method addTree\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(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String) \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
+ * Method enumerateSequenceSet.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSet elements\r
*/\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet() \r
+ public java.util.Enumeration enumerateSequenceSet(\r
+ ) {\r
+ return this._sequenceSetList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateTree\r
- * \r
+ * Method enumerateTree.\r
* \r
- * \r
- * @return Enumeration\r
+ * @return an Enumeration over all java.lang.String elements\r
*/\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
+ public java.util.Enumeration enumerateTree(\r
+ ) {\r
+ return this._treeList.elements();\r
+ }\r
\r
/**\r
- * Method getSequenceSet\r
- * \r
- * \r
+ * Method getSequenceSet.\r
* \r
* @param index\r
- * @return SequenceSet\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(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\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.elementAt(index);\r
- } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) \r
+ return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);\r
+ }\r
\r
/**\r
- * Method getSequenceSet\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
- * \r
- * \r
- * @return SequenceSet\r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() \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
+ * Method getSequenceSetCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getSequenceSetCount()\r
- {\r
- return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount() \r
+ public int getSequenceSetCount(\r
+ ) {\r
+ return this._sequenceSetList.size();\r
+ }\r
\r
/**\r
- * Method getTree\r
- * \r
- * \r
+ * Method getTree.\r
* \r
* @param index\r
- * @return String\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(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\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 (String)_treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int) \r
+ return (java.lang.String) _treeList.get(index);\r
+ }\r
\r
/**\r
- * Method getTree\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
- * \r
- * \r
- * @return String\r
+ * @return this collection as an Array\r
*/\r
- public java.lang.String[] getTree()\r
- {\r
- int size = _treeList.size();\r
- java.lang.String[] mArray = new java.lang.String[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (String)_treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- java.lang.String[] getTree() \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
+ * Method getTreeCount.\r
* \r
- * \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount() \r
+ public int getTreeCount(\r
+ ) {\r
+ return this._treeList.size();\r
+ }\r
\r
/**\r
- * Method isValid\r
- * \r
- * \r
+ * Method isValid.\r
* \r
- * @return boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\r
\r
/**\r
- * Method marshal\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(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\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
- } //-- void marshal(java.io.Writer) \r
+ }\r
\r
/**\r
- * Method marshal\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(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\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
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllSequenceSet\r
- * \r
*/\r
- public void removeAllSequenceSet()\r
- {\r
- _sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet() \r
+ public void removeAllSequenceSet(\r
+ ) {\r
+ this._sequenceSetList.clear();\r
+ }\r
\r
/**\r
- * Method removeAllTree\r
- * \r
*/\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
+ public void removeAllTree(\r
+ ) {\r
+ this._treeList.clear();\r
+ }\r
\r
/**\r
- * Method removeSequenceSet\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 SequenceSet\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetList.elementAt(index);\r
- _sequenceSetList.removeElementAt(index);\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
- } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) \r
+ }\r
\r
/**\r
- * Method removeTree\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 String\r
+ * @return the element removed from the collection\r
*/\r
- public java.lang.String removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (String)obj;\r
- } //-- java.lang.String removeTree(int) \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
- * Method setSequenceSet\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(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\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
- _sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
+ \r
+ this._sequenceSetList.set(index, vSequenceSet);\r
+ }\r
\r
/**\r
- * Method setSequenceSet\r
- * \r
* \r
* \r
- * @param sequenceSetArray\r
+ * @param vSequenceSetArray\r
*/\r
- public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)\r
- {\r
+ public void setSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {\r
//-- copy array\r
- _sequenceSetList.removeAllElements();\r
- for (int i = 0; i < sequenceSetArray.length; i++) {\r
- _sequenceSetList.addElement(sequenceSetArray[i]);\r
+ _sequenceSetList.clear();\r
+ \r
+ for (int i = 0; i < vSequenceSetArray.length; i++) {\r
+ this._sequenceSetList.add(vSequenceSetArray[i]);\r
}\r
- } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
+ }\r
\r
/**\r
- * Method setTree\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(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\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
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String) \r
+ \r
+ this._treeList.set(index, vTree);\r
+ }\r
\r
/**\r
- * Method setTree\r
* \r
* \r
- * \r
- * @param treeArray\r
+ * @param vTreeArray\r
*/\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
+ public void setTree(\r
+ final java.lang.String[] vTreeArray) {\r
//-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++) {\r
- _treeList.addElement(treeArray[i]);\r
+ _treeList.clear();\r
+ \r
+ for (int i = 0; i < vTreeArray.length; i++) {\r
+ this._treeList.add(vTreeArray[i]);\r
}\r
- } //-- void setTree(java.lang.String) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\r
* \r
* @param reader\r
- * @return Object\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 java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\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
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\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
- throws org.exolab.castor.xml.ValidationException\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
- } //-- void validate() \r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff