/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\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 java.util.*;\r
\r
-import org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class Sequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence\r
- extends jalview.schemabinding.version2.SequenceType implements java.io.\r
- Serializable\r
+public class Sequence extends jalview.schemabinding.version2.SequenceType \r
+implements java.io.Serializable\r
{\r
\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _DBRefList\r
- */\r
- private java.util.Vector _DBRefList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Sequence()\r
- {\r
- super();\r
- _DBRefList = new Vector();\r
- } //-- jalview.schemabinding.version2.Sequence()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addDBRef\r
- *\r
- *\r
- *\r
- * @param vDBRef\r
- */\r
- public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.addElement(vDBRef);\r
- } //-- void addDBRef(jalview.schemabinding.version2.DBRef)\r
-\r
- /**\r
- * Method addDBRef\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vDBRef\r
- */\r
- public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.insertElementAt(vDBRef, index);\r
- } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef)\r
-\r
- /**\r
- * Method enumerateDBRef\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateDBRef()\r
- {\r
- return _DBRefList.elements();\r
- } //-- java.util.Enumeration enumerateDBRef()\r
-\r
- /**\r
- * Method getDBRef\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _DBRefList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * dataset sequence id for this sequence. Will be created as\r
+ * union of sequences.\r
+ * \r
+ */\r
+ private java.lang.String _dsseqid;\r
+\r
+ /**\r
+ * Field _DBRefList.\r
+ */\r
+ private java.util.Vector _DBRefList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Sequence() {\r
+ super();\r
+ this._DBRefList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.addElement(vDBRef);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._DBRefList.add(index, vDBRef);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateDBRef.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.DBRef elements\r
+ */\r
+ public java.util.Enumeration enumerateDBRef(\r
+ ) {\r
+ return this._DBRefList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getDBRef.\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.DBRef at the given index\r
+ */\r
+ public jalview.schemabinding.version2.DBRef getDBRef(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getDBRef.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 jalview.schemabinding.version2.DBRef[] getDBRef(\r
+ ) {\r
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];\r
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);\r
}\r
\r
- return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.DBRef getDBRef(int)\r
-\r
- /**\r
- * Method getDBRef\r
- *\r
- *\r
- *\r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef[] getDBRef()\r
- {\r
- int size = _DBRefList.size();\r
- jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.\r
- version2.DBRef[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.\r
- elementAt(index);\r
+ /**\r
+ * Method getDBRefCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getDBRefCount(\r
+ ) {\r
+ return this._DBRefList.size();\r
}\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.DBRef[] getDBRef()\r
-\r
- /**\r
- * Method getDBRefCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getDBRefCount()\r
- {\r
- return _DBRefList.size();\r
- } //-- int getDBRefCount()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
+\r
+ /**\r
+ * Returns the value of field 'dsseqid'. The field 'dsseqid'\r
+ * has the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @return the value of field 'Dsseqid'.\r
+ */\r
+ public java.lang.String getDsseqid(\r
+ ) {\r
+ return this._dsseqid;\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 removeAllDBRef(\r
+ ) {\r
+ this._DBRefList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeDBRef.\r
+ * \r
+ * @param vDBRef\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeDBRef(\r
+ final jalview.schemabinding.version2.DBRef vDBRef) {\r
+ boolean removed = _DBRefList.remove(vDBRef);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeDBRefAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._DBRefList.remove(index);\r
+ return (jalview.schemabinding.version2.DBRef) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setDBRef(\r
+ final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size()) {\r
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._DBRefList.set(index, vDBRef);\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vDBRefArray\r
+ */\r
+ public void setDBRef(\r
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray) {\r
+ //-- copy array\r
+ _DBRefList.clear();\r
+ \r
+ for (int i = 0; i < vDBRefArray.length; i++) {\r
+ this._DBRefList.add(vDBRefArray[i]);\r
+ }\r
}\r
- return true;\r
- } //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Method removeAllDBRef\r
- *\r
- */\r
- public void removeAllDBRef()\r
- {\r
- _DBRefList.removeAllElements();\r
- } //-- void removeAllDBRef()\r
-\r
- /**\r
- * Method removeDBRef\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
- {\r
- java.lang.Object obj = _DBRefList.elementAt(index);\r
- _DBRefList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.DBRef) obj;\r
- } //-- jalview.schemabinding.version2.DBRef removeDBRef(int)\r
-\r
- /**\r
- * Method setDBRef\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vDBRef\r
- */\r
- public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _DBRefList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
+\r
+ /**\r
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has\r
+ * the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @param dsseqid the value of field 'dsseqid'.\r
+ */\r
+ public void setDsseqid(\r
+ final java.lang.String dsseqid) {\r
+ this._dsseqid = dsseqid;\r
}\r
- _DBRefList.setElementAt(vDBRef, index);\r
- } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef)\r
-\r
- /**\r
- * Method setDBRef\r
- *\r
- *\r
- *\r
- * @param DBRefArray\r
- */\r
- public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
- {\r
- //-- copy array\r
- _DBRefList.removeAllElements();\r
- for (int i = 0; i < DBRefArray.length; i++)\r
- {\r
- _DBRefList.addElement(DBRefArray[i]);\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\r
+ * jalview.schemabinding.version2.SequenceType\r
+ */\r
+ public static jalview.schemabinding.version2.SequenceType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.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
- } //-- void setDBRef(jalview.schemabinding.version2.DBRef)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff