*/\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+// ---------------------------------/\r
+// - Imported classes and packages -/\r
+// ---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends jalview.schemabinding.version2.SequenceType \r
-implements java.io.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
- //- Class/Member Variables -/\r
- //--------------------------/\r
+ /**\r
+ * dataset sequence id for this sequence. Will be created as union of\r
+ * sequences.\r
+ * \r
+ */\r
+ private java.lang.String _dsseqid;\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
+ * Field _DBRefList.\r
+ */\r
+ private java.util.Vector _DBRefList;\r
\r
- /**\r
- * Field _DBRefList.\r
- */\r
- private java.util.Vector _DBRefList;\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
\r
+ public Sequence()\r
+ {\r
+ super();\r
+ this._DBRefList = new java.util.Vector();\r
+ }\r
\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
\r
- public Sequence() {\r
- super();\r
- this._DBRefList = new java.util.Vector();\r
- }\r
+ /**\r
+ * \r
+ * \r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._DBRefList.addElement(vDBRef);\r
+ }\r
\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addDBRef(final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._DBRefList.add(index, vDBRef);\r
+ }\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ /**\r
+ * Method enumerateDBRef.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.DBRef\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateDBRef()\r
+ {\r
+ return this._DBRefList.elements();\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
+ * Method getDBRef.\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.DBRef at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.DBRef getDBRef(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index\r
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\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
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);\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
+ * Method getDBRef.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.DBRef[] getDBRef()\r
+ {\r
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];\r
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList\r
+ .toArray(array);\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
+ * Method getDBRefCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getDBRefCount()\r
+ {\r
+ return this._DBRefList.size();\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
+ * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following\r
+ * description: dataset sequence id for this sequence. Will be created as\r
+ * 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 getDBRefCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getDBRefCount(\r
- ) {\r
- return this._DBRefList.size();\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
+ return true;\r
+ }\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
+ * \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\r
+ * 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
- * 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
+ * @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\r
+ * 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
- * @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
+ public void removeAllDBRef()\r
+ {\r
+ this._DBRefList.clear();\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
+ * 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
+ {\r
+ boolean removed = _DBRefList.remove(vDBRef);\r
+ return removed;\r
+ }\r
\r
- /**\r
- */\r
- public void removeAllDBRef(\r
- ) {\r
- this._DBRefList.clear();\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(final int index)\r
+ {\r
+ java.lang.Object obj = this._DBRefList.remove(index);\r
+ return (jalview.schemabinding.version2.DBRef) obj;\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
+ * @param index\r
+ * @param vDBRef\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setDBRef(final int index,\r
+ final jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._DBRefList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index\r
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");\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
+ this._DBRefList.set(index, 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 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
+ /**\r
+ * \r
+ * \r
+ * @param vDBRefArray\r
+ */\r
+ public void setDBRef(\r
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray)\r
+ {\r
+ // -- copy array\r
+ _DBRefList.clear();\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
+ for (int i = 0; i < vDBRefArray.length; i++)\r
+ {\r
+ this._DBRefList.add(vDBRefArray[i]);\r
}\r
+ }\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
+ /**\r
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following\r
+ * description: dataset sequence id for this sequence. Will be created as\r
+ * union of sequences.\r
+ * \r
+ * \r
+ * @param dsseqid\r
+ * the value of field 'dsseqid'.\r
+ */\r
+ public void setDsseqid(final java.lang.String dsseqid)\r
+ {\r
+ this._dsseqid = dsseqid;\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\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
+ * 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\r
+ * schema\r
+ * @return the unmarshaled 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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.Sequence.class,\r
+ 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
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * 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