* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\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
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\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
/**\r
* Class Annotation.\r
* @version $Revision$ $Date$\r
*/\r
public class Annotation implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _description;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Annotation() {\r
super();\r
_annotationElementList = new Vector();\r
- } //-- jalview.binding.Annotation()\r
-\r
+ }\r
+ //-- jalview.binding.Annotation()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- *\r
- *\r
- *\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addAnnotationElement(\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Method addAnnotationElement\r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method deleteGraph\r
*\r
*/\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph()\r
+ public void deleteGraph() {\r
+ this._has_graph = false;\r
+ }\r
+ //-- void deleteGraph()\r
\r
/**\r
* Method enumerateAnnotationElement\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
+ public java.util.Enumeration enumerateAnnotationElement() {\r
return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement()\r
+ }\r
+ //-- java.util.Enumeration enumerateAnnotationElement()\r
\r
/**\r
* Method getAnnotationElement\r
* @return AnnotationElement\r
*/\r
public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationElementList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
+ }\r
+ //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
\r
/**\r
* Method getAnnotationElement\r
*\r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement[] getAnnotationElement()\r
- {\r
+ public jalview.binding.AnnotationElement[] getAnnotationElement() {\r
int size = _annotationElementList.size();\r
jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ }\r
+ //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
\r
/**\r
* Method getAnnotationElementCount\r
*\r
* @return int\r
*/\r
- public int getAnnotationElementCount()\r
- {\r
+ public int getAnnotationElementCount() {\r
return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount()\r
+ }\r
+ //-- int getAnnotationElementCount()\r
\r
/**\r
* Returns the value of field 'description'.\r
* @return String\r
* @return the value of field 'description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription() {\r
return this._description;\r
- } //-- java.lang.String getDescription()\r
+ }\r
+ //-- java.lang.String getDescription()\r
\r
/**\r
* Returns the value of field 'graph'.\r
* @return boolean\r
* @return the value of field 'graph'.\r
*/\r
- public boolean getGraph()\r
- {\r
+ public boolean getGraph() {\r
return this._graph;\r
- } //-- boolean getGraph()\r
+ }\r
+ //-- boolean getGraph()\r
\r
/**\r
* Returns the value of field 'label'.\r
* @return String\r
* @return the value of field 'label'.\r
*/\r
- public java.lang.String getLabel()\r
- {\r
+ public java.lang.String getLabel() {\r
return this._label;\r
- } //-- java.lang.String getLabel()\r
+ }\r
+ //-- java.lang.String getLabel()\r
\r
/**\r
* Method hasGraph\r
*\r
* @return boolean\r
*/\r
- public boolean hasGraph()\r
- {\r
+ public boolean hasGraph() {\r
return this._has_graph;\r
- } //-- boolean hasGraph()\r
+ }\r
+ //-- boolean hasGraph()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\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
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllAnnotationElement\r
*\r
*/\r
- public void removeAllAnnotationElement()\r
- {\r
+ public void removeAllAnnotationElement() {\r
_annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement()\r
+ }\r
+ //-- void removeAllAnnotationElement()\r
\r
/**\r
* Method removeAnnotationElement\r
* @param index\r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
- {\r
+ public jalview.binding.AnnotationElement removeAnnotationElement(int index) {\r
java.lang.Object obj = _annotationElementList.elementAt(index);\r
_annotationElementList.removeElementAt(index);\r
+\r
return (jalview.binding.AnnotationElement) obj;\r
- } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
+ }\r
+ //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
\r
/**\r
* Method setAnnotationElement\r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationElementList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method setAnnotationElement\r
*\r
* @param annotationElementArray\r
*/\r
- public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
- {\r
+ public void setAnnotationElement(\r
+ jalview.binding.AnnotationElement[] annotationElementArray) {\r
//-- copy array\r
_annotationElementList.removeAllElements();\r
+\r
for (int i = 0; i < annotationElementArray.length; i++) {\r
_annotationElementList.addElement(annotationElementArray[i]);\r
}\r
- } //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Sets the value of field 'description'.\r
*\r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String)\r
+ }\r
+ //-- void setDescription(java.lang.String)\r
\r
/**\r
* Sets the value of field 'graph'.\r
*\r
* @param graph the value of field 'graph'.\r
*/\r
- public void setGraph(boolean graph)\r
- {\r
+ public void setGraph(boolean graph) {\r
this._graph = graph;\r
this._has_graph = true;\r
- } //-- void setGraph(boolean)\r
+ }\r
+ //-- void setGraph(boolean)\r
\r
/**\r
* Sets the value of field 'label'.\r
*\r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label)\r
- {\r
+ public void setLabel(java.lang.String label) {\r
this._label = label;\r
- } //-- void setLabel(java.lang.String)\r
+ }\r
+ //-- void setLabel(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
* @return Object\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
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class,\r
+ reader);\r
+ }\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
+ public void validate() 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
+ //-- void validate()\r
}\r
git://source.jalview.org / jalview.git / blobdiff