/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 Alignment.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Alignment implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class Alignment implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.SequenceSet _sequenceSet;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public Alignment()\r
- {\r
+\r
+ public Alignment() {\r
super();\r
- }\r
+ } //-- jalview.binding.Alignment()\r
\r
- //-- jalview.binding.Alignment()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Returns the value of field 'annotation'.\r
+ * \r
+ * @return Annotation\r
+ * @return the value of field 'annotation'.\r
*/\r
public jalview.binding.Annotation getAnnotation()\r
{\r
return this._annotation;\r
- }\r
-\r
- //-- jalview.binding.Annotation getAnnotation() \r
+ } //-- jalview.binding.Annotation getAnnotation() \r
\r
/**\r
* Returns the value of field 'sequenceSet'.\r
- *\r
+ * \r
* @return SequenceSet\r
* @return the value of field 'sequenceSet'.\r
*/\r
public jalview.binding.SequenceSet getSequenceSet()\r
{\r
return this._sequenceSet;\r
- }\r
-\r
- //-- jalview.binding.SequenceSet getSequenceSet() \r
+ } //-- jalview.binding.SequenceSet getSequenceSet() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'annotation'.\r
- *\r
+ * \r
* @param annotation the value of field 'annotation'.\r
*/\r
public void setAnnotation(jalview.binding.Annotation annotation)\r
{\r
this._annotation = annotation;\r
- }\r
-\r
- //-- void setAnnotation(jalview.binding.Annotation) \r
+ } //-- void setAnnotation(jalview.binding.Annotation) \r
\r
/**\r
* Sets the value of field 'sequenceSet'.\r
- *\r
+ * \r
* @param sequenceSet the value of field 'sequenceSet'.\r
*/\r
public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
{\r
this._sequenceSet = sequenceSet;\r
- }\r
-\r
- //-- void setSequenceSet(jalview.binding.SequenceSet) \r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\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 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 Annotation.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Annotation\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _graph\r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _annotationElementList\r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Field _label\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Annotation()\r
- {\r
- super();\r
- _annotationElementList = new Vector();\r
- } //-- jalview.binding.Annotation()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- *\r
- *\r
- *\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(jalview.binding.AnnotationElement\r
- vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
-\r
- /**\r
- * Method addAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(int index,\r
- jalview.binding.AnnotationElement\r
- vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\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
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement()\r
-\r
- /**\r
- * Method getAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _annotationElementList.size()))\r
+public class Annotation implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _graph\r
+ */\r
+ private boolean _graph;\r
+\r
+ /**\r
+ * keeps track of state for field: _graph\r
+ */\r
+ private boolean _has_graph;\r
+\r
+ /**\r
+ * Field _annotationElementList\r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Field _label\r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Field _description\r
+ */\r
+ private java.lang.String _description;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Annotation() {\r
+ super();\r
+ _annotationElementList = new Vector();\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
+ _annotationElementList.addElement(vAnnotationElement);\r
+ } //-- void addAnnotationElement(jalview.binding.AnnotationElement) \r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.insertElementAt(vAnnotationElement, index);\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
+\r
+ /**\r
+ * Method enumerateAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
+ return _annotationElementList.elements();\r
+ } //-- java.util.Enumeration enumerateAnnotationElement() \r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\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
+ /**\r
+ * Method getAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ {\r
+ int size = _annotationElementList.size();\r
+ jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.AnnotationElement[] getAnnotationElement() \r
+\r
+ /**\r
+ * Method getAnnotationElementCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getAnnotationElementCount()\r
+ {\r
+ return _annotationElementList.size();\r
+ } //-- int getAnnotationElementCount() \r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ } //-- java.lang.String getDescription() \r
+\r
+ /**\r
+ * Returns the value of field 'graph'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'graph'.\r
+ */\r
+ public boolean getGraph()\r
+ {\r
+ return this._graph;\r
+ } //-- boolean getGraph() \r
+\r
+ /**\r
+ * Returns the value of field 'label'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'label'.\r
+ */\r
+ public java.lang.String getLabel()\r
+ {\r
+ return this._label;\r
+ } //-- java.lang.String getLabel() \r
+\r
+ /**\r
+ * Method hasGraph\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasGraph()\r
+ {\r
+ return this._has_graph;\r
+ } //-- boolean hasGraph() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllAnnotationElement\r
+ * \r
+ */\r
+ public void removeAllAnnotationElement()\r
+ {\r
+ _annotationElementList.removeAllElements();\r
+ } //-- void removeAllAnnotationElement() \r
+\r
+ /**\r
+ * Method removeAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
+ {\r
+ java.lang.Object obj = _annotationElementList.elementAt(index);\r
+ _annotationElementList.removeElementAt(index);\r
+ return (jalview.binding.AnnotationElement) obj;\r
+ } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) \r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _annotationElementList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _annotationElementList.setElementAt(vAnnotationElement, index);\r
+ } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) \r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ * \r
+ * \r
+ * \r
+ * @param annotationElementArray\r
+ */\r
+ public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
{\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(\r
- index);\r
- } //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
-\r
- /**\r
- * Method getAnnotationElement\r
- *\r
- *\r
- *\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- jalview.binding.AnnotationElement[] mArray = new jalview.binding.\r
- AnnotationElement[size];\r
- for (int index = 0; index < size; index++)\r
+ //-- copy array\r
+ _annotationElementList.removeAllElements();\r
+ for (int i = 0; i < annotationElementArray.length; i++) {\r
+ _annotationElementList.addElement(annotationElementArray[i]);\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
- mArray[index] = (jalview.binding.AnnotationElement)\r
- _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
-\r
- /**\r
- * Method getAnnotationElementCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount()\r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- *\r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription()\r
-\r
- /**\r
- * Returns the value of field 'graph'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph()\r
-\r
- /**\r
- * Returns the value of field 'label'.\r
- *\r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel()\r
- {\r
- return this._label;\r
- } //-- java.lang.String getLabel()\r
-\r
- /**\r
- * Method hasGraph\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
+ this._description = description;\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
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
+ this._graph = graph;\r
+ this._has_graph = true;\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
- return false;\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 removeAllAnnotationElement\r
- *\r
- */\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement()\r
-\r
- /**\r
- * Method removeAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
- return (jalview.binding.AnnotationElement) obj;\r
- } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
-\r
- /**\r
- * Method setAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index,\r
- jalview.binding.AnnotationElement\r
- vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _annotationElementList.size()))\r
+ this._label = label;\r
+ } //-- void setLabel(java.lang.String) \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, org.exolab.castor.xml.ValidationException\r
{\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
-\r
- /**\r
- * Method setAnnotationElement\r
- *\r
- *\r
- *\r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(jalview.binding.AnnotationElement[]\r
- annotationElementArray)\r
- {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++)\r
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.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
- _annotationElementList.addElement(annotationElementArray[i]);\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
- this._description = description;\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
- this._graph = graph;\r
- this._has_graph = true;\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
- this._label = label;\r
- } //-- void setLabel(java.lang.String)\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.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.\r
- Annotation.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
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 AnnotationElement.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class AnnotationElement implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class AnnotationElement implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_value;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public AnnotationElement()\r
- {\r
+\r
+ public AnnotationElement() {\r
super();\r
- }\r
+ } //-- jalview.binding.AnnotationElement()\r
+\r
\r
- //-- jalview.binding.AnnotationElement()\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Method deletePosition\r
+ * \r
*/\r
public void deletePosition()\r
{\r
- this._has_position = false;\r
- }\r
-\r
- //-- void deletePosition() \r
+ this._has_position= false;\r
+ } //-- void deletePosition() \r
\r
/**\r
* Method deleteValue\r
- *\r
+ * \r
*/\r
public void deleteValue()\r
{\r
- this._has_value = false;\r
- }\r
-\r
- //-- void deleteValue() \r
+ this._has_value= false;\r
+ } //-- void deleteValue() \r
\r
/**\r
* Returns the value of field 'description'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'description'.\r
*/\r
public java.lang.String getDescription()\r
{\r
return this._description;\r
- }\r
-\r
- //-- java.lang.String getDescription() \r
+ } //-- java.lang.String getDescription() \r
\r
/**\r
* Returns the value of field 'displayCharacter'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'displayCharacter'.\r
*/\r
public java.lang.String getDisplayCharacter()\r
{\r
return this._displayCharacter;\r
- }\r
-\r
- //-- java.lang.String getDisplayCharacter() \r
+ } //-- java.lang.String getDisplayCharacter() \r
\r
/**\r
* Returns the value of field 'position'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'position'.\r
*/\r
public int getPosition()\r
{\r
return this._position;\r
- }\r
-\r
- //-- int getPosition() \r
+ } //-- int getPosition() \r
\r
/**\r
* Returns the value of field 'secondaryStructure'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'secondaryStructure'.\r
*/\r
public java.lang.String getSecondaryStructure()\r
{\r
return this._secondaryStructure;\r
- }\r
-\r
- //-- java.lang.String getSecondaryStructure() \r
+ } //-- java.lang.String getSecondaryStructure() \r
\r
/**\r
* Returns the value of field 'value'.\r
- *\r
+ * \r
* @return float\r
* @return the value of field 'value'.\r
*/\r
public float getValue()\r
{\r
return this._value;\r
- }\r
-\r
- //-- float getValue() \r
+ } //-- float getValue() \r
\r
/**\r
* Method hasPosition\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasPosition()\r
{\r
return this._has_position;\r
- }\r
-\r
- //-- boolean hasPosition() \r
+ } //-- boolean hasPosition() \r
\r
/**\r
* Method hasValue\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasValue()\r
{\r
return this._has_value;\r
- }\r
-\r
- //-- boolean hasValue() \r
+ } //-- boolean hasValue() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'description'.\r
- *\r
+ * \r
* @param description the value of field 'description'.\r
*/\r
public void setDescription(java.lang.String description)\r
{\r
this._description = description;\r
- }\r
-\r
- //-- void setDescription(java.lang.String) \r
+ } //-- void setDescription(java.lang.String) \r
\r
/**\r
* Sets the value of field 'displayCharacter'.\r
- *\r
+ * \r
* @param displayCharacter the value of field 'displayCharacter'\r
*/\r
public void setDisplayCharacter(java.lang.String displayCharacter)\r
{\r
this._displayCharacter = displayCharacter;\r
- }\r
-\r
- //-- void setDisplayCharacter(java.lang.String) \r
+ } //-- void setDisplayCharacter(java.lang.String) \r
\r
/**\r
* Sets the value of field 'position'.\r
- *\r
+ * \r
* @param position the value of field 'position'.\r
*/\r
public void setPosition(int position)\r
{\r
this._position = position;\r
this._has_position = true;\r
- }\r
-\r
- //-- void setPosition(int) \r
+ } //-- void setPosition(int) \r
\r
/**\r
* Sets the value of field 'secondaryStructure'.\r
- *\r
+ * \r
* @param secondaryStructure the value of field\r
* 'secondaryStructure'.\r
*/\r
public void setSecondaryStructure(java.lang.String secondaryStructure)\r
{\r
this._secondaryStructure = secondaryStructure;\r
- }\r
-\r
- //-- void setSecondaryStructure(java.lang.String) \r
+ } //-- void setSecondaryStructure(java.lang.String) \r
\r
/**\r
* Sets the value of field 'value'.\r
- *\r
+ * \r
* @param value the value of field 'value'.\r
*/\r
public void setValue(float value)\r
{\r
this._value = value;\r
this._has_value = true;\r
- }\r
-\r
- //-- void setValue(float) \r
+ } //-- void setValue(float) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 Colour.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Colour implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class Colour implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _RGB;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public Colour()\r
- {\r
+\r
+ public Colour() {\r
super();\r
- }\r
+ } //-- jalview.binding.Colour()\r
+\r
\r
- //-- jalview.binding.Colour()\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- }\r
-\r
- //-- java.lang.String getName() \r
+ } //-- java.lang.String getName() \r
\r
/**\r
* Returns the value of field 'RGB'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'RGB'.\r
*/\r
public java.lang.String getRGB()\r
{\r
return this._RGB;\r
- }\r
-\r
- //-- java.lang.String getRGB() \r
+ } //-- java.lang.String getRGB() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'name'.\r
- *\r
+ * \r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- }\r
-\r
- //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String) \r
\r
/**\r
* Sets the value of field 'RGB'.\r
- *\r
+ * \r
* @param RGB the value of field 'RGB'.\r
*/\r
public void setRGB(java.lang.String RGB)\r
{\r
this._RGB = RGB;\r
- }\r
-\r
- //-- void setRGB(java.lang.String) \r
+ } //-- void setRGB(java.lang.String) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\r
import java.util.Enumeration;\r
import java.util.Vector;\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
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JGroup.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JGroup implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class JGroup implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _seqList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public JGroup()\r
- {\r
+\r
+ public JGroup() {\r
super();\r
_seqList = new Vector();\r
- }\r
+ } //-- jalview.binding.JGroup()\r
+\r
\r
- //-- jalview.binding.JGroup()\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @param vSeq DOCUMENT ME!\r
- *\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!\r
+ * Method addSeq\r
+ * \r
+ * \r
+ * \r
+ * @param vSeq\r
*/\r
- public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException\r
+ public void addSeq(int vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
_seqList.addElement(new java.lang.Integer(vSeq));\r
- }\r
-\r
- //-- void addSeq(int) \r
+ } //-- void addSeq(int) \r
\r
/**\r
* Method addSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSeq\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- }\r
-\r
- //-- void addSeq(int, int) \r
+ } //-- void addSeq(int, int) \r
\r
/**\r
* Method deleteColourText\r
- *\r
+ * \r
*/\r
public void deleteColourText()\r
{\r
- this._has_colourText = false;\r
- }\r
-\r
- //-- void deleteColourText() \r
+ this._has_colourText= false;\r
+ } //-- void deleteColourText() \r
\r
/**\r
* Method deleteConsThreshold\r
- *\r
+ * \r
*/\r
public void deleteConsThreshold()\r
{\r
- this._has_consThreshold = false;\r
- }\r
-\r
- //-- void deleteConsThreshold() \r
+ this._has_consThreshold= false;\r
+ } //-- void deleteConsThreshold() \r
\r
/**\r
* Method deleteDisplayBoxes\r
- *\r
+ * \r
*/\r
public void deleteDisplayBoxes()\r
{\r
- this._has_displayBoxes = false;\r
- }\r
-\r
- //-- void deleteDisplayBoxes() \r
+ this._has_displayBoxes= false;\r
+ } //-- void deleteDisplayBoxes() \r
\r
/**\r
* Method deleteDisplayText\r
- *\r
+ * \r
*/\r
public void deleteDisplayText()\r
{\r
- this._has_displayText = false;\r
- }\r
-\r
- //-- void deleteDisplayText() \r
+ this._has_displayText= false;\r
+ } //-- void deleteDisplayText() \r
\r
/**\r
* Method deleteEnd\r
- *\r
+ * \r
*/\r
public void deleteEnd()\r
{\r
- this._has_end = false;\r
- }\r
-\r
- //-- void deleteEnd() \r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
\r
/**\r
* Method deleteOutlineColour\r
- *\r
+ * \r
*/\r
public void deleteOutlineColour()\r
{\r
- this._has_outlineColour = false;\r
- }\r
-\r
- //-- void deleteOutlineColour() \r
+ this._has_outlineColour= false;\r
+ } //-- void deleteOutlineColour() \r
\r
/**\r
* Method deletePidThreshold\r
- *\r
+ * \r
*/\r
public void deletePidThreshold()\r
{\r
- this._has_pidThreshold = false;\r
- }\r
-\r
- //-- void deletePidThreshold() \r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
\r
/**\r
* Method deleteStart\r
- *\r
+ * \r
*/\r
public void deleteStart()\r
{\r
- this._has_start = false;\r
- }\r
-\r
- //-- void deleteStart() \r
+ this._has_start= false;\r
+ } //-- void deleteStart() \r
\r
/**\r
* Method enumerateSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSeq()\r
{\r
return _seqList.elements();\r
- }\r
-\r
- //-- java.util.Enumeration enumerateSeq() \r
+ } //-- java.util.Enumeration enumerateSeq() \r
\r
/**\r
* Returns the value of field 'colour'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'colour'.\r
*/\r
public java.lang.String getColour()\r
{\r
return this._colour;\r
- }\r
-\r
- //-- java.lang.String getColour() \r
+ } //-- java.lang.String getColour() \r
\r
/**\r
* Returns the value of field 'colourText'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'colourText'.\r
*/\r
public boolean getColourText()\r
{\r
return this._colourText;\r
- }\r
-\r
- //-- boolean getColourText() \r
+ } //-- boolean getColourText() \r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
public int getConsThreshold()\r
{\r
return this._consThreshold;\r
- }\r
-\r
- //-- int getConsThreshold() \r
+ } //-- int getConsThreshold() \r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'displayBoxes'.\r
*/\r
public boolean getDisplayBoxes()\r
{\r
return this._displayBoxes;\r
- }\r
-\r
- //-- boolean getDisplayBoxes() \r
+ } //-- boolean getDisplayBoxes() \r
\r
/**\r
* Returns the value of field 'displayText'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'displayText'.\r
*/\r
public boolean getDisplayText()\r
{\r
return this._displayText;\r
- }\r
-\r
- //-- boolean getDisplayText() \r
+ } //-- boolean getDisplayText() \r
\r
/**\r
* Returns the value of field 'end'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'end'.\r
*/\r
public int getEnd()\r
{\r
return this._end;\r
- }\r
-\r
- //-- int getEnd() \r
+ } //-- int getEnd() \r
\r
/**\r
* Returns the value of field 'name'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- }\r
-\r
- //-- java.lang.String getName() \r
+ } //-- java.lang.String getName() \r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'outlineColour'.\r
*/\r
public int getOutlineColour()\r
{\r
return this._outlineColour;\r
- }\r
-\r
- //-- int getOutlineColour() \r
+ } //-- int getOutlineColour() \r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
public int getPidThreshold()\r
{\r
return this._pidThreshold;\r
- }\r
-\r
- //-- int getPidThreshold() \r
+ } //-- int getPidThreshold() \r
\r
/**\r
* Method getSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return int\r
*/\r
- public int getSeq(int index) throws java.lang.IndexOutOfBoundsException\r
+ public int getSeq(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size()))\r
- {\r
+ if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
- return ((java.lang.Integer) _seqList.elementAt(index)).intValue();\r
- }\r
-\r
- //-- int getSeq(int) \r
+ \r
+ return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+ } //-- int getSeq(int) \r
\r
/**\r
* Method getSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
public int[] getSeq()\r
{\r
int size = _seqList.size();\r
int[] mArray = new int[size];\r
-\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
}\r
-\r
return mArray;\r
- }\r
-\r
- //-- int[] getSeq() \r
+ } //-- int[] getSeq() \r
\r
/**\r
* Method getSeqCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
public int getSeqCount()\r
{\r
return _seqList.size();\r
- }\r
-\r
- //-- int getSeqCount() \r
+ } //-- int getSeqCount() \r
\r
/**\r
* Returns the value of field 'start'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- }\r
-\r
- //-- int getStart() \r
+ } //-- int getStart() \r
\r
/**\r
* Method hasColourText\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasColourText()\r
{\r
return this._has_colourText;\r
- }\r
-\r
- //-- boolean hasColourText() \r
+ } //-- boolean hasColourText() \r
\r
/**\r
* Method hasConsThreshold\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasConsThreshold()\r
{\r
return this._has_consThreshold;\r
- }\r
-\r
- //-- boolean hasConsThreshold() \r
+ } //-- boolean hasConsThreshold() \r
\r
/**\r
* Method hasDisplayBoxes\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasDisplayBoxes()\r
{\r
return this._has_displayBoxes;\r
- }\r
-\r
- //-- boolean hasDisplayBoxes() \r
+ } //-- boolean hasDisplayBoxes() \r
\r
/**\r
* Method hasDisplayText\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasDisplayText()\r
{\r
return this._has_displayText;\r
- }\r
-\r
- //-- boolean hasDisplayText() \r
+ } //-- boolean hasDisplayText() \r
\r
/**\r
* Method hasEnd\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- }\r
-\r
- //-- boolean hasEnd() \r
+ } //-- boolean hasEnd() \r
\r
/**\r
* Method hasOutlineColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasOutlineColour()\r
{\r
return this._has_outlineColour;\r
- }\r
-\r
- //-- boolean hasOutlineColour() \r
+ } //-- boolean hasOutlineColour() \r
\r
/**\r
* Method hasPidThreshold\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasPidThreshold()\r
{\r
return this._has_pidThreshold;\r
- }\r
-\r
- //-- boolean hasPidThreshold() \r
+ } //-- boolean hasPidThreshold() \r
\r
/**\r
* Method hasStart\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- }\r
-\r
- //-- boolean hasStart() \r
+ } //-- boolean hasStart() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllSeq\r
- *\r
+ * \r
*/\r
public void removeAllSeq()\r
{\r
_seqList.removeAllElements();\r
- }\r
-\r
- //-- void removeAllSeq() \r
+ } //-- void removeAllSeq() \r
\r
/**\r
* Method removeSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return int\r
*/\r
{\r
java.lang.Object obj = _seqList.elementAt(index);\r
_seqList.removeElementAt(index);\r
-\r
- return ((java.lang.Integer) obj).intValue();\r
- }\r
-\r
- //-- int removeSeq(int) \r
+ return ((java.lang.Integer)obj).intValue();\r
+ } //-- int removeSeq(int) \r
\r
/**\r
* Sets the value of field 'colour'.\r
- *\r
+ * \r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(java.lang.String colour)\r
{\r
this._colour = colour;\r
- }\r
-\r
- //-- void setColour(java.lang.String) \r
+ } //-- void setColour(java.lang.String) \r
\r
/**\r
* Sets the value of field 'colourText'.\r
- *\r
+ * \r
* @param colourText the value of field 'colourText'.\r
*/\r
public void setColourText(boolean colourText)\r
{\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- }\r
-\r
- //-- void setColourText(boolean) \r
+ } //-- void setColourText(boolean) \r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
- *\r
+ * \r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
public void setConsThreshold(int consThreshold)\r
{\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- }\r
-\r
- //-- void setConsThreshold(int) \r
+ } //-- void setConsThreshold(int) \r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
- *\r
+ * \r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
public void setDisplayBoxes(boolean displayBoxes)\r
{\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- }\r
-\r
- //-- void setDisplayBoxes(boolean) \r
+ } //-- void setDisplayBoxes(boolean) \r
\r
/**\r
* Sets the value of field 'displayText'.\r
- *\r
+ * \r
* @param displayText the value of field 'displayText'.\r
*/\r
public void setDisplayText(boolean displayText)\r
{\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- }\r
-\r
- //-- void setDisplayText(boolean) \r
+ } //-- void setDisplayText(boolean) \r
\r
/**\r
* Sets the value of field 'end'.\r
- *\r
+ * \r
* @param end the value of field 'end'.\r
*/\r
public void setEnd(int end)\r
{\r
this._end = end;\r
this._has_end = true;\r
- }\r
-\r
- //-- void setEnd(int) \r
+ } //-- void setEnd(int) \r
\r
/**\r
* Sets the value of field 'name'.\r
- *\r
+ * \r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- }\r
-\r
- //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String) \r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
- *\r
+ * \r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
public void setOutlineColour(int outlineColour)\r
{\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- }\r
-\r
- //-- void setOutlineColour(int) \r
+ } //-- void setOutlineColour(int) \r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
- *\r
+ * \r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
public void setPidThreshold(int pidThreshold)\r
{\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- }\r
-\r
- //-- void setPidThreshold(int) \r
+ } //-- void setPidThreshold(int) \r
\r
/**\r
* Method setSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSeq\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size()))\r
- {\r
+ if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- }\r
-\r
- //-- void setSeq(int, int) \r
+ } //-- void setSeq(int, int) \r
\r
/**\r
* Method setSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param seqArray\r
*/\r
public void setSeq(int[] seqArray)\r
{\r
//-- copy array\r
_seqList.removeAllElements();\r
-\r
- for (int i = 0; i < seqArray.length; i++)\r
- {\r
+ for (int i = 0; i < seqArray.length; i++) {\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));\r
}\r
- }\r
-\r
- //-- void setSeq(int) \r
+ } //-- void setSeq(int) \r
\r
/**\r
* Sets the value of field 'start'.\r
- *\r
+ * \r
* @param start the value of field 'start'.\r
*/\r
public void setStart(int start)\r
{\r
this._start = start;\r
this._has_start = true;\r
- }\r
-\r
- //-- void setStart(int) \r
+ } //-- void setStart(int) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 JSeq.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JSeq implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class JSeq implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_id;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public JSeq()\r
- {\r
+\r
+ public JSeq() {\r
super();\r
- }\r
+ } //-- jalview.binding.JSeq()\r
\r
- //-- jalview.binding.JSeq()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Method deleteColour\r
+ * \r
*/\r
public void deleteColour()\r
{\r
- this._has_colour = false;\r
- }\r
-\r
- //-- void deleteColour() \r
+ this._has_colour= false;\r
+ } //-- void deleteColour() \r
\r
/**\r
* Method deleteEnd\r
- *\r
+ * \r
*/\r
public void deleteEnd()\r
{\r
- this._has_end = false;\r
- }\r
-\r
- //-- void deleteEnd() \r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
\r
/**\r
* Method deleteId\r
- *\r
+ * \r
*/\r
public void deleteId()\r
{\r
- this._has_id = false;\r
- }\r
-\r
- //-- void deleteId() \r
+ this._has_id= false;\r
+ } //-- void deleteId() \r
\r
/**\r
* Method deleteStart\r
- *\r
+ * \r
*/\r
public void deleteStart()\r
{\r
- this._has_start = false;\r
- }\r
-\r
- //-- void deleteStart() \r
+ this._has_start= false;\r
+ } //-- void deleteStart() \r
\r
/**\r
* Returns the value of field 'colour'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'colour'.\r
*/\r
public int getColour()\r
{\r
return this._colour;\r
- }\r
-\r
- //-- int getColour() \r
+ } //-- int getColour() \r
\r
/**\r
* Returns the value of field 'end'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'end'.\r
*/\r
public int getEnd()\r
{\r
return this._end;\r
- }\r
-\r
- //-- int getEnd() \r
+ } //-- int getEnd() \r
\r
/**\r
* Returns the value of field 'id'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'id'.\r
*/\r
public int getId()\r
{\r
return this._id;\r
- }\r
-\r
- //-- int getId() \r
+ } //-- int getId() \r
\r
/**\r
* Returns the value of field 'start'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- }\r
-\r
- //-- int getStart() \r
+ } //-- int getStart() \r
\r
/**\r
* Method hasColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasColour()\r
{\r
return this._has_colour;\r
- }\r
-\r
- //-- boolean hasColour() \r
+ } //-- boolean hasColour() \r
\r
/**\r
* Method hasEnd\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- }\r
-\r
- //-- boolean hasEnd() \r
+ } //-- boolean hasEnd() \r
\r
/**\r
* Method hasId\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasId()\r
{\r
return this._has_id;\r
- }\r
-\r
- //-- boolean hasId() \r
+ } //-- boolean hasId() \r
\r
/**\r
* Method hasStart\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- }\r
-\r
- //-- boolean hasStart() \r
+ } //-- boolean hasStart() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'colour'.\r
- *\r
+ * \r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(int colour)\r
{\r
this._colour = colour;\r
this._has_colour = true;\r
- }\r
-\r
- //-- void setColour(int) \r
+ } //-- void setColour(int) \r
\r
/**\r
* Sets the value of field 'end'.\r
- *\r
+ * \r
* @param end the value of field 'end'.\r
*/\r
public void setEnd(int end)\r
{\r
this._end = end;\r
this._has_end = true;\r
- }\r
-\r
- //-- void setEnd(int) \r
+ } //-- void setEnd(int) \r
\r
/**\r
* Sets the value of field 'id'.\r
- *\r
+ * \r
* @param id the value of field 'id'.\r
*/\r
public void setId(int id)\r
{\r
this._id = id;\r
this._has_id = true;\r
- }\r
-\r
- //-- void setId(int) \r
+ } //-- void setId(int) \r
\r
/**\r
* Sets the value of field 'start'.\r
- *\r
+ * \r
* @param start the value of field 'start'.\r
*/\r
public void setStart(int start)\r
{\r
this._start = start;\r
this._has_start = true;\r
- }\r
-\r
- //-- void setStart(int) \r
+ } //-- void setStart(int) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\r
import java.util.Date;\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
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JalviewModel.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModel implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class JalviewModel implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.JalviewModelSequence _jalviewModelSequence;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public JalviewModel()\r
- {\r
+\r
+ public JalviewModel() {\r
super();\r
- }\r
+ } //-- jalview.binding.JalviewModel()\r
\r
- //-- jalview.binding.JalviewModel()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Returns the value of field 'creationDate'.\r
+ * \r
+ * @return Date\r
+ * @return the value of field 'creationDate'.\r
*/\r
public java.util.Date getCreationDate()\r
{\r
return this._creationDate;\r
- }\r
-\r
- //-- java.util.Date getCreationDate() \r
+ } //-- java.util.Date getCreationDate() \r
\r
/**\r
* Returns the value of field 'jalviewModelSequence'.\r
- *\r
+ * \r
* @return JalviewModelSequence\r
* @return the value of field 'jalviewModelSequence'.\r
*/\r
public jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
{\r
return this._jalviewModelSequence;\r
- }\r
-\r
- //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() \r
+ } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() \r
\r
/**\r
* Returns the value of field 'vamsasModel'.\r
- *\r
+ * \r
* @return VamsasModel\r
* @return the value of field 'vamsasModel'.\r
*/\r
public jalview.binding.VamsasModel getVamsasModel()\r
{\r
return this._vamsasModel;\r
- }\r
-\r
- //-- jalview.binding.VamsasModel getVamsasModel() \r
+ } //-- jalview.binding.VamsasModel getVamsasModel() \r
\r
/**\r
* Returns the value of field 'version'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'version'.\r
*/\r
public java.lang.String getVersion()\r
{\r
return this._version;\r
- }\r
-\r
- //-- java.lang.String getVersion() \r
+ } //-- java.lang.String getVersion() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'creationDate'.\r
- *\r
+ * \r
* @param creationDate the value of field 'creationDate'.\r
*/\r
public void setCreationDate(java.util.Date creationDate)\r
{\r
this._creationDate = creationDate;\r
- }\r
-\r
- //-- void setCreationDate(java.util.Date) \r
+ } //-- void setCreationDate(java.util.Date) \r
\r
/**\r
* Sets the value of field 'jalviewModelSequence'.\r
- *\r
+ * \r
* @param jalviewModelSequence the value of field\r
* 'jalviewModelSequence'.\r
*/\r
- public void setJalviewModelSequence(\r
- jalview.binding.JalviewModelSequence jalviewModelSequence)\r
+ public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence)\r
{\r
this._jalviewModelSequence = jalviewModelSequence;\r
- }\r
-\r
- //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) \r
+ } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) \r
\r
/**\r
* Sets the value of field 'vamsasModel'.\r
- *\r
+ * \r
* @param vamsasModel the value of field 'vamsasModel'.\r
*/\r
public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)\r
{\r
this._vamsasModel = vamsasModel;\r
- }\r
-\r
- //-- void setVamsasModel(jalview.binding.VamsasModel) \r
+ } //-- void setVamsasModel(jalview.binding.VamsasModel) \r
\r
/**\r
* Sets the value of field 'version'.\r
- *\r
+ * \r
* @param version the value of field 'version'.\r
*/\r
public void setVersion(java.lang.String version)\r
{\r
this._version = version;\r
- }\r
-\r
- //-- void setVersion(java.lang.String) \r
+ } //-- void setVersion(java.lang.String) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\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 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 JalviewModelSequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelSequence\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _JSeqList\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModelSequence()\r
- {\r
- super();\r
- _JSeqList = new Vector();\r
- _JGroupList = new Vector();\r
- _viewportList = new Vector();\r
- _userColoursList = new Vector();\r
- _treeList = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addJGroup\r
- *\r
- *\r
- *\r
- * @param vJGroup\r
- */\r
- public void addJGroup(jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.binding.JGroup)\r
-\r
- /**\r
- * Method addJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.binding.JGroup)\r
-\r
- /**\r
- * Method addJSeq\r
- *\r
- *\r
- *\r
- * @param vJSeq\r
- */\r
- public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.binding.JSeq)\r
-\r
- /**\r
- * Method addJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq)\r
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param vTree\r
- */\r
- public void addTree(jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(jalview.binding.Tree)\r
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, jalview.binding.Tree)\r
-\r
- /**\r
- * Method addUserColours\r
- *\r
- *\r
- *\r
- * @param vUserColours\r
- */\r
- public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.binding.UserColours)\r
-\r
- /**\r
- * Method addUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void addUserColours(int index,\r
- jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.binding.UserColours)\r
-\r
- /**\r
- * Method addViewport\r
- *\r
- *\r
- *\r
- * @param vViewport\r
- */\r
- public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.binding.Viewport)\r
-\r
- /**\r
- * Method addViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vViewport\r
- */\r
- public void addViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.binding.Viewport)\r
-\r
- /**\r
- * Method enumerateJGroup\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
- return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup()\r
-\r
- /**\r
- * Method enumerateJSeq\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
- return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq()\r
-\r
- /**\r
- * Method enumerateTree\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree()\r
-\r
- /**\r
- * Method enumerateUserColours\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
- return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours()\r
-\r
- /**\r
- * Method enumerateViewport\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
- return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport()\r
-\r
- /**\r
- * Method getJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JGroupList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.binding.JGroup getJGroup(int)\r
-\r
- /**\r
- * Method getJGroup\r
- *\r
- *\r
- *\r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup[] getJGroup()\r
- {\r
- int size = _JGroupList.size();\r
- jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.JGroup[] getJGroup()\r
-\r
- /**\r
- * Method getJGroupCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getJGroupCount()\r
- {\r
- return _JGroupList.size();\r
- } //-- int getJGroupCount()\r
-\r
- /**\r
- * Method getJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JSeqList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.binding.JSeq getJSeq(int)\r
-\r
- /**\r
- * Method getJSeq\r
- *\r
- *\r
- *\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq[] getJSeq()\r
- {\r
- int size = _JSeqList.size();\r
- jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.JSeq[] getJSeq()\r
-\r
- /**\r
- * Method getJSeqCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getJSeqCount()\r
- {\r
- return _JSeqList.size();\r
- } //-- int getJSeqCount()\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _treeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.Tree) _treeList.elementAt(index);\r
- } //-- jalview.binding.Tree getTree(int)\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree[] getTree()\r
- {\r
- int size = _treeList.size();\r
- jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Tree[] getTree()\r
-\r
- /**\r
- * Method getTreeCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount()\r
-\r
- /**\r
- * Method getUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColoursList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.binding.UserColours getUserColours(int)\r
-\r
- /**\r
- * Method getUserColours\r
- *\r
- *\r
- *\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours[] getUserColours()\r
- {\r
- int size = _userColoursList.size();\r
- jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.UserColours[] getUserColours()\r
-\r
- /**\r
- * Method getUserColoursCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getUserColoursCount()\r
- {\r
- return _userColoursList.size();\r
- } //-- int getUserColoursCount()\r
-\r
- /**\r
- * Method getViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _viewportList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.binding.Viewport getViewport(int)\r
-\r
- /**\r
- * Method getViewport\r
- *\r
- *\r
- *\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport[] getViewport()\r
- {\r
- int size = _viewportList.size();\r
- jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Viewport[] getViewport()\r
-\r
- /**\r
- * Method getViewportCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getViewportCount()\r
- {\r
- return _viewportList.size();\r
- } //-- int getViewportCount()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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 removeAllJGroup\r
- *\r
- */\r
- public void removeAllJGroup()\r
- {\r
- _JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup()\r
-\r
- /**\r
- * Method removeAllJSeq\r
- *\r
- */\r
- public void removeAllJSeq()\r
- {\r
- _JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq()\r
-\r
- /**\r
- * Method removeAllTree\r
- *\r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree()\r
-\r
- /**\r
- * Method removeAllUserColours\r
- *\r
- */\r
- public void removeAllUserColours()\r
- {\r
- _userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours()\r
-\r
- /**\r
- * Method removeAllViewport\r
- *\r
- */\r
- public void removeAllViewport()\r
- {\r
- _viewportList.removeAllElements();\r
- } //-- void removeAllViewport()\r
-\r
- /**\r
- * Method removeJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup removeJGroup(int index)\r
- {\r
- java.lang.Object obj = _JGroupList.elementAt(index);\r
- _JGroupList.removeElementAt(index);\r
- return (jalview.binding.JGroup) obj;\r
- } //-- jalview.binding.JGroup removeJGroup(int)\r
-\r
- /**\r
- * Method removeJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq removeJSeq(int index)\r
- {\r
- java.lang.Object obj = _JSeqList.elementAt(index);\r
- _JSeqList.removeElementAt(index);\r
- return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int)\r
-\r
- /**\r
- * Method removeTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (jalview.binding.Tree) obj;\r
- } //-- jalview.binding.Tree removeTree(int)\r
-\r
- /**\r
- * Method removeUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours removeUserColours(int index)\r
- {\r
- java.lang.Object obj = _userColoursList.elementAt(index);\r
- _userColoursList.removeElementAt(index);\r
- return (jalview.binding.UserColours) obj;\r
- } //-- jalview.binding.UserColours removeUserColours(int)\r
-\r
- /**\r
- * Method removeViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport removeViewport(int index)\r
- {\r
- java.lang.Object obj = _viewportList.elementAt(index);\r
- _viewportList.removeElementAt(index);\r
- return (jalview.binding.Viewport) obj;\r
- } //-- jalview.binding.Viewport removeViewport(int)\r
-\r
- /**\r
- * Method setJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void setJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JGroupList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.binding.JGroup)\r
-\r
- /**\r
- * Method setJGroup\r
- *\r
- *\r
- *\r
- * @param JGroupArray\r
- */\r
- public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
- {\r
- //-- copy array\r
- _JGroupList.removeAllElements();\r
- for (int i = 0; i < JGroupArray.length; i++)\r
- {\r
- _JGroupList.addElement(JGroupArray[i]);\r
- }\r
- } //-- void setJGroup(jalview.binding.JGroup)\r
-\r
- /**\r
- * Method setJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void setJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JSeqList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.binding.JSeq)\r
-\r
- /**\r
- * Method setJSeq\r
- *\r
- *\r
- *\r
- * @param JSeqArray\r
- */\r
- public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
- {\r
- //-- copy array\r
- _JSeqList.removeAllElements();\r
- for (int i = 0; i < JSeqArray.length; i++)\r
- {\r
- _JSeqList.addElement(JSeqArray[i]);\r
- }\r
- } //-- void setJSeq(jalview.binding.JSeq)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _treeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, jalview.binding.Tree)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param treeArray\r
- */\r
- public void setTree(jalview.binding.Tree[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++)\r
- {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(jalview.binding.Tree)\r
-\r
- /**\r
- * Method setUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void setUserColours(int index,\r
- jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColoursList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.binding.UserColours)\r
-\r
- /**\r
- * Method setUserColours\r
- *\r
- *\r
- *\r
- * @param userColoursArray\r
- */\r
- public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
- {\r
- //-- copy array\r
- _userColoursList.removeAllElements();\r
- for (int i = 0; i < userColoursArray.length; i++)\r
- {\r
- _userColoursList.addElement(userColoursArray[i]);\r
- }\r
- } //-- void setUserColours(jalview.binding.UserColours)\r
-\r
- /**\r
- * Method setViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vViewport\r
- */\r
- public void setViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _viewportList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.binding.Viewport)\r
-\r
- /**\r
- * Method setViewport\r
- *\r
- *\r
- *\r
- * @param viewportArray\r
- */\r
- public void setViewport(jalview.binding.Viewport[] viewportArray)\r
- {\r
- //-- copy array\r
- _viewportList.removeAllElements();\r
- for (int i = 0; i < viewportArray.length; i++)\r
- {\r
- _viewportList.addElement(viewportArray[i]);\r
- }\r
- } //-- void setViewport(jalview.binding.Viewport)\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.binding.JalviewModelSequence) Unmarshaller.unmarshal(\r
- jalview.binding.JalviewModelSequence.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
+public class JalviewModelSequence implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _JSeqList\r
+ */\r
+ private java.util.Vector _JSeqList;\r
+\r
+ /**\r
+ * Field _JGroupList\r
+ */\r
+ private java.util.Vector _JGroupList;\r
+\r
+ /**\r
+ * Field _viewportList\r
+ */\r
+ private java.util.Vector _viewportList;\r
+\r
+ /**\r
+ * Field _userColoursList\r
+ */\r
+ private java.util.Vector _userColoursList;\r
+\r
+ /**\r
+ * Field _treeList\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JalviewModelSequence() {\r
+ super();\r
+ _JSeqList = new Vector();\r
+ _JGroupList = new Vector();\r
+ _viewportList = new Vector();\r
+ _userColoursList = new Vector();\r
+ _treeList = new Vector();\r
+ } //-- jalview.binding.JalviewModelSequence()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param vJGroup\r
+ */\r
+ public void addJGroup(jalview.binding.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _JGroupList.addElement(vJGroup);\r
+ } //-- void addJGroup(jalview.binding.JGroup) \r
+\r
+ /**\r
+ * Method addJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ */\r
+ public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _JGroupList.insertElementAt(vJGroup, index);\r
+ } //-- void addJGroup(int, jalview.binding.JGroup) \r
+\r
+ /**\r
+ * Method addJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param vJSeq\r
+ */\r
+ public void addJSeq(jalview.binding.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _JSeqList.addElement(vJSeq);\r
+ } //-- void addJSeq(jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method addJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ */\r
+ public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _JSeqList.insertElementAt(vJSeq, index);\r
+ } //-- void addJSeq(int, jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param vTree\r
+ */\r
+ public void addTree(jalview.binding.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _treeList.addElement(vTree);\r
+ } //-- void addTree(jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ */\r
+ public void addTree(int index, jalview.binding.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _treeList.insertElementAt(vTree, index);\r
+ } //-- void addTree(int, jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method addUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param vUserColours\r
+ */\r
+ public void addUserColours(jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _userColoursList.addElement(vUserColours);\r
+ } //-- void addUserColours(jalview.binding.UserColours) \r
+\r
+ /**\r
+ * Method addUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ */\r
+ public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _userColoursList.insertElementAt(vUserColours, index);\r
+ } //-- void addUserColours(int, jalview.binding.UserColours) \r
+\r
+ /**\r
+ * Method addViewport\r
+ * \r
+ * \r
+ * \r
+ * @param vViewport\r
+ */\r
+ public void addViewport(jalview.binding.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _viewportList.addElement(vViewport);\r
+ } //-- void addViewport(jalview.binding.Viewport) \r
+\r
+ /**\r
+ * Method addViewport\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ */\r
+ public void addViewport(int index, jalview.binding.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _viewportList.insertElementAt(vViewport, index);\r
+ } //-- void addViewport(int, jalview.binding.Viewport) \r
+\r
+ /**\r
+ * Method enumerateJGroup\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateJGroup()\r
+ {\r
+ return _JGroupList.elements();\r
+ } //-- java.util.Enumeration enumerateJGroup() \r
+\r
+ /**\r
+ * Method enumerateJSeq\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateJSeq()\r
+ {\r
+ return _JSeqList.elements();\r
+ } //-- java.util.Enumeration enumerateJSeq() \r
+\r
+ /**\r
+ * Method enumerateTree\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
+ return _treeList.elements();\r
+ } //-- java.util.Enumeration enumerateTree() \r
+\r
+ /**\r
+ * Method enumerateUserColours\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateUserColours()\r
+ {\r
+ return _userColoursList.elements();\r
+ } //-- java.util.Enumeration enumerateUserColours() \r
+\r
+ /**\r
+ * Method enumerateViewport\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateViewport()\r
+ {\r
+ return _viewportList.elements();\r
+ } //-- java.util.Enumeration enumerateViewport() \r
+\r
+ /**\r
+ * Method getJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return JGroup\r
+ */\r
+ public jalview.binding.JGroup getJGroup(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _JGroupList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
+ } //-- jalview.binding.JGroup getJGroup(int) \r
+\r
+ /**\r
+ * Method getJGroup\r
+ * \r
+ * \r
+ * \r
+ * @return JGroup\r
+ */\r
+ public jalview.binding.JGroup[] getJGroup()\r
+ {\r
+ int size = _JGroupList.size();\r
+ jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.JGroup[] getJGroup() \r
+\r
+ /**\r
+ * Method getJGroupCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getJGroupCount()\r
+ {\r
+ return _JGroupList.size();\r
+ } //-- int getJGroupCount() \r
+\r
+ /**\r
+ * Method getJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return JSeq\r
+ */\r
+ public jalview.binding.JSeq getJSeq(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _JSeqList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
+ } //-- jalview.binding.JSeq getJSeq(int) \r
+\r
+ /**\r
+ * Method getJSeq\r
+ * \r
+ * \r
+ * \r
+ * @return JSeq\r
+ */\r
+ public jalview.binding.JSeq[] getJSeq()\r
+ {\r
+ int size = _JSeqList.size();\r
+ jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.JSeq[] getJSeq() \r
+\r
+ /**\r
+ * Method getJSeqCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getJSeqCount()\r
+ {\r
+ return _JSeqList.size();\r
+ } //-- int getJSeqCount() \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree 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
+ }\r
+ \r
+ return (jalview.binding.Tree) _treeList.elementAt(index);\r
+ } //-- jalview.binding.Tree getTree(int) \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree[] getTree()\r
+ {\r
+ int size = _treeList.size();\r
+ jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Tree[] getTree() \r
+\r
+ /**\r
+ * Method getTreeCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getTreeCount()\r
+ {\r
+ return _treeList.size();\r
+ } //-- int getTreeCount() \r
+\r
+ /**\r
+ * Method getUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return UserColours\r
+ */\r
+ public jalview.binding.UserColours getUserColours(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _userColoursList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+ } //-- jalview.binding.UserColours getUserColours(int) \r
+\r
+ /**\r
+ * Method getUserColours\r
+ * \r
+ * \r
+ * \r
+ * @return UserColours\r
+ */\r
+ public jalview.binding.UserColours[] getUserColours()\r
+ {\r
+ int size = _userColoursList.size();\r
+ jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.UserColours[] getUserColours() \r
+\r
+ /**\r
+ * Method getUserColoursCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getUserColoursCount()\r
+ {\r
+ return _userColoursList.size();\r
+ } //-- int getUserColoursCount() \r
+\r
+ /**\r
+ * Method getViewport\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Viewport\r
+ */\r
+ public jalview.binding.Viewport getViewport(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _viewportList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
+ } //-- jalview.binding.Viewport getViewport(int) \r
+\r
+ /**\r
+ * Method getViewport\r
+ * \r
+ * \r
+ * \r
+ * @return Viewport\r
+ */\r
+ public jalview.binding.Viewport[] getViewport()\r
+ {\r
+ int size = _viewportList.size();\r
+ jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Viewport[] getViewport() \r
+\r
+ /**\r
+ * Method getViewportCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getViewportCount()\r
+ {\r
+ return _viewportList.size();\r
+ } //-- int getViewportCount() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllJGroup\r
+ * \r
+ */\r
+ public void removeAllJGroup()\r
+ {\r
+ _JGroupList.removeAllElements();\r
+ } //-- void removeAllJGroup() \r
+\r
+ /**\r
+ * Method removeAllJSeq\r
+ * \r
+ */\r
+ public void removeAllJSeq()\r
+ {\r
+ _JSeqList.removeAllElements();\r
+ } //-- void removeAllJSeq() \r
+\r
+ /**\r
+ * Method removeAllTree\r
+ * \r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ _treeList.removeAllElements();\r
+ } //-- void removeAllTree() \r
+\r
+ /**\r
+ * Method removeAllUserColours\r
+ * \r
+ */\r
+ public void removeAllUserColours()\r
+ {\r
+ _userColoursList.removeAllElements();\r
+ } //-- void removeAllUserColours() \r
+\r
+ /**\r
+ * Method removeAllViewport\r
+ * \r
+ */\r
+ public void removeAllViewport()\r
+ {\r
+ _viewportList.removeAllElements();\r
+ } //-- void removeAllViewport() \r
+\r
+ /**\r
+ * Method removeJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return JGroup\r
+ */\r
+ public jalview.binding.JGroup removeJGroup(int index)\r
+ {\r
+ java.lang.Object obj = _JGroupList.elementAt(index);\r
+ _JGroupList.removeElementAt(index);\r
+ return (jalview.binding.JGroup) obj;\r
+ } //-- jalview.binding.JGroup removeJGroup(int) \r
+\r
+ /**\r
+ * Method removeJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return JSeq\r
+ */\r
+ public jalview.binding.JSeq removeJSeq(int index)\r
+ {\r
+ java.lang.Object obj = _JSeqList.elementAt(index);\r
+ _JSeqList.removeElementAt(index);\r
+ return (jalview.binding.JSeq) obj;\r
+ } //-- jalview.binding.JSeq removeJSeq(int) \r
+\r
+ /**\r
+ * Method removeTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree removeTree(int index)\r
+ {\r
+ java.lang.Object obj = _treeList.elementAt(index);\r
+ _treeList.removeElementAt(index);\r
+ return (jalview.binding.Tree) obj;\r
+ } //-- jalview.binding.Tree removeTree(int) \r
+\r
+ /**\r
+ * Method removeUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return UserColours\r
+ */\r
+ public jalview.binding.UserColours removeUserColours(int index)\r
+ {\r
+ java.lang.Object obj = _userColoursList.elementAt(index);\r
+ _userColoursList.removeElementAt(index);\r
+ return (jalview.binding.UserColours) obj;\r
+ } //-- jalview.binding.UserColours removeUserColours(int) \r
+\r
+ /**\r
+ * Method removeViewport\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Viewport\r
+ */\r
+ public jalview.binding.Viewport removeViewport(int index)\r
+ {\r
+ java.lang.Object obj = _viewportList.elementAt(index);\r
+ _viewportList.removeElementAt(index);\r
+ return (jalview.binding.Viewport) obj;\r
+ } //-- jalview.binding.Viewport removeViewport(int) \r
+\r
+ /**\r
+ * Method setJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ */\r
+ public void setJGroup(int index, jalview.binding.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _JGroupList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _JGroupList.setElementAt(vJGroup, index);\r
+ } //-- void setJGroup(int, jalview.binding.JGroup) \r
+\r
+ /**\r
+ * Method setJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param JGroupArray\r
+ */\r
+ public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
+ {\r
+ //-- copy array\r
+ _JGroupList.removeAllElements();\r
+ for (int i = 0; i < JGroupArray.length; i++) {\r
+ _JGroupList.addElement(JGroupArray[i]);\r
+ }\r
+ } //-- void setJGroup(jalview.binding.JGroup) \r
+\r
+ /**\r
+ * Method setJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ */\r
+ public void setJSeq(int index, jalview.binding.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _JSeqList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _JSeqList.setElementAt(vJSeq, index);\r
+ } //-- void setJSeq(int, jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method setJSeq\r
+ * \r
+ * \r
+ * \r
+ * @param JSeqArray\r
+ */\r
+ public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
+ {\r
+ //-- copy array\r
+ _JSeqList.removeAllElements();\r
+ for (int i = 0; i < JSeqArray.length; i++) {\r
+ _JSeqList.addElement(JSeqArray[i]);\r
+ }\r
+ } //-- void setJSeq(jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ */\r
+ public void setTree(int index, jalview.binding.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _treeList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _treeList.setElementAt(vTree, index);\r
+ } //-- void setTree(int, jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param treeArray\r
+ */\r
+ public void setTree(jalview.binding.Tree[] treeArray)\r
+ {\r
+ //-- copy array\r
+ _treeList.removeAllElements();\r
+ for (int i = 0; i < treeArray.length; i++) {\r
+ _treeList.addElement(treeArray[i]);\r
+ }\r
+ } //-- void setTree(jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method setUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ */\r
+ public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _userColoursList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _userColoursList.setElementAt(vUserColours, index);\r
+ } //-- void setUserColours(int, jalview.binding.UserColours) \r
+\r
+ /**\r
+ * Method setUserColours\r
+ * \r
+ * \r
+ * \r
+ * @param userColoursArray\r
+ */\r
+ public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
+ {\r
+ //-- copy array\r
+ _userColoursList.removeAllElements();\r
+ for (int i = 0; i < userColoursArray.length; i++) {\r
+ _userColoursList.addElement(userColoursArray[i]);\r
+ }\r
+ } //-- void setUserColours(jalview.binding.UserColours) \r
+\r
+ /**\r
+ * Method setViewport\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ */\r
+ public void setViewport(int index, jalview.binding.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _viewportList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _viewportList.setElementAt(vViewport, index);\r
+ } //-- void setViewport(int, jalview.binding.Viewport) \r
+\r
+ /**\r
+ * Method setViewport\r
+ * \r
+ * \r
+ * \r
+ * @param viewportArray\r
+ */\r
+ public void setViewport(jalview.binding.Viewport[] viewportArray)\r
+ {\r
+ //-- copy array\r
+ _viewportList.removeAllElements();\r
+ for (int i = 0; i < viewportArray.length; i++) {\r
+ _viewportList.addElement(viewportArray[i]);\r
+ }\r
+ } //-- void setViewport(jalview.binding.Viewport) \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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\r
import java.util.Enumeration;\r
import java.util.Vector;\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
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class JalviewUserColours.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewUserColours implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class JalviewUserColours implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
+ * Field _schemeName\r
+ */\r
+ private java.lang.String _schemeName;\r
+\r
+ /**\r
* Field _colourList\r
*/\r
private java.util.Vector _colourList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public JalviewUserColours()\r
- {\r
+\r
+ public JalviewUserColours() {\r
super();\r
_colourList = new Vector();\r
- }\r
+ } //-- jalview.binding.JalviewUserColours()\r
+\r
\r
- //-- jalview.binding.JalviewUserColours()\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @param vColour DOCUMENT ME!\r
- *\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!\r
+ * Method addColour\r
+ * \r
+ * \r
+ * \r
+ * @param vColour\r
*/\r
public void addColour(jalview.binding.Colour vColour)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_colourList.addElement(vColour);\r
- }\r
-\r
- //-- void addColour(jalview.binding.Colour) \r
+ } //-- void addColour(jalview.binding.Colour) \r
\r
/**\r
* Method addColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vColour\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_colourList.insertElementAt(vColour, index);\r
- }\r
-\r
- //-- void addColour(int, jalview.binding.Colour) \r
+ } //-- void addColour(int, jalview.binding.Colour) \r
\r
/**\r
* Method enumerateColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateColour()\r
{\r
return _colourList.elements();\r
- }\r
-\r
- //-- java.util.Enumeration enumerateColour() \r
+ } //-- java.util.Enumeration enumerateColour() \r
\r
/**\r
* Method getColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Colour\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size()))\r
- {\r
+ if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Colour) _colourList.elementAt(index);\r
- }\r
-\r
- //-- jalview.binding.Colour getColour(int) \r
+ } //-- jalview.binding.Colour getColour(int) \r
\r
/**\r
* Method getColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Colour\r
*/\r
public jalview.binding.Colour[] getColour()\r
{\r
int size = _colourList.size();\r
jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];\r
-\r
- for (int index = 0; index < size; index++)\r
- {\r
+ for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
-\r
- //-- jalview.binding.Colour[] getColour() \r
+ } //-- jalview.binding.Colour[] getColour() \r
\r
/**\r
* Method getColourCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
public int getColourCount()\r
{\r
return _colourList.size();\r
- }\r
+ } //-- int getColourCount() \r
\r
- //-- int getColourCount() \r
+ /**\r
+ * Returns the value of field 'schemeName'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'schemeName'.\r
+ */\r
+ public java.lang.String getSchemeName()\r
+ {\r
+ return this._schemeName;\r
+ } //-- java.lang.String getSchemeName() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllColour\r
- *\r
+ * \r
*/\r
public void removeAllColour()\r
{\r
_colourList.removeAllElements();\r
- }\r
-\r
- //-- void removeAllColour() \r
+ } //-- void removeAllColour() \r
\r
/**\r
* Method removeColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Colour\r
*/\r
{\r
java.lang.Object obj = _colourList.elementAt(index);\r
_colourList.removeElementAt(index);\r
-\r
return (jalview.binding.Colour) obj;\r
- }\r
-\r
- //-- jalview.binding.Colour removeColour(int) \r
+ } //-- jalview.binding.Colour removeColour(int) \r
\r
/**\r
* Method setColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vColour\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size()))\r
- {\r
+ if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_colourList.setElementAt(vColour, index);\r
- }\r
-\r
- //-- void setColour(int, jalview.binding.Colour) \r
+ } //-- void setColour(int, jalview.binding.Colour) \r
\r
/**\r
* Method setColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param colourArray\r
*/\r
public void setColour(jalview.binding.Colour[] colourArray)\r
{\r
//-- copy array\r
_colourList.removeAllElements();\r
-\r
- for (int i = 0; i < colourArray.length; i++)\r
- {\r
+ for (int i = 0; i < colourArray.length; i++) {\r
_colourList.addElement(colourArray[i]);\r
}\r
- }\r
+ } //-- void setColour(jalview.binding.Colour) \r
\r
- //-- void setColour(jalview.binding.Colour) \r
+ /**\r
+ * Sets the value of field 'schemeName'.\r
+ * \r
+ * @param schemeName the value of field 'schemeName'.\r
+ */\r
+ public void setSchemeName(java.lang.String schemeName)\r
+ {\r
+ this._schemeName = schemeName;\r
+ } //-- void setSchemeName(java.lang.String) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\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 Sequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence\r
- extends SequenceType implements java.io.Serializable\r
+public class Sequence extends SequenceType \r
+implements java.io.Serializable\r
{\r
\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
\r
- public Sequence()\r
- {\r
- super();\r
- } //-- jalview.binding.Sequence()\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ public Sequence() {\r
+ super();\r
+ } //-- jalview.binding.Sequence()\r
\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
+ //- Methods -/\r
+ //-----------/\r
\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \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
+ * Method marshal\r
+ * \r
+ * \r
+ * \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
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \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.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.\r
- Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.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
+ * 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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\r
import java.util.Enumeration;\r
import java.util.Vector;\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
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class SequenceSet.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceSet implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+public class SequenceSet implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _annotationList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public SequenceSet()\r
- {\r
+\r
+ public SequenceSet() {\r
super();\r
_sequenceList = new Vector();\r
_annotationList = new Vector();\r
- }\r
+ } //-- jalview.binding.SequenceSet()\r
+\r
\r
- //-- jalview.binding.SequenceSet()\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @param vAnnotation DOCUMENT ME!\r
- *\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!\r
+ * Method addAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param vAnnotation\r
*/\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.addElement(vAnnotation);\r
- }\r
-\r
- //-- void addAnnotation(jalview.binding.Annotation) \r
+ } //-- void addAnnotation(jalview.binding.Annotation) \r
\r
/**\r
* Method addAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.insertElementAt(vAnnotation, index);\r
- }\r
-\r
- //-- void addAnnotation(int, jalview.binding.Annotation) \r
+ } //-- void addAnnotation(int, jalview.binding.Annotation) \r
\r
/**\r
* Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vSequence\r
*/\r
public void addSequence(jalview.binding.Sequence vSequence)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceList.addElement(vSequence);\r
- }\r
-\r
- //-- void addSequence(jalview.binding.Sequence) \r
+ } //-- void addSequence(jalview.binding.Sequence) \r
\r
/**\r
* Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceList.insertElementAt(vSequence, index);\r
- }\r
-\r
- //-- void addSequence(int, jalview.binding.Sequence) \r
+ } //-- void addSequence(int, jalview.binding.Sequence) \r
\r
/**\r
* Method deleteAligned\r
- *\r
+ * \r
*/\r
public void deleteAligned()\r
{\r
- this._has_aligned = false;\r
- }\r
-\r
- //-- void deleteAligned() \r
+ this._has_aligned= false;\r
+ } //-- void deleteAligned() \r
\r
/**\r
* Method enumerateAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateAnnotation()\r
{\r
return _annotationList.elements();\r
- }\r
-\r
- //-- java.util.Enumeration enumerateAnnotation() \r
+ } //-- java.util.Enumeration enumerateAnnotation() \r
\r
/**\r
* Method enumerateSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSequence()\r
{\r
return _sequenceList.elements();\r
- }\r
-\r
- //-- java.util.Enumeration enumerateSequence() \r
+ } //-- java.util.Enumeration enumerateSequence() \r
\r
/**\r
* Returns the value of field 'aligned'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'aligned'.\r
*/\r
public boolean getAligned()\r
{\r
return this._aligned;\r
- }\r
-\r
- //-- boolean getAligned() \r
+ } //-- boolean getAligned() \r
\r
/**\r
* Method getAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Annotation\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size()))\r
- {\r
+ if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- }\r
-\r
- //-- jalview.binding.Annotation getAnnotation(int) \r
+ } //-- jalview.binding.Annotation getAnnotation(int) \r
\r
/**\r
* Method getAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Annotation\r
*/\r
public jalview.binding.Annotation[] getAnnotation()\r
{\r
int size = _annotationList.size();\r
jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];\r
-\r
- for (int index = 0; index < size; index++)\r
- {\r
+ for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
-\r
- //-- jalview.binding.Annotation[] getAnnotation() \r
+ } //-- jalview.binding.Annotation[] getAnnotation() \r
\r
/**\r
* Method getAnnotationCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
public int getAnnotationCount()\r
{\r
return _annotationList.size();\r
- }\r
-\r
- //-- int getAnnotationCount() \r
+ } //-- int getAnnotationCount() \r
\r
/**\r
* Returns the value of field 'gapChar'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'gapChar'.\r
*/\r
public java.lang.String getGapChar()\r
{\r
return this._gapChar;\r
- }\r
-\r
- //-- java.lang.String getGapChar() \r
+ } //-- java.lang.String getGapChar() \r
\r
/**\r
* Method getSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Sequence\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size()))\r
- {\r
+ if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- }\r
-\r
- //-- jalview.binding.Sequence getSequence(int) \r
+ } //-- jalview.binding.Sequence getSequence(int) \r
\r
/**\r
* Method getSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Sequence\r
*/\r
public jalview.binding.Sequence[] getSequence()\r
{\r
int size = _sequenceList.size();\r
jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];\r
-\r
- for (int index = 0; index < size; index++)\r
- {\r
+ for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
-\r
- //-- jalview.binding.Sequence[] getSequence() \r
+ } //-- jalview.binding.Sequence[] getSequence() \r
\r
/**\r
* Method getSequenceCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
public int getSequenceCount()\r
{\r
return _sequenceList.size();\r
- }\r
-\r
- //-- int getSequenceCount() \r
+ } //-- int getSequenceCount() \r
\r
/**\r
* Method hasAligned\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasAligned()\r
{\r
return this._has_aligned;\r
- }\r
-\r
- //-- boolean hasAligned() \r
+ } //-- boolean hasAligned() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllAnnotation\r
- *\r
+ * \r
*/\r
public void removeAllAnnotation()\r
{\r
_annotationList.removeAllElements();\r
- }\r
-\r
- //-- void removeAllAnnotation() \r
+ } //-- void removeAllAnnotation() \r
\r
/**\r
* Method removeAllSequence\r
- *\r
+ * \r
*/\r
public void removeAllSequence()\r
{\r
_sequenceList.removeAllElements();\r
- }\r
-\r
- //-- void removeAllSequence() \r
+ } //-- void removeAllSequence() \r
\r
/**\r
* Method removeAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Annotation\r
*/\r
{\r
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
-\r
return (jalview.binding.Annotation) obj;\r
- }\r
-\r
- //-- jalview.binding.Annotation removeAnnotation(int) \r
+ } //-- jalview.binding.Annotation removeAnnotation(int) \r
\r
/**\r
* Method removeSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Sequence\r
*/\r
{\r
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
-\r
return (jalview.binding.Sequence) obj;\r
- }\r
-\r
- //-- jalview.binding.Sequence removeSequence(int) \r
+ } //-- jalview.binding.Sequence removeSequence(int) \r
\r
/**\r
* Sets the value of field 'aligned'.\r
- *\r
+ * \r
* @param aligned the value of field 'aligned'.\r
*/\r
public void setAligned(boolean aligned)\r
{\r
this._aligned = aligned;\r
this._has_aligned = true;\r
- }\r
-\r
- //-- void setAligned(boolean) \r
+ } //-- void setAligned(boolean) \r
\r
/**\r
* Method setAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size()))\r
- {\r
+ if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_annotationList.setElementAt(vAnnotation, index);\r
- }\r
-\r
- //-- void setAnnotation(int, jalview.binding.Annotation) \r
+ } //-- void setAnnotation(int, jalview.binding.Annotation) \r
\r
/**\r
* Method setAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param annotationArray\r
*/\r
public void setAnnotation(jalview.binding.Annotation[] annotationArray)\r
{\r
//-- copy array\r
_annotationList.removeAllElements();\r
-\r
- for (int i = 0; i < annotationArray.length; i++)\r
- {\r
+ for (int i = 0; i < annotationArray.length; i++) {\r
_annotationList.addElement(annotationArray[i]);\r
}\r
- }\r
-\r
- //-- void setAnnotation(jalview.binding.Annotation) \r
+ } //-- void setAnnotation(jalview.binding.Annotation) \r
\r
/**\r
* Sets the value of field 'gapChar'.\r
- *\r
+ * \r
* @param gapChar the value of field 'gapChar'.\r
*/\r
public void setGapChar(java.lang.String gapChar)\r
{\r
this._gapChar = gapChar;\r
- }\r
-\r
- //-- void setGapChar(java.lang.String) \r
+ } //-- void setGapChar(java.lang.String) \r
\r
/**\r
* Method setSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
//-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size()))\r
- {\r
+ if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_sequenceList.setElementAt(vSequence, index);\r
- }\r
-\r
- //-- void setSequence(int, jalview.binding.Sequence) \r
+ } //-- void setSequence(int, jalview.binding.Sequence) \r
\r
/**\r
* Method setSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param sequenceArray\r
*/\r
public void setSequence(jalview.binding.Sequence[] sequenceArray)\r
{\r
//-- copy array\r
_sequenceList.removeAllElements();\r
-\r
- for (int i = 0; i < sequenceArray.length; i++)\r
- {\r
+ for (int i = 0; i < sequenceArray.length; i++) {\r
_sequenceList.addElement(sequenceArray[i]);\r
}\r
- }\r
-\r
- //-- void setSequence(jalview.binding.Sequence) \r
+ } //-- void setSequence(jalview.binding.Sequence) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\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 SequenceType.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceType\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _sequence\r
- */\r
- private java.lang.String _sequence;\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceType()\r
- {\r
- super();\r
- } //-- jalview.binding.SequenceType()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId()\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- *\r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName()\r
-\r
- /**\r
- * Returns the value of field 'sequence'.\r
- *\r
- * @return String\r
- * @return the value of field 'sequence'.\r
- */\r
- public java.lang.String getSequence()\r
- {\r
- return this._sequence;\r
- } //-- java.lang.String getSequence()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
+public class SequenceType implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _sequence\r
+ */\r
+ private java.lang.String _sequence;\r
+\r
+ /**\r
+ * Field _name\r
+ */\r
+ private java.lang.String _name;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceType() {\r
+ super();\r
+ } //-- jalview.binding.SequenceType()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ } //-- java.lang.String getId() \r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'name'.\r
+ */\r
+ public java.lang.String getName()\r
+ {\r
+ return this._name;\r
+ } //-- java.lang.String getName() \r
+\r
+ /**\r
+ * Returns the value of field 'sequence'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'sequence'.\r
+ */\r
+ public java.lang.String getSequence()\r
+ {\r
+ return this._sequence;\r
+ } //-- java.lang.String getSequence() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ } //-- void setId(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(java.lang.String name)\r
+ {\r
+ this._name = name;\r
+ } //-- void setName(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'sequence'.\r
+ * \r
+ * @param sequence the value of field 'sequence'.\r
+ */\r
+ public void setSequence(java.lang.String sequence)\r
+ {\r
+ this._sequence = sequence;\r
+ } //-- void setSequence(java.lang.String) \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, org.exolab.castor.xml.ValidationException\r
{\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.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
- return false;\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
- * Sets the value of field 'id'.\r
- *\r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- *\r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'sequence'.\r
- *\r
- * @param sequence the value of field 'sequence'.\r
- */\r
- public void setSequence(java.lang.String sequence)\r
- {\r
- this._sequence = sequence;\r
- } //-- void setSequence(java.lang.String)\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.binding.SequenceType) Unmarshaller.unmarshal(jalview.\r
- binding.SequenceType.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
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 Tree.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Tree implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
+public class Tree implements java.io.Serializable {\r
\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
\r
- /**\r
- * Field _currentTree\r
- */\r
- private boolean _currentTree;\r
-\r
- /**\r
- * keeps track of state for field: _currentTree\r
- */\r
- private boolean _has_currentTree;\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
\r
/**\r
- * Field _fitToWindow\r
+ * Field _width\r
*/\r
- private boolean _fitToWindow;\r
+ private int _width;\r
\r
/**\r
- * keeps track of state for field: _fitToWindow\r
+ * keeps track of state for field: _width\r
*/\r
- private boolean _has_fitToWindow;\r
+ private boolean _has_width;\r
\r
/**\r
- * Field _showDistances\r
+ * Field _height\r
*/\r
- private boolean _showDistances;\r
+ private int _height;\r
\r
/**\r
- * keeps track of state for field: _showDistances\r
+ * keeps track of state for field: _height\r
*/\r
- private boolean _has_showDistances;\r
+ private boolean _has_height;\r
\r
/**\r
- * Field _showBootstrap\r
+ * Field _xpos\r
*/\r
- private boolean _showBootstrap;\r
+ private int _xpos;\r
\r
/**\r
- * keeps track of state for field: _showBootstrap\r
+ * keeps track of state for field: _xpos\r
*/\r
- private boolean _has_showBootstrap;\r
+ private boolean _has_xpos;\r
\r
/**\r
- * Field _markUnlinked\r
+ * Field _ypos\r
*/\r
- private boolean _markUnlinked;\r
+ private int _ypos;\r
\r
/**\r
- * keeps track of state for field: _markUnlinked\r
+ * keeps track of state for field: _ypos\r
*/\r
- private boolean _has_markUnlinked;\r
+ private boolean _has_ypos;\r
\r
/**\r
* Field _fontSize\r
private boolean _has_threshold;\r
\r
/**\r
- * Field _xpos\r
+ * Field _showBootstrap\r
*/\r
- private int _xpos;\r
+ private boolean _showBootstrap;\r
\r
/**\r
- * keeps track of state for field: _xpos\r
+ * keeps track of state for field: _showBootstrap\r
*/\r
- private boolean _has_xpos;\r
+ private boolean _has_showBootstrap;\r
\r
/**\r
- * Field _ypos\r
+ * Field _showDistances\r
*/\r
- private int _ypos;\r
+ private boolean _showDistances;\r
\r
/**\r
- * keeps track of state for field: _ypos\r
+ * keeps track of state for field: _showDistances\r
*/\r
- private boolean _has_ypos;\r
+ private boolean _has_showDistances;\r
\r
/**\r
- * Field _width\r
+ * Field _markUnlinked\r
*/\r
- private int _width;\r
+ private boolean _markUnlinked;\r
\r
/**\r
- * keeps track of state for field: _width\r
+ * keeps track of state for field: _markUnlinked\r
*/\r
- private boolean _has_width;\r
+ private boolean _has_markUnlinked;\r
\r
/**\r
- * Field _height\r
+ * Field _fitToWindow\r
*/\r
- private int _height;\r
+ private boolean _fitToWindow;\r
\r
/**\r
- * keeps track of state for field: _height\r
+ * keeps track of state for field: _fitToWindow\r
*/\r
- private boolean _has_height;\r
+ private boolean _has_fitToWindow;\r
+\r
+ /**\r
+ * Field _currentTree\r
+ */\r
+ private boolean _currentTree;\r
+\r
+ /**\r
+ * keeps track of state for field: _currentTree\r
+ */\r
+ private boolean _has_currentTree;\r
+\r
+ /**\r
+ * Field _title\r
+ */\r
+ private java.lang.String _title;\r
\r
/**\r
* Field _newick\r
*/\r
private java.lang.String _newick;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public Tree()\r
- {\r
+\r
+ public Tree() {\r
super();\r
- }\r
+ } //-- jalview.binding.Tree()\r
\r
- //-- jalview.binding.Tree()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Method deleteCurrentTree\r
+ * \r
*/\r
public void deleteCurrentTree()\r
{\r
- this._has_currentTree = false;\r
- }\r
-\r
- //-- void deleteCurrentTree() \r
+ this._has_currentTree= false;\r
+ } //-- void deleteCurrentTree() \r
\r
/**\r
* Method deleteFitToWindow\r
- *\r
+ * \r
*/\r
public void deleteFitToWindow()\r
{\r
- this._has_fitToWindow = false;\r
- }\r
-\r
- //-- void deleteFitToWindow() \r
+ this._has_fitToWindow= false;\r
+ } //-- void deleteFitToWindow() \r
\r
/**\r
* Method deleteFontSize\r
- *\r
+ * \r
*/\r
public void deleteFontSize()\r
{\r
- this._has_fontSize = false;\r
- }\r
-\r
- //-- void deleteFontSize() \r
+ this._has_fontSize= false;\r
+ } //-- void deleteFontSize() \r
\r
/**\r
* Method deleteHeight\r
- *\r
+ * \r
*/\r
public void deleteHeight()\r
{\r
- this._has_height = false;\r
- }\r
-\r
- //-- void deleteHeight() \r
+ this._has_height= false;\r
+ } //-- void deleteHeight() \r
\r
/**\r
* Method deleteMarkUnlinked\r
- *\r
+ * \r
*/\r
public void deleteMarkUnlinked()\r
{\r
- this._has_markUnlinked = false;\r
- }\r
-\r
- //-- void deleteMarkUnlinked() \r
+ this._has_markUnlinked= false;\r
+ } //-- void deleteMarkUnlinked() \r
\r
/**\r
* Method deleteShowBootstrap\r
- *\r
+ * \r
*/\r
public void deleteShowBootstrap()\r
{\r
- this._has_showBootstrap = false;\r
- }\r
-\r
- //-- void deleteShowBootstrap() \r
+ this._has_showBootstrap= false;\r
+ } //-- void deleteShowBootstrap() \r
\r
/**\r
* Method deleteShowDistances\r
- *\r
+ * \r
*/\r
public void deleteShowDistances()\r
{\r
- this._has_showDistances = false;\r
- }\r
-\r
- //-- void deleteShowDistances() \r
+ this._has_showDistances= false;\r
+ } //-- void deleteShowDistances() \r
\r
/**\r
* Method deleteThreshold\r
- *\r
+ * \r
*/\r
public void deleteThreshold()\r
{\r
- this._has_threshold = false;\r
- }\r
-\r
- //-- void deleteThreshold() \r
+ this._has_threshold= false;\r
+ } //-- void deleteThreshold() \r
\r
/**\r
* Method deleteWidth\r
- *\r
+ * \r
*/\r
public void deleteWidth()\r
{\r
- this._has_width = false;\r
- }\r
-\r
- //-- void deleteWidth() \r
+ this._has_width= false;\r
+ } //-- void deleteWidth() \r
\r
/**\r
* Method deleteXpos\r
- *\r
+ * \r
*/\r
public void deleteXpos()\r
{\r
- this._has_xpos = false;\r
- }\r
-\r
- //-- void deleteXpos() \r
+ this._has_xpos= false;\r
+ } //-- void deleteXpos() \r
\r
/**\r
* Method deleteYpos\r
- *\r
+ * \r
*/\r
public void deleteYpos()\r
{\r
- this._has_ypos = false;\r
- }\r
-\r
- //-- void deleteYpos() \r
+ this._has_ypos= false;\r
+ } //-- void deleteYpos() \r
\r
/**\r
* Returns the value of field 'currentTree'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'currentTree'.\r
*/\r
public boolean getCurrentTree()\r
{\r
return this._currentTree;\r
- }\r
-\r
- //-- boolean getCurrentTree() \r
+ } //-- boolean getCurrentTree() \r
\r
/**\r
* Returns the value of field 'fitToWindow'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'fitToWindow'.\r
*/\r
public boolean getFitToWindow()\r
{\r
return this._fitToWindow;\r
- }\r
-\r
- //-- boolean getFitToWindow() \r
+ } //-- boolean getFitToWindow() \r
\r
/**\r
* Returns the value of field 'fontSize'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'fontSize'.\r
*/\r
public int getFontSize()\r
{\r
return this._fontSize;\r
- }\r
-\r
- //-- int getFontSize() \r
+ } //-- int getFontSize() \r
\r
/**\r
* Returns the value of field 'height'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'height'.\r
*/\r
public int getHeight()\r
{\r
return this._height;\r
- }\r
-\r
- //-- int getHeight() \r
+ } //-- int getHeight() \r
\r
/**\r
* Returns the value of field 'markUnlinked'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'markUnlinked'.\r
*/\r
public boolean getMarkUnlinked()\r
{\r
return this._markUnlinked;\r
- }\r
-\r
- //-- boolean getMarkUnlinked() \r
+ } //-- boolean getMarkUnlinked() \r
\r
/**\r
* Returns the value of field 'newick'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'newick'.\r
*/\r
public java.lang.String getNewick()\r
{\r
return this._newick;\r
- }\r
-\r
- //-- java.lang.String getNewick() \r
+ } //-- java.lang.String getNewick() \r
\r
/**\r
* Returns the value of field 'showBootstrap'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showBootstrap'.\r
*/\r
public boolean getShowBootstrap()\r
{\r
return this._showBootstrap;\r
- }\r
-\r
- //-- boolean getShowBootstrap() \r
+ } //-- boolean getShowBootstrap() \r
\r
/**\r
* Returns the value of field 'showDistances'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showDistances'.\r
*/\r
public boolean getShowDistances()\r
{\r
return this._showDistances;\r
- }\r
-\r
- //-- boolean getShowDistances() \r
+ } //-- boolean getShowDistances() \r
\r
/**\r
* Returns the value of field 'threshold'.\r
- *\r
+ * \r
* @return float\r
* @return the value of field 'threshold'.\r
*/\r
public float getThreshold()\r
{\r
return this._threshold;\r
- }\r
-\r
- //-- float getThreshold() \r
+ } //-- float getThreshold() \r
\r
/**\r
* Returns the value of field 'title'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'title'.\r
*/\r
public java.lang.String getTitle()\r
{\r
return this._title;\r
- }\r
-\r
- //-- java.lang.String getTitle() \r
+ } //-- java.lang.String getTitle() \r
\r
/**\r
* Returns the value of field 'width'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'width'.\r
*/\r
public int getWidth()\r
{\r
return this._width;\r
- }\r
-\r
- //-- int getWidth() \r
+ } //-- int getWidth() \r
\r
/**\r
* Returns the value of field 'xpos'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'xpos'.\r
*/\r
public int getXpos()\r
{\r
return this._xpos;\r
- }\r
-\r
- //-- int getXpos() \r
+ } //-- int getXpos() \r
\r
/**\r
* Returns the value of field 'ypos'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'ypos'.\r
*/\r
public int getYpos()\r
{\r
return this._ypos;\r
- }\r
-\r
- //-- int getYpos() \r
+ } //-- int getYpos() \r
\r
/**\r
* Method hasCurrentTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasCurrentTree()\r
{\r
return this._has_currentTree;\r
- }\r
-\r
- //-- boolean hasCurrentTree() \r
+ } //-- boolean hasCurrentTree() \r
\r
/**\r
* Method hasFitToWindow\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasFitToWindow()\r
{\r
return this._has_fitToWindow;\r
- }\r
-\r
- //-- boolean hasFitToWindow() \r
+ } //-- boolean hasFitToWindow() \r
\r
/**\r
* Method hasFontSize\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasFontSize()\r
{\r
return this._has_fontSize;\r
- }\r
-\r
- //-- boolean hasFontSize() \r
+ } //-- boolean hasFontSize() \r
\r
/**\r
* Method hasHeight\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasHeight()\r
{\r
return this._has_height;\r
- }\r
-\r
- //-- boolean hasHeight() \r
+ } //-- boolean hasHeight() \r
\r
/**\r
* Method hasMarkUnlinked\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasMarkUnlinked()\r
{\r
return this._has_markUnlinked;\r
- }\r
-\r
- //-- boolean hasMarkUnlinked() \r
+ } //-- boolean hasMarkUnlinked() \r
\r
/**\r
* Method hasShowBootstrap\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasShowBootstrap()\r
{\r
return this._has_showBootstrap;\r
- }\r
-\r
- //-- boolean hasShowBootstrap() \r
+ } //-- boolean hasShowBootstrap() \r
\r
/**\r
* Method hasShowDistances\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasShowDistances()\r
{\r
return this._has_showDistances;\r
- }\r
-\r
- //-- boolean hasShowDistances() \r
+ } //-- boolean hasShowDistances() \r
\r
/**\r
* Method hasThreshold\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasThreshold()\r
{\r
return this._has_threshold;\r
- }\r
-\r
- //-- boolean hasThreshold() \r
+ } //-- boolean hasThreshold() \r
\r
/**\r
* Method hasWidth\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasWidth()\r
{\r
return this._has_width;\r
- }\r
-\r
- //-- boolean hasWidth() \r
+ } //-- boolean hasWidth() \r
\r
/**\r
* Method hasXpos\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasXpos()\r
{\r
return this._has_xpos;\r
- }\r
-\r
- //-- boolean hasXpos() \r
+ } //-- boolean hasXpos() \r
\r
/**\r
* Method hasYpos\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasYpos()\r
{\r
return this._has_ypos;\r
- }\r
-\r
- //-- boolean hasYpos() \r
+ } //-- boolean hasYpos() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'currentTree'.\r
- *\r
+ * \r
* @param currentTree the value of field 'currentTree'.\r
*/\r
public void setCurrentTree(boolean currentTree)\r
{\r
this._currentTree = currentTree;\r
this._has_currentTree = true;\r
- }\r
-\r
- //-- void setCurrentTree(boolean) \r
+ } //-- void setCurrentTree(boolean) \r
\r
/**\r
* Sets the value of field 'fitToWindow'.\r
- *\r
+ * \r
* @param fitToWindow the value of field 'fitToWindow'.\r
*/\r
public void setFitToWindow(boolean fitToWindow)\r
{\r
this._fitToWindow = fitToWindow;\r
this._has_fitToWindow = true;\r
- }\r
-\r
- //-- void setFitToWindow(boolean) \r
+ } //-- void setFitToWindow(boolean) \r
\r
/**\r
* Sets the value of field 'fontSize'.\r
- *\r
+ * \r
* @param fontSize the value of field 'fontSize'.\r
*/\r
public void setFontSize(int fontSize)\r
{\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- }\r
-\r
- //-- void setFontSize(int) \r
+ } //-- void setFontSize(int) \r
\r
/**\r
* Sets the value of field 'height'.\r
- *\r
+ * \r
* @param height the value of field 'height'.\r
*/\r
public void setHeight(int height)\r
{\r
this._height = height;\r
this._has_height = true;\r
- }\r
-\r
- //-- void setHeight(int) \r
+ } //-- void setHeight(int) \r
\r
/**\r
* Sets the value of field 'markUnlinked'.\r
- *\r
+ * \r
* @param markUnlinked the value of field 'markUnlinked'.\r
*/\r
public void setMarkUnlinked(boolean markUnlinked)\r
{\r
this._markUnlinked = markUnlinked;\r
this._has_markUnlinked = true;\r
- }\r
-\r
- //-- void setMarkUnlinked(boolean) \r
+ } //-- void setMarkUnlinked(boolean) \r
\r
/**\r
* Sets the value of field 'newick'.\r
- *\r
+ * \r
* @param newick the value of field 'newick'.\r
*/\r
public void setNewick(java.lang.String newick)\r
{\r
this._newick = newick;\r
- }\r
-\r
- //-- void setNewick(java.lang.String) \r
+ } //-- void setNewick(java.lang.String) \r
\r
/**\r
* Sets the value of field 'showBootstrap'.\r
- *\r
+ * \r
* @param showBootstrap the value of field 'showBootstrap'.\r
*/\r
public void setShowBootstrap(boolean showBootstrap)\r
{\r
this._showBootstrap = showBootstrap;\r
this._has_showBootstrap = true;\r
- }\r
-\r
- //-- void setShowBootstrap(boolean) \r
+ } //-- void setShowBootstrap(boolean) \r
\r
/**\r
* Sets the value of field 'showDistances'.\r
- *\r
+ * \r
* @param showDistances the value of field 'showDistances'.\r
*/\r
public void setShowDistances(boolean showDistances)\r
{\r
this._showDistances = showDistances;\r
this._has_showDistances = true;\r
- }\r
-\r
- //-- void setShowDistances(boolean) \r
+ } //-- void setShowDistances(boolean) \r
\r
/**\r
* Sets the value of field 'threshold'.\r
- *\r
+ * \r
* @param threshold the value of field 'threshold'.\r
*/\r
public void setThreshold(float threshold)\r
{\r
this._threshold = threshold;\r
this._has_threshold = true;\r
- }\r
-\r
- //-- void setThreshold(float) \r
+ } //-- void setThreshold(float) \r
\r
/**\r
* Sets the value of field 'title'.\r
- *\r
+ * \r
* @param title the value of field 'title'.\r
*/\r
public void setTitle(java.lang.String title)\r
{\r
this._title = title;\r
- }\r
-\r
- //-- void setTitle(java.lang.String) \r
+ } //-- void setTitle(java.lang.String) \r
\r
/**\r
* Sets the value of field 'width'.\r
- *\r
+ * \r
* @param width the value of field 'width'.\r
*/\r
public void setWidth(int width)\r
{\r
this._width = width;\r
this._has_width = true;\r
- }\r
-\r
- //-- void setWidth(int) \r
+ } //-- void setWidth(int) \r
\r
/**\r
* Sets the value of field 'xpos'.\r
- *\r
+ * \r
* @param xpos the value of field 'xpos'.\r
*/\r
public void setXpos(int xpos)\r
{\r
this._xpos = xpos;\r
this._has_xpos = true;\r
- }\r
-\r
- //-- void setXpos(int) \r
+ } //-- void setXpos(int) \r
\r
/**\r
* Sets the value of field 'ypos'.\r
- *\r
+ * \r
* @param ypos the value of field 'ypos'.\r
*/\r
public void setYpos(int ypos)\r
{\r
this._ypos = ypos;\r
this._has_ypos = true;\r
- }\r
-\r
- //-- void setYpos(int) \r
+ } //-- void setYpos(int) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\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 UserColourScheme.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColourScheme\r
- extends JalviewUserColours implements java.io.Serializable\r
+public class UserColourScheme extends JalviewUserColours \r
+implements java.io.Serializable\r
{\r
\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
\r
- public UserColourScheme()\r
- {\r
- super();\r
- } //-- jalview.binding.UserColourScheme()\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ public UserColourScheme() {\r
+ super();\r
+ } //-- jalview.binding.UserColourScheme()\r
\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
+ //- Methods -/\r
+ //-----------/\r
\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \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
+ * Method marshal\r
+ * \r
+ * \r
+ * \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
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \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.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.\r
- binding.UserColourScheme.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.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
+ * 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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\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 UserColours.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColours\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _userColourScheme\r
- */\r
- private jalview.binding.UserColourScheme _userColourScheme;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public UserColours()\r
- {\r
- super();\r
- } //-- jalview.binding.UserColours()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId()\r
-\r
- /**\r
- * Returns the value of field 'userColourScheme'.\r
- *\r
- * @return UserColourScheme\r
- * @return the value of field 'userColourScheme'.\r
- */\r
- public jalview.binding.UserColourScheme getUserColourScheme()\r
- {\r
- return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
+public class UserColours implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _userColourScheme\r
+ */\r
+ private jalview.binding.UserColourScheme _userColourScheme;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public UserColours() {\r
+ super();\r
+ } //-- jalview.binding.UserColours()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ } //-- java.lang.String getId() \r
+\r
+ /**\r
+ * Returns the value of field 'userColourScheme'.\r
+ * \r
+ * @return UserColourScheme\r
+ * @return the value of field 'userColourScheme'.\r
+ */\r
+ public jalview.binding.UserColourScheme getUserColourScheme()\r
+ {\r
+ return this._userColourScheme;\r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ } //-- void setId(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'userColourScheme'.\r
+ * \r
+ * @param userColourScheme the value of field 'userColourScheme'\r
+ */\r
+ public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
+ {\r
+ this._userColourScheme = userColourScheme;\r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \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, org.exolab.castor.xml.ValidationException\r
{\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.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
- return false;\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
- * Sets the value of field 'id'.\r
- *\r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'userColourScheme'.\r
- *\r
- * @param userColourScheme the value of field 'userColourScheme'\r
- */\r
- public void setUserColourScheme(jalview.binding.UserColourScheme\r
- userColourScheme)\r
- {\r
- this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\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.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.\r
- UserColours.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
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\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 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
* @version $Revision$ $Date$\r
*/\r
-public class VAMSAS\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _alignmentList\r
- */\r
- private java.util.Vector _alignmentList;\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _sequenceSetList\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VAMSAS()\r
- {\r
- super();\r
- _alignmentList = new Vector();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.binding.VAMSAS()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAlignment\r
- *\r
- *\r
- *\r
- * @param vAlignment\r
- */\r
- public void addAlignment(jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.addElement(vAlignment);\r
- } //-- void addAlignment(jalview.binding.Alignment)\r
-\r
- /**\r
- * Method addAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAlignment\r
- */\r
- public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.insertElementAt(vAlignment, index);\r
- } //-- void addAlignment(int, jalview.binding.Alignment)\r
-\r
- /**\r
- * Method addSequenceSet\r
- *\r
- *\r
- *\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method addSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(int index,\r
- jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param vTree\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
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\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
-\r
- /**\r
- * Method enumerateAlignment\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAlignment()\r
- {\r
- return _alignmentList.elements();\r
- } //-- java.util.Enumeration enumerateAlignment()\r
-\r
- /**\r
- * Method enumerateSequenceSet\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet()\r
-\r
- /**\r
- * Method enumerateTree\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree()\r
-\r
- /**\r
- * Method getAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _alignmentList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- } //-- jalview.binding.Alignment getAlignment(int)\r
-\r
- /**\r
- * Method getAlignment\r
- *\r
- *\r
- *\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment[] getAlignment()\r
- {\r
- int size = _alignmentList.size();\r
- jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Alignment[] getAlignment()\r
-\r
- /**\r
- * Method getAlignmentCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getAlignmentCount()\r
- {\r
- return _alignmentList.size();\r
- } //-- int getAlignmentCount()\r
-\r
- /**\r
- * Method getSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceSetList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.binding.SequenceSet getSequenceSet(int)\r
-\r
- /**\r
- * Method getSequenceSet\r
- *\r
- *\r
- *\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.SequenceSet[] getSequenceSet()\r
-\r
- /**\r
- * Method getSequenceSetCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getSequenceSetCount()\r
- {\r
- return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount()\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return String\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
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (String) _treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int)\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @return String\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
- {\r
- mArray[index] = (String) _treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- java.lang.String[] getTree()\r
-\r
- /**\r
- * Method getTreeCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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 removeAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment removeAlignment(int index)\r
- {\r
- java.lang.Object obj = _alignmentList.elementAt(index);\r
- _alignmentList.removeElementAt(index);\r
- return (jalview.binding.Alignment) obj;\r
- } //-- jalview.binding.Alignment removeAlignment(int)\r
-\r
- /**\r
- * Method removeAllAlignment\r
- *\r
- */\r
- public void removeAllAlignment()\r
- {\r
- _alignmentList.removeAllElements();\r
- } //-- void removeAllAlignment()\r
-\r
- /**\r
- * Method removeAllSequenceSet\r
- *\r
- */\r
- public void removeAllSequenceSet()\r
- {\r
- _sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet()\r
-\r
- /**\r
- * Method removeAllTree\r
- *\r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree()\r
-\r
- /**\r
- * Method removeSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet removeSequenceSet(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetList.elementAt(index);\r
- _sequenceSetList.removeElementAt(index);\r
- return (jalview.binding.SequenceSet) obj;\r
- } //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
-\r
- /**\r
- * Method removeTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return String\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
-\r
- /**\r
- * Method setAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAlignment\r
- */\r
- public void setAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _alignmentList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _alignmentList.setElementAt(vAlignment, index);\r
- } //-- void setAlignment(int, jalview.binding.Alignment)\r
-\r
- /**\r
- * Method setAlignment\r
- *\r
- *\r
- *\r
- * @param alignmentArray\r
- */\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
- {\r
- //-- copy array\r
- _alignmentList.removeAllElements();\r
- for (int i = 0; i < alignmentArray.length; i++)\r
- {\r
- _alignmentList.addElement(alignmentArray[i]);\r
- }\r
- } //-- void setAlignment(jalview.binding.Alignment)\r
-\r
- /**\r
- * Method setSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void setSequenceSet(int index,\r
- jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceSetList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method setSequenceSet\r
- *\r
- *\r
- *\r
- * @param sequenceSetArray\r
- */\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
- {\r
- //-- copy array\r
- _sequenceSetList.removeAllElements();\r
- for (int i = 0; i < sequenceSetArray.length; i++)\r
- {\r
- _sequenceSetList.addElement(sequenceSetArray[i]);\r
- }\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\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
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param treeArray\r
- */\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++)\r
- {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(java.lang.String)\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.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.\r
- VAMSAS.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
+public class VAMSAS implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _alignmentList\r
+ */\r
+ private java.util.Vector _alignmentList;\r
+\r
+ /**\r
+ * Field _treeList\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _sequenceSetList\r
+ */\r
+ private java.util.Vector _sequenceSetList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VAMSAS() {\r
+ super();\r
+ _alignmentList = new Vector();\r
+ _treeList = new Vector();\r
+ _sequenceSetList = new Vector();\r
+ } //-- jalview.binding.VAMSAS()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param vAlignment\r
+ */\r
+ public void addAlignment(jalview.binding.Alignment vAlignment)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _alignmentList.addElement(vAlignment);\r
+ } //-- void addAlignment(jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method addAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlignment\r
+ */\r
+ public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _alignmentList.insertElementAt(vAlignment, index);\r
+ } //-- void addAlignment(int, jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method addSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param vSequenceSet\r
+ */\r
+ public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceSetList.addElement(vSequenceSet);\r
+ } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method addSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ */\r
+ public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceSetList.insertElementAt(vSequenceSet, index);\r
+ } //-- void addSequenceSet(int, jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param vTree\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
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\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
+\r
+ /**\r
+ * Method enumerateAlignment\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAlignment()\r
+ {\r
+ return _alignmentList.elements();\r
+ } //-- java.util.Enumeration enumerateAlignment() \r
+\r
+ /**\r
+ * Method enumerateSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSet()\r
+ {\r
+ return _sequenceSetList.elements();\r
+ } //-- java.util.Enumeration enumerateSequenceSet() \r
+\r
+ /**\r
+ * Method enumerateTree\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
+ return _treeList.elements();\r
+ } //-- java.util.Enumeration enumerateTree() \r
+\r
+ /**\r
+ * Method getAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.Alignment getAlignment(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _alignmentList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
+ } //-- jalview.binding.Alignment getAlignment(int) \r
+\r
+ /**\r
+ * Method getAlignment\r
+ * \r
+ * \r
+ * \r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.Alignment[] getAlignment()\r
+ {\r
+ int size = _alignmentList.size();\r
+ jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Alignment[] getAlignment() \r
+\r
+ /**\r
+ * Method getAlignmentCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getAlignmentCount()\r
+ {\r
+ return _alignmentList.size();\r
+ } //-- int getAlignmentCount() \r
+\r
+ /**\r
+ * Method getSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.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
+ }\r
+ \r
+ return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
+ } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
+\r
+ /**\r
+ * Method getSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.SequenceSet[] getSequenceSet()\r
+ {\r
+ int size = _sequenceSetList.size();\r
+ jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.SequenceSet[] getSequenceSet() \r
+\r
+ /**\r
+ * Method getSequenceSetCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getSequenceSetCount()\r
+ {\r
+ return _sequenceSetList.size();\r
+ } //-- int getSequenceSetCount() \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return String\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
+ }\r
+ \r
+ return (String)_treeList.elementAt(index);\r
+ } //-- java.lang.String getTree(int) \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @return String\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
+\r
+ /**\r
+ * Method getTreeCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getTreeCount()\r
+ {\r
+ return _treeList.size();\r
+ } //-- int getTreeCount() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.Alignment removeAlignment(int index)\r
+ {\r
+ java.lang.Object obj = _alignmentList.elementAt(index);\r
+ _alignmentList.removeElementAt(index);\r
+ return (jalview.binding.Alignment) obj;\r
+ } //-- jalview.binding.Alignment removeAlignment(int) \r
+\r
+ /**\r
+ * Method removeAllAlignment\r
+ * \r
+ */\r
+ public void removeAllAlignment()\r
+ {\r
+ _alignmentList.removeAllElements();\r
+ } //-- void removeAllAlignment() \r
+\r
+ /**\r
+ * Method removeAllSequenceSet\r
+ * \r
+ */\r
+ public void removeAllSequenceSet()\r
+ {\r
+ _sequenceSetList.removeAllElements();\r
+ } //-- void removeAllSequenceSet() \r
+\r
+ /**\r
+ * Method removeAllTree\r
+ * \r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ _treeList.removeAllElements();\r
+ } //-- void removeAllTree() \r
+\r
+ /**\r
+ * Method removeSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.SequenceSet removeSequenceSet(int index)\r
+ {\r
+ java.lang.Object obj = _sequenceSetList.elementAt(index);\r
+ _sequenceSetList.removeElementAt(index);\r
+ return (jalview.binding.SequenceSet) obj;\r
+ } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
+\r
+ /**\r
+ * Method removeTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return String\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
+\r
+ /**\r
+ * Method setAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlignment\r
+ */\r
+ public void setAlignment(int index, jalview.binding.Alignment vAlignment)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _alignmentList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _alignmentList.setElementAt(vAlignment, index);\r
+ } //-- void setAlignment(int, jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method setAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param alignmentArray\r
+ */\r
+ public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
+ {\r
+ //-- copy array\r
+ _alignmentList.removeAllElements();\r
+ for (int i = 0; i < alignmentArray.length; i++) {\r
+ _alignmentList.addElement(alignmentArray[i]);\r
+ }\r
+ } //-- void setAlignment(jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method setSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ */\r
+ public void setSequenceSet(int index, jalview.binding.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
+ }\r
+ _sequenceSetList.setElementAt(vSequenceSet, index);\r
+ } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method setSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param sequenceSetArray\r
+ */\r
+ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
+ {\r
+ //-- copy array\r
+ _sequenceSetList.removeAllElements();\r
+ for (int i = 0; i < sequenceSetArray.length; i++) {\r
+ _sequenceSetList.addElement(sequenceSetArray[i]);\r
+ }\r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\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
+ }\r
+ _treeList.setElementAt(vTree, index);\r
+ } //-- void setTree(int, java.lang.String) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param treeArray\r
+ */\r
+ public void setTree(java.lang.String[] treeArray)\r
+ {\r
+ //-- copy array\r
+ _treeList.removeAllElements();\r
+ for (int i = 0; i < treeArray.length; i++) {\r
+ _treeList.addElement(treeArray[i]);\r
+ }\r
+ } //-- void setTree(java.lang.String) \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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
/*\r
- * This class was automatically generated with\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
*/\r
-package jalview.binding;\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
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\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 VamsasModel.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class VamsasModel extends VAMSAS implements java.io.Serializable\r
+public class VamsasModel extends VAMSAS \r
+implements java.io.Serializable\r
{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public VamsasModel()\r
- {\r
+\r
+ public VamsasModel() {\r
super();\r
- }\r
+ } //-- jalview.binding.VamsasModel()\r
\r
- //-- jalview.binding.VamsasModel()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
//-----------/\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
*/\r
public boolean isValid()\r
{\r
- try\r
- {\r
+ try {\r
validate();\r
}\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
-\r
- //-- boolean isValid() \r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
+ return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
+ public void validate()\r
+ 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
+ } //-- void validate() \r
\r
- //-- void validate() \r
}\r
/*\r
- * This class was automatically generated with\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
\r
package jalview.binding;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\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 Viewport.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Viewport\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _conservationSelected\r
- */\r
- private boolean _conservationSelected;\r
-\r
- /**\r
- * keeps track of state for field: _conservationSelected\r
- */\r
- private boolean _has_conservationSelected;\r
-\r
- /**\r
- * Field _pidSelected\r
- */\r
- private boolean _pidSelected;\r
-\r
- /**\r
- * keeps track of state for field: _pidSelected\r
- */\r
- private boolean _has_pidSelected;\r
-\r
- /**\r
- * Field _bgColour\r
- */\r
- private java.lang.String _bgColour;\r
-\r
- /**\r
- * Field _consThreshold\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _showFullId\r
- */\r
- private boolean _showFullId;\r
-\r
- /**\r
- * keeps track of state for field: _showFullId\r
- */\r
- private boolean _has_showFullId;\r
-\r
- /**\r
- * Field _showText\r
- */\r
- private boolean _showText;\r
-\r
- /**\r
- * keeps track of state for field: _showText\r
- */\r
- private boolean _has_showText;\r
-\r
- /**\r
- * Field _showColourText\r
- */\r
- private boolean _showColourText;\r
-\r
- /**\r
- * keeps track of state for field: _showColourText\r
- */\r
- private boolean _has_showColourText;\r
-\r
- /**\r
- * Field _showBoxes\r
- */\r
- private boolean _showBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _showBoxes\r
- */\r
- private boolean _has_showBoxes;\r
-\r
- /**\r
- * Field _wrapAlignment\r
- */\r
- private boolean _wrapAlignment;\r
-\r
- /**\r
- * keeps track of state for field: _wrapAlignment\r
- */\r
- private boolean _has_wrapAlignment;\r
-\r
- /**\r
- * Field _renderGaps\r
- */\r
- private boolean _renderGaps;\r
-\r
- /**\r
- * keeps track of state for field: _renderGaps\r
- */\r
- private boolean _has_renderGaps;\r
-\r
- /**\r
- * Field _showSequenceFeatures\r
- */\r
- private boolean _showSequenceFeatures;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceFeatures\r
- */\r
- private boolean _has_showSequenceFeatures;\r
-\r
- /**\r
- * Field _showAnnotation\r
- */\r
- private boolean _showAnnotation;\r
-\r
- /**\r
- * keeps track of state for field: _showAnnotation\r
- */\r
- private boolean _has_showAnnotation;\r
-\r
- /**\r
- * Field _showConservation\r
- */\r
- private boolean _showConservation;\r
-\r
- /**\r
- * keeps track of state for field: _showConservation\r
- */\r
- private boolean _has_showConservation;\r
-\r
- /**\r
- * Field _showQuality\r
- */\r
- private boolean _showQuality;\r
-\r
- /**\r
- * keeps track of state for field: _showQuality\r
- */\r
- private boolean _has_showQuality;\r
-\r
- /**\r
- * Field _showIdentity\r
- */\r
- private boolean _showIdentity;\r
-\r
- /**\r
- * keeps track of state for field: _showIdentity\r
- */\r
- private boolean _has_showIdentity;\r
-\r
- /**\r
- * Field _xpos\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _startRes\r
- */\r
- private int _startRes;\r
-\r
- /**\r
- * keeps track of state for field: _startRes\r
- */\r
- private boolean _has_startRes;\r
-\r
- /**\r
- * Field _startSeq\r
- */\r
- private int _startSeq;\r
-\r
- /**\r
- * keeps track of state for field: _startSeq\r
- */\r
- private boolean _has_startSeq;\r
-\r
- /**\r
- * Field _fontName\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Viewport()\r
- {\r
- super();\r
- } //-- jalview.binding.Viewport()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteConsThreshold\r
- *\r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold = false;\r
- } //-- void deleteConsThreshold()\r
-\r
- /**\r
- * Method deleteConservationSelected\r
- *\r
- */\r
- public void deleteConservationSelected()\r
- {\r
- this._has_conservationSelected = false;\r
- } //-- void deleteConservationSelected()\r
-\r
- /**\r
- * Method deleteFontSize\r
- *\r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize = false;\r
- } //-- void deleteFontSize()\r
-\r
- /**\r
- * Method deleteFontStyle\r
- *\r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle = false;\r
- } //-- void deleteFontStyle()\r
-\r
- /**\r
- * Method deleteHeight\r
- *\r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height = false;\r
- } //-- void deleteHeight()\r
-\r
- /**\r
- * Method deletePidSelected\r
- *\r
- */\r
- public void deletePidSelected()\r
- {\r
- this._has_pidSelected = false;\r
- } //-- void deletePidSelected()\r
-\r
- /**\r
- * Method deletePidThreshold\r
- *\r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold = false;\r
- } //-- void deletePidThreshold()\r
-\r
- /**\r
- * Method deleteRenderGaps\r
- *\r
- */\r
- public void deleteRenderGaps()\r
- {\r
- this._has_renderGaps = false;\r
- } //-- void deleteRenderGaps()\r
-\r
- /**\r
- * Method deleteShowAnnotation\r
- *\r
- */\r
- public void deleteShowAnnotation()\r
- {\r
- this._has_showAnnotation = false;\r
- } //-- void deleteShowAnnotation()\r
-\r
- /**\r
- * Method deleteShowBoxes\r
- *\r
- */\r
- public void deleteShowBoxes()\r
- {\r
- this._has_showBoxes = false;\r
- } //-- void deleteShowBoxes()\r
-\r
- /**\r
- * Method deleteShowColourText\r
- *\r
- */\r
- public void deleteShowColourText()\r
- {\r
- this._has_showColourText = false;\r
- } //-- void deleteShowColourText()\r
-\r
- /**\r
- * Method deleteShowConservation\r
- *\r
- */\r
- public void deleteShowConservation()\r
- {\r
- this._has_showConservation = false;\r
- } //-- void deleteShowConservation()\r
-\r
- /**\r
- * Method deleteShowFullId\r
- *\r
- */\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId = false;\r
- } //-- void deleteShowFullId()\r
-\r
- /**\r
- * Method deleteShowIdentity\r
- *\r
- */\r
- public void deleteShowIdentity()\r
- {\r
- this._has_showIdentity = false;\r
- } //-- void deleteShowIdentity()\r
-\r
- /**\r
- * Method deleteShowQuality\r
- *\r
- */\r
- public void deleteShowQuality()\r
- {\r
- this._has_showQuality = false;\r
- } //-- void deleteShowQuality()\r
-\r
- /**\r
- * Method deleteShowSequenceFeatures\r
- *\r
- */\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures = false;\r
- } //-- void deleteShowSequenceFeatures()\r
-\r
- /**\r
- * Method deleteShowText\r
- *\r
- */\r
- public void deleteShowText()\r
- {\r
- this._has_showText = false;\r
- } //-- void deleteShowText()\r
-\r
- /**\r
- * Method deleteStartRes\r
- *\r
- */\r
- public void deleteStartRes()\r
- {\r
- this._has_startRes = false;\r
- } //-- void deleteStartRes()\r
-\r
- /**\r
- * Method deleteStartSeq\r
- *\r
- */\r
- public void deleteStartSeq()\r
- {\r
- this._has_startSeq = false;\r
- } //-- void deleteStartSeq()\r
-\r
- /**\r
- * Method deleteWidth\r
- *\r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width = false;\r
- } //-- void deleteWidth()\r
-\r
- /**\r
- * Method deleteWrapAlignment\r
- *\r
- */\r
- public void deleteWrapAlignment()\r
- {\r
- this._has_wrapAlignment = false;\r
- } //-- void deleteWrapAlignment()\r
-\r
- /**\r
- * Method deleteXpos\r
- *\r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos = false;\r
- } //-- void deleteXpos()\r
-\r
- /**\r
- * Method deleteYpos\r
- *\r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos = false;\r
- } //-- void deleteYpos()\r
-\r
- /**\r
- * Returns the value of field 'bgColour'.\r
- *\r
- * @return String\r
- * @return the value of field 'bgColour'.\r
- */\r
- public java.lang.String getBgColour()\r
- {\r
- return this._bgColour;\r
- } //-- java.lang.String getBgColour()\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- *\r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- } //-- int getConsThreshold()\r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'conservationSelected'.\r
- */\r
- public boolean getConservationSelected()\r
- {\r
- return this._conservationSelected;\r
- } //-- boolean getConservationSelected()\r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- *\r
- * @return String\r
- * @return the value of field 'fontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- } //-- java.lang.String getFontName()\r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- *\r
- * @return int\r
- * @return the value of field 'fontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- } //-- int getFontSize()\r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- *\r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- } //-- int getFontStyle()\r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- *\r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight()\r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'pidSelected'.\r
- */\r
- public boolean getPidSelected()\r
- {\r
- return this._pidSelected;\r
- } //-- boolean getPidSelected()\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- *\r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- } //-- int getPidThreshold()\r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'renderGaps'.\r
- */\r
- public boolean getRenderGaps()\r
- {\r
- return this._renderGaps;\r
- } //-- boolean getRenderGaps()\r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showAnnotation'.\r
- */\r
- public boolean getShowAnnotation()\r
- {\r
- return this._showAnnotation;\r
- } //-- boolean getShowAnnotation()\r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showBoxes'.\r
- */\r
- public boolean getShowBoxes()\r
- {\r
- return this._showBoxes;\r
- } //-- boolean getShowBoxes()\r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showColourText'.\r
- */\r
- public boolean getShowColourText()\r
- {\r
- return this._showColourText;\r
- } //-- boolean getShowColourText()\r
-\r
- /**\r
- * Returns the value of field 'showConservation'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showConservation'.\r
- */\r
- public boolean getShowConservation()\r
- {\r
- return this._showConservation;\r
- } //-- boolean getShowConservation()\r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showFullId'.\r
- */\r
- public boolean getShowFullId()\r
- {\r
- return this._showFullId;\r
- } //-- boolean getShowFullId()\r
-\r
- /**\r
- * Returns the value of field 'showIdentity'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showIdentity'.\r
- */\r
- public boolean getShowIdentity()\r
- {\r
- return this._showIdentity;\r
- } //-- boolean getShowIdentity()\r
-\r
- /**\r
- * Returns the value of field 'showQuality'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showQuality'.\r
- */\r
- public boolean getShowQuality()\r
- {\r
- return this._showQuality;\r
- } //-- boolean getShowQuality()\r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showSequenceFeatures'.\r
- */\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures()\r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showText'.\r
- */\r
- public boolean getShowText()\r
- {\r
- return this._showText;\r
- } //-- boolean getShowText()\r
-\r
- /**\r
- * Returns the value of field 'startRes'.\r
- *\r
- * @return int\r
- * @return the value of field 'startRes'.\r
- */\r
- public int getStartRes()\r
- {\r
- return this._startRes;\r
- } //-- int getStartRes()\r
-\r
- /**\r
- * Returns the value of field 'startSeq'.\r
- *\r
- * @return int\r
- * @return the value of field 'startSeq'.\r
- */\r
- public int getStartSeq()\r
- {\r
- return this._startSeq;\r
- } //-- int getStartSeq()\r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- *\r
- * @return String\r
- * @return the value of field 'title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- } //-- java.lang.String getTitle()\r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- *\r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth()\r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'wrapAlignment'.\r
- */\r
- public boolean getWrapAlignment()\r
- {\r
- return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment()\r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- *\r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos()\r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- *\r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos()\r
-\r
- /**\r
- * Method hasConsThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold()\r
-\r
- /**\r
- * Method hasConservationSelected\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasConservationSelected()\r
- {\r
- return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected()\r
-\r
- /**\r
- * Method hasFontSize\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- } //-- boolean hasFontSize()\r
-\r
- /**\r
- * Method hasFontStyle\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- } //-- boolean hasFontStyle()\r
-\r
- /**\r
- * Method hasHeight\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight()\r
-\r
- /**\r
- * Method hasPidSelected\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasPidSelected()\r
- {\r
- return this._has_pidSelected;\r
- } //-- boolean hasPidSelected()\r
-\r
- /**\r
- * Method hasPidThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold()\r
-\r
- /**\r
- * Method hasRenderGaps\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasRenderGaps()\r
- {\r
- return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps()\r
-\r
- /**\r
- * Method hasShowAnnotation\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowAnnotation()\r
- {\r
- return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation()\r
-\r
- /**\r
- * Method hasShowBoxes\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowBoxes()\r
- {\r
- return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes()\r
-\r
- /**\r
- * Method hasShowColourText\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowColourText()\r
- {\r
- return this._has_showColourText;\r
- } //-- boolean hasShowColourText()\r
-\r
- /**\r
- * Method hasShowConservation\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowConservation()\r
- {\r
- return this._has_showConservation;\r
- } //-- boolean hasShowConservation()\r
-\r
- /**\r
- * Method hasShowFullId\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowFullId()\r
- {\r
- return this._has_showFullId;\r
- } //-- boolean hasShowFullId()\r
-\r
- /**\r
- * Method hasShowIdentity\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowIdentity()\r
- {\r
- return this._has_showIdentity;\r
- } //-- boolean hasShowIdentity()\r
-\r
- /**\r
- * Method hasShowQuality\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowQuality()\r
- {\r
- return this._has_showQuality;\r
- } //-- boolean hasShowQuality()\r
-\r
- /**\r
- * Method hasShowSequenceFeatures\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowSequenceFeatures()\r
- {\r
- return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures()\r
-\r
- /**\r
- * Method hasShowText\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowText()\r
- {\r
- return this._has_showText;\r
- } //-- boolean hasShowText()\r
-\r
- /**\r
- * Method hasStartRes\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasStartRes()\r
- {\r
- return this._has_startRes;\r
- } //-- boolean hasStartRes()\r
-\r
- /**\r
- * Method hasStartSeq\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasStartSeq()\r
- {\r
- return this._has_startSeq;\r
- } //-- boolean hasStartSeq()\r
-\r
- /**\r
- * Method hasWidth\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth()\r
-\r
- /**\r
- * Method hasWrapAlignment\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasWrapAlignment()\r
- {\r
- return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment()\r
-\r
- /**\r
- * Method hasXpos\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos()\r
-\r
- /**\r
- * Method hasYpos\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\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
- * Sets the value of field 'bgColour'.\r
- *\r
- * @param bgColour the value of field 'bgColour'.\r
- */\r
- public void setBgColour(java.lang.String bgColour)\r
- {\r
- this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- *\r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int)\r
-\r
- /**\r
- * Sets the value of field 'conservationSelected'.\r
- *\r
- * @param conservationSelected the value of field\r
- * 'conservationSelected'.\r
- */\r
- public void setConservationSelected(boolean conservationSelected)\r
- {\r
- this._conservationSelected = conservationSelected;\r
- this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean)\r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- *\r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- *\r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- } //-- void setFontSize(int)\r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- *\r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- } //-- void setFontStyle(int)\r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- *\r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int)\r
-\r
- /**\r
- * Sets the value of field 'pidSelected'.\r
- *\r
- * @param pidSelected the value of field 'pidSelected'.\r
- */\r
- public void setPidSelected(boolean pidSelected)\r
- {\r
- this._pidSelected = pidSelected;\r
- this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean)\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- *\r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int)\r
-\r
- /**\r
- * Sets the value of field 'renderGaps'.\r
- *\r
- * @param renderGaps the value of field 'renderGaps'.\r
- */\r
- public void setRenderGaps(boolean renderGaps)\r
- {\r
- this._renderGaps = renderGaps;\r
- this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showAnnotation'.\r
- *\r
- * @param showAnnotation the value of field 'showAnnotation'.\r
- */\r
- public void setShowAnnotation(boolean showAnnotation)\r
- {\r
- this._showAnnotation = showAnnotation;\r
- this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showBoxes'.\r
- *\r
- * @param showBoxes the value of field 'showBoxes'.\r
- */\r
- public void setShowBoxes(boolean showBoxes)\r
- {\r
- this._showBoxes = showBoxes;\r
- this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showColourText'.\r
- *\r
- * @param showColourText the value of field 'showColourText'.\r
- */\r
- public void setShowColourText(boolean showColourText)\r
- {\r
- this._showColourText = showColourText;\r
- this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showConservation'.\r
- *\r
- * @param showConservation the value of field 'showConservation'\r
- */\r
- public void setShowConservation(boolean showConservation)\r
- {\r
- this._showConservation = showConservation;\r
- this._has_showConservation = true;\r
- } //-- void setShowConservation(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showFullId'.\r
- *\r
- * @param showFullId the value of field 'showFullId'.\r
- */\r
- public void setShowFullId(boolean showFullId)\r
- {\r
- this._showFullId = showFullId;\r
- this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showIdentity'.\r
- *\r
- * @param showIdentity the value of field 'showIdentity'.\r
- */\r
- public void setShowIdentity(boolean showIdentity)\r
- {\r
- this._showIdentity = showIdentity;\r
- this._has_showIdentity = true;\r
- } //-- void setShowIdentity(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showQuality'.\r
- *\r
- * @param showQuality the value of field 'showQuality'.\r
- */\r
- public void setShowQuality(boolean showQuality)\r
- {\r
- this._showQuality = showQuality;\r
- this._has_showQuality = true;\r
- } //-- void setShowQuality(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showSequenceFeatures'.\r
- *\r
- * @param showSequenceFeatures the value of field\r
- * 'showSequenceFeatures'.\r
- */\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
- {\r
- this._showSequenceFeatures = showSequenceFeatures;\r
- this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showText'.\r
- *\r
- * @param showText the value of field 'showText'.\r
- */\r
- public void setShowText(boolean showText)\r
- {\r
- this._showText = showText;\r
- this._has_showText = true;\r
- } //-- void setShowText(boolean)\r
-\r
- /**\r
- * Sets the value of field 'startRes'.\r
- *\r
- * @param startRes the value of field 'startRes'.\r
- */\r
- public void setStartRes(int startRes)\r
- {\r
- this._startRes = startRes;\r
- this._has_startRes = true;\r
- } //-- void setStartRes(int)\r
-\r
- /**\r
- * Sets the value of field 'startSeq'.\r
- *\r
- * @param startSeq the value of field 'startSeq'.\r
- */\r
- public void setStartSeq(int startSeq)\r
- {\r
- this._startSeq = startSeq;\r
- this._has_startSeq = true;\r
- } //-- void setStartSeq(int)\r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- *\r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(java.lang.String title)\r
- {\r
- this._title = title;\r
- } //-- void setTitle(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- *\r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int)\r
-\r
- /**\r
- * Sets the value of field 'wrapAlignment'.\r
- *\r
- * @param wrapAlignment the value of field 'wrapAlignment'.\r
- */\r
- public void setWrapAlignment(boolean wrapAlignment)\r
- {\r
- this._wrapAlignment = wrapAlignment;\r
- this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean)\r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- *\r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int)\r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- *\r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(int)\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.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.\r
- Viewport.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
+public class Viewport implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _conservationSelected\r
+ */\r
+ private boolean _conservationSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _conservationSelected\r
+ */\r
+ private boolean _has_conservationSelected;\r
+\r
+ /**\r
+ * Field _pidSelected\r
+ */\r
+ private boolean _pidSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidSelected\r
+ */\r
+ private boolean _has_pidSelected;\r
+\r
+ /**\r
+ * Field _bgColour\r
+ */\r
+ private java.lang.String _bgColour;\r
+\r
+ /**\r
+ * Field _consThreshold\r
+ */\r
+ private int _consThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _consThreshold\r
+ */\r
+ private boolean _has_consThreshold;\r
+\r
+ /**\r
+ * Field _pidThreshold\r
+ */\r
+ private int _pidThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidThreshold\r
+ */\r
+ private boolean _has_pidThreshold;\r
+\r
+ /**\r
+ * Field _title\r
+ */\r
+ private java.lang.String _title;\r
+\r
+ /**\r
+ * Field _showFullId\r
+ */\r
+ private boolean _showFullId;\r
+\r
+ /**\r
+ * keeps track of state for field: _showFullId\r
+ */\r
+ private boolean _has_showFullId;\r
+\r
+ /**\r
+ * Field _showText\r
+ */\r
+ private boolean _showText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showText\r
+ */\r
+ private boolean _has_showText;\r
+\r
+ /**\r
+ * Field _showColourText\r
+ */\r
+ private boolean _showColourText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showColourText\r
+ */\r
+ private boolean _has_showColourText;\r
+\r
+ /**\r
+ * Field _showBoxes\r
+ */\r
+ private boolean _showBoxes;\r
+\r
+ /**\r
+ * keeps track of state for field: _showBoxes\r
+ */\r
+ private boolean _has_showBoxes;\r
+\r
+ /**\r
+ * Field _wrapAlignment\r
+ */\r
+ private boolean _wrapAlignment;\r
+\r
+ /**\r
+ * keeps track of state for field: _wrapAlignment\r
+ */\r
+ private boolean _has_wrapAlignment;\r
+\r
+ /**\r
+ * Field _renderGaps\r
+ */\r
+ private boolean _renderGaps;\r
+\r
+ /**\r
+ * keeps track of state for field: _renderGaps\r
+ */\r
+ private boolean _has_renderGaps;\r
+\r
+ /**\r
+ * Field _showSequenceFeatures\r
+ */\r
+ private boolean _showSequenceFeatures;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceFeatures\r
+ */\r
+ private boolean _has_showSequenceFeatures;\r
+\r
+ /**\r
+ * Field _showAnnotation\r
+ */\r
+ private boolean _showAnnotation;\r
+\r
+ /**\r
+ * keeps track of state for field: _showAnnotation\r
+ */\r
+ private boolean _has_showAnnotation;\r
+\r
+ /**\r
+ * Field _showConservation\r
+ */\r
+ private boolean _showConservation;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConservation\r
+ */\r
+ private boolean _has_showConservation;\r
+\r
+ /**\r
+ * Field _showQuality\r
+ */\r
+ private boolean _showQuality;\r
+\r
+ /**\r
+ * keeps track of state for field: _showQuality\r
+ */\r
+ private boolean _has_showQuality;\r
+\r
+ /**\r
+ * Field _showIdentity\r
+ */\r
+ private boolean _showIdentity;\r
+\r
+ /**\r
+ * keeps track of state for field: _showIdentity\r
+ */\r
+ private boolean _has_showIdentity;\r
+\r
+ /**\r
+ * Field _xpos\r
+ */\r
+ private int _xpos;\r
+\r
+ /**\r
+ * keeps track of state for field: _xpos\r
+ */\r
+ private boolean _has_xpos;\r
+\r
+ /**\r
+ * Field _ypos\r
+ */\r
+ private int _ypos;\r
+\r
+ /**\r
+ * keeps track of state for field: _ypos\r
+ */\r
+ private boolean _has_ypos;\r
+\r
+ /**\r
+ * Field _width\r
+ */\r
+ private int _width;\r
+\r
+ /**\r
+ * keeps track of state for field: _width\r
+ */\r
+ private boolean _has_width;\r
+\r
+ /**\r
+ * Field _height\r
+ */\r
+ private int _height;\r
+\r
+ /**\r
+ * keeps track of state for field: _height\r
+ */\r
+ private boolean _has_height;\r
+\r
+ /**\r
+ * Field _startRes\r
+ */\r
+ private int _startRes;\r
+\r
+ /**\r
+ * keeps track of state for field: _startRes\r
+ */\r
+ private boolean _has_startRes;\r
+\r
+ /**\r
+ * Field _startSeq\r
+ */\r
+ private int _startSeq;\r
+\r
+ /**\r
+ * keeps track of state for field: _startSeq\r
+ */\r
+ private boolean _has_startSeq;\r
+\r
+ /**\r
+ * Field _fontName\r
+ */\r
+ private java.lang.String _fontName;\r
+\r
+ /**\r
+ * Field _fontSize\r
+ */\r
+ private int _fontSize;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontSize\r
+ */\r
+ private boolean _has_fontSize;\r
+\r
+ /**\r
+ * Field _fontStyle\r
+ */\r
+ private int _fontStyle;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontStyle\r
+ */\r
+ private boolean _has_fontStyle;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Viewport() {\r
+ super();\r
+ } //-- jalview.binding.Viewport()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteConsThreshold\r
+ * \r
+ */\r
+ public void deleteConsThreshold()\r
+ {\r
+ this._has_consThreshold= false;\r
+ } //-- void deleteConsThreshold() \r
+\r
+ /**\r
+ * Method deleteConservationSelected\r
+ * \r
+ */\r
+ public void deleteConservationSelected()\r
+ {\r
+ this._has_conservationSelected= false;\r
+ } //-- void deleteConservationSelected() \r
+\r
+ /**\r
+ * Method deleteFontSize\r
+ * \r
+ */\r
+ public void deleteFontSize()\r
+ {\r
+ this._has_fontSize= false;\r
+ } //-- void deleteFontSize() \r
+\r
+ /**\r
+ * Method deleteFontStyle\r
+ * \r
+ */\r
+ public void deleteFontStyle()\r
+ {\r
+ this._has_fontStyle= false;\r
+ } //-- void deleteFontStyle() \r
+\r
+ /**\r
+ * Method deleteHeight\r
+ * \r
+ */\r
+ public void deleteHeight()\r
+ {\r
+ this._has_height= false;\r
+ } //-- void deleteHeight() \r
+\r
+ /**\r
+ * Method deletePidSelected\r
+ * \r
+ */\r
+ public void deletePidSelected()\r
+ {\r
+ this._has_pidSelected= false;\r
+ } //-- void deletePidSelected() \r
+\r
+ /**\r
+ * Method deletePidThreshold\r
+ * \r
+ */\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
+\r
+ /**\r
+ * Method deleteRenderGaps\r
+ * \r
+ */\r
+ public void deleteRenderGaps()\r
+ {\r
+ this._has_renderGaps= false;\r
+ } //-- void deleteRenderGaps() \r
+\r
+ /**\r
+ * Method deleteShowAnnotation\r
+ * \r
+ */\r
+ public void deleteShowAnnotation()\r
+ {\r
+ this._has_showAnnotation= false;\r
+ } //-- void deleteShowAnnotation() \r
+\r
+ /**\r
+ * Method deleteShowBoxes\r
+ * \r
+ */\r
+ public void deleteShowBoxes()\r
+ {\r
+ this._has_showBoxes= false;\r
+ } //-- void deleteShowBoxes() \r
+\r
+ /**\r
+ * Method deleteShowColourText\r
+ * \r
+ */\r
+ public void deleteShowColourText()\r
+ {\r
+ this._has_showColourText= false;\r
+ } //-- void deleteShowColourText() \r
+\r
+ /**\r
+ * Method deleteShowConservation\r
+ * \r
+ */\r
+ public void deleteShowConservation()\r
+ {\r
+ this._has_showConservation= false;\r
+ } //-- void deleteShowConservation() \r
+\r
+ /**\r
+ * Method deleteShowFullId\r
+ * \r
+ */\r
+ public void deleteShowFullId()\r
+ {\r
+ this._has_showFullId= false;\r
+ } //-- void deleteShowFullId() \r
+\r
+ /**\r
+ * Method deleteShowIdentity\r
+ * \r
+ */\r
+ public void deleteShowIdentity()\r
+ {\r
+ this._has_showIdentity= false;\r
+ } //-- void deleteShowIdentity() \r
+\r
+ /**\r
+ * Method deleteShowQuality\r
+ * \r
+ */\r
+ public void deleteShowQuality()\r
+ {\r
+ this._has_showQuality= false;\r
+ } //-- void deleteShowQuality() \r
+\r
+ /**\r
+ * Method deleteShowSequenceFeatures\r
+ * \r
+ */\r
+ public void deleteShowSequenceFeatures()\r
+ {\r
+ this._has_showSequenceFeatures= false;\r
+ } //-- void deleteShowSequenceFeatures() \r
+\r
+ /**\r
+ * Method deleteShowText\r
+ * \r
+ */\r
+ public void deleteShowText()\r
+ {\r
+ this._has_showText= false;\r
+ } //-- void deleteShowText() \r
+\r
+ /**\r
+ * Method deleteStartRes\r
+ * \r
+ */\r
+ public void deleteStartRes()\r
+ {\r
+ this._has_startRes= false;\r
+ } //-- void deleteStartRes() \r
+\r
+ /**\r
+ * Method deleteStartSeq\r
+ * \r
+ */\r
+ public void deleteStartSeq()\r
+ {\r
+ this._has_startSeq= false;\r
+ } //-- void deleteStartSeq() \r
+\r
+ /**\r
+ * Method deleteWidth\r
+ * \r
+ */\r
+ public void deleteWidth()\r
+ {\r
+ this._has_width= false;\r
+ } //-- void deleteWidth() \r
+\r
+ /**\r
+ * Method deleteWrapAlignment\r
+ * \r
+ */\r
+ public void deleteWrapAlignment()\r
+ {\r
+ this._has_wrapAlignment= false;\r
+ } //-- void deleteWrapAlignment() \r
+\r
+ /**\r
+ * Method deleteXpos\r
+ * \r
+ */\r
+ public void deleteXpos()\r
+ {\r
+ this._has_xpos= false;\r
+ } //-- void deleteXpos() \r
+\r
+ /**\r
+ * Method deleteYpos\r
+ * \r
+ */\r
+ public void deleteYpos()\r
+ {\r
+ this._has_ypos= false;\r
+ } //-- void deleteYpos() \r
+\r
+ /**\r
+ * Returns the value of field 'bgColour'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'bgColour'.\r
+ */\r
+ public java.lang.String getBgColour()\r
+ {\r
+ return this._bgColour;\r
+ } //-- java.lang.String getBgColour() \r
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'consThreshold'.\r
+ */\r
+ public int getConsThreshold()\r
+ {\r
+ return this._consThreshold;\r
+ } //-- int getConsThreshold() \r
+\r
+ /**\r
+ * Returns the value of field 'conservationSelected'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'conservationSelected'.\r
+ */\r
+ public boolean getConservationSelected()\r
+ {\r
+ return this._conservationSelected;\r
+ } //-- boolean getConservationSelected() \r
+\r
+ /**\r
+ * Returns the value of field 'fontName'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'fontName'.\r
+ */\r
+ public java.lang.String getFontName()\r
+ {\r
+ return this._fontName;\r
+ } //-- java.lang.String getFontName() \r
+\r
+ /**\r
+ * Returns the value of field 'fontSize'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'fontSize'.\r
+ */\r
+ public int getFontSize()\r
+ {\r
+ return this._fontSize;\r
+ } //-- int getFontSize() \r
+\r
+ /**\r
+ * Returns the value of field 'fontStyle'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'fontStyle'.\r
+ */\r
+ public int getFontStyle()\r
+ {\r
+ return this._fontStyle;\r
+ } //-- int getFontStyle() \r
+\r
+ /**\r
+ * Returns the value of field 'height'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'height'.\r
+ */\r
+ public int getHeight()\r
+ {\r
+ return this._height;\r
+ } //-- int getHeight() \r
+\r
+ /**\r
+ * Returns the value of field 'pidSelected'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'pidSelected'.\r
+ */\r
+ public boolean getPidSelected()\r
+ {\r
+ return this._pidSelected;\r
+ } //-- boolean getPidSelected() \r
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'pidThreshold'.\r
+ */\r
+ public int getPidThreshold()\r
+ {\r
+ return this._pidThreshold;\r
+ } //-- int getPidThreshold() \r
+\r
+ /**\r
+ * Returns the value of field 'renderGaps'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'renderGaps'.\r
+ */\r
+ public boolean getRenderGaps()\r
+ {\r
+ return this._renderGaps;\r
+ } //-- boolean getRenderGaps() \r
+\r
+ /**\r
+ * Returns the value of field 'showAnnotation'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showAnnotation'.\r
+ */\r
+ public boolean getShowAnnotation()\r
+ {\r
+ return this._showAnnotation;\r
+ } //-- boolean getShowAnnotation() \r
+\r
+ /**\r
+ * Returns the value of field 'showBoxes'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showBoxes'.\r
+ */\r
+ public boolean getShowBoxes()\r
+ {\r
+ return this._showBoxes;\r
+ } //-- boolean getShowBoxes() \r
+\r
+ /**\r
+ * Returns the value of field 'showColourText'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showColourText'.\r
+ */\r
+ public boolean getShowColourText()\r
+ {\r
+ return this._showColourText;\r
+ } //-- boolean getShowColourText() \r
+\r
+ /**\r
+ * Returns the value of field 'showConservation'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showConservation'.\r
+ */\r
+ public boolean getShowConservation()\r
+ {\r
+ return this._showConservation;\r
+ } //-- boolean getShowConservation() \r
+\r
+ /**\r
+ * Returns the value of field 'showFullId'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showFullId'.\r
+ */\r
+ public boolean getShowFullId()\r
+ {\r
+ return this._showFullId;\r
+ } //-- boolean getShowFullId() \r
+\r
+ /**\r
+ * Returns the value of field 'showIdentity'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showIdentity'.\r
+ */\r
+ public boolean getShowIdentity()\r
+ {\r
+ return this._showIdentity;\r
+ } //-- boolean getShowIdentity() \r
+\r
+ /**\r
+ * Returns the value of field 'showQuality'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showQuality'.\r
+ */\r
+ public boolean getShowQuality()\r
+ {\r
+ return this._showQuality;\r
+ } //-- boolean getShowQuality() \r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showSequenceFeatures'.\r
+ */\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return this._showSequenceFeatures;\r
+ } //-- boolean getShowSequenceFeatures() \r
+\r
+ /**\r
+ * Returns the value of field 'showText'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showText'.\r
+ */\r
+ public boolean getShowText()\r
+ {\r
+ return this._showText;\r
+ } //-- boolean getShowText() \r
+\r
+ /**\r
+ * Returns the value of field 'startRes'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'startRes'.\r
+ */\r
+ public int getStartRes()\r
+ {\r
+ return this._startRes;\r
+ } //-- int getStartRes() \r
+\r
+ /**\r
+ * Returns the value of field 'startSeq'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'startSeq'.\r
+ */\r
+ public int getStartSeq()\r
+ {\r
+ return this._startSeq;\r
+ } //-- int getStartSeq() \r
+\r
+ /**\r
+ * Returns the value of field 'title'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'title'.\r
+ */\r
+ public java.lang.String getTitle()\r
+ {\r
+ return this._title;\r
+ } //-- java.lang.String getTitle() \r
+\r
+ /**\r
+ * Returns the value of field 'width'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'width'.\r
+ */\r
+ public int getWidth()\r
+ {\r
+ return this._width;\r
+ } //-- int getWidth() \r
+\r
+ /**\r
+ * Returns the value of field 'wrapAlignment'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'wrapAlignment'.\r
+ */\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return this._wrapAlignment;\r
+ } //-- boolean getWrapAlignment() \r
+\r
+ /**\r
+ * Returns the value of field 'xpos'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'xpos'.\r
+ */\r
+ public int getXpos()\r
+ {\r
+ return this._xpos;\r
+ } //-- int getXpos() \r
+\r
+ /**\r
+ * Returns the value of field 'ypos'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'ypos'.\r
+ */\r
+ public int getYpos()\r
+ {\r
+ return this._ypos;\r
+ } //-- int getYpos() \r
+\r
+ /**\r
+ * Method hasConsThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasConsThreshold()\r
+ {\r
+ return this._has_consThreshold;\r
+ } //-- boolean hasConsThreshold() \r
+\r
+ /**\r
+ * Method hasConservationSelected\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasConservationSelected()\r
+ {\r
+ return this._has_conservationSelected;\r
+ } //-- boolean hasConservationSelected() \r
+\r
+ /**\r
+ * Method hasFontSize\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasFontSize()\r
+ {\r
+ return this._has_fontSize;\r
+ } //-- boolean hasFontSize() \r
+\r
+ /**\r
+ * Method hasFontStyle\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasFontStyle()\r
+ {\r
+ return this._has_fontStyle;\r
+ } //-- boolean hasFontStyle() \r
+\r
+ /**\r
+ * Method hasHeight\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasHeight()\r
+ {\r
+ return this._has_height;\r
+ } //-- boolean hasHeight() \r
+\r
+ /**\r
+ * Method hasPidSelected\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasPidSelected()\r
+ {\r
+ return this._has_pidSelected;\r
+ } //-- boolean hasPidSelected() \r
+\r
+ /**\r
+ * Method hasPidThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasPidThreshold()\r
+ {\r
+ return this._has_pidThreshold;\r
+ } //-- boolean hasPidThreshold() \r
+\r
+ /**\r
+ * Method hasRenderGaps\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasRenderGaps()\r
+ {\r
+ return this._has_renderGaps;\r
+ } //-- boolean hasRenderGaps() \r
+\r
+ /**\r
+ * Method hasShowAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowAnnotation()\r
+ {\r
+ return this._has_showAnnotation;\r
+ } //-- boolean hasShowAnnotation() \r
+\r
+ /**\r
+ * Method hasShowBoxes\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowBoxes()\r
+ {\r
+ return this._has_showBoxes;\r
+ } //-- boolean hasShowBoxes() \r
+\r
+ /**\r
+ * Method hasShowColourText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowColourText()\r
+ {\r
+ return this._has_showColourText;\r
+ } //-- boolean hasShowColourText() \r
+\r
+ /**\r
+ * Method hasShowConservation\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowConservation()\r
+ {\r
+ return this._has_showConservation;\r
+ } //-- boolean hasShowConservation() \r
+\r
+ /**\r
+ * Method hasShowFullId\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowFullId()\r
+ {\r
+ return this._has_showFullId;\r
+ } //-- boolean hasShowFullId() \r
+\r
+ /**\r
+ * Method hasShowIdentity\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowIdentity()\r
+ {\r
+ return this._has_showIdentity;\r
+ } //-- boolean hasShowIdentity() \r
+\r
+ /**\r
+ * Method hasShowQuality\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowQuality()\r
+ {\r
+ return this._has_showQuality;\r
+ } //-- boolean hasShowQuality() \r
+\r
+ /**\r
+ * Method hasShowSequenceFeatures\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowSequenceFeatures()\r
+ {\r
+ return this._has_showSequenceFeatures;\r
+ } //-- boolean hasShowSequenceFeatures() \r
+\r
+ /**\r
+ * Method hasShowText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowText()\r
+ {\r
+ return this._has_showText;\r
+ } //-- boolean hasShowText() \r
+\r
+ /**\r
+ * Method hasStartRes\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStartRes()\r
+ {\r
+ return this._has_startRes;\r
+ } //-- boolean hasStartRes() \r
+\r
+ /**\r
+ * Method hasStartSeq\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStartSeq()\r
+ {\r
+ return this._has_startSeq;\r
+ } //-- boolean hasStartSeq() \r
+\r
+ /**\r
+ * Method hasWidth\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasWidth()\r
+ {\r
+ return this._has_width;\r
+ } //-- boolean hasWidth() \r
+\r
+ /**\r
+ * Method hasWrapAlignment\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasWrapAlignment()\r
+ {\r
+ return this._has_wrapAlignment;\r
+ } //-- boolean hasWrapAlignment() \r
+\r
+ /**\r
+ * Method hasXpos\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasXpos()\r
+ {\r
+ return this._has_xpos;\r
+ } //-- boolean hasXpos() \r
+\r
+ /**\r
+ * Method hasYpos\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasYpos()\r
+ {\r
+ return this._has_ypos;\r
+ } //-- boolean hasYpos() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\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, 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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'bgColour'.\r
+ * \r
+ * @param bgColour the value of field 'bgColour'.\r
+ */\r
+ public void setBgColour(java.lang.String bgColour)\r
+ {\r
+ this._bgColour = bgColour;\r
+ } //-- void setBgColour(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(int consThreshold)\r
+ {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ } //-- void setConsThreshold(int) \r
+\r
+ /**\r
+ * Sets the value of field 'conservationSelected'.\r
+ * \r
+ * @param conservationSelected the value of field\r
+ * 'conservationSelected'.\r
+ */\r
+ public void setConservationSelected(boolean conservationSelected)\r
+ {\r
+ this._conservationSelected = conservationSelected;\r
+ this._has_conservationSelected = true;\r
+ } //-- void setConservationSelected(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName the value of field 'fontName'.\r
+ */\r
+ public void setFontName(java.lang.String fontName)\r
+ {\r
+ this._fontName = fontName;\r
+ } //-- void setFontName(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(int fontSize)\r
+ {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ } //-- void setFontSize(int) \r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(int fontStyle)\r
+ {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ } //-- void setFontStyle(int) \r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height the value of field 'height'.\r
+ */\r
+ public void setHeight(int height)\r
+ {\r
+ this._height = height;\r
+ this._has_height = true;\r
+ } //-- void setHeight(int) \r
+\r
+ /**\r
+ * Sets the value of field 'pidSelected'.\r
+ * \r
+ * @param pidSelected the value of field 'pidSelected'.\r
+ */\r
+ public void setPidSelected(boolean pidSelected)\r
+ {\r
+ this._pidSelected = pidSelected;\r
+ this._has_pidSelected = true;\r
+ } //-- void setPidSelected(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(int pidThreshold)\r
+ {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ } //-- void setPidThreshold(int) \r
+\r
+ /**\r
+ * Sets the value of field 'renderGaps'.\r
+ * \r
+ * @param renderGaps the value of field 'renderGaps'.\r
+ */\r
+ public void setRenderGaps(boolean renderGaps)\r
+ {\r
+ this._renderGaps = renderGaps;\r
+ this._has_renderGaps = true;\r
+ } //-- void setRenderGaps(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showAnnotation'.\r
+ * \r
+ * @param showAnnotation the value of field 'showAnnotation'.\r
+ */\r
+ public void setShowAnnotation(boolean showAnnotation)\r
+ {\r
+ this._showAnnotation = showAnnotation;\r
+ this._has_showAnnotation = true;\r
+ } //-- void setShowAnnotation(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showBoxes'.\r
+ * \r
+ * @param showBoxes the value of field 'showBoxes'.\r
+ */\r
+ public void setShowBoxes(boolean showBoxes)\r
+ {\r
+ this._showBoxes = showBoxes;\r
+ this._has_showBoxes = true;\r
+ } //-- void setShowBoxes(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showColourText'.\r
+ * \r
+ * @param showColourText the value of field 'showColourText'.\r
+ */\r
+ public void setShowColourText(boolean showColourText)\r
+ {\r
+ this._showColourText = showColourText;\r
+ this._has_showColourText = true;\r
+ } //-- void setShowColourText(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showConservation'.\r
+ * \r
+ * @param showConservation the value of field 'showConservation'\r
+ */\r
+ public void setShowConservation(boolean showConservation)\r
+ {\r
+ this._showConservation = showConservation;\r
+ this._has_showConservation = true;\r
+ } //-- void setShowConservation(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showFullId'.\r
+ * \r
+ * @param showFullId the value of field 'showFullId'.\r
+ */\r
+ public void setShowFullId(boolean showFullId)\r
+ {\r
+ this._showFullId = showFullId;\r
+ this._has_showFullId = true;\r
+ } //-- void setShowFullId(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showIdentity'.\r
+ * \r
+ * @param showIdentity the value of field 'showIdentity'.\r
+ */\r
+ public void setShowIdentity(boolean showIdentity)\r
+ {\r
+ this._showIdentity = showIdentity;\r
+ this._has_showIdentity = true;\r
+ } //-- void setShowIdentity(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showQuality'.\r
+ * \r
+ * @param showQuality the value of field 'showQuality'.\r
+ */\r
+ public void setShowQuality(boolean showQuality)\r
+ {\r
+ this._showQuality = showQuality;\r
+ this._has_showQuality = true;\r
+ } //-- void setShowQuality(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @param showSequenceFeatures the value of field\r
+ * 'showSequenceFeatures'.\r
+ */\r
+ public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
+ {\r
+ this._showSequenceFeatures = showSequenceFeatures;\r
+ this._has_showSequenceFeatures = true;\r
+ } //-- void setShowSequenceFeatures(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showText'.\r
+ * \r
+ * @param showText the value of field 'showText'.\r
+ */\r
+ public void setShowText(boolean showText)\r
+ {\r
+ this._showText = showText;\r
+ this._has_showText = true;\r
+ } //-- void setShowText(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'startRes'.\r
+ * \r
+ * @param startRes the value of field 'startRes'.\r
+ */\r
+ public void setStartRes(int startRes)\r
+ {\r
+ this._startRes = startRes;\r
+ this._has_startRes = true;\r
+ } //-- void setStartRes(int) \r
+\r
+ /**\r
+ * Sets the value of field 'startSeq'.\r
+ * \r
+ * @param startSeq the value of field 'startSeq'.\r
+ */\r
+ public void setStartSeq(int startSeq)\r
+ {\r
+ this._startSeq = startSeq;\r
+ this._has_startSeq = true;\r
+ } //-- void setStartSeq(int) \r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title the value of field 'title'.\r
+ */\r
+ public void setTitle(java.lang.String title)\r
+ {\r
+ this._title = title;\r
+ } //-- void setTitle(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width the value of field 'width'.\r
+ */\r
+ public void setWidth(int width)\r
+ {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ } //-- void setWidth(int) \r
+\r
+ /**\r
+ * Sets the value of field 'wrapAlignment'.\r
+ * \r
+ * @param wrapAlignment the value of field 'wrapAlignment'.\r
+ */\r
+ public void setWrapAlignment(boolean wrapAlignment)\r
+ {\r
+ this._wrapAlignment = wrapAlignment;\r
+ this._has_wrapAlignment = true;\r
+ } //-- void setWrapAlignment(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos the value of field 'xpos'.\r
+ */\r
+ public void setXpos(int xpos)\r
+ {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ } //-- void setXpos(int) \r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos the value of field 'ypos'.\r
+ */\r
+ public void setYpos(int ypos)\r
+ {\r
+ this._ypos = ypos;\r
+ this._has_ypos = true;\r
+ } //-- void setYpos(int) \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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
git://source.jalview.org / jalview.git / commitdiff