/*\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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public Alignment() {\r
super();\r
- }\r
- //-- jalview.binding.Alignment()\r
- //-----------/\r
+ } //-- jalview.binding.Alignment()\r
\r
- public jalview.binding.Annotation getAnnotation() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\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
- //-- 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
+ public jalview.binding.SequenceSet getSequenceSet()\r
+ {\r
return this._sequenceSet;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setAnnotation(jalview.binding.Annotation annotation)\r
+ {\r
this._annotation = annotation;\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
+ public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
+ {\r
this._sequenceSet = sequenceSet;\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
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 Annotation.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class Annotation implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _description;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public Annotation() {\r
super();\r
_annotationElementList = new Vector();\r
- }\r
- //-- jalview.binding.Annotation()\r
- //-----------/\r
+ } //-- jalview.binding.Annotation()\r
+\r
\r
- public void addAnnotationElement(\r
- jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\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
- }\r
- //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
+ } //-- void addAnnotationElement(jalview.binding.AnnotationElement) \r
\r
/**\r
* Method addAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void addAnnotationElement(int index,\r
- jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_annotationElementList.insertElementAt(vAnnotationElement, index);\r
- }\r
- //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) \r
\r
/**\r
* Method deleteGraph\r
- *\r
+ * \r
*/\r
- public void deleteGraph() {\r
- this._has_graph = false;\r
- }\r
- //-- void deleteGraph()\r
+ public void deleteGraph()\r
+ {\r
+ this._has_graph= false;\r
+ } //-- void deleteGraph() \r
\r
/**\r
* Method enumerateAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAnnotationElement() {\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
return _annotationElementList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateAnnotationElement()\r
+ } //-- java.util.Enumeration enumerateAnnotationElement() \r
\r
/**\r
* Method getAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return AnnotationElement\r
*/\r
public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
+ } //-- jalview.binding.AnnotationElement getAnnotationElement(int) \r
\r
/**\r
* Method getAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement[] getAnnotationElement() {\r
+ public jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ {\r
int size = _annotationElementList.size();\r
jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ } //-- jalview.binding.AnnotationElement[] getAnnotationElement() \r
\r
/**\r
* Method getAnnotationElementCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getAnnotationElementCount() {\r
+ public int getAnnotationElementCount()\r
+ {\r
return _annotationElementList.size();\r
- }\r
- //-- int getAnnotationElementCount()\r
+ } //-- int getAnnotationElementCount() \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
+ public java.lang.String getDescription()\r
+ {\r
return this._description;\r
- }\r
- //-- java.lang.String getDescription()\r
+ } //-- java.lang.String getDescription() \r
\r
/**\r
* Returns the value of field 'graph'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'graph'.\r
*/\r
- public boolean getGraph() {\r
+ public boolean getGraph()\r
+ {\r
return this._graph;\r
- }\r
- //-- boolean getGraph()\r
+ } //-- boolean getGraph() \r
\r
/**\r
* Returns the value of field 'label'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'label'.\r
*/\r
- public java.lang.String getLabel() {\r
+ public java.lang.String getLabel()\r
+ {\r
return this._label;\r
- }\r
- //-- java.lang.String getLabel()\r
+ } //-- java.lang.String getLabel() \r
\r
/**\r
* Method hasGraph\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasGraph() {\r
+ public boolean hasGraph()\r
+ {\r
return this._has_graph;\r
- }\r
- //-- boolean hasGraph()\r
+ } //-- boolean hasGraph() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllAnnotationElement\r
- *\r
+ * \r
*/\r
- public void removeAllAnnotationElement() {\r
+ public void removeAllAnnotationElement()\r
+ {\r
_annotationElementList.removeAllElements();\r
- }\r
- //-- void removeAllAnnotationElement()\r
+ } //-- void removeAllAnnotationElement() \r
\r
/**\r
* Method removeAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index) {\r
+ public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
+ {\r
java.lang.Object obj = _annotationElementList.elementAt(index);\r
_annotationElementList.removeElementAt(index);\r
-\r
return (jalview.binding.AnnotationElement) obj;\r
- }\r
- //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
+ } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) \r
\r
/**\r
* Method setAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void setAnnotationElement(int index,\r
- jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\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
-\r
_annotationElementList.setElementAt(vAnnotationElement, index);\r
- }\r
- //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) \r
\r
/**\r
* Method setAnnotationElement\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param annotationElementArray\r
*/\r
- public void setAnnotationElement(\r
- jalview.binding.AnnotationElement[] annotationElementArray) {\r
+ public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
+ {\r
//-- copy array\r
_annotationElementList.removeAllElements();\r
-\r
for (int i = 0; i < annotationElementArray.length; i++) {\r
_annotationElementList.addElement(annotationElementArray[i]);\r
}\r
- }\r
- //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
+ } //-- void setAnnotationElement(jalview.binding.AnnotationElement) \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
+ public void setDescription(java.lang.String description)\r
+ {\r
this._description = description;\r
- }\r
- //-- void setDescription(java.lang.String)\r
+ } //-- void setDescription(java.lang.String) \r
\r
/**\r
* Sets the value of field 'graph'.\r
- *\r
+ * \r
* @param graph the value of field 'graph'.\r
*/\r
- public void setGraph(boolean graph) {\r
+ public void setGraph(boolean graph)\r
+ {\r
this._graph = graph;\r
this._has_graph = true;\r
- }\r
- //-- void setGraph(boolean)\r
+ } //-- void setGraph(boolean) \r
\r
/**\r
* Sets the value of field 'label'.\r
- *\r
+ * \r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label) {\r
+ public void setLabel(java.lang.String label)\r
+ {\r
this._label = label;\r
- }\r
- //-- void setLabel(java.lang.String)\r
+ } //-- void setLabel(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
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public AnnotationElement() {\r
super();\r
- }\r
- //-- jalview.binding.AnnotationElement()\r
- //-----------/\r
+ } //-- jalview.binding.AnnotationElement()\r
\r
- public void deletePosition() {\r
- this._has_position = false;\r
- }\r
- //-- void deletePosition()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deletePosition\r
+ * \r
+ */\r
+ public void deletePosition()\r
+ {\r
+ this._has_position= false;\r
+ } //-- void deletePosition() \r
\r
/**\r
* Method deleteValue\r
- *\r
+ * \r
*/\r
- public void deleteValue() {\r
- this._has_value = false;\r
- }\r
- //-- void deleteValue()\r
+ public void deleteValue()\r
+ {\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
+ public java.lang.String getDescription()\r
+ {\r
return this._description;\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
+ public java.lang.String getDisplayCharacter()\r
+ {\r
return this._displayCharacter;\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
+ public int getPosition()\r
+ {\r
return this._position;\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
+ public java.lang.String getSecondaryStructure()\r
+ {\r
return this._secondaryStructure;\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
+ public float getValue()\r
+ {\r
return this._value;\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
+ public boolean hasPosition()\r
+ {\r
return this._has_position;\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
+ public boolean hasValue()\r
+ {\r
return this._has_value;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setDescription(java.lang.String description)\r
+ {\r
this._description = description;\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
+ public void setDisplayCharacter(java.lang.String displayCharacter)\r
+ {\r
this._displayCharacter = displayCharacter;\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
+ public void setPosition(int position)\r
+ {\r
this._position = position;\r
this._has_position = true;\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
+ public void setSecondaryStructure(java.lang.String secondaryStructure)\r
+ {\r
this._secondaryStructure = secondaryStructure;\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
+ public void setValue(float value)\r
+ {\r
this._value = value;\r
this._has_value = true;\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
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public Colour() {\r
super();\r
- }\r
- //-- jalview.binding.Colour()\r
- //-----------/\r
+ } //-- jalview.binding.Colour()\r
+\r
\r
- public java.lang.String getName() {\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\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
- }\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
+ public java.lang.String getRGB()\r
+ {\r
return this._RGB;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setName(java.lang.String name)\r
+ {\r
this._name = name;\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
+ public void setRGB(java.lang.String RGB)\r
+ {\r
this._RGB = RGB;\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
- return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public JGroup() {\r
super();\r
_seqList = new Vector();\r
- }\r
- //-- jalview.binding.JGroup()\r
- //-----------/\r
+ } //-- jalview.binding.JGroup()\r
+\r
\r
- public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException {\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addSeq\r
+ * \r
+ * \r
+ * \r
+ * @param vSeq\r
+ */\r
+ public void addSeq(int vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_seqList.addElement(new java.lang.Integer(vSeq));\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
public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- }\r
- //-- void addSeq(int, int)\r
+ } //-- void addSeq(int, int) \r
\r
/**\r
* Method deleteColourText\r
- *\r
+ * \r
*/\r
- public void deleteColourText() {\r
- this._has_colourText = false;\r
- }\r
- //-- void deleteColourText()\r
+ public void deleteColourText()\r
+ {\r
+ this._has_colourText= false;\r
+ } //-- void deleteColourText() \r
\r
/**\r
* Method deleteConsThreshold\r
- *\r
+ * \r
*/\r
- public void deleteConsThreshold() {\r
- this._has_consThreshold = false;\r
- }\r
- //-- void deleteConsThreshold()\r
+ public void deleteConsThreshold()\r
+ {\r
+ this._has_consThreshold= false;\r
+ } //-- void deleteConsThreshold() \r
\r
/**\r
* Method deleteDisplayBoxes\r
- *\r
+ * \r
*/\r
- public void deleteDisplayBoxes() {\r
- this._has_displayBoxes = false;\r
- }\r
- //-- void deleteDisplayBoxes()\r
+ public void deleteDisplayBoxes()\r
+ {\r
+ this._has_displayBoxes= false;\r
+ } //-- void deleteDisplayBoxes() \r
\r
/**\r
* Method deleteDisplayText\r
- *\r
+ * \r
*/\r
- public void deleteDisplayText() {\r
- this._has_displayText = false;\r
- }\r
- //-- void deleteDisplayText()\r
+ public void deleteDisplayText()\r
+ {\r
+ this._has_displayText= false;\r
+ } //-- void deleteDisplayText() \r
\r
/**\r
* Method deleteEnd\r
- *\r
+ * \r
*/\r
- public void deleteEnd() {\r
- this._has_end = false;\r
- }\r
- //-- void deleteEnd()\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
\r
/**\r
* Method deleteOutlineColour\r
- *\r
+ * \r
*/\r
- public void deleteOutlineColour() {\r
- this._has_outlineColour = false;\r
- }\r
- //-- void deleteOutlineColour()\r
+ public void deleteOutlineColour()\r
+ {\r
+ this._has_outlineColour= false;\r
+ } //-- void deleteOutlineColour() \r
\r
/**\r
* Method deletePidThreshold\r
- *\r
+ * \r
*/\r
- public void deletePidThreshold() {\r
- this._has_pidThreshold = false;\r
- }\r
- //-- void deletePidThreshold()\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
\r
/**\r
* Method deleteStart\r
- *\r
+ * \r
*/\r
- public void deleteStart() {\r
- this._has_start = false;\r
- }\r
- //-- void deleteStart()\r
+ public void deleteStart()\r
+ {\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
+ public java.util.Enumeration enumerateSeq()\r
+ {\r
return _seqList.elements();\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
+ public java.lang.String getColour()\r
+ {\r
return this._colour;\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
+ public boolean getColourText()\r
+ {\r
return this._colourText;\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
+ public int getConsThreshold()\r
+ {\r
return this._consThreshold;\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
+ public boolean getDisplayBoxes()\r
+ {\r
return this._displayBoxes;\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
+ public boolean getDisplayText()\r
+ {\r
return this._displayText;\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
+ public int getEnd()\r
+ {\r
return this._end;\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
+ public java.lang.String getName()\r
+ {\r
return this._name;\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
+ public int getOutlineColour()\r
+ {\r
return this._outlineColour;\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
+ public int getPidThreshold()\r
+ {\r
return this._pidThreshold;\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
throw new IndexOutOfBoundsException();\r
}\r
-\r
- return ((java.lang.Integer) _seqList.elementAt(index)).intValue();\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
+ 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
- mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();\r
+ mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
}\r
-\r
return mArray;\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
+ public int getSeqCount()\r
+ {\r
return _seqList.size();\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
+ public int getStart()\r
+ {\r
return this._start;\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
+ public boolean hasColourText()\r
+ {\r
return this._has_colourText;\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
+ public boolean hasConsThreshold()\r
+ {\r
return this._has_consThreshold;\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
+ public boolean hasDisplayBoxes()\r
+ {\r
return this._has_displayBoxes;\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
+ public boolean hasDisplayText()\r
+ {\r
return this._has_displayText;\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
+ public boolean hasEnd()\r
+ {\r
return this._has_end;\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
+ public boolean hasOutlineColour()\r
+ {\r
return this._has_outlineColour;\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
+ public boolean hasPidThreshold()\r
+ {\r
return this._has_pidThreshold;\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
+ public boolean hasStart()\r
+ {\r
return this._has_start;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void removeAllSeq()\r
+ {\r
_seqList.removeAllElements();\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
- public int removeSeq(int index) {\r
+ public int removeSeq(int index)\r
+ {\r
java.lang.Object obj = _seqList.elementAt(index);\r
_seqList.removeElementAt(index);\r
-\r
- return ((java.lang.Integer) obj).intValue();\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
+ public void setColour(java.lang.String colour)\r
+ {\r
this._colour = colour;\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
+ public void setColourText(boolean colourText)\r
+ {\r
this._colourText = colourText;\r
this._has_colourText = true;\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
+ public void setConsThreshold(int consThreshold)\r
+ {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\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
+ public void setDisplayBoxes(boolean displayBoxes)\r
+ {\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\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
+ public void setDisplayText(boolean displayText)\r
+ {\r
this._displayText = displayText;\r
this._has_displayText = true;\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
+ public void setEnd(int end)\r
+ {\r
this._end = end;\r
this._has_end = true;\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
+ public void setName(java.lang.String name)\r
+ {\r
this._name = name;\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
+ public void setOutlineColour(int outlineColour)\r
+ {\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\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
+ public void setPidThreshold(int pidThreshold)\r
+ {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\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
public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);\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
+ public void setSeq(int[] seqArray)\r
+ {\r
//-- copy array\r
_seqList.removeAllElements();\r
-\r
for (int i = 0; i < seqArray.length; i++) {\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));\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
+ public void setStart(int start)\r
+ {\r
this._start = start;\r
this._has_start = true;\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
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public JSeq() {\r
super();\r
- }\r
- //-- jalview.binding.JSeq()\r
- //-----------/\r
+ } //-- jalview.binding.JSeq()\r
\r
- public void deleteColour() {\r
- this._has_colour = false;\r
- }\r
- //-- void deleteColour()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteColour\r
+ * \r
+ */\r
+ public void deleteColour()\r
+ {\r
+ this._has_colour= false;\r
+ } //-- void deleteColour() \r
\r
/**\r
* Method deleteEnd\r
- *\r
+ * \r
*/\r
- public void deleteEnd() {\r
- this._has_end = false;\r
- }\r
- //-- void deleteEnd()\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
\r
/**\r
* Method deleteId\r
- *\r
+ * \r
*/\r
- public void deleteId() {\r
- this._has_id = false;\r
- }\r
- //-- void deleteId()\r
+ public void deleteId()\r
+ {\r
+ this._has_id= false;\r
+ } //-- void deleteId() \r
\r
/**\r
* Method deleteStart\r
- *\r
+ * \r
*/\r
- public void deleteStart() {\r
- this._has_start = false;\r
- }\r
- //-- void deleteStart()\r
+ public void deleteStart()\r
+ {\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
+ public int getColour()\r
+ {\r
return this._colour;\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
+ public int getEnd()\r
+ {\r
return this._end;\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
+ public int getId()\r
+ {\r
return this._id;\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
+ public int getStart()\r
+ {\r
return this._start;\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
+ public boolean hasColour()\r
+ {\r
return this._has_colour;\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
+ public boolean hasEnd()\r
+ {\r
return this._has_end;\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
+ public boolean hasId()\r
+ {\r
return this._has_id;\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
+ public boolean hasStart()\r
+ {\r
return this._has_start;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setColour(int colour)\r
+ {\r
this._colour = colour;\r
this._has_colour = true;\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
+ public void setEnd(int end)\r
+ {\r
this._end = end;\r
this._has_end = true;\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
+ public void setId(int id)\r
+ {\r
this._id = id;\r
this._has_id = true;\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
+ public void setStart(int start)\r
+ {\r
this._start = start;\r
this._has_start = true;\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
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public JalviewModel() {\r
super();\r
- }\r
- //-- jalview.binding.JalviewModel()\r
- //-----------/\r
+ } //-- jalview.binding.JalviewModel()\r
\r
- public java.util.Date getCreationDate() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\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
- //-- 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
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
+ {\r
return this._jalviewModelSequence;\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
+ public jalview.binding.VamsasModel getVamsasModel()\r
+ {\r
return this._vamsasModel;\r
- }\r
- //-- jalview.binding.VamsasModel getVamsasModel()\r
+ } //-- jalview.binding.VamsasModel getVamsasModel() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setCreationDate(java.util.Date creationDate)\r
+ {\r
this._creationDate = creationDate;\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
- //-- 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
+ public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)\r
+ {\r
this._vamsasModel = vamsasModel;\r
- }\r
- //-- void setVamsasModel(jalview.binding.VamsasModel)\r
+ } //-- void setVamsasModel(jalview.binding.VamsasModel) \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
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 JalviewModelSequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\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
- //- 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
- }\r
- //-- jalview.binding.JalviewModelSequence()\r
- //-----------/\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JGroupList.addElement(vJGroup);\r
- }\r
- //-- void addJGroup(jalview.binding.JGroup)\r
+ } //-- void addJGroup(jalview.binding.JGroup) \r
\r
/**\r
* Method addJGroup\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JGroupList.insertElementAt(vJGroup, index);\r
- }\r
- //-- void addJGroup(int, jalview.binding.JGroup)\r
+ } //-- void addJGroup(int, jalview.binding.JGroup) \r
\r
/**\r
* Method addJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vJSeq\r
*/\r
public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JSeqList.addElement(vJSeq);\r
- }\r
- //-- void addJSeq(jalview.binding.JSeq)\r
+ } //-- void addJSeq(jalview.binding.JSeq) \r
\r
/**\r
* Method addJSeq\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JSeqList.insertElementAt(vJSeq, index);\r
- }\r
- //-- void addJSeq(int, jalview.binding.JSeq)\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
+ * \r
+ * \r
+ * \r
* @param vUserColours\r
*/\r
public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColoursList.addElement(vUserColours);\r
- }\r
- //-- void addUserColours(jalview.binding.UserColours)\r
+ } //-- void addUserColours(jalview.binding.UserColours) \r
\r
/**\r
* Method addUserColours\r
- *\r
- *\r
- *\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
+ public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColoursList.insertElementAt(vUserColours, index);\r
- }\r
- //-- void addUserColours(int, jalview.binding.UserColours)\r
+ } //-- void addUserColours(int, jalview.binding.UserColours) \r
\r
/**\r
* Method addViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vViewport\r
*/\r
public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_viewportList.addElement(vViewport);\r
- }\r
- //-- void addViewport(jalview.binding.Viewport)\r
+ } //-- void addViewport(jalview.binding.Viewport) \r
\r
/**\r
* Method addViewport\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_viewportList.insertElementAt(vViewport, index);\r
- }\r
- //-- void addViewport(int, jalview.binding.Viewport)\r
+ } //-- void addViewport(int, jalview.binding.Viewport) \r
\r
/**\r
* Method enumerateJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJGroup() {\r
+ public java.util.Enumeration enumerateJGroup()\r
+ {\r
return _JGroupList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateJGroup()\r
+ } //-- java.util.Enumeration enumerateJGroup() \r
\r
/**\r
* Method enumerateJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJSeq() {\r
+ public java.util.Enumeration enumerateJSeq()\r
+ {\r
return _JSeqList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateJSeq()\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
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateUserColours() {\r
+ public java.util.Enumeration enumerateUserColours()\r
+ {\r
return _userColoursList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateUserColours()\r
+ } //-- java.util.Enumeration enumerateUserColours() \r
\r
/**\r
* Method enumerateViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateViewport() {\r
+ public java.util.Enumeration enumerateViewport()\r
+ {\r
return _viewportList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateViewport()\r
+ } //-- java.util.Enumeration enumerateViewport() \r
\r
/**\r
* Method getJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JGroup\r
*/\r
public jalview.binding.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- }\r
- //-- jalview.binding.JGroup getJGroup(int)\r
+ } //-- jalview.binding.JGroup getJGroup(int) \r
\r
/**\r
* Method getJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup[] getJGroup() {\r
+ public jalview.binding.JGroup[] getJGroup()\r
+ {\r
int size = _JGroupList.size();\r
jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.JGroup[] getJGroup()\r
+ } //-- jalview.binding.JGroup[] getJGroup() \r
\r
/**\r
* Method getJGroupCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getJGroupCount() {\r
+ public int getJGroupCount()\r
+ {\r
return _JGroupList.size();\r
- }\r
- //-- int getJGroupCount()\r
+ } //-- int getJGroupCount() \r
\r
/**\r
* Method getJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JSeq\r
*/\r
public jalview.binding.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- }\r
- //-- jalview.binding.JSeq getJSeq(int)\r
+ } //-- jalview.binding.JSeq getJSeq(int) \r
\r
/**\r
* Method getJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq[] getJSeq() {\r
+ public jalview.binding.JSeq[] getJSeq()\r
+ {\r
int size = _JSeqList.size();\r
jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.JSeq[] getJSeq()\r
+ } //-- jalview.binding.JSeq[] getJSeq() \r
\r
/**\r
* Method getJSeqCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getJSeqCount() {\r
+ public int getJSeqCount()\r
+ {\r
return _JSeqList.size();\r
- }\r
- //-- int getJSeqCount()\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
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColours\r
*/\r
public jalview.binding.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- }\r
- //-- jalview.binding.UserColours getUserColours(int)\r
+ } //-- jalview.binding.UserColours getUserColours(int) \r
\r
/**\r
* Method getUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours[] getUserColours() {\r
+ public jalview.binding.UserColours[] getUserColours()\r
+ {\r
int size = _userColoursList.size();\r
jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.UserColours[] getUserColours()\r
+ } //-- jalview.binding.UserColours[] getUserColours() \r
\r
/**\r
* Method getUserColoursCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getUserColoursCount() {\r
+ public int getUserColoursCount()\r
+ {\r
return _userColoursList.size();\r
- }\r
- //-- int getUserColoursCount()\r
+ } //-- int getUserColoursCount() \r
\r
/**\r
* Method getViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Viewport\r
*/\r
public jalview.binding.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- }\r
- //-- jalview.binding.Viewport getViewport(int)\r
+ } //-- jalview.binding.Viewport getViewport(int) \r
\r
/**\r
* Method getViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport[] getViewport() {\r
+ public jalview.binding.Viewport[] getViewport()\r
+ {\r
int size = _viewportList.size();\r
jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Viewport[] getViewport()\r
+ } //-- jalview.binding.Viewport[] getViewport() \r
\r
/**\r
* Method getViewportCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getViewportCount() {\r
+ public int getViewportCount()\r
+ {\r
return _viewportList.size();\r
- }\r
- //-- int getViewportCount()\r
+ } //-- int getViewportCount() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllJGroup\r
- *\r
+ * \r
*/\r
- public void removeAllJGroup() {\r
+ public void removeAllJGroup()\r
+ {\r
_JGroupList.removeAllElements();\r
- }\r
- //-- void removeAllJGroup()\r
+ } //-- void removeAllJGroup() \r
\r
/**\r
* Method removeAllJSeq\r
- *\r
+ * \r
*/\r
- public void removeAllJSeq() {\r
+ public void removeAllJSeq()\r
+ {\r
_JSeqList.removeAllElements();\r
- }\r
- //-- void removeAllJSeq()\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
*/\r
- public void removeAllUserColours() {\r
+ public void removeAllUserColours()\r
+ {\r
_userColoursList.removeAllElements();\r
- }\r
- //-- void removeAllUserColours()\r
+ } //-- void removeAllUserColours() \r
\r
/**\r
* Method removeAllViewport\r
- *\r
+ * \r
*/\r
- public void removeAllViewport() {\r
+ public void removeAllViewport()\r
+ {\r
_viewportList.removeAllElements();\r
- }\r
- //-- void removeAllViewport()\r
+ } //-- void removeAllViewport() \r
\r
/**\r
* Method removeJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup removeJGroup(int index) {\r
+ public jalview.binding.JGroup removeJGroup(int index)\r
+ {\r
java.lang.Object obj = _JGroupList.elementAt(index);\r
_JGroupList.removeElementAt(index);\r
-\r
return (jalview.binding.JGroup) obj;\r
- }\r
- //-- jalview.binding.JGroup removeJGroup(int)\r
+ } //-- jalview.binding.JGroup removeJGroup(int) \r
\r
/**\r
* Method removeJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq removeJSeq(int index) {\r
+ public jalview.binding.JSeq removeJSeq(int index)\r
+ {\r
java.lang.Object obj = _JSeqList.elementAt(index);\r
_JSeqList.removeElementAt(index);\r
-\r
return (jalview.binding.JSeq) obj;\r
- }\r
- //-- jalview.binding.JSeq removeJSeq(int)\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
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours removeUserColours(int index) {\r
+ public jalview.binding.UserColours removeUserColours(int index)\r
+ {\r
java.lang.Object obj = _userColoursList.elementAt(index);\r
_userColoursList.removeElementAt(index);\r
-\r
return (jalview.binding.UserColours) obj;\r
- }\r
- //-- jalview.binding.UserColours removeUserColours(int)\r
+ } //-- jalview.binding.UserColours removeUserColours(int) \r
\r
/**\r
* Method removeViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport removeViewport(int index) {\r
+ public jalview.binding.Viewport removeViewport(int index)\r
+ {\r
java.lang.Object obj = _viewportList.elementAt(index);\r
_viewportList.removeElementAt(index);\r
-\r
return (jalview.binding.Viewport) obj;\r
- }\r
- //-- jalview.binding.Viewport removeViewport(int)\r
+ } //-- jalview.binding.Viewport removeViewport(int) \r
\r
/**\r
* Method setJGroup\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_JGroupList.setElementAt(vJGroup, index);\r
- }\r
- //-- void setJGroup(int, jalview.binding.JGroup)\r
+ } //-- void setJGroup(int, jalview.binding.JGroup) \r
\r
/**\r
* Method setJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param JGroupArray\r
*/\r
- public void setJGroup(jalview.binding.JGroup[] JGroupArray) {\r
+ public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
+ {\r
//-- copy array\r
_JGroupList.removeAllElements();\r
-\r
for (int i = 0; i < JGroupArray.length; i++) {\r
_JGroupList.addElement(JGroupArray[i]);\r
}\r
- }\r
- //-- void setJGroup(jalview.binding.JGroup)\r
+ } //-- void setJGroup(jalview.binding.JGroup) \r
\r
/**\r
* Method setJSeq\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_JSeqList.setElementAt(vJSeq, index);\r
- }\r
- //-- void setJSeq(int, jalview.binding.JSeq)\r
+ } //-- void setJSeq(int, jalview.binding.JSeq) \r
\r
/**\r
* Method setJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param JSeqArray\r
*/\r
- public void setJSeq(jalview.binding.JSeq[] JSeqArray) {\r
+ public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
+ {\r
//-- copy array\r
_JSeqList.removeAllElements();\r
-\r
for (int i = 0; i < JSeqArray.length; i++) {\r
_JSeqList.addElement(JSeqArray[i]);\r
}\r
- }\r
- //-- void setJSeq(jalview.binding.JSeq)\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
+ * \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
+ 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
-\r
_userColoursList.setElementAt(vUserColours, index);\r
- }\r
- //-- void setUserColours(int, jalview.binding.UserColours)\r
+ } //-- void setUserColours(int, jalview.binding.UserColours) \r
\r
/**\r
* Method setUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param userColoursArray\r
*/\r
- public void setUserColours(jalview.binding.UserColours[] userColoursArray) {\r
+ public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
+ {\r
//-- copy array\r
_userColoursList.removeAllElements();\r
-\r
for (int i = 0; i < userColoursArray.length; i++) {\r
_userColoursList.addElement(userColoursArray[i]);\r
}\r
- }\r
- //-- void setUserColours(jalview.binding.UserColours)\r
+ } //-- void setUserColours(jalview.binding.UserColours) \r
\r
/**\r
* Method setViewport\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_viewportList.setElementAt(vViewport, index);\r
- }\r
- //-- void setViewport(int, jalview.binding.Viewport)\r
+ } //-- void setViewport(int, jalview.binding.Viewport) \r
\r
/**\r
* Method setViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param viewportArray\r
*/\r
- public void setViewport(jalview.binding.Viewport[] viewportArray) {\r
+ public void setViewport(jalview.binding.Viewport[] viewportArray)\r
+ {\r
//-- copy array\r
_viewportList.removeAllElements();\r
-\r
for (int i = 0; i < viewportArray.length; i++) {\r
_viewportList.addElement(viewportArray[i]);\r
}\r
- }\r
- //-- void setViewport(jalview.binding.Viewport)\r
+ } //-- void setViewport(jalview.binding.Viewport) \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
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 JalviewModelSequence2.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2 implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _items;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public JalviewModelSequence2() {\r
super();\r
_items = new Vector();\r
- }\r
- //-- jalview.binding.JalviewModelSequence2()\r
- //-----------/\r
+ } //-- jalview.binding.JalviewModelSequence2()\r
+\r
\r
- public void addJalviewModelSequence2Item(\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addJalviewModelSequence2Item\r
+ * \r
+ * \r
+ * \r
+ * @param vJalviewModelSequence2Item\r
+ */\r
+ public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_items.addElement(vJalviewModelSequence2Item);\r
- }\r
- //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
+ } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
\r
/**\r
* Method addJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
- public void addJalviewModelSequence2Item(int index,\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_items.insertElementAt(vJalviewModelSequence2Item, index);\r
- }\r
- //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
+ } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
\r
/**\r
* Method enumerateJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJalviewModelSequence2Item() {\r
+ public java.util.Enumeration enumerateJalviewModelSequence2Item()\r
+ {\r
return _items.elements();\r
- }\r
- //-- java.util.Enumeration enumerateJalviewModelSequence2Item()\r
+ } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() \r
\r
/**\r
* Method getJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(\r
- int index) throws java.lang.IndexOutOfBoundsException {\r
+ public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _items.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
- }\r
- //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)\r
+ } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) \r
\r
/**\r
* Method getJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() {\r
+ public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
+ {\r
int size = _items.size();\r
jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
+ } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() \r
\r
/**\r
* Method getJalviewModelSequence2ItemCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getJalviewModelSequence2ItemCount() {\r
+ public int getJalviewModelSequence2ItemCount()\r
+ {\r
return _items.size();\r
- }\r
- //-- int getJalviewModelSequence2ItemCount()\r
+ } //-- int getJalviewModelSequence2ItemCount() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllJalviewModelSequence2Item\r
- *\r
+ * \r
*/\r
- public void removeAllJalviewModelSequence2Item() {\r
+ public void removeAllJalviewModelSequence2Item()\r
+ {\r
_items.removeAllElements();\r
- }\r
- //-- void removeAllJalviewModelSequence2Item()\r
+ } //-- void removeAllJalviewModelSequence2Item() \r
\r
/**\r
* Method removeJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(\r
- int index) {\r
+ public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index)\r
+ {\r
java.lang.Object obj = _items.elementAt(index);\r
_items.removeElementAt(index);\r
-\r
return (jalview.binding.JalviewModelSequence2Item) obj;\r
- }\r
- //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int)\r
+ } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) \r
\r
/**\r
* Method setJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
- public void setJalviewModelSequence2Item(int index,\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _items.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_items.setElementAt(vJalviewModelSequence2Item, index);\r
- }\r
- //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
+ } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
\r
/**\r
* Method setJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param jalviewModelSequence2ItemArray\r
*/\r
- public void setJalviewModelSequence2Item(\r
- jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) {\r
+ public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)\r
+ {\r
//-- copy array\r
_items.removeAllElements();\r
-\r
for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {\r
_items.addElement(jalviewModelSequence2ItemArray[i]);\r
}\r
- }\r
- //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
+ } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \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
- return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.binding;\r
\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-import java.io.Serializable;\r
\r
+import java.io.Serializable;\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class JalviewModelSequence2Item.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2Item implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _userColourSchemeList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public JalviewModelSequence2Item() {\r
super();\r
_userColourSchemeList = new Vector();\r
- }\r
- //-- jalview.binding.JalviewModelSequence2Item()\r
- //-----------/\r
+ } //-- jalview.binding.JalviewModelSequence2Item()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
- public void addUserColourScheme(\r
- jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ /**\r
+ * Method addUserColourScheme\r
+ * \r
+ * \r
+ * \r
+ * @param vUserColourScheme\r
+ */\r
+ public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColourSchemeList.addElement(vUserColourScheme);\r
- }\r
- //-- void addUserColourScheme(jalview.binding.UserColourScheme)\r
+ } //-- void addUserColourScheme(jalview.binding.UserColourScheme) \r
\r
/**\r
* Method addUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vUserColourScheme\r
*/\r
- public void addUserColourScheme(int index,\r
- jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColourSchemeList.insertElementAt(vUserColourScheme, index);\r
- }\r
- //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)\r
+ } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) \r
\r
/**\r
* Method enumerateUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateUserColourScheme() {\r
+ public java.util.Enumeration enumerateUserColourScheme()\r
+ {\r
return _userColourSchemeList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateUserColourScheme()\r
+ } //-- java.util.Enumeration enumerateUserColourScheme() \r
\r
/**\r
* Method getUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColourScheme\r
*/\r
public jalview.binding.UserColourScheme getUserColourScheme(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColourSchemeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
- }\r
- //-- jalview.binding.UserColourScheme getUserColourScheme(int)\r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme(int) \r
\r
/**\r
* Method getUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return UserColourScheme\r
*/\r
- public jalview.binding.UserColourScheme[] getUserColourScheme() {\r
+ public jalview.binding.UserColourScheme[] getUserColourScheme()\r
+ {\r
int size = _userColourSchemeList.size();\r
jalview.binding.UserColourScheme[] mArray = new jalview.binding.UserColourScheme[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.UserColourScheme[] getUserColourScheme()\r
+ } //-- jalview.binding.UserColourScheme[] getUserColourScheme() \r
\r
/**\r
* Method getUserColourSchemeCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getUserColourSchemeCount() {\r
+ public int getUserColourSchemeCount()\r
+ {\r
return _userColourSchemeList.size();\r
- }\r
- //-- int getUserColourSchemeCount()\r
+ } //-- int getUserColourSchemeCount() \r
\r
/**\r
* Method removeAllUserColourScheme\r
- *\r
+ * \r
*/\r
- public void removeAllUserColourScheme() {\r
+ public void removeAllUserColourScheme()\r
+ {\r
_userColourSchemeList.removeAllElements();\r
- }\r
- //-- void removeAllUserColourScheme()\r
+ } //-- void removeAllUserColourScheme() \r
\r
/**\r
* Method removeUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColourScheme\r
*/\r
- public jalview.binding.UserColourScheme removeUserColourScheme(int index) {\r
+ public jalview.binding.UserColourScheme removeUserColourScheme(int index)\r
+ {\r
java.lang.Object obj = _userColourSchemeList.elementAt(index);\r
_userColourSchemeList.removeElementAt(index);\r
-\r
return (jalview.binding.UserColourScheme) obj;\r
- }\r
- //-- jalview.binding.UserColourScheme removeUserColourScheme(int)\r
+ } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) \r
\r
/**\r
* Method setUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vUserColourScheme\r
*/\r
- public void setUserColourScheme(int index,\r
- jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColourSchemeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_userColourSchemeList.setElementAt(vUserColourScheme, index);\r
- }\r
- //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)\r
+ } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) \r
\r
/**\r
* Method setUserColourScheme\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param userColourSchemeArray\r
*/\r
- public void setUserColourScheme(\r
- jalview.binding.UserColourScheme[] userColourSchemeArray) {\r
+ public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)\r
+ {\r
//-- copy array\r
_userColourSchemeList.removeAllElements();\r
-\r
for (int i = 0; i < userColourSchemeArray.length; i++) {\r
_userColourSchemeList.addElement(userColourSchemeArray[i]);\r
}\r
- }\r
- //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _colourList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public JalviewUserColours() {\r
super();\r
_colourList = new Vector();\r
- }\r
- //-- jalview.binding.JalviewUserColours()\r
- //-----------/\r
+ } //-- jalview.binding.JalviewUserColours()\r
+\r
\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addColour\r
+ * \r
+ * \r
+ * \r
+ * @param vColour\r
+ */\r
public void addColour(jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_colourList.addElement(vColour);\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
public void addColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_colourList.insertElementAt(vColour, index);\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
+ public java.util.Enumeration enumerateColour()\r
+ {\r
return _colourList.elements();\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
public jalview.binding.Colour getColour(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Colour) _colourList.elementAt(index);\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
+ 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
mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
}\r
-\r
return mArray;\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
+ public int getColourCount()\r
+ {\r
return _colourList.size();\r
- }\r
- //-- int getColourCount()\r
+ } //-- int getColourCount() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void removeAllColour()\r
+ {\r
_colourList.removeAllElements();\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
- public jalview.binding.Colour removeColour(int index) {\r
+ public jalview.binding.Colour removeColour(int index)\r
+ {\r
java.lang.Object obj = _colourList.elementAt(index);\r
_colourList.removeElementAt(index);\r
-\r
return (jalview.binding.Colour) obj;\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
public void setColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_colourList.setElementAt(vColour, index);\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
+ 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
_colourList.addElement(colourArray[i]);\r
}\r
- }\r
- //-- void setColour(jalview.binding.Colour)\r
+ } //-- void setColour(jalview.binding.Colour) \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
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.binding;\r
\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-import java.io.Serializable;\r
\r
+import java.io.Serializable;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class JalviewUserColoursItem.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class JalviewUserColoursItem implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.Colour _colour;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public JalviewUserColoursItem() {\r
super();\r
- }\r
- //-- jalview.binding.JalviewUserColoursItem()\r
- //-----------/\r
+ } //-- jalview.binding.JalviewUserColoursItem()\r
\r
- public jalview.binding.Colour getColour() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return Colour\r
+ * @return the value of field 'colour'.\r
+ */\r
+ public jalview.binding.Colour getColour()\r
+ {\r
return this._colour;\r
- }\r
- //-- jalview.binding.Colour getColour()\r
+ } //-- jalview.binding.Colour getColour() \r
\r
/**\r
* Sets the value of field 'colour'.\r
- *\r
+ * \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(jalview.binding.Colour colour) {\r
+ public void setColour(jalview.binding.Colour colour)\r
+ {\r
this._colour = colour;\r
- }\r
- //-- void setColour(jalview.binding.Colour)\r
+ } //-- void setColour(jalview.binding.Colour) \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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 Residue.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class Residue implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_RGB;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public Residue() {\r
super();\r
- }\r
- //-- jalview.binding.Residue()\r
- //-----------/\r
+ } //-- jalview.binding.Residue()\r
\r
- public void deleteRGB() {\r
- this._has_RGB = false;\r
- }\r
- //-- void deleteRGB()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteRGB\r
+ * \r
+ */\r
+ public void deleteRGB()\r
+ {\r
+ this._has_RGB= false;\r
+ } //-- void deleteRGB() \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
+ public java.lang.String getName()\r
+ {\r
return this._name;\r
- }\r
- //-- java.lang.String getName()\r
+ } //-- java.lang.String getName() \r
\r
/**\r
* Returns the value of field 'RGB'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'RGB'.\r
*/\r
- public int getRGB() {\r
+ public int getRGB()\r
+ {\r
return this._RGB;\r
- }\r
- //-- int getRGB()\r
+ } //-- int getRGB() \r
\r
/**\r
* Method hasRGB\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasRGB() {\r
+ public boolean hasRGB()\r
+ {\r
return this._has_RGB;\r
- }\r
- //-- boolean hasRGB()\r
+ } //-- boolean hasRGB() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void setName(java.lang.String name)\r
+ {\r
this._name = name;\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(int RGB) {\r
+ public void setRGB(int RGB)\r
+ {\r
this._RGB = RGB;\r
this._has_RGB = true;\r
- }\r
- //-- void setRGB(int)\r
+ } //-- void setRGB(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
- return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 Sequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends SequenceType implements java.io.Serializable {\r
- //----------------/\r
- //- Constructors -/\r
+public class Sequence extends SequenceType \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
+\r
public Sequence() {\r
super();\r
- }\r
- //-- jalview.binding.Sequence()\r
- //-----------/\r
+ } //-- jalview.binding.Sequence()\r
\r
- public boolean isValid() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
- return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //- Class/Member Variables -/\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
+\r
public SequenceSet() {\r
super();\r
_sequenceList = new Vector();\r
_annotationList = new Vector();\r
- }\r
- //-- jalview.binding.SequenceSet()\r
- //-----------/\r
+ } //-- jalview.binding.SequenceSet()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
+ /**\r
+ * Method addAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param vAnnotation\r
+ */\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_annotationList.addElement(vAnnotation);\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
public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_annotationList.insertElementAt(vAnnotation, index);\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceList.addElement(vSequence);\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
public void addSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceList.insertElementAt(vSequence, index);\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
- this._has_aligned = false;\r
- }\r
- //-- void deleteAligned()\r
+ public void deleteAligned()\r
+ {\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
+ public java.util.Enumeration enumerateAnnotation()\r
+ {\r
return _annotationList.elements();\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
+ public java.util.Enumeration enumerateSequence()\r
+ {\r
return _sequenceList.elements();\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
+ public boolean getAligned()\r
+ {\r
return this._aligned;\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
public jalview.binding.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\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
+ 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
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
-\r
return mArray;\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
+ public int getAnnotationCount()\r
+ {\r
return _annotationList.size();\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
+ public java.lang.String getGapChar()\r
+ {\r
return this._gapChar;\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
public jalview.binding.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\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
+ 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
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
-\r
return mArray;\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
+ public int getSequenceCount()\r
+ {\r
return _sequenceList.size();\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
+ public boolean hasAligned()\r
+ {\r
return this._has_aligned;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
+ public void removeAllAnnotation()\r
+ {\r
_annotationList.removeAllElements();\r
- }\r
- //-- void removeAllAnnotation()\r
+ } //-- void removeAllAnnotation() \r
\r
/**\r
* Method removeAllSequence\r
- *\r
+ * \r
*/\r
- public void removeAllSequence() {\r
+ public void removeAllSequence()\r
+ {\r
_sequenceList.removeAllElements();\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
- public jalview.binding.Annotation removeAnnotation(int index) {\r
+ public jalview.binding.Annotation removeAnnotation(int index)\r
+ {\r
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
-\r
return (jalview.binding.Annotation) obj;\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
- public jalview.binding.Sequence removeSequence(int index) {\r
+ public jalview.binding.Sequence removeSequence(int index)\r
+ {\r
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
-\r
return (jalview.binding.Sequence) obj;\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
+ public void setAligned(boolean aligned)\r
+ {\r
this._aligned = aligned;\r
this._has_aligned = true;\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
public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_annotationList.setElementAt(vAnnotation, index);\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
+ 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
_annotationList.addElement(annotationArray[i]);\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
+ public void setGapChar(java.lang.String gapChar)\r
+ {\r
this._gapChar = gapChar;\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
public void setSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_sequenceList.setElementAt(vSequence, index);\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
+ 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
_sequenceList.addElement(sequenceArray[i]);\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
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 SequenceType.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class SequenceType implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _name;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public SequenceType() {\r
super();\r
- }\r
- //-- jalview.binding.SequenceType()\r
- //-----------/\r
+ } //-- jalview.binding.SequenceType()\r
+\r
\r
- public java.lang.String getId() {\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
- }\r
- //-- java.lang.String getId()\r
+ } //-- java.lang.String getId() \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
+ public java.lang.String getName()\r
+ {\r
return this._name;\r
- }\r
- //-- java.lang.String getName()\r
+ } //-- java.lang.String getName() \r
\r
/**\r
* Returns the value of field 'sequence'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'sequence'.\r
*/\r
- public java.lang.String getSequence() {\r
+ public java.lang.String getSequence()\r
+ {\r
return this._sequence;\r
- }\r
- //-- java.lang.String getSequence()\r
+ } //-- java.lang.String getSequence() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'id'.\r
- *\r
+ * \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id) {\r
+ public void setId(java.lang.String id)\r
+ {\r
this._id = id;\r
- }\r
- //-- void setId(java.lang.String)\r
+ } //-- void setId(java.lang.String) \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
+ public void setName(java.lang.String name)\r
+ {\r
this._name = name;\r
- }\r
- //-- void setName(java.lang.String)\r
+ } //-- void setName(java.lang.String) \r
\r
/**\r
* Sets the value of field 'sequence'.\r
- *\r
+ * \r
* @param sequence the value of field 'sequence'.\r
*/\r
- public void setSequence(java.lang.String sequence) {\r
+ public void setSequence(java.lang.String sequence)\r
+ {\r
this._sequence = sequence;\r
- }\r
- //-- void setSequence(java.lang.String)\r
+ } //-- void setSequence(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
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
*/\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
+ } //-- void validate() \r
+\r
}\r
--- /dev/null
+/*\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
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import 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
+ * @version $Revision$ $Date$\r
+ */\r
+public class Tree implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\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
+ /**\r
+ * Field _fitToWindow\r
+ */\r
+ private boolean _fitToWindow;\r
+\r
+ /**\r
+ * keeps track of state for field: _fitToWindow\r
+ */\r
+ private boolean _has_fitToWindow;\r
+\r
+ /**\r
+ * Field _showDistances\r
+ */\r
+ private boolean _showDistances;\r
+\r
+ /**\r
+ * keeps track of state for field: _showDistances\r
+ */\r
+ private boolean _has_showDistances;\r
+\r
+ /**\r
+ * Field _showBootstrap\r
+ */\r
+ private boolean _showBootstrap;\r
+\r
+ /**\r
+ * keeps track of state for field: _showBootstrap\r
+ */\r
+ private boolean _has_showBootstrap;\r
+\r
+ /**\r
+ * Field _markUnlinked\r
+ */\r
+ private boolean _markUnlinked;\r
+\r
+ /**\r
+ * keeps track of state for field: _markUnlinked\r
+ */\r
+ private boolean _has_markUnlinked;\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 _threshold\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\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 _newick\r
+ */\r
+ private java.lang.String _newick;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Tree() {\r
+ super();\r
+ } //-- jalview.binding.Tree()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteCurrentTree\r
+ * \r
+ */\r
+ public void deleteCurrentTree()\r
+ {\r
+ this._has_currentTree= false;\r
+ } //-- void deleteCurrentTree() \r
+\r
+ /**\r
+ * Method deleteFitToWindow\r
+ * \r
+ */\r
+ public void deleteFitToWindow()\r
+ {\r
+ this._has_fitToWindow= false;\r
+ } //-- void deleteFitToWindow() \r
+\r
+ /**\r
+ * Method deleteFontSize\r
+ * \r
+ */\r
+ public void deleteFontSize()\r
+ {\r
+ this._has_fontSize= false;\r
+ } //-- void deleteFontSize() \r
+\r
+ /**\r
+ * Method deleteHeight\r
+ * \r
+ */\r
+ public void deleteHeight()\r
+ {\r
+ this._has_height= false;\r
+ } //-- void deleteHeight() \r
+\r
+ /**\r
+ * Method deleteMarkUnlinked\r
+ * \r
+ */\r
+ public void deleteMarkUnlinked()\r
+ {\r
+ this._has_markUnlinked= false;\r
+ } //-- void deleteMarkUnlinked() \r
+\r
+ /**\r
+ * Method deleteShowBootstrap\r
+ * \r
+ */\r
+ public void deleteShowBootstrap()\r
+ {\r
+ this._has_showBootstrap= false;\r
+ } //-- void deleteShowBootstrap() \r
+\r
+ /**\r
+ * Method deleteShowDistances\r
+ * \r
+ */\r
+ public void deleteShowDistances()\r
+ {\r
+ this._has_showDistances= false;\r
+ } //-- void deleteShowDistances() \r
+\r
+ /**\r
+ * Method deleteThreshold\r
+ * \r
+ */\r
+ public void deleteThreshold()\r
+ {\r
+ this._has_threshold= false;\r
+ } //-- void deleteThreshold() \r
+\r
+ /**\r
+ * Method deleteWidth\r
+ * \r
+ */\r
+ public void deleteWidth()\r
+ {\r
+ this._has_width= false;\r
+ } //-- void deleteWidth() \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 'currentTree'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'currentTree'.\r
+ */\r
+ public boolean getCurrentTree()\r
+ {\r
+ return this._currentTree;\r
+ } //-- boolean getCurrentTree() \r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'fitToWindow'.\r
+ */\r
+ public boolean getFitToWindow()\r
+ {\r
+ return this._fitToWindow;\r
+ } //-- boolean getFitToWindow() \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 '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 'markUnlinked'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'markUnlinked'.\r
+ */\r
+ public boolean getMarkUnlinked()\r
+ {\r
+ return this._markUnlinked;\r
+ } //-- boolean getMarkUnlinked() \r
+\r
+ /**\r
+ * Returns the value of field 'newick'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'newick'.\r
+ */\r
+ public java.lang.String getNewick()\r
+ {\r
+ return this._newick;\r
+ } //-- java.lang.String getNewick() \r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showBootstrap'.\r
+ */\r
+ public boolean getShowBootstrap()\r
+ {\r
+ return this._showBootstrap;\r
+ } //-- boolean getShowBootstrap() \r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showDistances'.\r
+ */\r
+ public boolean getShowDistances()\r
+ {\r
+ return this._showDistances;\r
+ } //-- boolean getShowDistances() \r
+\r
+ /**\r
+ * Returns the value of field 'threshold'.\r
+ * \r
+ * @return float\r
+ * @return the value of field 'threshold'.\r
+ */\r
+ public float getThreshold()\r
+ {\r
+ return this._threshold;\r
+ } //-- float getThreshold() \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 '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 hasCurrentTree\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasCurrentTree()\r
+ {\r
+ return this._has_currentTree;\r
+ } //-- boolean hasCurrentTree() \r
+\r
+ /**\r
+ * Method hasFitToWindow\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasFitToWindow()\r
+ {\r
+ return this._has_fitToWindow;\r
+ } //-- boolean hasFitToWindow() \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 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 hasMarkUnlinked\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasMarkUnlinked()\r
+ {\r
+ return this._has_markUnlinked;\r
+ } //-- boolean hasMarkUnlinked() \r
+\r
+ /**\r
+ * Method hasShowBootstrap\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowBootstrap()\r
+ {\r
+ return this._has_showBootstrap;\r
+ } //-- boolean hasShowBootstrap() \r
+\r
+ /**\r
+ * Method hasShowDistances\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowDistances()\r
+ {\r
+ return this._has_showDistances;\r
+ } //-- boolean hasShowDistances() \r
+\r
+ /**\r
+ * Method hasThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasThreshold()\r
+ {\r
+ return this._has_threshold;\r
+ } //-- boolean hasThreshold() \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 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 'currentTree'.\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
+ } //-- void setCurrentTree(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'fitToWindow'.\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
+ } //-- void setFitToWindow(boolean) \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 '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 'markUnlinked'.\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
+ } //-- void setMarkUnlinked(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'newick'.\r
+ * \r
+ * @param newick the value of field 'newick'.\r
+ */\r
+ public void setNewick(java.lang.String newick)\r
+ {\r
+ this._newick = newick;\r
+ } //-- void setNewick(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'showBootstrap'.\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
+ } //-- void setShowBootstrap(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showDistances'.\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
+ } //-- void setShowDistances(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'threshold'.\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
+ } //-- void setThreshold(float) \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 '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.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 UserColour.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class UserColour implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.UserColourScheme _userColourScheme;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public UserColour() {\r
super();\r
- }\r
- //-- jalview.binding.UserColour()\r
- //-----------/\r
+ } //-- jalview.binding.UserColour()\r
\r
- public void deleteId() {\r
- this._has_id = false;\r
- }\r
- //-- void deleteId()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteId\r
+ * \r
+ */\r
+ public void deleteId()\r
+ {\r
+ this._has_id= false;\r
+ } //-- void deleteId() \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
+ public int getId()\r
+ {\r
return this._id;\r
- }\r
- //-- int getId()\r
+ } //-- int getId() \r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
- *\r
+ * \r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
- public jalview.binding.UserColourScheme getUserColourScheme() {\r
+ public jalview.binding.UserColourScheme getUserColourScheme()\r
+ {\r
return this._userColourScheme;\r
- }\r
- //-- jalview.binding.UserColourScheme getUserColourScheme()\r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
\r
/**\r
* Method hasId\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasId() {\r
+ public boolean hasId()\r
+ {\r
return this._has_id;\r
- }\r
- //-- boolean hasId()\r
+ } //-- boolean hasId() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \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
+ public void setId(int id)\r
+ {\r
this._id = id;\r
this._has_id = true;\r
- }\r
- //-- void setId(int)\r
+ } //-- void setId(int) \r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
- *\r
+ * \r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
- public void setUserColourScheme(\r
- jalview.binding.UserColourScheme userColourScheme) {\r
+ public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
+ {\r
this._userColourScheme = userColourScheme;\r
- }\r
- //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \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
- return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 UserColourScheme.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class UserColourScheme extends JalviewUserColours\r
- implements java.io.Serializable {\r
- //----------------/\r
- //- Constructors -/\r
+public class UserColourScheme extends JalviewUserColours \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
+\r
public UserColourScheme() {\r
super();\r
- }\r
- //-- jalview.binding.UserColourScheme()\r
- //-----------/\r
+ } //-- jalview.binding.UserColourScheme()\r
\r
- public boolean isValid() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
- return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 UserColours.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class UserColours implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.UserColourScheme _userColourScheme;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public UserColours() {\r
super();\r
- }\r
- //-- jalview.binding.UserColours()\r
- //-----------/\r
+ } //-- jalview.binding.UserColours()\r
\r
- public java.lang.String getId() {\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
- }\r
- //-- java.lang.String getId()\r
+ } //-- java.lang.String getId() \r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
- *\r
+ * \r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
- public jalview.binding.UserColourScheme getUserColourScheme() {\r
+ public jalview.binding.UserColourScheme getUserColourScheme()\r
+ {\r
return this._userColourScheme;\r
- }\r
- //-- jalview.binding.UserColourScheme getUserColourScheme()\r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'id'.\r
- *\r
+ * \r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id) {\r
+ public void setId(java.lang.String id)\r
+ {\r
this._id = id;\r
- }\r
- //-- void setId(java.lang.String)\r
+ } //-- void setId(java.lang.String) \r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
- *\r
+ * \r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
- public void setUserColourScheme(\r
- jalview.binding.UserColourScheme userColourScheme) {\r
+ public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
+ {\r
this._userColourScheme = userColourScheme;\r
- }\r
- //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \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
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
*/\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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 VAMSAS.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class VAMSAS implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _sequenceSetList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public VAMSAS() {\r
super();\r
_alignmentList = new Vector();\r
_treeList = new Vector();\r
_sequenceSetList = new Vector();\r
- }\r
- //-- jalview.binding.VAMSAS()\r
- //-----------/\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_alignmentList.addElement(vAlignment);\r
- }\r
- //-- void addAlignment(jalview.binding.Alignment)\r
+ } //-- void addAlignment(jalview.binding.Alignment) \r
\r
/**\r
* Method addAlignment\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_alignmentList.insertElementAt(vAlignment, index);\r
- }\r
- //-- void addAlignment(int, jalview.binding.Alignment)\r
+ } //-- void addAlignment(int, jalview.binding.Alignment) \r
\r
/**\r
* Method addSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vSequenceSet\r
*/\r
public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceSetList.addElement(vSequenceSet);\r
- }\r
- //-- void addSequenceSet(jalview.binding.SequenceSet)\r
+ } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
\r
/**\r
* Method addSequenceSet\r
- *\r
- *\r
- *\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
+ public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceSetList.insertElementAt(vSequenceSet, index);\r
- }\r
- //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
+ } //-- void addSequenceSet(int, jalview.binding.SequenceSet) \r
\r
/**\r
* Method addTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vTree\r
*/\r
public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_treeList.addElement(vTree);\r
- }\r
- //-- void addTree(java.lang.String)\r
+ } //-- void addTree(java.lang.String) \r
\r
/**\r
* Method addTree\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_treeList.insertElementAt(vTree, index);\r
- }\r
- //-- void addTree(int, java.lang.String)\r
+ } //-- void addTree(int, java.lang.String) \r
\r
/**\r
* Method enumerateAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAlignment() {\r
+ public java.util.Enumeration enumerateAlignment()\r
+ {\r
return _alignmentList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateAlignment()\r
+ } //-- java.util.Enumeration enumerateAlignment() \r
\r
/**\r
* Method enumerateSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSequenceSet() {\r
+ public java.util.Enumeration enumerateSequenceSet()\r
+ {\r
return _sequenceSetList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateSequenceSet()\r
+ } //-- java.util.Enumeration enumerateSequenceSet() \r
\r
/**\r
* Method enumerateTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateTree() {\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
return _treeList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateTree()\r
+ } //-- java.util.Enumeration enumerateTree() \r
\r
/**\r
* Method getAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Alignment\r
*/\r
public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- }\r
- //-- jalview.binding.Alignment getAlignment(int)\r
+ } //-- jalview.binding.Alignment getAlignment(int) \r
\r
/**\r
* Method getAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment[] getAlignment() {\r
+ public jalview.binding.Alignment[] getAlignment()\r
+ {\r
int size = _alignmentList.size();\r
jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Alignment[] getAlignment()\r
+ } //-- jalview.binding.Alignment[] getAlignment() \r
\r
/**\r
* Method getAlignmentCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getAlignmentCount() {\r
+ public int getAlignmentCount()\r
+ {\r
return _alignmentList.size();\r
- }\r
- //-- int getAlignmentCount()\r
+ } //-- int getAlignmentCount() \r
\r
/**\r
* Method getSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return SequenceSet\r
*/\r
public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- //-- jalview.binding.SequenceSet getSequenceSet(int)\r
+ } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
\r
/**\r
* Method getSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet[] getSequenceSet() {\r
+ public jalview.binding.SequenceSet[] getSequenceSet()\r
+ {\r
int size = _sequenceSetList.size();\r
jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.SequenceSet[] getSequenceSet()\r
+ } //-- jalview.binding.SequenceSet[] getSequenceSet() \r
\r
/**\r
* Method getSequenceSetCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getSequenceSetCount() {\r
+ public int getSequenceSetCount()\r
+ {\r
return _sequenceSetList.size();\r
- }\r
- //-- int getSequenceSetCount()\r
+ } //-- int getSequenceSetCount() \r
\r
/**\r
* Method getTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return String\r
*/\r
public java.lang.String getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
- }\r
- //-- java.lang.String getTree(int)\r
+ \r
+ return (String)_treeList.elementAt(index);\r
+ } //-- java.lang.String getTree(int) \r
\r
/**\r
* Method getTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return String\r
*/\r
- public java.lang.String[] getTree() {\r
+ public java.lang.String[] getTree()\r
+ {\r
int size = _treeList.size();\r
java.lang.String[] mArray = new java.lang.String[size];\r
-\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = (String) _treeList.elementAt(index);\r
+ mArray[index] = (String)_treeList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- java.lang.String[] getTree()\r
+ } //-- java.lang.String[] getTree() \r
\r
/**\r
* Method getTreeCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getTreeCount() {\r
+ public int getTreeCount()\r
+ {\r
return _treeList.size();\r
- }\r
- //-- int getTreeCount()\r
+ } //-- int getTreeCount() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment removeAlignment(int index) {\r
+ public jalview.binding.Alignment removeAlignment(int index)\r
+ {\r
java.lang.Object obj = _alignmentList.elementAt(index);\r
_alignmentList.removeElementAt(index);\r
-\r
return (jalview.binding.Alignment) obj;\r
- }\r
- //-- jalview.binding.Alignment removeAlignment(int)\r
+ } //-- jalview.binding.Alignment removeAlignment(int) \r
\r
/**\r
* Method removeAllAlignment\r
- *\r
+ * \r
*/\r
- public void removeAllAlignment() {\r
+ public void removeAllAlignment()\r
+ {\r
_alignmentList.removeAllElements();\r
- }\r
- //-- void removeAllAlignment()\r
+ } //-- void removeAllAlignment() \r
\r
/**\r
* Method removeAllSequenceSet\r
- *\r
+ * \r
*/\r
- public void removeAllSequenceSet() {\r
+ public void removeAllSequenceSet()\r
+ {\r
_sequenceSetList.removeAllElements();\r
- }\r
- //-- void removeAllSequenceSet()\r
+ } //-- void removeAllSequenceSet() \r
\r
/**\r
* Method removeAllTree\r
- *\r
+ * \r
*/\r
- public void removeAllTree() {\r
+ public void removeAllTree()\r
+ {\r
_treeList.removeAllElements();\r
- }\r
- //-- void removeAllTree()\r
+ } //-- void removeAllTree() \r
\r
/**\r
* Method removeSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet removeSequenceSet(int index) {\r
+ public jalview.binding.SequenceSet removeSequenceSet(int index)\r
+ {\r
java.lang.Object obj = _sequenceSetList.elementAt(index);\r
_sequenceSetList.removeElementAt(index);\r
-\r
return (jalview.binding.SequenceSet) obj;\r
- }\r
- //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
+ } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
\r
/**\r
* Method removeTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return String\r
*/\r
- public java.lang.String removeTree(int index) {\r
+ public java.lang.String removeTree(int index)\r
+ {\r
java.lang.Object obj = _treeList.elementAt(index);\r
_treeList.removeElementAt(index);\r
-\r
- return (String) obj;\r
- }\r
- //-- java.lang.String removeTree(int)\r
+ return (String)obj;\r
+ } //-- java.lang.String removeTree(int) \r
\r
/**\r
* Method setAlignment\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _alignmentList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_alignmentList.setElementAt(vAlignment, index);\r
- }\r
- //-- void setAlignment(int, jalview.binding.Alignment)\r
+ } //-- void setAlignment(int, jalview.binding.Alignment) \r
\r
/**\r
* Method setAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param alignmentArray\r
*/\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray) {\r
+ public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
+ {\r
//-- copy array\r
_alignmentList.removeAllElements();\r
-\r
for (int i = 0; i < alignmentArray.length; i++) {\r
_alignmentList.addElement(alignmentArray[i]);\r
}\r
- }\r
- //-- void setAlignment(jalview.binding.Alignment)\r
+ } //-- void setAlignment(jalview.binding.Alignment) \r
\r
/**\r
* Method setSequenceSet\r
- *\r
- *\r
- *\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
+ 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
-\r
_sequenceSetList.setElementAt(vSequenceSet, index);\r
- }\r
- //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
+ } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
\r
/**\r
* Method setSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param sequenceSetArray\r
*/\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) {\r
+ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
+ {\r
//-- copy array\r
_sequenceSetList.removeAllElements();\r
-\r
for (int i = 0; i < sequenceSetArray.length; i++) {\r
_sequenceSetList.addElement(sequenceSetArray[i]);\r
}\r
- }\r
- //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
\r
/**\r
* Method setTree\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _treeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_treeList.setElementAt(vTree, index);\r
- }\r
- //-- void setTree(int, java.lang.String)\r
+ } //-- void setTree(int, java.lang.String) \r
\r
/**\r
* Method setTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param treeArray\r
*/\r
- public void setTree(java.lang.String[] treeArray) {\r
+ public void setTree(java.lang.String[] treeArray)\r
+ {\r
//-- copy array\r
_treeList.removeAllElements();\r
-\r
for (int i = 0; i < treeArray.length; i++) {\r
_treeList.addElement(treeArray[i]);\r
}\r
- }\r
- //-- void setTree(java.lang.String)\r
+ } //-- void setTree(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
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\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
+ } //-- 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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-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
- //----------------/\r
- //- Constructors -/\r
+public class VamsasModel extends VAMSAS \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
+\r
public VamsasModel() {\r
super();\r
- }\r
- //-- jalview.binding.VamsasModel()\r
- //-----------/\r
+ } //-- jalview.binding.VamsasModel()\r
\r
- public boolean isValid() {\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- 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
- return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\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
+ } //-- void validate() \r
+\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-/*\r
- * 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 Viewport.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class Viewport implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_fontStyle;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public Viewport() {\r
super();\r
- }\r
- //-- jalview.binding.Viewport()\r
- //-----------/\r
+ } //-- jalview.binding.Viewport()\r
\r
- public void deleteConsThreshold() {\r
- this._has_consThreshold = false;\r
- }\r
- //-- void deleteConsThreshold()\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
*/\r
- public void deleteConservationSelected() {\r
- this._has_conservationSelected = false;\r
- }\r
- //-- void deleteConservationSelected()\r
+ public void deleteConservationSelected()\r
+ {\r
+ this._has_conservationSelected= false;\r
+ } //-- void deleteConservationSelected() \r
\r
/**\r
* Method deleteFontSize\r
- *\r
+ * \r
*/\r
- public void deleteFontSize() {\r
- this._has_fontSize = false;\r
- }\r
- //-- void deleteFontSize()\r
+ public void deleteFontSize()\r
+ {\r
+ this._has_fontSize= false;\r
+ } //-- void deleteFontSize() \r
\r
/**\r
* Method deleteFontStyle\r
- *\r
+ * \r
*/\r
- public void deleteFontStyle() {\r
- this._has_fontStyle = false;\r
- }\r
- //-- void deleteFontStyle()\r
+ public void deleteFontStyle()\r
+ {\r
+ this._has_fontStyle= false;\r
+ } //-- void deleteFontStyle() \r
\r
/**\r
* Method deleteHeight\r
- *\r
+ * \r
*/\r
- public void deleteHeight() {\r
- this._has_height = false;\r
- }\r
- //-- void deleteHeight()\r
+ public void deleteHeight()\r
+ {\r
+ this._has_height= false;\r
+ } //-- void deleteHeight() \r
\r
/**\r
* Method deletePidSelected\r
- *\r
+ * \r
*/\r
- public void deletePidSelected() {\r
- this._has_pidSelected = false;\r
- }\r
- //-- void deletePidSelected()\r
+ public void deletePidSelected()\r
+ {\r
+ this._has_pidSelected= false;\r
+ } //-- void deletePidSelected() \r
\r
/**\r
* Method deletePidThreshold\r
- *\r
+ * \r
*/\r
- public void deletePidThreshold() {\r
- this._has_pidThreshold = false;\r
- }\r
- //-- void deletePidThreshold()\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
\r
/**\r
* Method deleteRenderGaps\r
- *\r
+ * \r
*/\r
- public void deleteRenderGaps() {\r
- this._has_renderGaps = false;\r
- }\r
- //-- void deleteRenderGaps()\r
+ public void deleteRenderGaps()\r
+ {\r
+ this._has_renderGaps= false;\r
+ } //-- void deleteRenderGaps() \r
\r
/**\r
* Method deleteShowAnnotation\r
- *\r
+ * \r
*/\r
- public void deleteShowAnnotation() {\r
- this._has_showAnnotation = false;\r
- }\r
- //-- void deleteShowAnnotation()\r
+ public void deleteShowAnnotation()\r
+ {\r
+ this._has_showAnnotation= false;\r
+ } //-- void deleteShowAnnotation() \r
\r
/**\r
* Method deleteShowBoxes\r
- *\r
+ * \r
*/\r
- public void deleteShowBoxes() {\r
- this._has_showBoxes = false;\r
- }\r
- //-- void deleteShowBoxes()\r
+ public void deleteShowBoxes()\r
+ {\r
+ this._has_showBoxes= false;\r
+ } //-- void deleteShowBoxes() \r
\r
/**\r
* Method deleteShowColourText\r
- *\r
+ * \r
*/\r
- public void deleteShowColourText() {\r
- this._has_showColourText = false;\r
- }\r
- //-- void deleteShowColourText()\r
+ public void deleteShowColourText()\r
+ {\r
+ this._has_showColourText= false;\r
+ } //-- void deleteShowColourText() \r
\r
/**\r
* Method deleteShowConservation\r
- *\r
+ * \r
*/\r
- public void deleteShowConservation() {\r
- this._has_showConservation = false;\r
- }\r
- //-- void deleteShowConservation()\r
+ public void deleteShowConservation()\r
+ {\r
+ this._has_showConservation= false;\r
+ } //-- void deleteShowConservation() \r
\r
/**\r
* Method deleteShowFullId\r
- *\r
+ * \r
*/\r
- public void deleteShowFullId() {\r
- this._has_showFullId = false;\r
- }\r
- //-- void deleteShowFullId()\r
+ public void deleteShowFullId()\r
+ {\r
+ this._has_showFullId= false;\r
+ } //-- void deleteShowFullId() \r
\r
/**\r
* Method deleteShowIdentity\r
- *\r
+ * \r
*/\r
- public void deleteShowIdentity() {\r
- this._has_showIdentity = false;\r
- }\r
- //-- void deleteShowIdentity()\r
+ public void deleteShowIdentity()\r
+ {\r
+ this._has_showIdentity= false;\r
+ } //-- void deleteShowIdentity() \r
\r
/**\r
* Method deleteShowQuality\r
- *\r
+ * \r
*/\r
- public void deleteShowQuality() {\r
- this._has_showQuality = false;\r
- }\r
- //-- void deleteShowQuality()\r
+ public void deleteShowQuality()\r
+ {\r
+ this._has_showQuality= false;\r
+ } //-- void deleteShowQuality() \r
\r
/**\r
* Method deleteShowSequenceFeatures\r
- *\r
+ * \r
*/\r
- public void deleteShowSequenceFeatures() {\r
- this._has_showSequenceFeatures = false;\r
- }\r
- //-- void deleteShowSequenceFeatures()\r
+ public void deleteShowSequenceFeatures()\r
+ {\r
+ this._has_showSequenceFeatures= false;\r
+ } //-- void deleteShowSequenceFeatures() \r
\r
/**\r
* Method deleteShowText\r
- *\r
+ * \r
*/\r
- public void deleteShowText() {\r
- this._has_showText = false;\r
- }\r
- //-- void deleteShowText()\r
+ public void deleteShowText()\r
+ {\r
+ this._has_showText= false;\r
+ } //-- void deleteShowText() \r
\r
/**\r
* Method deleteStartRes\r
- *\r
+ * \r
*/\r
- public void deleteStartRes() {\r
- this._has_startRes = false;\r
- }\r
- //-- void deleteStartRes()\r
+ public void deleteStartRes()\r
+ {\r
+ this._has_startRes= false;\r
+ } //-- void deleteStartRes() \r
\r
/**\r
* Method deleteStartSeq\r
- *\r
+ * \r
*/\r
- public void deleteStartSeq() {\r
- this._has_startSeq = false;\r
- }\r
- //-- void deleteStartSeq()\r
+ public void deleteStartSeq()\r
+ {\r
+ this._has_startSeq= false;\r
+ } //-- void deleteStartSeq() \r
\r
/**\r
* Method deleteWidth\r
- *\r
+ * \r
*/\r
- public void deleteWidth() {\r
- this._has_width = false;\r
- }\r
- //-- void deleteWidth()\r
+ public void deleteWidth()\r
+ {\r
+ this._has_width= false;\r
+ } //-- void deleteWidth() \r
\r
/**\r
* Method deleteWrapAlignment\r
- *\r
+ * \r
*/\r
- public void deleteWrapAlignment() {\r
- this._has_wrapAlignment = false;\r
- }\r
- //-- void deleteWrapAlignment()\r
+ public void deleteWrapAlignment()\r
+ {\r
+ this._has_wrapAlignment= false;\r
+ } //-- void deleteWrapAlignment() \r
\r
/**\r
* Method deleteXpos\r
- *\r
+ * \r
*/\r
- public void deleteXpos() {\r
- this._has_xpos = false;\r
- }\r
- //-- void deleteXpos()\r
+ public void deleteXpos()\r
+ {\r
+ this._has_xpos= false;\r
+ } //-- void deleteXpos() \r
\r
/**\r
* Method deleteYpos\r
- *\r
+ * \r
*/\r
- public void deleteYpos() {\r
- this._has_ypos = false;\r
- }\r
- //-- void deleteYpos()\r
+ public void deleteYpos()\r
+ {\r
+ this._has_ypos= false;\r
+ } //-- void deleteYpos() \r
\r
/**\r
* Returns the value of field 'bgColour'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'bgColour'.\r
*/\r
- public java.lang.String getBgColour() {\r
+ public java.lang.String getBgColour()\r
+ {\r
return this._bgColour;\r
- }\r
- //-- java.lang.String getBgColour()\r
+ } //-- java.lang.String getBgColour() \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
+ public int getConsThreshold()\r
+ {\r
return this._consThreshold;\r
- }\r
- //-- int getConsThreshold()\r
+ } //-- int getConsThreshold() \r
\r
/**\r
* Returns the value of field 'conservationSelected'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'conservationSelected'.\r
*/\r
- public boolean getConservationSelected() {\r
+ public boolean getConservationSelected()\r
+ {\r
return this._conservationSelected;\r
- }\r
- //-- boolean getConservationSelected()\r
+ } //-- boolean getConservationSelected() \r
\r
/**\r
* Returns the value of field 'fontName'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'fontName'.\r
*/\r
- public java.lang.String getFontName() {\r
+ public java.lang.String getFontName()\r
+ {\r
return this._fontName;\r
- }\r
- //-- java.lang.String getFontName()\r
+ } //-- java.lang.String getFontName() \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
+ public int getFontSize()\r
+ {\r
return this._fontSize;\r
- }\r
- //-- int getFontSize()\r
+ } //-- int getFontSize() \r
\r
/**\r
* Returns the value of field 'fontStyle'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'fontStyle'.\r
*/\r
- public int getFontStyle() {\r
+ public int getFontStyle()\r
+ {\r
return this._fontStyle;\r
- }\r
- //-- int getFontStyle()\r
+ } //-- int getFontStyle() \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
+ public int getHeight()\r
+ {\r
return this._height;\r
- }\r
- //-- int getHeight()\r
+ } //-- int getHeight() \r
\r
/**\r
* Returns the value of field 'pidSelected'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'pidSelected'.\r
*/\r
- public boolean getPidSelected() {\r
+ public boolean getPidSelected()\r
+ {\r
return this._pidSelected;\r
- }\r
- //-- boolean getPidSelected()\r
+ } //-- boolean getPidSelected() \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
+ public int getPidThreshold()\r
+ {\r
return this._pidThreshold;\r
- }\r
- //-- int getPidThreshold()\r
+ } //-- int getPidThreshold() \r
\r
/**\r
* Returns the value of field 'renderGaps'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'renderGaps'.\r
*/\r
- public boolean getRenderGaps() {\r
+ public boolean getRenderGaps()\r
+ {\r
return this._renderGaps;\r
- }\r
- //-- boolean getRenderGaps()\r
+ } //-- boolean getRenderGaps() \r
\r
/**\r
* Returns the value of field 'showAnnotation'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showAnnotation'.\r
*/\r
- public boolean getShowAnnotation() {\r
+ public boolean getShowAnnotation()\r
+ {\r
return this._showAnnotation;\r
- }\r
- //-- boolean getShowAnnotation()\r
+ } //-- boolean getShowAnnotation() \r
\r
/**\r
* Returns the value of field 'showBoxes'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showBoxes'.\r
*/\r
- public boolean getShowBoxes() {\r
+ public boolean getShowBoxes()\r
+ {\r
return this._showBoxes;\r
- }\r
- //-- boolean getShowBoxes()\r
+ } //-- boolean getShowBoxes() \r
\r
/**\r
* Returns the value of field 'showColourText'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showColourText'.\r
*/\r
- public boolean getShowColourText() {\r
+ public boolean getShowColourText()\r
+ {\r
return this._showColourText;\r
- }\r
- //-- boolean getShowColourText()\r
+ } //-- boolean getShowColourText() \r
\r
/**\r
* Returns the value of field 'showConservation'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showConservation'.\r
*/\r
- public boolean getShowConservation() {\r
+ public boolean getShowConservation()\r
+ {\r
return this._showConservation;\r
- }\r
- //-- boolean getShowConservation()\r
+ } //-- boolean getShowConservation() \r
\r
/**\r
* Returns the value of field 'showFullId'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showFullId'.\r
*/\r
- public boolean getShowFullId() {\r
+ public boolean getShowFullId()\r
+ {\r
return this._showFullId;\r
- }\r
- //-- boolean getShowFullId()\r
+ } //-- boolean getShowFullId() \r
\r
/**\r
* Returns the value of field 'showIdentity'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showIdentity'.\r
*/\r
- public boolean getShowIdentity() {\r
+ public boolean getShowIdentity()\r
+ {\r
return this._showIdentity;\r
- }\r
- //-- boolean getShowIdentity()\r
+ } //-- boolean getShowIdentity() \r
\r
/**\r
* Returns the value of field 'showQuality'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showQuality'.\r
*/\r
- public boolean getShowQuality() {\r
+ public boolean getShowQuality()\r
+ {\r
return this._showQuality;\r
- }\r
- //-- boolean getShowQuality()\r
+ } //-- boolean getShowQuality() \r
\r
/**\r
* Returns the value of field 'showSequenceFeatures'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showSequenceFeatures'.\r
*/\r
- public boolean getShowSequenceFeatures() {\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
return this._showSequenceFeatures;\r
- }\r
- //-- boolean getShowSequenceFeatures()\r
+ } //-- boolean getShowSequenceFeatures() \r
\r
/**\r
* Returns the value of field 'showText'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'showText'.\r
*/\r
- public boolean getShowText() {\r
+ public boolean getShowText()\r
+ {\r
return this._showText;\r
- }\r
- //-- boolean getShowText()\r
+ } //-- boolean getShowText() \r
\r
/**\r
* Returns the value of field 'startRes'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'startRes'.\r
*/\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return this._startRes;\r
- }\r
- //-- int getStartRes()\r
+ } //-- int getStartRes() \r
\r
/**\r
* Returns the value of field 'startSeq'.\r
- *\r
+ * \r
* @return int\r
* @return the value of field 'startSeq'.\r
*/\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return this._startSeq;\r
- }\r
- //-- int getStartSeq()\r
+ } //-- int getStartSeq() \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
+ public java.lang.String getTitle()\r
+ {\r
return this._title;\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
+ public int getWidth()\r
+ {\r
return this._width;\r
- }\r
- //-- int getWidth()\r
+ } //-- int getWidth() \r
\r
/**\r
* Returns the value of field 'wrapAlignment'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'wrapAlignment'.\r
*/\r
- public boolean getWrapAlignment() {\r
+ public boolean getWrapAlignment()\r
+ {\r
return this._wrapAlignment;\r
- }\r
- //-- boolean getWrapAlignment()\r
+ } //-- boolean getWrapAlignment() \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
+ public int getXpos()\r
+ {\r
return this._xpos;\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
+ public int getYpos()\r
+ {\r
return this._ypos;\r
- }\r
- //-- int getYpos()\r
+ } //-- int getYpos() \r
\r
/**\r
* Method hasConsThreshold\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasConsThreshold() {\r
+ public boolean hasConsThreshold()\r
+ {\r
return this._has_consThreshold;\r
- }\r
- //-- boolean hasConsThreshold()\r
+ } //-- boolean hasConsThreshold() \r
\r
/**\r
* Method hasConservationSelected\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasConservationSelected() {\r
+ public boolean hasConservationSelected()\r
+ {\r
return this._has_conservationSelected;\r
- }\r
- //-- boolean hasConservationSelected()\r
+ } //-- boolean hasConservationSelected() \r
\r
/**\r
* Method hasFontSize\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasFontSize() {\r
+ public boolean hasFontSize()\r
+ {\r
return this._has_fontSize;\r
- }\r
- //-- boolean hasFontSize()\r
+ } //-- boolean hasFontSize() \r
\r
/**\r
* Method hasFontStyle\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasFontStyle() {\r
+ public boolean hasFontStyle()\r
+ {\r
return this._has_fontStyle;\r
- }\r
- //-- boolean hasFontStyle()\r
+ } //-- boolean hasFontStyle() \r
\r
/**\r
* Method hasHeight\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasHeight() {\r
+ public boolean hasHeight()\r
+ {\r
return this._has_height;\r
- }\r
- //-- boolean hasHeight()\r
+ } //-- boolean hasHeight() \r
\r
/**\r
* Method hasPidSelected\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasPidSelected() {\r
+ public boolean hasPidSelected()\r
+ {\r
return this._has_pidSelected;\r
- }\r
- //-- boolean hasPidSelected()\r
+ } //-- boolean hasPidSelected() \r
\r
/**\r
* Method hasPidThreshold\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasPidThreshold() {\r
+ public boolean hasPidThreshold()\r
+ {\r
return this._has_pidThreshold;\r
- }\r
- //-- boolean hasPidThreshold()\r
+ } //-- boolean hasPidThreshold() \r
\r
/**\r
* Method hasRenderGaps\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasRenderGaps() {\r
+ public boolean hasRenderGaps()\r
+ {\r
return this._has_renderGaps;\r
- }\r
- //-- boolean hasRenderGaps()\r
+ } //-- boolean hasRenderGaps() \r
\r
/**\r
* Method hasShowAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowAnnotation() {\r
+ public boolean hasShowAnnotation()\r
+ {\r
return this._has_showAnnotation;\r
- }\r
- //-- boolean hasShowAnnotation()\r
+ } //-- boolean hasShowAnnotation() \r
\r
/**\r
* Method hasShowBoxes\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowBoxes() {\r
+ public boolean hasShowBoxes()\r
+ {\r
return this._has_showBoxes;\r
- }\r
- //-- boolean hasShowBoxes()\r
+ } //-- boolean hasShowBoxes() \r
\r
/**\r
* Method hasShowColourText\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowColourText() {\r
+ public boolean hasShowColourText()\r
+ {\r
return this._has_showColourText;\r
- }\r
- //-- boolean hasShowColourText()\r
+ } //-- boolean hasShowColourText() \r
\r
/**\r
* Method hasShowConservation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowConservation() {\r
+ public boolean hasShowConservation()\r
+ {\r
return this._has_showConservation;\r
- }\r
- //-- boolean hasShowConservation()\r
+ } //-- boolean hasShowConservation() \r
\r
/**\r
* Method hasShowFullId\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowFullId() {\r
+ public boolean hasShowFullId()\r
+ {\r
return this._has_showFullId;\r
- }\r
- //-- boolean hasShowFullId()\r
+ } //-- boolean hasShowFullId() \r
\r
/**\r
* Method hasShowIdentity\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowIdentity() {\r
+ public boolean hasShowIdentity()\r
+ {\r
return this._has_showIdentity;\r
- }\r
- //-- boolean hasShowIdentity()\r
+ } //-- boolean hasShowIdentity() \r
\r
/**\r
* Method hasShowQuality\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowQuality() {\r
+ public boolean hasShowQuality()\r
+ {\r
return this._has_showQuality;\r
- }\r
- //-- boolean hasShowQuality()\r
+ } //-- boolean hasShowQuality() \r
\r
/**\r
* Method hasShowSequenceFeatures\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowSequenceFeatures() {\r
+ public boolean hasShowSequenceFeatures()\r
+ {\r
return this._has_showSequenceFeatures;\r
- }\r
- //-- boolean hasShowSequenceFeatures()\r
+ } //-- boolean hasShowSequenceFeatures() \r
\r
/**\r
* Method hasShowText\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasShowText() {\r
+ public boolean hasShowText()\r
+ {\r
return this._has_showText;\r
- }\r
- //-- boolean hasShowText()\r
+ } //-- boolean hasShowText() \r
\r
/**\r
* Method hasStartRes\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasStartRes() {\r
+ public boolean hasStartRes()\r
+ {\r
return this._has_startRes;\r
- }\r
- //-- boolean hasStartRes()\r
+ } //-- boolean hasStartRes() \r
\r
/**\r
* Method hasStartSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasStartSeq() {\r
+ public boolean hasStartSeq()\r
+ {\r
return this._has_startSeq;\r
- }\r
- //-- boolean hasStartSeq()\r
+ } //-- boolean hasStartSeq() \r
\r
/**\r
* Method hasWidth\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasWidth() {\r
+ public boolean hasWidth()\r
+ {\r
return this._has_width;\r
- }\r
- //-- boolean hasWidth()\r
+ } //-- boolean hasWidth() \r
\r
/**\r
* Method hasWrapAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasWrapAlignment() {\r
+ public boolean hasWrapAlignment()\r
+ {\r
return this._has_wrapAlignment;\r
- }\r
- //-- boolean hasWrapAlignment()\r
+ } //-- boolean hasWrapAlignment() \r
\r
/**\r
* Method hasXpos\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasXpos() {\r
+ public boolean hasXpos()\r
+ {\r
return this._has_xpos;\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
+ public boolean hasYpos()\r
+ {\r
return this._has_ypos;\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
+ public boolean isValid()\r
+ {\r
try {\r
validate();\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
- //-- 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
- //-- 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
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Sets the value of field 'bgColour'.\r
- *\r
+ * \r
* @param bgColour the value of field 'bgColour'.\r
*/\r
- public void setBgColour(java.lang.String bgColour) {\r
+ public void setBgColour(java.lang.String bgColour)\r
+ {\r
this._bgColour = bgColour;\r
- }\r
- //-- void setBgColour(java.lang.String)\r
+ } //-- void setBgColour(java.lang.String) \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
+ public void setConsThreshold(int consThreshold)\r
+ {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- }\r
- //-- void setConsThreshold(int)\r
+ } //-- void setConsThreshold(int) \r
\r
/**\r
* Sets the value of field 'conservationSelected'.\r
- *\r
+ * \r
* @param conservationSelected the value of field\r
* 'conservationSelected'.\r
*/\r
- public void setConservationSelected(boolean conservationSelected) {\r
+ public void setConservationSelected(boolean conservationSelected)\r
+ {\r
this._conservationSelected = conservationSelected;\r
this._has_conservationSelected = true;\r
- }\r
- //-- void setConservationSelected(boolean)\r
+ } //-- void setConservationSelected(boolean) \r
\r
/**\r
* Sets the value of field 'fontName'.\r
- *\r
+ * \r
* @param fontName the value of field 'fontName'.\r
*/\r
- public void setFontName(java.lang.String fontName) {\r
+ public void setFontName(java.lang.String fontName)\r
+ {\r
this._fontName = fontName;\r
- }\r
- //-- void setFontName(java.lang.String)\r
+ } //-- void setFontName(java.lang.String) \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
+ public void setFontSize(int fontSize)\r
+ {\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- }\r
- //-- void setFontSize(int)\r
+ } //-- void setFontSize(int) \r
\r
/**\r
* Sets the value of field 'fontStyle'.\r
- *\r
+ * \r
* @param fontStyle the value of field 'fontStyle'.\r
*/\r
- public void setFontStyle(int fontStyle) {\r
+ public void setFontStyle(int fontStyle)\r
+ {\r
this._fontStyle = fontStyle;\r
this._has_fontStyle = true;\r
- }\r
- //-- void setFontStyle(int)\r
+ } //-- void setFontStyle(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
+ public void setHeight(int height)\r
+ {\r
this._height = height;\r
this._has_height = true;\r
- }\r
- //-- void setHeight(int)\r
+ } //-- void setHeight(int) \r
\r
/**\r
* Sets the value of field 'pidSelected'.\r
- *\r
+ * \r
* @param pidSelected the value of field 'pidSelected'.\r
*/\r
- public void setPidSelected(boolean pidSelected) {\r
+ public void setPidSelected(boolean pidSelected)\r
+ {\r
this._pidSelected = pidSelected;\r
this._has_pidSelected = true;\r
- }\r
- //-- void setPidSelected(boolean)\r
+ } //-- void setPidSelected(boolean) \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
+ public void setPidThreshold(int pidThreshold)\r
+ {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- }\r
- //-- void setPidThreshold(int)\r
+ } //-- void setPidThreshold(int) \r
\r
/**\r
* Sets the value of field 'renderGaps'.\r
- *\r
+ * \r
* @param renderGaps the value of field 'renderGaps'.\r
*/\r
- public void setRenderGaps(boolean renderGaps) {\r
+ public void setRenderGaps(boolean renderGaps)\r
+ {\r
this._renderGaps = renderGaps;\r
this._has_renderGaps = true;\r
- }\r
- //-- void setRenderGaps(boolean)\r
+ } //-- void setRenderGaps(boolean) \r
\r
/**\r
* Sets the value of field 'showAnnotation'.\r
- *\r
+ * \r
* @param showAnnotation the value of field 'showAnnotation'.\r
*/\r
- public void setShowAnnotation(boolean showAnnotation) {\r
+ public void setShowAnnotation(boolean showAnnotation)\r
+ {\r
this._showAnnotation = showAnnotation;\r
this._has_showAnnotation = true;\r
- }\r
- //-- void setShowAnnotation(boolean)\r
+ } //-- void setShowAnnotation(boolean) \r
\r
/**\r
* Sets the value of field 'showBoxes'.\r
- *\r
+ * \r
* @param showBoxes the value of field 'showBoxes'.\r
*/\r
- public void setShowBoxes(boolean showBoxes) {\r
+ public void setShowBoxes(boolean showBoxes)\r
+ {\r
this._showBoxes = showBoxes;\r
this._has_showBoxes = true;\r
- }\r
- //-- void setShowBoxes(boolean)\r
+ } //-- void setShowBoxes(boolean) \r
\r
/**\r
* Sets the value of field 'showColourText'.\r
- *\r
+ * \r
* @param showColourText the value of field 'showColourText'.\r
*/\r
- public void setShowColourText(boolean showColourText) {\r
+ public void setShowColourText(boolean showColourText)\r
+ {\r
this._showColourText = showColourText;\r
this._has_showColourText = true;\r
- }\r
- //-- void setShowColourText(boolean)\r
+ } //-- void setShowColourText(boolean) \r
\r
/**\r
* Sets the value of field 'showConservation'.\r
- *\r
+ * \r
* @param showConservation the value of field 'showConservation'\r
*/\r
- public void setShowConservation(boolean showConservation) {\r
+ public void setShowConservation(boolean showConservation)\r
+ {\r
this._showConservation = showConservation;\r
this._has_showConservation = true;\r
- }\r
- //-- void setShowConservation(boolean)\r
+ } //-- void setShowConservation(boolean) \r
\r
/**\r
* Sets the value of field 'showFullId'.\r
- *\r
+ * \r
* @param showFullId the value of field 'showFullId'.\r
*/\r
- public void setShowFullId(boolean showFullId) {\r
+ public void setShowFullId(boolean showFullId)\r
+ {\r
this._showFullId = showFullId;\r
this._has_showFullId = true;\r
- }\r
- //-- void setShowFullId(boolean)\r
+ } //-- void setShowFullId(boolean) \r
\r
/**\r
* Sets the value of field 'showIdentity'.\r
- *\r
+ * \r
* @param showIdentity the value of field 'showIdentity'.\r
*/\r
- public void setShowIdentity(boolean showIdentity) {\r
+ public void setShowIdentity(boolean showIdentity)\r
+ {\r
this._showIdentity = showIdentity;\r
this._has_showIdentity = true;\r
- }\r
- //-- void setShowIdentity(boolean)\r
+ } //-- void setShowIdentity(boolean) \r
\r
/**\r
* Sets the value of field 'showQuality'.\r
- *\r
+ * \r
* @param showQuality the value of field 'showQuality'.\r
*/\r
- public void setShowQuality(boolean showQuality) {\r
+ public void setShowQuality(boolean showQuality)\r
+ {\r
this._showQuality = showQuality;\r
this._has_showQuality = true;\r
- }\r
- //-- void setShowQuality(boolean)\r
+ } //-- void setShowQuality(boolean) \r
\r
/**\r
* Sets the value of field 'showSequenceFeatures'.\r
- *\r
+ * \r
* @param showSequenceFeatures the value of field\r
* 'showSequenceFeatures'.\r
*/\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures) {\r
+ public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
+ {\r
this._showSequenceFeatures = showSequenceFeatures;\r
this._has_showSequenceFeatures = true;\r
- }\r
- //-- void setShowSequenceFeatures(boolean)\r
+ } //-- void setShowSequenceFeatures(boolean) \r
\r
/**\r
* Sets the value of field 'showText'.\r
- *\r
+ * \r
* @param showText the value of field 'showText'.\r
*/\r
- public void setShowText(boolean showText) {\r
+ public void setShowText(boolean showText)\r
+ {\r
this._showText = showText;\r
this._has_showText = true;\r
- }\r
- //-- void setShowText(boolean)\r
+ } //-- void setShowText(boolean) \r
\r
/**\r
* Sets the value of field 'startRes'.\r
- *\r
+ * \r
* @param startRes the value of field 'startRes'.\r
*/\r
- public void setStartRes(int startRes) {\r
+ public void setStartRes(int startRes)\r
+ {\r
this._startRes = startRes;\r
this._has_startRes = true;\r
- }\r
- //-- void setStartRes(int)\r
+ } //-- void setStartRes(int) \r
\r
/**\r
* Sets the value of field 'startSeq'.\r
- *\r
+ * \r
* @param startSeq the value of field 'startSeq'.\r
*/\r
- public void setStartSeq(int startSeq) {\r
+ public void setStartSeq(int startSeq)\r
+ {\r
this._startSeq = startSeq;\r
this._has_startSeq = true;\r
- }\r
- //-- void setStartSeq(int)\r
+ } //-- void setStartSeq(int) \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
+ public void setTitle(java.lang.String title)\r
+ {\r
this._title = title;\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
+ public void setWidth(int width)\r
+ {\r
this._width = width;\r
this._has_width = true;\r
- }\r
- //-- void setWidth(int)\r
+ } //-- void setWidth(int) \r
\r
/**\r
* Sets the value of field 'wrapAlignment'.\r
- *\r
+ * \r
* @param wrapAlignment the value of field 'wrapAlignment'.\r
*/\r
- public void setWrapAlignment(boolean wrapAlignment) {\r
+ public void setWrapAlignment(boolean wrapAlignment)\r
+ {\r
this._wrapAlignment = wrapAlignment;\r
this._has_wrapAlignment = true;\r
- }\r
- //-- void setWrapAlignment(boolean)\r
+ } //-- void setWrapAlignment(boolean) \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
+ public void setXpos(int xpos)\r
+ {\r
this._xpos = xpos;\r
this._has_xpos = true;\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
+ public void setYpos(int ypos)\r
+ {\r
this._ypos = ypos;\r
this._has_ypos = true;\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
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\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
+ } //-- void validate() \r
+\r
}\r
git://source.jalview.org / jalview.git / commitdiff