* 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
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
+import java.util.*;\r
\r
+import org.exolab.castor.xml.*;\r
\r
/**\r
* Class Annotation.\r
*\r
* @version $Revision$ $Date$\r
*/\r
-public class Annotation implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _graph\r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _annotationElementList\r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Field _label\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public Annotation() {\r
- super();\r
- _annotationElementList = new Vector();\r
+public class Annotation\r
+ implements java.io.Serializable\r
+{\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _graph\r
+ */\r
+ private boolean _graph;\r
+\r
+ /**\r
+ * keeps track of state for field: _graph\r
+ */\r
+ private boolean _has_graph;\r
+\r
+ /**\r
+ * Field _annotationElementList\r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Field _label\r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Field _description\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Annotation()\r
+ {\r
+ super();\r
+ _annotationElementList = new Vector();\r
+ } //-- jalview.binding.Annotation()\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(jalview.binding.AnnotationElement\r
+ vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.addElement(vAnnotationElement);\r
+ } //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
+\r
+ /**\r
+ * Method addAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void addAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement\r
+ vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationElementList.insertElementAt(vAnnotationElement, index);\r
+ } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
+\r
+ /**\r
+ * Method deleteGraph\r
+ *\r
+ */\r
+ public void deleteGraph()\r
+ {\r
+ this._has_graph = false;\r
+ } //-- void deleteGraph()\r
+\r
+ /**\r
+ * Method enumerateAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
+ return _annotationElementList.elements();\r
+ } //-- java.util.Enumeration enumerateAnnotationElement()\r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ( (index < 0) || (index > _annotationElementList.size()))\r
+ {\r
+ throw new IndexOutOfBoundsException();\r
}\r
- //-- jalview.binding.Annotation()\r
- //-----------/\r
\r
- public void addAnnotationElement(\r
- jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- }\r
- //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
-\r
- /**\r
- * Method addAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(int index,\r
- jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- }\r
- //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
-\r
- /**\r
- * Method deleteGraph\r
- *\r
- */\r
- public void deleteGraph() {\r
- this._has_graph = false;\r
- }\r
- //-- void deleteGraph()\r
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement() {\r
- return _annotationElementList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateAnnotationElement()\r
-\r
- /**\r
- * Method getAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
-\r
- /**\r
- * Method getAnnotationElement\r
- *\r
- *\r
- *\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement[] getAnnotationElement() {\r
- 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
-\r
- /**\r
- * Method getAnnotationElementCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getAnnotationElementCount() {\r
- return _annotationElementList.size();\r
- }\r
- //-- int getAnnotationElementCount()\r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- *\r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription() {\r
- return this._description;\r
- }\r
- //-- java.lang.String getDescription()\r
-\r
- /**\r
- * Returns the value of field 'graph'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph() {\r
- return this._graph;\r
+ return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(\r
+ index);\r
+ } //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
+\r
+ /**\r
+ * Method getAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ {\r
+ int size = _annotationElementList.size();\r
+ jalview.binding.AnnotationElement[] mArray = new jalview.binding.\r
+ AnnotationElement[size];\r
+ for (int index = 0; index < size; index++)\r
+ {\r
+ mArray[index] = (jalview.binding.AnnotationElement)\r
+ _annotationElementList.elementAt(index);\r
}\r
- //-- boolean getGraph()\r
-\r
- /**\r
- * Returns the value of field 'label'.\r
- *\r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel() {\r
- return this._label;\r
+ return mArray;\r
+ } //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
+\r
+ /**\r
+ * Method getAnnotationElementCount\r
+ *\r
+ *\r
+ *\r
+ * @return int\r
+ */\r
+ public int getAnnotationElementCount()\r
+ {\r
+ return _annotationElementList.size();\r
+ } //-- int getAnnotationElementCount()\r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ } //-- java.lang.String getDescription()\r
+\r
+ /**\r
+ * Returns the value of field 'graph'.\r
+ *\r
+ * @return boolean\r
+ * @return the value of field 'graph'.\r
+ */\r
+ public boolean getGraph()\r
+ {\r
+ return this._graph;\r
+ } //-- boolean getGraph()\r
+\r
+ /**\r
+ * Returns the value of field 'label'.\r
+ *\r
+ * @return String\r
+ * @return the value of field 'label'.\r
+ */\r
+ public java.lang.String getLabel()\r
+ {\r
+ return this._label;\r
+ } //-- java.lang.String getLabel()\r
+\r
+ /**\r
+ * Method hasGraph\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean hasGraph()\r
+ {\r
+ return this._has_graph;\r
+ } //-- boolean hasGraph()\r
+\r
+ /**\r
+ * Method isValid\r
+ *\r
+ *\r
+ *\r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try\r
+ {\r
+ validate();\r
}\r
- //-- java.lang.String getLabel()\r
-\r
- /**\r
- * Method hasGraph\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasGraph() {\r
- return this._has_graph;\r
+ catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
}\r
- //-- boolean hasGraph()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid() {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
-\r
- return true;\r
+ return true;\r
+ } //-- boolean isValid()\r
+\r
+ /**\r
+ * Method marshal\r
+ *\r
+ *\r
+ *\r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+\r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer)\r
+\r
+ /**\r
+ * Method marshal\r
+ *\r
+ *\r
+ *\r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+\r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
+\r
+ /**\r
+ * Method removeAllAnnotationElement\r
+ *\r
+ */\r
+ public void removeAllAnnotationElement()\r
+ {\r
+ _annotationElementList.removeAllElements();\r
+ } //-- void removeAllAnnotationElement()\r
+\r
+ /**\r
+ * Method removeAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @return AnnotationElement\r
+ */\r
+ public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
+ {\r
+ java.lang.Object obj = _annotationElementList.elementAt(index);\r
+ _annotationElementList.removeElementAt(index);\r
+ return (jalview.binding.AnnotationElement) obj;\r
+ } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param index\r
+ * @param vAnnotationElement\r
+ */\r
+ public void setAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement\r
+ vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ( (index < 0) || (index > _annotationElementList.size()))\r
+ {\r
+ throw new IndexOutOfBoundsException();\r
}\r
- //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
+ _annotationElementList.setElementAt(vAnnotationElement, index);\r
+ } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
+\r
+ /**\r
+ * Method setAnnotationElement\r
+ *\r
+ *\r
+ *\r
+ * @param annotationElementArray\r
+ */\r
+ public void setAnnotationElement(jalview.binding.AnnotationElement[]\r
+ annotationElementArray)\r
+ {\r
+ //-- copy array\r
+ _annotationElementList.removeAllElements();\r
+ for (int i = 0; i < annotationElementArray.length; i++)\r
+ {\r
+ _annotationElementList.addElement(annotationElementArray[i]);\r
}\r
- //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
- //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Method removeAllAnnotationElement\r
- *\r
- */\r
- public void removeAllAnnotationElement() {\r
- _annotationElementList.removeAllElements();\r
- }\r
- //-- void removeAllAnnotationElement()\r
-\r
- /**\r
- * Method removeAnnotationElement\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index) {\r
- 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
-\r
- /**\r
- * Method setAnnotationElement\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
- //-- 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
-\r
- /**\r
- * Method setAnnotationElement\r
- *\r
- *\r
- *\r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(\r
- jalview.binding.AnnotationElement[] annotationElementArray) {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
-\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
- }\r
- }\r
- //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- *\r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description) {\r
- this._description = description;\r
- }\r
- //-- void setDescription(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'graph'.\r
- *\r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph) {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- }\r
- //-- void setGraph(boolean)\r
-\r
- /**\r
- * Sets the value of field 'label'.\r
- *\r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(java.lang.String label) {\r
- this._label = label;\r
- }\r
- //-- void setLabel(java.lang.String)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException {\r
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate() throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
- //-- void validate()\r
+ } //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
+\r
+ /**\r
+ * Sets the value of field 'description'.\r
+ *\r
+ * @param description the value of field 'description'.\r
+ */\r
+ public void setDescription(java.lang.String description)\r
+ {\r
+ this._description = description;\r
+ } //-- void setDescription(java.lang.String)\r
+\r
+ /**\r
+ * Sets the value of field 'graph'.\r
+ *\r
+ * @param graph the value of field 'graph'.\r
+ */\r
+ public void setGraph(boolean graph)\r
+ {\r
+ this._graph = graph;\r
+ this._has_graph = true;\r
+ } //-- void setGraph(boolean)\r
+\r
+ /**\r
+ * Sets the value of field 'label'.\r
+ *\r
+ * @param label the value of field 'label'.\r
+ */\r
+ public void setLabel(java.lang.String label)\r
+ {\r
+ this._label = label;\r
+ } //-- void setLabel(java.lang.String)\r
+\r
+ /**\r
+ * Method unmarshal\r
+ *\r
+ *\r
+ *\r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.\r
+ Annotation.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
+\r
+ /**\r
+ * Method validate\r
+ *\r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
+ Validator();\r
+ validator.validate(this);\r
+ } //-- void validate()\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff