2 * This class was automatically generated with
\r
3 * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
\r
8 package org.vamsas.objects.core;
\r
10 //---------------------------------/
\r
11 //- Imported classes and packages -/
\r
12 //---------------------------------/
\r
14 import java.io.IOException;
\r
15 import java.io.Reader;
\r
16 import java.io.Serializable;
\r
17 import java.io.Writer;
\r
18 import org.exolab.castor.xml.MarshalException;
\r
19 import org.exolab.castor.xml.Marshaller;
\r
20 import org.exolab.castor.xml.Unmarshaller;
\r
21 import org.exolab.castor.xml.ValidationException;
\r
22 import org.xml.sax.ContentHandler;
\r
25 * This is annotation over the
\r
26 * coordinate frame defined by all
\r
27 * the columns in the alignment.
\r
30 * @version $Revision$ $Date$
\r
32 public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation
\r
33 implements java.io.Serializable
\r
37 //--------------------------/
\r
38 //- Class/Member Variables -/
\r
39 //--------------------------/
\r
52 private boolean _graph;
\r
55 * keeps track of state for field: _graph
\r
57 private boolean _has_graph;
\r
62 private org.vamsas.objects.core.Provenance _provenance;
\r
69 public AlignmentAnnotation()
\r
72 } //-- org.vamsas.objects.core.AlignmentAnnotation()
\r
80 * Method deleteGraph
\r
83 public void deleteGraph()
\r
85 this._has_graph= false;
\r
86 } //-- void deleteGraph()
\r
89 * Note: hashCode() has not been overriden
\r
94 public boolean equals(java.lang.Object obj)
\r
99 if (super.equals(obj)==false)
\r
102 if (obj instanceof AlignmentAnnotation) {
\r
104 AlignmentAnnotation temp = (AlignmentAnnotation)obj;
\r
105 if (this._graph != temp._graph)
\r
107 if (this._has_graph != temp._has_graph)
\r
109 if (this._provenance != null) {
\r
110 if (temp._provenance == null) return false;
\r
111 else if (!(this._provenance.equals(temp._provenance)))
\r
114 else if (temp._provenance != null)
\r
119 } //-- boolean equals(java.lang.Object)
\r
122 * Returns the value of field 'graph'. The field 'graph' has
\r
123 * the following description: TODO: decide if
\r
128 * annotationElement
\r
134 * @return the value of field 'graph'.
\r
136 public boolean getGraph()
\r
138 return this._graph;
\r
139 } //-- boolean getGraph()
\r
142 * Returns the value of field 'provenance'.
\r
144 * @return Provenance
\r
145 * @return the value of field 'provenance'.
\r
147 public org.vamsas.objects.core.Provenance getProvenance()
\r
149 return this._provenance;
\r
150 } //-- org.vamsas.objects.core.Provenance getProvenance()
\r
159 public boolean hasGraph()
\r
161 return this._has_graph;
\r
162 } //-- boolean hasGraph()
\r
171 public boolean isValid()
\r
176 catch (org.exolab.castor.xml.ValidationException vex) {
\r
180 } //-- boolean isValid()
\r
189 public void marshal(java.io.Writer out)
\r
190 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
193 Marshaller.marshal(this, out);
\r
194 } //-- void marshal(java.io.Writer)
\r
203 public void marshal(org.xml.sax.ContentHandler handler)
\r
204 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
207 Marshaller.marshal(this, handler);
\r
208 } //-- void marshal(org.xml.sax.ContentHandler)
\r
211 * Sets the value of field 'graph'. The field 'graph' has the
\r
212 * following description: TODO: decide if
\r
217 * annotationElement
\r
222 * @param graph the value of field 'graph'.
\r
224 public void setGraph(boolean graph)
\r
226 this._graph = graph;
\r
227 this._has_graph = true;
\r
228 } //-- void setGraph(boolean)
\r
231 * Sets the value of field 'provenance'.
\r
233 * @param provenance the value of field 'provenance'.
\r
235 public void setProvenance(org.vamsas.objects.core.Provenance provenance)
\r
237 this._provenance = provenance;
\r
238 } //-- void setProvenance(org.vamsas.objects.core.Provenance)
\r
246 * @return RangeType
\r
248 public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
\r
249 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
251 return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader);
\r
252 } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
\r
258 public void validate()
\r
259 throws org.exolab.castor.xml.ValidationException
\r
261 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
262 validator.validate(this);
\r
263 } //-- void validate()
\r