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