2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.binding;
21 //---------------------------------/
22 //- Imported classes and packages -/
23 //---------------------------------/
25 import org.exolab.castor.xml.Marshaller;
26 import org.exolab.castor.xml.Unmarshaller;
31 * @version $Revision$ $Date$
33 public class Alignment implements java.io.Serializable
36 // --------------------------/
37 // - Class/Member Variables -/
38 // --------------------------/
43 private jalview.binding.Annotation _annotation;
48 private jalview.binding.SequenceSet _sequenceSet;
64 * Returns the value of field 'annotation'.
66 * @return the value of field 'Annotation'.
68 public jalview.binding.Annotation getAnnotation()
70 return this._annotation;
74 * Returns the value of field 'sequenceSet'.
76 * @return the value of field 'SequenceSet'.
78 public jalview.binding.SequenceSet getSequenceSet()
80 return this._sequenceSet;
86 * @return true if this object is valid according to the schema
88 public boolean isValid()
93 } catch (org.exolab.castor.xml.ValidationException vex)
104 * @throws org.exolab.castor.xml.MarshalException
105 * if object is null or if any SAXException is thrown during
107 * @throws org.exolab.castor.xml.ValidationException
108 * if this object is an invalid instance according to the schema
110 public void marshal(final java.io.Writer out)
111 throws org.exolab.castor.xml.MarshalException,
112 org.exolab.castor.xml.ValidationException
114 Marshaller.marshal(this, out);
121 * @throws java.io.IOException
122 * if an IOException occurs during marshaling
123 * @throws org.exolab.castor.xml.ValidationException
124 * if this object is an invalid instance according to the schema
125 * @throws org.exolab.castor.xml.MarshalException
126 * if object is null or if any SAXException is thrown during
129 public void marshal(final org.xml.sax.ContentHandler handler)
130 throws java.io.IOException,
131 org.exolab.castor.xml.MarshalException,
132 org.exolab.castor.xml.ValidationException
134 Marshaller.marshal(this, handler);
138 * Sets the value of field 'annotation'.
141 * the value of field 'annotation'.
143 public void setAnnotation(final jalview.binding.Annotation annotation)
145 this._annotation = annotation;
149 * Sets the value of field 'sequenceSet'.
152 * the value of field 'sequenceSet'.
154 public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
156 this._sequenceSet = sequenceSet;
163 * @throws org.exolab.castor.xml.MarshalException
164 * if object is null or if any SAXException is thrown during
166 * @throws org.exolab.castor.xml.ValidationException
167 * if this object is an invalid instance according to the schema
168 * @return the unmarshaled jalview.binding.Alignment
170 public static jalview.binding.Alignment unmarshal(
171 final java.io.Reader reader)
172 throws org.exolab.castor.xml.MarshalException,
173 org.exolab.castor.xml.ValidationException
175 return (jalview.binding.Alignment) Unmarshaller.unmarshal(
176 jalview.binding.Alignment.class, reader);
182 * @throws org.exolab.castor.xml.ValidationException
183 * if this object is an invalid instance according to the schema
185 public void validate() throws org.exolab.castor.xml.ValidationException
187 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
188 validator.validate(this);