Source code: org/biomage/Array/FeatureDefect.java
1 /***************************************************************************
2 * *
3 * C O P Y R I G H T N O T I C E *
4 * Copyright (c) 2001 by: *
5 * * The MicroArray Gene Expression Database group (MGED) *
6 * * Rosetta Inpharmatics *
7 * *
8 * All Rights Reserved. *
9 * *
10 * Permission is hereby granted, free of charge, to any person *
11 * obtaining a copy of this software and associated documentation files *
12 * (the "Software"), to deal in the Software without restriction, *
13 * including without limitation the rights to use, copy, modify, merge, *
14 * publish, distribute, sublicense, and/or sell copies of the Software, *
15 * and to permit persons to whom the Software is furnished to do so, *
16 * subject to the following conditions: *
17 * *
18 * The above copyright notice and this permission notice shall be *
19 * included in all copies or substantial portions of the Software. *
20 * *
21 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, *
22 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF *
23 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND *
24 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS *
25 * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN *
26 * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN *
27 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE *
28 * SOFTWARE. *
29 ***************************************************************************
30 * *
31 * Created by the create_mage_java_classes java program based on the *
32 * information in the xmi file created from the MAGE-OM UML model, *
33 * copyright European Bioinformatics Institute (EBI) for MGED and Rosetta *
34 * Informatics. *
35 * *
36 * The ideas and work are built on the previous work in perl of Jason *
37 * Stewart, Open Informatics, and Robert M. Hubley, Institute for Systems *
38 * Biology *
39 * *
40 * @author Michael Miller, Rosetta Inpharmatics *
41 * @version Revision: 1.0 *
42 * @date Thu, Feb 21, 2002 10:46:03 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.Array
49 *
50 */
51 package org.biomage.Array;
52
53 /**
54 * Import list for FeatureDefect
55 *
56 */
57 import java.io.Serializable;
58 import java.util.*;
59 import org.xml.sax.Attributes;
60 import java.io.Writer;
61 import java.io.IOException;
62 import org.biomage.Interface.HasPositionDelta;
63 import org.biomage.Interface.HasFeature;
64 import org.biomage.Interface.HasDefectType;
65 import org.biomage.Common.Extendable;
66 import org.biomage.Description.OntologyEntry;
67 import org.biomage.DesignElement.Feature;
68
69 /**
70 * Stores the defect information for a feature.
71 *
72 */
73 public
74 class FeatureDefect
75 extends Extendable
76 implements Serializable,
77 HasPositionDelta,
78 HasFeature,
79 HasDefectType
80 {
81 /**
82 * How the feature deviates in position from the ArrayDesign.
83 *
84 */
85 private PositionDelta positionDelta;
86
87
88 /**
89 * The feature that was manufactured defectively.
90 *
91 */
92 private Feature feature;
93
94
95 /**
96 * Indicates the type of defect (e.g. a missing feature or a moved
97 * feature).
98 *
99 */
100 private OntologyEntry defectType;
101
102
103 /**
104 * Default constructor.
105 *
106 */
107 public
108 FeatureDefect()
109 {
110 super();
111 }
112
113 /**
114 * Attribute constructor.
115 *
116 * Looks up the attributes in the parameter and casts them from strings
117 * appropriately
118 * @param atts: the attribute list.
119 *
120 */
121 // TODO Work in progress (attribute constructor).
122 public
123 FeatureDefect(Attributes atts)
124 {
125 super(atts);
126
127 }
128
129 /**
130 * writeMAGEML
131 * <p>
132 * This method is responsible for assembling the attribute and
133 * association data into XML. It creates the object tag and then calls
134 * the writeAttributes and writeAssociation methods.
135 * <p>
136 *
137 */
138 public
139 void
140 writeMAGEML(Writer out)
141 throws IOException
142 {
143 out.write("<FeatureDefect");
144 writeAttributes(out);
145 out.write(">");
146 writeAssociations(out);
147 out.write("</FeatureDefect>");
148 }
149
150 /**
151 * writeAttributes
152 * <p>
153 * This method is responsible for assembling the attribute data into
154 * XML. It calls the super method to write out all attributes of this
155 * class and it's ancestors.
156 * <p>
157 *
158 */
159 public
160 void
161 writeAttributes(Writer out)
162 throws IOException
163 {
164 super.writeAttributes(out);
165 }
166
167 /**
168 * writeAssociations
169 * <p>
170 * This method is responsible for assembling the association data
171 * into XML. It calls the super method to write out all associations of
172 * this class's ancestors.
173 * <p>
174 *
175 */
176 public
177 void
178 writeAssociations(Writer out)
179 throws IOException
180 {
181 super.writeAssociations(out);
182 if ( defectType != null ){
183 out.write("<DefectType_assn>");
184 defectType.writeMAGEML(out);
185 out.write("</DefectType_assn>");
186 }
187 if ( positionDelta != null ){
188 out.write("<PositionDelta_assn>");
189 positionDelta.writeMAGEML(out);
190 out.write("</PositionDelta_assn>");
191 }
192 if ( feature != null ){
193 out.write("<Feature_assnref>");
194 out.write("<Feature_ref identifier=\"" + feature.getIdentifier() + "\"/>");
195 out.write("</Feature_assnref>");
196 }
197 }
198
199 /**
200 * Set method for positionDelta
201 * <p>
202 * @param value to set
203 * <p>
204 *
205 */
206 public
207 void
208 setPositionDelta(
209 PositionDelta positionDelta
210 )
211 {
212 this.positionDelta = positionDelta;
213 }
214
215 /**
216 * Get method for positionDelta
217 * <p>
218 * @return value of the attribute
219 * <p>
220 *
221 */
222 public
223 PositionDelta
224 getPositionDelta()
225 {
226 return positionDelta;
227 }
228
229 /**
230 * Set method for feature
231 * <p>
232 * @param value to set
233 * <p>
234 *
235 */
236 public
237 void
238 setFeature(
239 Feature feature
240 )
241 {
242 this.feature = feature;
243 }
244
245 /**
246 * Get method for feature
247 * <p>
248 * @return value of the attribute
249 * <p>
250 *
251 */
252 public
253 Feature
254 getFeature()
255 {
256 return feature;
257 }
258
259 /**
260 * Set method for defectType
261 * <p>
262 * @param value to set
263 * <p>
264 *
265 */
266 public
267 void
268 setDefectType(
269 OntologyEntry defectType
270 )
271 {
272 this.defectType = defectType;
273 }
274
275 /**
276 * Get method for defectType
277 * <p>
278 * @return value of the attribute
279 * <p>
280 *
281 */
282 public
283 OntologyEntry
284 getDefectType()
285 {
286 return defectType;
287 }
288
289 }