Source code: org/biomage/BioAssay/DerivedBioAssay.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 10:46:11 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.BioAssay
49 *
50 */
51 package org.biomage.BioAssay;
52
53 /**
54 * Import list for DerivedBioAssay
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.HasDerivedBioAssayData;
63 import org.biomage.Interface.HasType;
64 import org.biomage.BioAssayData.DerivedBioAssayData;
65 import org.biomage.Description.OntologyEntry;
66
67 /**
68 * A BioAssay that is created by the Transformation BioEvent from one or
69 * more MeasuredBioAssays or DerivedBioAssays.
70 *
71 */
72 public
73 class DerivedBioAssay
74 extends BioAssay
75 implements Serializable,
76 HasDerivedBioAssayData,
77 HasType
78 {
79 /**
80 * The data associated with the DerivedBioAssay.
81 *
82 */
83 private DerivedBioAssayData_list derivedBioAssayData = new DerivedBioAssayData_list();
84
85 /**
86 * The derivation type, for instance collapsed spot replicate,
87 * ratio, averaged intensity, bioassay replicates, etc.
88 *
89 */
90 private OntologyEntry type;
91
92
93 /**
94 * Default constructor.
95 *
96 */
97 public
98 DerivedBioAssay()
99 {
100 super();
101 }
102
103 /**
104 * Attribute constructor.
105 *
106 * Looks up the attributes in the parameter and casts them from strings
107 * appropriately
108 * @param atts: the attribute list.
109 *
110 */
111 // TODO Work in progress (attribute constructor).
112 public
113 DerivedBioAssay(Attributes atts)
114 {
115 super(atts);
116
117 }
118
119 /**
120 * writeMAGEML
121 * <p>
122 * This method is responsible for assembling the attribute and
123 * association data into XML. It creates the object tag and then calls
124 * the writeAttributes and writeAssociation methods.
125 * <p>
126 *
127 */
128 public
129 void
130 writeMAGEML(Writer out)
131 throws IOException
132 {
133 out.write("<DerivedBioAssay");
134 writeAttributes(out);
135 out.write(">");
136 writeAssociations(out);
137 out.write("</DerivedBioAssay>");
138 }
139
140 /**
141 * writeAttributes
142 * <p>
143 * This method is responsible for assembling the attribute data into
144 * XML. It calls the super method to write out all attributes of this
145 * class and it's ancestors.
146 * <p>
147 *
148 */
149 public
150 void
151 writeAttributes(Writer out)
152 throws IOException
153 {
154 super.writeAttributes(out);
155 }
156
157 /**
158 * writeAssociations
159 * <p>
160 * This method is responsible for assembling the association data
161 * into XML. It calls the super method to write out all associations of
162 * this class's ancestors.
163 * <p>
164 *
165 */
166 public
167 void
168 writeAssociations(Writer out)
169 throws IOException
170 {
171 super.writeAssociations(out);
172 if ( type != null ){
173 out.write("<Type_assn>");
174 type.writeMAGEML(out);
175 out.write("</Type_assn>");
176 }
177 if ( derivedBioAssayData.size() > 0 ){
178 out.write("<DerivedBioAssayData_assnreflist>");
179 for ( int i = 0; i < derivedBioAssayData.size(); i++) {
180 out.write("<DerivedBioAssayData_ref identifier=\"" + ((DerivedBioAssayData)derivedBioAssayData.elementAt(i)).getIdentifier() + "\"/>");
181 }
182 out.write("</DerivedBioAssayData_assnreflist>");
183 }
184 }
185
186 /**
187 * Set method for derivedBioAssayData
188 * <p>
189 * @param value to set
190 * <p>
191 *
192 */
193 public
194 void
195 setDerivedBioAssayData(
196 DerivedBioAssayData_list derivedBioAssayData
197 )
198 {
199 ((List)this.derivedBioAssayData).addAll((List)derivedBioAssayData);
200 }
201
202 /**
203 * Get method for derivedBioAssayData
204 * <p>
205 * @return value of the attribute
206 * <p>
207 *
208 */
209 public
210 DerivedBioAssayData_list
211 getDerivedBioAssayData()
212 {
213 return derivedBioAssayData;
214 }
215
216 /**
217 * Method to add DerivedBioAssayData to DerivedBioAssayData_list
218 *
219 */
220 public
221 void
222 addToDerivedBioAssayData(
223 DerivedBioAssayData derivedBioAssayData
224 )
225 {
226 this.derivedBioAssayData.add(derivedBioAssayData);
227 }
228
229 /**
230 * Method to add DerivedBioAssayData at position to
231 * DerivedBioAssayData_list
232 *
233 */
234 public
235 void
236 addToDerivedBioAssayData(
237 int position,
238 DerivedBioAssayData derivedBioAssayData
239 )
240 {
241 this.derivedBioAssayData.add(position, derivedBioAssayData);
242 }
243
244 /**
245 * Method to get DerivedBioAssayData from DerivedBioAssayData_list
246 *
247 */
248 public
249 DerivedBioAssayData
250 getFromDerivedBioAssayData(
251 int position
252 )
253 {
254 return (DerivedBioAssayData) this.derivedBioAssayData.get(position);
255 }
256
257 /**
258 * Method to remove by position from DerivedBioAssayData_list
259 *
260 */
261 public
262 void
263 removeElementAtFromDerivedBioAssayData(
264 int position
265 )
266 {
267 this.derivedBioAssayData.removeElementAt(position);
268 }
269
270 /**
271 * Method to remove first DerivedBioAssayData from
272 * DerivedBioAssayData_list
273 *
274 */
275 public
276 void
277 removeFromDerivedBioAssayData(
278 DerivedBioAssayData derivedBioAssayData
279 )
280 {
281 this.derivedBioAssayData.remove(derivedBioAssayData);
282 }
283
284 /**
285 * Set method for type
286 * <p>
287 * @param value to set
288 * <p>
289 *
290 */
291 public
292 void
293 setType(
294 OntologyEntry type
295 )
296 {
297 this.type = type;
298 }
299
300 /**
301 * Get method for type
302 * <p>
303 * @return value of the attribute
304 * <p>
305 *
306 */
307 public
308 OntologyEntry
309 getType()
310 {
311 return type;
312 }
313
314 }