Source code: org/biomage/Array/ManufactureLIMSBiomaterial.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 10:46:07 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.Array
49 *
50 */
51 package org.biomage.Array;
52
53 /**
54 * Import list for ManufactureLIMSBiomaterial
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
63 /**
64 * Stores the location from which a biomaterial was obtained.
65 *
66 */
67 public
68 class ManufactureLIMSBiomaterial
69 extends ManufactureLIMS
70 implements Serializable
71 {
72 /**
73 * The plate from which a biomaterial was obtained.
74 *
75 */
76 String bioMaterialPlateIdentifier;
77
78 /**
79 * The plate row from which a biomaterial was obtained. Specified
80 * by a letter.
81 *
82 */
83 String bioMaterialPlateRow;
84
85 /**
86 * The plate column from which a biomaterial was obtained.
87 * Specified by a number.
88 *
89 */
90 String bioMaterialPlateCol;
91
92 /**
93 * Default constructor.
94 *
95 */
96 public
97 ManufactureLIMSBiomaterial()
98 {
99 super();
100 }
101
102 /**
103 * Attribute constructor.
104 *
105 * Looks up the attributes in the parameter and casts them from strings
106 * appropriately
107 * @param atts: the attribute list.
108 *
109 */
110 // TODO Work in progress (attribute constructor).
111 public
112 ManufactureLIMSBiomaterial(Attributes atts)
113 {
114 super(atts);
115
116 {
117 int nIndex = atts.getIndex("", "bioMaterialPlateIdentifier");
118 if (nIndex != -1)
119 {
120 bioMaterialPlateIdentifier = atts.getValue(nIndex);
121 }
122 }
123
124 {
125 int nIndex = atts.getIndex("", "bioMaterialPlateRow");
126 if (nIndex != -1)
127 {
128 bioMaterialPlateRow = atts.getValue(nIndex);
129 }
130 }
131
132 {
133 int nIndex = atts.getIndex("", "bioMaterialPlateCol");
134 if (nIndex != -1)
135 {
136 bioMaterialPlateCol = atts.getValue(nIndex);
137 }
138 }
139
140 }
141
142 /**
143 * writeMAGEML
144 * <p>
145 * This method is responsible for assembling the attribute and
146 * association data into XML. It creates the object tag and then calls
147 * the writeAttributes and writeAssociation methods.
148 * <p>
149 *
150 */
151 public
152 void
153 writeMAGEML(Writer out)
154 throws IOException
155 {
156 out.write("<ManufactureLIMSBiomaterial");
157 writeAttributes(out);
158 out.write(">");
159 writeAssociations(out);
160 out.write("</ManufactureLIMSBiomaterial>");
161 }
162
163 /**
164 * writeAttributes
165 * <p>
166 * This method is responsible for assembling the attribute data into
167 * XML. It calls the super method to write out all attributes of this
168 * class and it's ancestors.
169 * <p>
170 *
171 */
172 public
173 void
174 writeAttributes(Writer out)
175 throws IOException
176 {
177 super.writeAttributes(out);
178 if ( bioMaterialPlateIdentifier != null ) {
179 out.write(" bioMaterialPlateIdentifier=\"" + bioMaterialPlateIdentifier + "\"");
180 }
181 if ( bioMaterialPlateRow != null ) {
182 out.write(" bioMaterialPlateRow=\"" + bioMaterialPlateRow + "\"");
183 }
184 if ( bioMaterialPlateCol != null ) {
185 out.write(" bioMaterialPlateCol=\"" + bioMaterialPlateCol + "\"");
186 }
187 }
188
189 /**
190 * writeAssociations
191 * <p>
192 * This method is responsible for assembling the association data
193 * into XML. It calls the super method to write out all associations of
194 * this class's ancestors.
195 * <p>
196 *
197 */
198 public
199 void
200 writeAssociations(Writer out)
201 throws IOException
202 {
203 super.writeAssociations(out);
204 }
205
206 /**
207 * Set method for bioMaterialPlateIdentifier
208 * <p>
209 * @param value to set
210 * <p>
211 *
212 */
213 public
214 void
215 setBioMaterialPlateIdentifier(
216 String bioMaterialPlateIdentifier
217 )
218 {
219 this.bioMaterialPlateIdentifier = bioMaterialPlateIdentifier;
220 }
221
222 /**
223 * Get method for bioMaterialPlateIdentifier
224 * <p>
225 * @return value of the attribute
226 * <p>
227 *
228 */
229 public
230 String
231 getBioMaterialPlateIdentifier()
232 {
233 return bioMaterialPlateIdentifier;
234 }
235
236 /**
237 * Set method for bioMaterialPlateRow
238 * <p>
239 * @param value to set
240 * <p>
241 *
242 */
243 public
244 void
245 setBioMaterialPlateRow(
246 String bioMaterialPlateRow
247 )
248 {
249 this.bioMaterialPlateRow = bioMaterialPlateRow;
250 }
251
252 /**
253 * Get method for bioMaterialPlateRow
254 * <p>
255 * @return value of the attribute
256 * <p>
257 *
258 */
259 public
260 String
261 getBioMaterialPlateRow()
262 {
263 return bioMaterialPlateRow;
264 }
265
266 /**
267 * Set method for bioMaterialPlateCol
268 * <p>
269 * @param value to set
270 * <p>
271 *
272 */
273 public
274 void
275 setBioMaterialPlateCol(
276 String bioMaterialPlateCol
277 )
278 {
279 this.bioMaterialPlateCol = bioMaterialPlateCol;
280 }
281
282 /**
283 * Get method for bioMaterialPlateCol
284 * <p>
285 * @return value of the attribute
286 * <p>
287 *
288 */
289 public
290 String
291 getBioMaterialPlateCol()
292 {
293 return bioMaterialPlateCol;
294 }
295
296 }