Source code: org/biomage/BioAssayData/DesignElementMapping.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 10:46:20 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.BioAssayData
49 *
50 */
51 package org.biomage.BioAssayData;
52
53 /**
54 * Import list for DesignElementMapping
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.HasDesignElementMaps;
63 import org.biomage.Common.Extendable;
64
65 /**
66 * Container of the mappings of the input DesignElement dimensions to
67 * the output DesignElement dimension.
68 *
69 */
70 public
71 class DesignElementMapping
72 extends Extendable
73 implements Serializable,
74 HasDesignElementMaps
75 {
76 /**
77 * The maps for the DesignElements.
78 *
79 */
80 private DesignElementMaps_list designElementMaps = new DesignElementMaps_list();
81
82 /**
83 * Default constructor.
84 *
85 */
86 public
87 DesignElementMapping()
88 {
89 super();
90 }
91
92 /**
93 * Attribute constructor.
94 *
95 * Looks up the attributes in the parameter and casts them from strings
96 * appropriately
97 * @param atts: the attribute list.
98 *
99 */
100 // TODO Work in progress (attribute constructor).
101 public
102 DesignElementMapping(Attributes atts)
103 {
104 super(atts);
105
106 }
107
108 /**
109 * writeMAGEML
110 * <p>
111 * This method is responsible for assembling the attribute and
112 * association data into XML. It creates the object tag and then calls
113 * the writeAttributes and writeAssociation methods.
114 * <p>
115 *
116 */
117 public
118 void
119 writeMAGEML(Writer out)
120 throws IOException
121 {
122 out.write("<DesignElementMapping");
123 writeAttributes(out);
124 out.write(">");
125 writeAssociations(out);
126 out.write("</DesignElementMapping>");
127 }
128
129 /**
130 * writeAttributes
131 * <p>
132 * This method is responsible for assembling the attribute data into
133 * XML. It calls the super method to write out all attributes of this
134 * class and it's ancestors.
135 * <p>
136 *
137 */
138 public
139 void
140 writeAttributes(Writer out)
141 throws IOException
142 {
143 super.writeAttributes(out);
144 }
145
146 /**
147 * writeAssociations
148 * <p>
149 * This method is responsible for assembling the association data
150 * into XML. It calls the super method to write out all associations of
151 * this class's ancestors.
152 * <p>
153 *
154 */
155 public
156 void
157 writeAssociations(Writer out)
158 throws IOException
159 {
160 super.writeAssociations(out);
161 if ( designElementMaps.size() > 0 ){
162 out.write("<DesignElementMaps_assnreflist>");
163 for ( int i = 0; i < designElementMaps.size(); i++) {
164 out.write("<DesignElementMap_ref identifier=\"" + ((DesignElementMap)designElementMaps.elementAt(i)).getIdentifier() + "\"/>");
165 }
166 out.write("</DesignElementMaps_assnreflist>");
167 }
168 }
169
170 /**
171 * Set method for designElementMaps
172 * <p>
173 * @param value to set
174 * <p>
175 *
176 */
177 public
178 void
179 setDesignElementMaps(
180 DesignElementMaps_list designElementMaps
181 )
182 {
183 ((List)this.designElementMaps).addAll((List)designElementMaps);
184 }
185
186 /**
187 * Get method for designElementMaps
188 * <p>
189 * @return value of the attribute
190 * <p>
191 *
192 */
193 public
194 DesignElementMaps_list
195 getDesignElementMaps()
196 {
197 return designElementMaps;
198 }
199
200 /**
201 * Method to add DesignElementMap to DesignElementMaps_list
202 *
203 */
204 public
205 void
206 addToDesignElementMaps(
207 DesignElementMap designElementMap
208 )
209 {
210 this.designElementMaps.add(designElementMap);
211 }
212
213 /**
214 * Method to add DesignElementMap at position to
215 * DesignElementMaps_list
216 *
217 */
218 public
219 void
220 addToDesignElementMaps(
221 int position,
222 DesignElementMap designElementMap
223 )
224 {
225 this.designElementMaps.add(position, designElementMap);
226 }
227
228 /**
229 * Method to get DesignElementMap from DesignElementMaps_list
230 *
231 */
232 public
233 DesignElementMap
234 getFromDesignElementMaps(
235 int position
236 )
237 {
238 return (DesignElementMap) this.designElementMaps.get(position);
239 }
240
241 /**
242 * Method to remove by position from DesignElementMaps_list
243 *
244 */
245 public
246 void
247 removeElementAtFromDesignElementMaps(
248 int position
249 )
250 {
251 this.designElementMaps.removeElementAt(position);
252 }
253
254 /**
255 * Method to remove first DesignElementMap from
256 * DesignElementMaps_list
257 *
258 */
259 public
260 void
261 removeFromDesignElementMaps(
262 DesignElementMap designElementMap
263 )
264 {
265 this.designElementMaps.remove(designElementMap);
266 }
267
268 }