Source code: org/biomage/DesignElement/DesignElement.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 10:46:42 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.DesignElement
49 *
50 */
51 package org.biomage.DesignElement;
52
53 /**
54 * Import list for DesignElement
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.HasControlType;
63 import org.biomage.Common.Identifiable;
64 import org.biomage.Description.OntologyEntry;
65
66 /**
67 * An element of an array. This is generally of type feature but can be
68 * specified as reporters or compositeSequence for arrays that are
69 * abstracted from a physical array.
70 *
71 */
72 public
73 abstract
74 class DesignElement
75 extends Identifiable
76 implements Serializable,
77 HasControlType
78 {
79 /**
80 * If the design element represents a control, the type of control
81 * it is (normalization, deletion, negative, positive, etc.)
82 *
83 */
84 private OntologyEntry controlType;
85
86
87 /**
88 * Default constructor.
89 *
90 */
91 public
92 DesignElement()
93 {
94 super();
95 }
96
97 /**
98 * Attribute constructor.
99 *
100 * Looks up the attributes in the parameter and casts them from strings
101 * appropriately
102 * @param atts: the attribute list.
103 *
104 */
105 // TODO Work in progress (attribute constructor).
106 public
107 DesignElement(Attributes atts)
108 {
109 super(atts);
110
111 }
112
113 /**
114 * writeMAGEML
115 * <p>
116 * This method is responsible for assembling the attribute and
117 * association data into XML. It creates the object tag and then calls
118 * the writeAttributes and writeAssociation methods.
119 * <p>
120 *
121 */
122 public
123 void
124 writeMAGEML(Writer out)
125 throws IOException
126 {
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 ( controlType != null ){
162 out.write("<ControlType_assn>");
163 controlType.writeMAGEML(out);
164 out.write("</ControlType_assn>");
165 }
166 }
167
168 /**
169 * Set method for controlType
170 * <p>
171 * @param value to set
172 * <p>
173 *
174 */
175 public
176 void
177 setControlType(
178 OntologyEntry controlType
179 )
180 {
181 this.controlType = controlType;
182 }
183
184 /**
185 * Get method for controlType
186 * <p>
187 * @return value of the attribute
188 * <p>
189 *
190 */
191 public
192 OntologyEntry
193 getControlType()
194 {
195 return controlType;
196 }
197
198 }