Source code: org/biomage/BioAssayData/DesignElementDimension.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 10:46:19 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.BioAssayData
49 *
50 */
51 package org.biomage.BioAssayData;
52
53 /**
54 * Import list for DesignElementDimension
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.Common.Identifiable;
63
64 /**
65 * An ordered list of designElements. It will be realized as one of its
66 * three subclasses.
67 *
68 */
69 public
70 abstract
71 class DesignElementDimension
72 extends Identifiable
73 implements Serializable
74 {
75 /**
76 * Default constructor.
77 *
78 */
79 public
80 DesignElementDimension()
81 {
82 super();
83 }
84
85 /**
86 * Attribute constructor.
87 *
88 * Looks up the attributes in the parameter and casts them from strings
89 * appropriately
90 * @param atts: the attribute list.
91 *
92 */
93 // TODO Work in progress (attribute constructor).
94 public
95 DesignElementDimension(Attributes atts)
96 {
97 super(atts);
98
99 }
100
101 /**
102 * writeMAGEML
103 * <p>
104 * This method is responsible for assembling the attribute and
105 * association data into XML. It creates the object tag and then calls
106 * the writeAttributes and writeAssociation methods.
107 * <p>
108 *
109 */
110 public
111 void
112 writeMAGEML(Writer out)
113 throws IOException
114 {
115 }
116
117 /**
118 * writeAttributes
119 * <p>
120 * This method is responsible for assembling the attribute data into
121 * XML. It calls the super method to write out all attributes of this
122 * class and it's ancestors.
123 * <p>
124 *
125 */
126 public
127 void
128 writeAttributes(Writer out)
129 throws IOException
130 {
131 super.writeAttributes(out);
132 }
133
134 /**
135 * writeAssociations
136 * <p>
137 * This method is responsible for assembling the association data
138 * into XML. It calls the super method to write out all associations of
139 * this class's ancestors.
140 * <p>
141 *
142 */
143 public
144 void
145 writeAssociations(Writer out)
146 throws IOException
147 {
148 super.writeAssociations(out);
149 }
150
151 }