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