Source code: org/biomage/BioAssayData/MeasuredBioAssayData.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 MeasuredBioAssayData
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 * The data associated with the MeasuredBioAssay produced by
65 * FeatureExtraction.
66 *
67 */
68 public
69 class MeasuredBioAssayData
70 extends BioAssayData
71 implements Serializable
72 {
73 /**
74 * Default constructor.
75 *
76 */
77 public
78 MeasuredBioAssayData()
79 {
80 super();
81 }
82
83 /**
84 * Attribute constructor.
85 *
86 * Looks up the attributes in the parameter and casts them from strings
87 * appropriately
88 * @param atts: the attribute list.
89 *
90 */
91 // TODO Work in progress (attribute constructor).
92 public
93 MeasuredBioAssayData(Attributes atts)
94 {
95 super(atts);
96
97 }
98
99 /**
100 * writeMAGEML
101 * <p>
102 * This method is responsible for assembling the attribute and
103 * association data into XML. It creates the object tag and then calls
104 * the writeAttributes and writeAssociation methods.
105 * <p>
106 *
107 */
108 public
109 void
110 writeMAGEML(Writer out)
111 throws IOException
112 {
113 out.write("<MeasuredBioAssayData");
114 writeAttributes(out);
115 out.write(">");
116 writeAssociations(out);
117 out.write("</MeasuredBioAssayData>");
118 }
119
120 /**
121 * writeAttributes
122 * <p>
123 * This method is responsible for assembling the attribute data into
124 * XML. It calls the super method to write out all attributes of this
125 * class and it's ancestors.
126 * <p>
127 *
128 */
129 public
130 void
131 writeAttributes(Writer out)
132 throws IOException
133 {
134 super.writeAttributes(out);
135 }
136
137 /**
138 * writeAssociations
139 * <p>
140 * This method is responsible for assembling the association data
141 * into XML. It calls the super method to write out all associations of
142 * this class's ancestors.
143 * <p>
144 *
145 */
146 public
147 void
148 writeAssociations(Writer out)
149 throws IOException
150 {
151 super.writeAssociations(out);
152 }
153
154 }