Source code: org/biomage/BQS/BQS_package.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 10:46:53 AM *
43 * *
44 ***************************************************************************
45 */
46
47 /**
48 * org.biomage.BQS
49 *
50 */
51 package org.biomage.BQS;
52
53 /**
54 * Import list for BQS_package
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 * Allows a reference to an article, book or other publication to be
65 * specified for searching repositories.
66 *
67 */
68 public
69 class BQS_package
70 implements Serializable
71 {
72 /**
73 * Default constructor.
74 *
75 */
76 public
77 BQS_package()
78 {
79 }
80
81 /**
82 * Attribute constructor.
83 *
84 * Looks up the attributes in the parameter and casts them from strings
85 * appropriately
86 * @param atts: the attribute list.
87 *
88 */
89 // TODO Work in progress (attribute constructor).
90 public
91 BQS_package(Attributes atts)
92 {
93 }
94
95 /**
96 * writeMAGEML
97 * <p>
98 * This method is responsible for assembling the attribute and
99 * association data into XML. It creates the object tag and then calls
100 * the writeAttributes and writeAssociation methods.
101 * <p>
102 *
103 */
104 public
105 void
106 writeMAGEML(Writer out)
107 throws IOException
108 {
109 out.write("<BQS_package");
110 writeAttributes(out);
111 out.write(">");
112 writeAssociations(out);
113 out.write("</BQS_package>");
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 }
131
132 /**
133 * writeAssociations
134 * <p>
135 * This method is responsible for assembling the association data
136 * into XML. It calls the super method to write out all associations of
137 * this class's ancestors.
138 * <p>
139 *
140 */
141 public
142 void
143 writeAssociations(Writer out)
144 throws IOException
145 {
146 }
147
148 }