source: trunk/doc/src/docbook/appendix/raw_data_types.xml @ 3944

Last change on this file since 3944 was 3944, checked in by Martin Svensson, 14 years ago

References #819 The class-tag and interface-tag are now linking to the javadoc for the tagged class or interface.
Updated the source files of the documentation.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 3.6 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE appendix PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: raw_data_types.xml 3944 2007-11-09 15:31:00Z martin $
7 
8  Copyright (C) 2007 Nicklas Nordborg
9 
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12 
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 2
16  of the License, or (at your option) any later version.
17 
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22 
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<appendix id="appendix.rawdatatypes">
30  <title>Platforms and raw-data-types.xml reference</title>
31 
32  <para>
33    Raw data can be stored either as files attached to items or in
34    the database.
35    The <classname docapi="net.sf.basedb.core">Platform</classname> item has information
36    about this. Configuration information for the database tables
37    and columns used to store raw data in the database is found in the
38    <filename>raw-data-types.xml</filename> file. For detailed information
39    see <xref linkend="core_api.data_in_files" />.
40  </para>
41 
42  <sect1 id="appendix.rawdatatypes.platforms">
43    <title>Default platforms/variants installed with BASE</title>
44   
45    <informaltable>
46      <tgroup cols="7">
47        <colspec colname="platform.name" />
48        <colspec colname="platform.id" />
49        <colspec colname="variant.name" />
50        <colspec colname="variant.id" />
51        <colspec colname="filetype.item" />
52        <colspec colname="filetype.name" />
53        <colspec colname="filetype.id" />
54        <thead>
55          <row>
56            <entry namest="platform.name" nameend="platform.id">Platform</entry>
57            <entry namest="variant.name" nameend="variant.id">Variants</entry>
58            <entry namest="filetype.item" nameend="filetype.id">Data file types</entry>
59          </row>
60          <row>
61            <entry>Name</entry>
62            <entry>ID</entry>
63            <entry>Name</entry>
64            <entry>ID</entry>
65            <entry>Item</entry>
66            <entry>Name</entry>
67            <entry>ID</entry>
68          </row>
69        </thead>
70        <tbody>
71          <row>
72            <entry morerows="2">Generic</entry>
73            <entry morerows="2">generic</entry>
74            <entry morerows="2">-</entry>
75            <entry morerows="2">-</entry>
76
77            <entry morerows="1">Array design</entry>
78            <entry>Reporter map</entry>
79            <entry>generic.reportermap</entry>
80          </row>
81          <row>
82            <entry>Print map</entry>
83            <entry>generic.printmap</entry>
84          </row>
85          <row>
86            <entry>Raw bioassay</entry>
87            <entry>Generic raw data</entry>
88            <entry>generic.rawdata</entry>
89          </row>
90          <row>
91            <entry morerows="1">Affymetrix</entry>
92            <entry morerows="1">affymetrix</entry>
93            <entry morerows="1">-</entry>
94            <entry morerows="1">-</entry>
95            <entry>Array design</entry>
96            <entry>CDF file</entry>
97            <entry>affymetrix.cdf</entry>
98          </row>
99          <row>
100            <entry>Raw bioassay</entry>
101            <entry>CEL file</entry>
102            <entry>affymetrix.cel</entry>
103          </row>
104        </tbody>
105      </tgroup>
106    </informaltable>
107   
108 
109  </sect1>
110 
111  <sect1 id="appendix.rawdatatypes.ref">
112    <title>raw-data-types.xml reference</title>
113   
114    <para>
115      TODO
116    </para>
117   
118  </sect1>
119
120</appendix>
121
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