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1   /*
2    *                Doelan development code
3    *
4    * This code may be freely distributed and modified under the
5    * terms of the GNU General Public Licence.  This should
6    * be distributed with the code. If you do not have a copy,
7    * see:
8    *
9    *      http://www.gnu.org/copyleft/gpl.txt
10   *
11   * Copyright (c) 2004-2005 ENS Microarray Platform
12   * Copyright for this code is held jointly by the individual
13   * authors.  These should be listed in @author doc comments.
14   *
15   * For more information on the Doelan project and its aims,
16   * or to join the Doelan mailing list, visit the home page
17   * at:
18   *
19   *      http://www.transcriptome.ens.fr/doelan
20   */
21  
22  package fr.ens.transcriptome.doelan;
23  
24  import fr.ens.transcriptome.doelan.algorithms.DoelanConfigure;
25  import fr.ens.transcriptome.doelan.algorithms.DoelanExecuteGlobalTests;
26  import fr.ens.transcriptome.doelan.algorithms.DoelanGenerateReport;
27  import fr.ens.transcriptome.doelan.algorithms.DoelanLoadGenepixData;
28  import fr.ens.transcriptome.doelan.algorithms.DoelanShowReport;
29  import fr.ens.transcriptome.doelan.tests.AbsentSpotTest;
30  import fr.ens.transcriptome.doelan.tests.BadFeatureTest;
31  import fr.ens.transcriptome.doelan.tests.GenericTest;
32  import fr.ens.transcriptome.doelan.tests.GlobalMaxBadFeatureRemoved;
33  import fr.ens.transcriptome.doelan.tests.GlobalMaxBadFeaturesTest;
34  import fr.ens.transcriptome.doelan.tests.HeterogeneousFeatureTest;
35  import fr.ens.transcriptome.doelan.tests.MaxDiameterFeatureTest;
36  import fr.ens.transcriptome.doelan.tests.MinDiameterFeatureTest;
37  import fr.ens.transcriptome.doelan.tests.NotFoundFeatureTest;
38  import fr.ens.transcriptome.doelan.tests.SaturatedPixelsTest;
39  import fr.ens.transcriptome.doelan.tests.MinimalIntensityTest;
40  import fr.ens.transcriptome.nividic.util.Version;
41  
42  /***
43   * Default values of the application.
44   * @author Laurent Jourdren
45   */
46  public final class Defaults {
47  
48    /*** Config file. */
49    public static final String CONFIG_FILE = "/files/app.properties";
50    /*** Debug mode. */
51    public static final boolean DEBUG = false;
52    /*** sub directory for data. */
53    public static final String SUBDIR_DATA = "data";
54    /*** sub directory for the reports. */
55    public static final String SUBDIR_REPORT = "reports";
56    /*** Default test suite list file. */
57    public static final String TEST_SUITE_LIST_FILE = "default.tsl";
58    /*** Name of the application. */
59    public static final String APP_NAME = "Doelan";
60    /*** Name of the application. */
61    public static final String APP_DESCRITPION = "a microarray quality test suite software";
62    /*** Version of the application. */
63    public static final String VERSION = "??.??";
64    /*** Default version of the tests. */
65    public static final Version DEFAULT_TEST_VERSION = new Version("1.0.1");
66    /*** Copyrigth date. */
67    public static final String COPYRIGHT_DATE = "2004-200x";
68    /*** Manufacturer. */
69    public static final String MANUFACTURER = "École Normale Supérieure Microarray Platform";
70    /*** Authors */
71    public static final String AUTHORS = "Laurent Jourdren";
72    /*** Web site. */
73    public static final String WEBSITE = "http://transcriptome.ens.fr/doelan";
74    /*** Web site. */
75    public static final String MANUFACTURER_WEBSITE = "http://transcriptome.ens.fr/doelan";
76  
77    /*** Licence. */
78    public static final String LICENCE = "General Public Licence";
79    /*** Internals modules. */
80    public static final Class[] INTERNALS_MODULES = {AbsentSpotTest.class,
81    //DiameterFeatureTest.class,
82        MinDiameterFeatureTest.class, MaxDiameterFeatureTest.class,
83        DoelanLoadGenepixData.class, DoelanExecuteGlobalTests.class,
84        DoelanGenerateReport.class, DoelanShowReport.class,
85        NotFoundFeatureTest.class, BadFeatureTest.class,
86        SaturatedPixelsTest.class, HeterogeneousFeatureTest.class,
87        MinimalIntensityTest.class, GlobalMaxBadFeaturesTest.class,
88        GlobalMaxBadFeatureRemoved.class, DoelanConfigure.class,
89        GenericTest.class};
90  
91    /*** Main window width. */
92    public static final int WINDOW_WIDTH = 800;
93    /*** Main window height. */
94    public static final int WINDOW_HEIGHT = 600;
95  
96    /*** Array plot width. */
97    public static final int ARRAY_PLOT_WIDTH = 600;
98    /*** Array plot margin. */
99    public static final int ARRAY_PLOT_MARGIN = 10;
100 
101   /*** Chart plot width. */
102   public static final int DOLEAN_CHART_WIDTH = 500;
103   /*** Chart plot height. */
104   public static final int DOELAN_CHART_HEIGHT = 400;
105 
106   /*** Type of workflow for doelan test suite. */
107   public static final String DOELAN_WORKFLOW_TYPE = "DoelanTestSuite";
108   /*** Version of the workflow for doelan test suite. */
109   public static final String DOELAN_WORKFLOW_VERSION = "1.0";
110   /*** Annatation key for the version of the test suite workflow. */
111   public static final String DOELAN_WORKFLOW_VERSION_ANNOTATION_KEY = "doelan.workflow.version";
112   /*** Annaotation key of the type of the chip. */
113   public static final String CHIP_TYPE_ANNOTATION_KEY = "doelan.chip.type";
114   /*** Annatotation key of the test suite name. */
115   public static final String TEST_SUITE_NAME_ANNOTATION_KEY = "doelan.testsuite.name";
116   /*** The identifier of the rejected spots. */
117   public static final String REJECTED_SPOT_IDENTIFIER = "rejected";
118 
119 }