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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
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 }