1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.metadata;
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21 import java.io.File;
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23 import compbio.runner.Util;
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24 import compbio.runner.msa.ClustalW;
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25 import compbio.runner.msa.Muscle;
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26 import compbio.runner.msa.Tcoffee;
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27 import compbio.util.SysPrefs;
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29 public class AllTestSuit {
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31 public static final PresetManager<ClustalW> CLUSTAL_PRESETS = Util
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32 .getPresets(ClustalW.class);
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33 public static final RunnerConfig<ClustalW> CLUSTAL_PARAMETERS = Util
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34 .getSupportedOptions(ClustalW.class);
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35 public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = compbio.engine.client.Util
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36 .getLimits(new ClustalW().getType());
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38 public static final PresetManager<Tcoffee> TCOFFEE_PRESETS = Util
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39 .getPresets(Tcoffee.class);
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40 public static final RunnerConfig<Tcoffee> TCOFFEE_PARAMETERS = Util
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41 .getSupportedOptions(Tcoffee.class);
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42 public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = compbio.engine.client.Util
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43 .getLimits(new Tcoffee().getType());
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45 public static final PresetManager<Muscle> MUSCLE_PRESETS = Util
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46 .getPresets(Muscle.class);
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47 public static final RunnerConfig<Muscle> MUSCLE_PARAMETERS = Util
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48 .getSupportedOptions(Muscle.class);
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49 public static final LimitsManager<Muscle> MUSCLE_LIMITS = compbio.engine.client.Util
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50 .getLimits(new Muscle().getType());
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52 public final static String test_group_cluster = "cluster";
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53 public final static String test_group_runner = "runner";
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54 public final static String test_group_non_windows = "non_windows";
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55 public final static String test_group_windows_only = "windows_only";
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56 public final static String test_group_engine = "engine";
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57 public final static String test_group_long = "performance";
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58 public final static String test_group_webservices = "webservices";
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61 * For this to work execution must start from the project directory!
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63 public static final String CURRENT_DIRECTORY = SysPrefs
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64 .getCurrentDirectory() + File.separator;
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66 public static final String TEST_DATA_PATH = "testsrc" + File.separator
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67 + "testdata" + File.separator;
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69 public static final String TEST_DATA_PATH_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY
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72 // For cluster execution paths MUST BE ABSOLUTE as cluster hosts will not be
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73 // able to access the task otherwise
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74 public static final String OUTPUT_DIR_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY
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75 + File.separator + "local_jobsout" + File.separator;
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77 public static final String RUNNER_TEST_LOGGER = "RunnerLogger";
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79 public static final String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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82 public static final String test_alignment_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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83 + "TO1381.fasta.aln";
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85 public static final String test_input_real = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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86 + "50x500Protein.fasta";
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88 public static final String test_input_dna = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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91 public static final String test_input_large = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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92 + "1000x3000Dna.fasta";
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