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