2 * This file is part of the Vamsas Client version 0.2.
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3 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
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4 * Andrew Waterhouse and Dominik Lindner.
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6 * Earlier versions have also been incorporated into Jalview version 2.4
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7 * since 2008, and TOPALi version 2 since 2007.
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9 * The Vamsas Client is free software: you can redistribute it and/or modify
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10 * it under the terms of the GNU Lesser General Public License as published by
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11 * the Free Software Foundation, either version 3 of the License, or
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12 * (at your option) any later version.
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14 * The Vamsas Client is distributed in the hope that it will be useful,
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15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 * GNU Lesser General Public License for more details.
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19 * You should have received a copy of the GNU Lesser General Public License
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20 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
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22 package uk.ac.vamsas.test.objects;
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24 import org.apache.commons.logging.Log;
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25 import org.apache.commons.logging.LogFactory;
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27 import uk.ac.vamsas.objects.core.*;
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28 import uk.ac.vamsas.objects.utils.*;
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29 import uk.ac.vamsas.objects.utils.document.*;
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30 import uk.ac.vamsas.test.simpleclient.ArchiveReports;
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33 * @author jim test XSD-Java binding classes in uk.ac.vamsas.objects.core
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36 static Log log = LogFactory.getLog(Core.class);
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40 * complete any automatically completable entries in the dataset
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44 public static String user = "uk.ac.vamsas.test.objects.Core";
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46 public static void complete(DataSet ds) {
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47 Sequence[] q = ds.getSequence();
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48 for (int i = 0, j = q.length; i < j; i++) {
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49 q[i].setStart(i + 1);
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50 q[i].setEnd(q[i].getSequence().length() + i + 1);
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54 public static VAMSAS getDemoVamsas() {
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55 VAMSAS v = new VAMSAS();
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56 DataSet ds = new DataSet();
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57 ds.addSequence(Seq.newSequence("Dummy1", "ASDFLEQ",
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58 SymbolDictionary.STANDARD_AA, 5, 11));
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59 ds.addSequence(Seq.newSequence("Dummy2", "ASFLEQ",
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60 SymbolDictionary.STANDARD_AA, 5, 10));
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61 ds.addSequence(Seq.newSequence("Dummy3", "ADFEQ",
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62 SymbolDictionary.STANDARD_AA, 3, 7));
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63 ds.setProvenance(ProvenanceStuff.newProvenance(user,
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64 "constructed some dummy sequences"));
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67 Alignment al = new Alignment();
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68 al.setProvenance(ProvenanceStuff.newProvenance(user,
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69 "Created dummy alignment"));
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70 // rely on newAlignmentSequence to set start/end correctly
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71 al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds
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72 .getSequence(0), -1, -1));
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73 al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds
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74 .getSequence(1), -1, -1));
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75 al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds
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76 .getSequence(2), -1, -1));
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78 ds.addAlignment(al);
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79 // TODO: create annotations
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80 // TODO: create tree
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87 public static void main(String[] args) {
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90 * test constants and controlled vocab utils
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92 System.out.println("VersionEntries.compare(invalid, ALPHA) returned "
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93 + VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
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94 System.out.println("VersionEntries.compare(ALPHA, invalid) returned "
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95 + VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));
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96 System.out.println("VersionEntries.compare(BETA, ALPHA) returned "
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97 + VersionEntries.compare(VersionEntries.BETA_VERSION,
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98 VersionEntries.ALPHA_VERSION));
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99 System.out.println("VersionEntries.compare(ALPHA, BETA) returned "
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100 + VersionEntries.compare(VersionEntries.ALPHA_VERSION,
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101 VersionEntries.BETA_VERSION));
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102 System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "
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103 + VersionEntries.compare(VersionEntries.ALPHA_VERSION,
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104 VersionEntries.ALPHA_VERSION));
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105 System.out.println("VersionEntries.compare(invalid, invalid) returned "
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106 + VersionEntries.compare("invalid", "invalid"));
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107 System.out.println("VersionEntries.latestVersion()="
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108 + VersionEntries.latestVersion() + ", dict_aa="
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109 + SymbolDictionary.STANDARD_AA + ", dict_na="
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110 + SymbolDictionary.STANDARD_NA);
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112 * Test utils and autogenerated Vobject interfaces
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115 VamsasDocument doc = DocumentStuff.newVamsasDocument(
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116 new VAMSAS[] { getDemoVamsas() }, ProvenanceStuff.newProvenance(
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117 "org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
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118 VersionEntries.latestVersion());
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119 ArchiveReports.reportDocument(doc, null, true, System.out);
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