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package eu.etaxonomy.cdm.api.service;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNotNull;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.junit.Before;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
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/**
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* @author m.venin
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* @created 16.12.2010
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* @version 1.0
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*/
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public class IdentificationKeyGeneratorTest {
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private static final Logger logger = Logger.getLogger(IdentificationKeyGeneratorTest.class);
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private Feature feature1;
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private Feature feature2;
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private Feature feature3;
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private Feature feature4;
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private Taxon taxon1;
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private Taxon taxon2;
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private Taxon taxon3;
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private Taxon taxon4;
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private Taxon taxon5;
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private Taxon taxon6;
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private Taxon taxon7;
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private Taxon taxon8;
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private TaxonDescription taxond1;
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private TaxonDescription taxond2;
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private TaxonDescription taxond3;
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private TaxonDescription taxond4;
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private TaxonDescription taxond5;
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private TaxonDescription taxond6;
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private TaxonDescription taxond7;
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private TaxonDescription taxond8;
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private Set<TaxonDescription> taxa;
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private List<Feature> features;
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private PolytomousKeyGenerator generator;
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@Before
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public void setUp() throws Exception {
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feature1 = Feature.NewInstance("","Shape of the head","");
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feature2 = Feature.NewInstance("","Presence of wings","");
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feature3 = Feature.NewInstance("","Length of wings","");
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feature4 = Feature.NewInstance("","Colour","");
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NonViralName tn1 = NonViralName.NewInstance(null);
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NonViralName tn2 = NonViralName.NewInstance(null);
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NonViralName tn3 = NonViralName.NewInstance(null);
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NonViralName tn4 = NonViralName.NewInstance(null);
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NonViralName tn5 = NonViralName.NewInstance(null);
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NonViralName tn6 = NonViralName.NewInstance(null);
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NonViralName tn7 = NonViralName.NewInstance(null);
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NonViralName tn8 = NonViralName.NewInstance(null);
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taxon1 = Taxon.NewInstance(tn1, null);
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taxon2 = Taxon.NewInstance(tn2, null);
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taxon3 = Taxon.NewInstance(tn3, null);
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taxon4 = Taxon.NewInstance(tn4, null);
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taxon5 = Taxon.NewInstance(tn5, null);
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taxon6 = Taxon.NewInstance(tn6, null);
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taxon7 = Taxon.NewInstance(tn7, null);
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taxon8 = Taxon.NewInstance(tn8, null);
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taxond1 = TaxonDescription.NewInstance(taxon1);
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taxond2 = TaxonDescription.NewInstance(taxon2);
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taxond3 = TaxonDescription.NewInstance(taxon3);
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taxond4 = TaxonDescription.NewInstance(taxon4);
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taxond5 = TaxonDescription.NewInstance(taxon5);
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taxond6 = TaxonDescription.NewInstance(taxon6);
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taxond7 = TaxonDescription.NewInstance(taxon7);
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taxond8 = TaxonDescription.NewInstance(taxon8);
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CategoricalData catd11 = CategoricalData.NewInstance();
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catd11.setFeature(feature1);
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StateData sd11 = StateData.NewInstance();
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State s11 = State.NewInstance("","Triangular","");
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State s12 = State.NewInstance("","Circular","");
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sd11.setState(s11);
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catd11.addState(sd11);
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CategoricalData catd12 = CategoricalData.NewInstance();
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catd12.setFeature(feature1);
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StateData sd12 = StateData.NewInstance();
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sd12.setState(s11);
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catd12.addState(sd12);
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CategoricalData catd13 = CategoricalData.NewInstance();
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catd13.setFeature(feature1);
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StateData sd13 = StateData.NewInstance();
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sd13.setState(s11);
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catd13.addState(sd13);
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CategoricalData catd14 = CategoricalData.NewInstance();
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catd14.setFeature(feature1);
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StateData sd14 = StateData.NewInstance();
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sd14.setState(s11);
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catd14.addState(sd14);
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CategoricalData catd15 = CategoricalData.NewInstance();
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catd15.setFeature(feature1);
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StateData sd15 = StateData.NewInstance();
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sd15.setState(s12);
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catd15.addState(sd15);
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CategoricalData catd16 = CategoricalData.NewInstance();
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catd16.setFeature(feature1);
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StateData sd16 = StateData.NewInstance();
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sd16.setState(s12);
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catd16.addState(sd16);
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CategoricalData catd17 = CategoricalData.NewInstance();
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catd17.setFeature(feature1);
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StateData sd17 = StateData.NewInstance();
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sd17.setState(s12);
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catd17.addState(sd17);
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CategoricalData catd18 = CategoricalData.NewInstance();
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catd18.setFeature(feature1);
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StateData sd18 = StateData.NewInstance();
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sd18.setState(s12);
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catd18.addState(sd18);
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/*************************/
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CategoricalData catd21 = CategoricalData.NewInstance();
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catd21.setFeature(feature2);
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StateData sd21 = StateData.NewInstance();
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State s21 = State.NewInstance("","Yes","");
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State s22 = State.NewInstance("","No","");
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sd21.setState(s21);
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catd21.addState(sd21);
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CategoricalData catd22 = CategoricalData.NewInstance();
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catd22.setFeature(feature2);
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StateData sd22 = StateData.NewInstance();
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sd22.setState(s21);
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catd22.addState(sd22);
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CategoricalData catd23 = CategoricalData.NewInstance();
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catd23.setFeature(feature2);
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StateData sd23 = StateData.NewInstance();
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sd23.setState(s21);
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catd23.addState(sd23);
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CategoricalData catd24 = CategoricalData.NewInstance();
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catd24.setFeature(feature2);
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StateData sd24 = StateData.NewInstance();
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sd24.setState(s21);
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catd24.addState(sd24);
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CategoricalData catd25 = CategoricalData.NewInstance();
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catd25.setFeature(feature2);
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StateData sd25 = StateData.NewInstance();
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sd25.setState(s21);
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catd25.addState(sd25);
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CategoricalData catd26 = CategoricalData.NewInstance();
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catd26.setFeature(feature2);
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StateData sd26 = StateData.NewInstance();
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sd26.setState(s21);
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catd26.addState(sd26);
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CategoricalData catd27 = CategoricalData.NewInstance();
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catd27.setFeature(feature2);
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StateData sd27 = StateData.NewInstance();
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sd27.setState(s21);
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catd27.addState(sd27);
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CategoricalData catd28 = CategoricalData.NewInstance();
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catd28.setFeature(feature2);
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StateData sd28 = StateData.NewInstance();
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sd28.setState(s22);
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catd28.addState(sd28);
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/*************************/
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QuantitativeData qtd31 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv311 = StatisticalMeasurementValue.NewInstance();
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smv311.setValue(0);
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StatisticalMeasure sm311 = StatisticalMeasure.MIN();
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smv311.setType(sm311);
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StatisticalMeasurementValue smv312 = StatisticalMeasurementValue.NewInstance();
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smv312.setValue(3);
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StatisticalMeasure sm312 = StatisticalMeasure.MAX();
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smv312.setType(sm312);
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qtd31.addStatisticalValue(smv311);
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qtd31.addStatisticalValue(smv312);
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QuantitativeData qtd32 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv321 = StatisticalMeasurementValue.NewInstance();
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smv321.setValue(0);
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StatisticalMeasure sm321 = StatisticalMeasure.MIN();
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smv321.setType(sm321);
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StatisticalMeasurementValue smv322 = StatisticalMeasurementValue.NewInstance();
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smv322.setValue(3);
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StatisticalMeasure sm322 = StatisticalMeasure.MAX();
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smv322.setType(sm322);
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qtd32.addStatisticalValue(smv321);
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qtd32.addStatisticalValue(smv322);
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QuantitativeData qtd33 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv331 = StatisticalMeasurementValue.NewInstance();
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smv331.setValue(6);
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StatisticalMeasure sm331 = StatisticalMeasure.MIN();
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smv331.setType(sm331);
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StatisticalMeasurementValue smv332 = StatisticalMeasurementValue.NewInstance();
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smv332.setValue(9);
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StatisticalMeasure sm332 = StatisticalMeasure.MAX();
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smv332.setType(sm332);
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qtd33.addStatisticalValue(smv331);
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qtd33.addStatisticalValue(smv332);
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QuantitativeData qtd34 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv341 = StatisticalMeasurementValue.NewInstance();
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smv341.setValue(6);
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StatisticalMeasure sm341 = StatisticalMeasure.MIN();
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smv341.setType(sm341);
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StatisticalMeasurementValue smv342 = StatisticalMeasurementValue.NewInstance();
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smv342.setValue(9);
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StatisticalMeasure sm342 = StatisticalMeasure.MAX();
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smv342.setType(sm342);
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qtd34.addStatisticalValue(smv341);
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qtd34.addStatisticalValue(smv342);
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QuantitativeData qtd35 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv351 = StatisticalMeasurementValue.NewInstance();
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smv351.setValue(0);
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StatisticalMeasure sm351 = StatisticalMeasure.MIN();
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smv351.setType(sm351);
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StatisticalMeasurementValue smv352 = StatisticalMeasurementValue.NewInstance();
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smv352.setValue(3);
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StatisticalMeasure sm352 = StatisticalMeasure.MAX();
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smv352.setType(sm352);
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qtd35.addStatisticalValue(smv351);
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qtd35.addStatisticalValue(smv352);
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QuantitativeData qtd36 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv361 = StatisticalMeasurementValue.NewInstance();
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smv361.setValue(0);
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StatisticalMeasure sm361 = StatisticalMeasure.MIN();
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smv361.setType(sm361);
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StatisticalMeasurementValue smv362 = StatisticalMeasurementValue.NewInstance();
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smv362.setValue(3);
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StatisticalMeasure sm362 = StatisticalMeasure.MAX();
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smv362.setType(sm362);
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qtd36.addStatisticalValue(smv361);
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qtd36.addStatisticalValue(smv362);
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QuantitativeData qtd37 = QuantitativeData.NewInstance();
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StatisticalMeasurementValue smv371 = StatisticalMeasurementValue.NewInstance();
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smv371.setValue(6);
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StatisticalMeasure sm371 = StatisticalMeasure.MIN();
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smv371.setType(sm371);
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StatisticalMeasurementValue smv372 = StatisticalMeasurementValue.NewInstance();
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smv372.setValue(9);
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StatisticalMeasure sm372 = StatisticalMeasure.MAX();
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smv372.setType(sm372);
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qtd37.addStatisticalValue(smv371);
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qtd37.addStatisticalValue(smv372);
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// QuantitativeData qtd38 = QuantitativeData.NewInstance();
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// StatisticalMeasurementValue smv381 = StatisticalMeasurementValue.NewInstance();
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// smv381.setValue(6);
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// StatisticalMeasure sm381 = StatisticalMeasure.MIN();
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// smv381.setType(sm381);
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// StatisticalMeasurementValue smv382 = StatisticalMeasurementValue.NewInstance();
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// smv382.setValue(9);
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// StatisticalMeasure sm382 = StatisticalMeasure.MAX();
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// smv382.setType(sm382);
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// qtd38.addStatisticalValue(smv381);
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// qtd38.addStatisticalValue(smv382);
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/*************************/
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CategoricalData catd41 = CategoricalData.NewInstance();
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catd41.setFeature(feature4);
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StateData sd41 = StateData.NewInstance();
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State s41 = State.NewInstance("","Blue","");
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State s42 = State.NewInstance("","Yellow","");
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sd41.setState(s41);
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catd41.addState(sd41);
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CategoricalData catd42 = CategoricalData.NewInstance();
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catd42.setFeature(feature4);
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StateData sd42 = StateData.NewInstance();
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sd42.setState(s42);
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catd42.addState(sd42);
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CategoricalData catd43 = CategoricalData.NewInstance();
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catd43.setFeature(feature4);
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StateData sd43 = StateData.NewInstance();
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sd43.setState(s41);
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catd43.addState(sd43);
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CategoricalData catd44 = CategoricalData.NewInstance();
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catd44.setFeature(feature4);
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StateData sd44 = StateData.NewInstance();
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sd44.setState(s42);
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catd44.addState(sd44);
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CategoricalData catd45 = CategoricalData.NewInstance();
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catd45.setFeature(feature4);
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StateData sd45 = StateData.NewInstance();
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sd45.setState(s41);
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catd45.addState(sd45);
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CategoricalData catd46 = CategoricalData.NewInstance();
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catd46.setFeature(feature4);
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StateData sd46 = StateData.NewInstance();
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sd46.setState(s41);
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catd46.addState(sd46);
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342
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CategoricalData catd47 = CategoricalData.NewInstance();
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catd47.setFeature(feature4);
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StateData sd47 = StateData.NewInstance();
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sd47.setState(s41);
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catd47.addState(sd47);
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CategoricalData catd48 = CategoricalData.NewInstance();
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catd48.setFeature(feature4);
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StateData sd48 = StateData.NewInstance();
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sd48.setState(s41);
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catd48.addState(sd48);
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/*************************/
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356
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357
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taxond1.addElement(catd11);
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taxond1.addElement(catd21);
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taxond1.addElement(qtd31);
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taxond1.addElement(catd41);
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taxond2.addElement(catd12);
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taxond2.addElement(catd22);
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taxond2.addElement(qtd32);
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taxond2.addElement(catd42);
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taxond3.addElement(catd13);
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taxond3.addElement(catd23);
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taxond3.addElement(qtd33);
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taxond3.addElement(catd43);
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taxond4.addElement(catd14);
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taxond4.addElement(catd24);
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taxond4.addElement(qtd34);
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taxond4.addElement(catd44);
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taxond5.addElement(catd15);
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taxond5.addElement(catd25);
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taxond5.addElement(qtd35);
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taxond5.addElement(catd45);
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381
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382
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taxond6.addElement(catd16);
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taxond6.addElement(catd26);
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taxond6.addElement(qtd36);
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taxond6.addElement(catd46);
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taxond7.addElement(catd17);
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taxond7.addElement(catd27);
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taxond7.addElement(qtd37);
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taxond7.addElement(catd47);
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391
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392
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taxond8.addElement(catd18);
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taxond8.addElement(catd28);
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// taxond8.addElement(qtd38); // This taxon has no wings
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395
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taxond8.addElement(catd48);
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396
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397
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/*************************/
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398
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|
399
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features = new ArrayList<Feature>();
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400
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features.add(feature1);
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401
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features.add(feature2);
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402
|
features.add(feature3);
|
403
|
features.add(feature4);
|
404
|
|
405
|
taxa = new HashSet<TaxonDescription>();
|
406
|
taxa.add(taxond1);
|
407
|
taxa.add(taxond2);
|
408
|
taxa.add(taxond3);
|
409
|
taxa.add(taxond4);
|
410
|
taxa.add(taxond5);
|
411
|
taxa.add(taxond6);
|
412
|
taxa.add(taxond7);
|
413
|
taxa.add(taxond8);
|
414
|
|
415
|
}
|
416
|
|
417
|
//*************************** TESTS *********************** /
|
418
|
|
419
|
|
420
|
@Test
|
421
|
public void testInvoke() {
|
422
|
generator = new PolytomousKeyGenerator();
|
423
|
generator.setFeatures(features);
|
424
|
generator.setTaxa(taxa);
|
425
|
assertNotNull("Key should exist.",generator.invoke());
|
426
|
}
|
427
|
|
428
|
@Test
|
429
|
public void testInvokeMergeModeON() {
|
430
|
// generator = new IdentificationKeyGenerator();
|
431
|
// generator.setFeatures(features);
|
432
|
// generator.setTaxa(taxa);
|
433
|
// generator.mergeModeON();
|
434
|
// generator.invoke();
|
435
|
// assertNotNull("Key should exist (merge mode ON).",generator.invoke());;
|
436
|
}
|
437
|
|
438
|
@Test
|
439
|
public void testInvokeWithDependencies() {
|
440
|
// generator = new IdentificationKeyGenerator();
|
441
|
// generator.setFeatures(features);
|
442
|
// generator.setTaxa(taxa);
|
443
|
//// generator.setDependencies(tree);// TODO create a tree with dependencies to test this function
|
444
|
// generator.invoke();
|
445
|
// assertNotNull("Key should exist (dependencies are present).",generator.invoke());;
|
446
|
}
|
447
|
|
448
|
}
|