001    package calhoun.analysis.crf.test;
002    
003    
004    import java.util.List;
005    
006    import org.apache.commons.logging.Log;
007    import org.apache.commons.logging.LogFactory;
008    
009    import calhoun.analysis.crf.Conrad;
010    import calhoun.analysis.crf.io.TrainingSequence;
011    import calhoun.util.AbstractTestCase;
012    
013    public class GapConjunctionFeaturesTest extends AbstractTestCase {
014            private static final Log log = LogFactory.getLog(GapConjunctionFeaturesTest.class);
015            boolean debug = log.isDebugEnabled();
016            
017            public void testGapFeature() throws Exception {
018    
019                    String configFile = "test/input/multipleAlignmentUnitTest/basic_ModelDSComp.xml";
020                    String inputFile = "test/input/multipleAlignmentUnitTest/tiny_5way.txt";
021                    
022                    Conrad crf = new Conrad(configFile);
023                    List<? extends TrainingSequence<?>> t = crf.getInputHandler().readTrainingData(inputFile);
024    
025                    crf.train(t);
026                    double[] weights = crf.getWeights();
027    
028                    System.out.println("The weights are: ");
029                    for (int i=0; i<weights.length; i++ ) { System.out.print("\t"+weights[i]);           }
030                    System.out.println();
031            }
032            
033    }