001    package calhoun.analysis.crf.io;
002    
003    import java.io.IOException;
004    import java.util.ArrayList;
005    import java.util.Collections;
006    import java.util.HashMap;
007    import java.util.Iterator;
008    import java.util.List;
009    import java.util.Map;
010    
011    import org.apache.commons.logging.Log;
012    import org.apache.commons.logging.LogFactory;
013    
014    import calhoun.analysis.crf.io.GTFInputInterval13.CDS;
015    import calhoun.util.Assert;
016    import calhoun.util.FileUtil;
017    
018    public class GTFInputInterval29 extends GTFInputInterval13 {
019            private static final long serialVersionUID = 4413724139445660884L;
020            private static final Log log = LogFactory.getLog(GTFInputInterval29.class);
021            
022            public void readTrainingSequences(Object location, List<TrainingSequence<Map<String, Object>>> seqs) throws IOException {
023                    super.readTrainingSequences(location, seqs);
024                    
025                    for (Iterator iter = seqs.iterator(); iter.hasNext();) {
026                            TrainingSequence<Map<String, Object>> seq = (TrainingSequence<Map<String, Object>>)iter.next();
027                            int[] states = seq.getY();
028                            states = SequenceConverter.convertSeqFromInterval13ToInterval29(states);
029                            seq.setY(states);
030                    }
031            }
032    }