Package org.broad.igv.feature.tribble

Examples of org.broad.igv.feature.tribble.PSLCodec


public class PSLAlignmentParser implements AlignmentParser {

    PSLCodec codec;

    public PSLAlignmentParser() {
        codec = new PSLCodec(); //genome);
    }
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            public void run() {
                try {

                    Genome genome = IGV.hasInstance() ? GenomeManager.getInstance().getCurrentGenome() : null;
                    PSLCodec codec = new PSLCodec(genome, true);

                    // TODO -- something better than this!
                    String db = genome.getId();
                    String species = genome.getSpecies();
                    if (species == null) species = genome.getDisplayName();

                    List<String> tokensList = blat(species, db, userSeq);

                    // Convert tokens to features
                    List<PSLRecord> features = new ArrayList<PSLRecord>(tokensList.size());
                    for (String tokens : tokensList) {
                        PSLRecord f = codec.decode(tokens);
                        if (f != null) {
                            features.add(f);
                        }
                    }
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