this.isTwoStrandFeature = isTwoStrandFeature;
}
public void convert() throws IOException, BioException, ParserException {
// find all of the given feature from the given sequence
GFFEntrySet gffEntries = new GFFEntrySet();
GFFRecordFilter.FeatureFilter fFilter = new GFFRecordFilter.FeatureFilter();
fFilter.setFeature(featureName);
GFFRecordFilter.SequenceFilter sFilter = new GFFRecordFilter.SequenceFilter();
sFilter.setSeqName(seqName);
// have to and the filters together
GFFAndFilter aFilter = new GFFAndFilter(fFilter, sFilter);
GFFFilterer filterer = new GFFFilterer(gffEntries.getAddHandler(), aFilter);
// parse the gff file
GFFParser parser = new GFFParser();
parser.parse(new BufferedReader(new InputStreamReader(new FileInputStream(new File(gffFileName)))), filterer);
// find all of the features
// output to the out file the tube information
//outFile = new PrintWriter(new BufferedWriter(new FileWriter(outFileName)));
Iterator entriesIterator = gffEntries.lineIterator();
// make sure to sort the records
sorter = new TreeMap<Integer, GFFRecord>();
// add everything to the treeMap to ensure it is sorted