Examples of SeqReader

Examples of edu.msu.cme.rdp.readseq.readers.SeqReader

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        if (format == null) {
            format = CmdOptions.DEFAULT_FORMAT;
        }
        ClassifierFactory factory = ClassifierFactory.getFactory(gene);
        Classifier aClassifier = factory.createClassifier();
        SeqReader parser = new SequenceReader(new File(inputFile));
        BufferedWriter wt = new BufferedWriter(new FileWriter(outFile));
        Sequence pSeq = null;

        try {
            while ((pSeq = parser.readNextSequence()) != null) {
                try {
                    ClassificationResult result = aClassifier.classify(new ClassifierSequence(pSeq), min_bootstrap_words);
                    wt.write(ClassificationResultFormatter.getOutput(result, format));

                } catch (ShortSequenceException e) {
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