Examples of edu.msu.cme.rdp.classifier.Classifier.classify()

Class edu.msu.cme.rdp.classifier.Classifier

Examples of edu.msu.cme.rdp.classifier.Classifier.classify()

edu.msu.cme.rdp.classifier.Classifier.classify()
Takes a query sequence, returns the classification result. For each query sequence, first assign it to a genus node using all the words for calculation. Then randomly chooses one-eighth of the all overlapping words in the query to calculate the joint probability. The number of times a genus was selected out of the number of bootstrap trials was used as an estimate of confidence in the assignment to that genus. @throws ShortSequenceException if the sequence length is less than the minimum sequence length.


        try {
            parser = new SequenceReader(inStream1);
            while((pSeq = parser.readNextSequence()) != null) {
                try {
                    ClassificationResult result = aClassifier.classify(pSeq);
                    root = reconstructTree(result, root, SAMPLE1);
                    wt.write(ClassificationResultFormatter.getOutput(result, format));


                } catch (ShortSequenceException e) {
                    System.out.println(e.getMessage());

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            }


            parser = new SequenceReader(inStream2);
            while((pSeq = parser.readNextSequence()) != null) {
                try {
                    ClassificationResult result = aClassifier.classify(pSeq);
                    root = reconstructTree(result, root, SAMPLE2);
                    wt.write(ClassificationResultFormatter.getOutput(result, format));


                } catch (ShortSequenceException e) {
                    System.out.println(e.getMessage());

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        String sequence = "";
        infile.readLine();
        sequence = infile.readLine();
        sequence = sequence.toUpperCase();
        ClassifierSequence pSeq = new ClassifierSequence("name", "title", sequence);
        ClassificationResult result = aClassifier.classify(pSeq);
        
        Iterator it = result.getAssignments().iterator();
        RankAssignment classResult = (RankAssignment) it.next();
        assertEquals(classResult.getBestClass().getName() , rootTree.getName());
        assertEquals(classResult.getConfidence(), 1.0, 0.1);

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        // test the second sequence
        infile.readLine();
        sequence = infile.readLine();
        sequence = sequence.toUpperCase();
        pSeq = new ClassifierSequence("name", "title", sequence);
        result = aClassifier.classify(pSeq);
        
        
        it = result.getAssignments().iterator();
        classResult = (RankAssignment) it.next();
        assertEquals(classResult.getBestClass().getName() , rootTree.getName());

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