Examples of edu.msu.cme.rdp.classifier.train.validation.TreeFactory.buildTree()

    
    
    
    public void calSabSimilarity(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException{        
        TreeFactory factory = new TreeFactory(new FileReader(taxonFile));
        factory.buildTree();
        // get the lineage of the trainSeqFile  
        LineageSequenceParser trainParser = new LineageSequenceParser(new File(trainSeqFile));
        HashMap<String, List<String>> lineageMap = new HashMap<String, List<String>>();
        while (trainParser.hasNext()) {
            LineageSequence seq = (LineageSequence) trainParser.next();

    
    }
    
    public void calPairwiseSimilaritye(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException, OverlapCheckFailedException{        
        TreeFactory factory = new TreeFactory(new FileReader(taxonFile));
        factory.buildTree();
        // get the lineage of the trainSeqFile  
        LineageSequenceParser trainParser = new LineageSequenceParser(new File(trainSeqFile));
        ArrayList<LineageSequence> trainSeqList = new ArrayList<LineageSequence>();
        while (trainParser.hasNext()) {
            LineageSequence seq = (LineageSequence) trainParser.next();

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