Example usage for org.apache.commons.math.stat.descriptive.moment StandardDeviation evaluate

Introduction

In this page you can find the example usage for org.apache.commons.math.stat.descriptive.moment StandardDeviation evaluate.

Prototype

public double evaluate(final double[] values, final double mean) 

Source Link

Document

Returns the Standard Deviation of the entries in the input array, using the precomputed mean value.

Usage

From source file:net.sf.jdmf.util.MathCalculator.java

/**
 * Calculates the standard deviation of all attribute values.
 * // w  ww .  j  a  v  a 2  s  .  co  m
 * @param attributeValues attribute values
 * @return the standard deviation
 */
public Double calculateStandardDeviation(Comparable[] attributeValues, Double mean) {
    StandardDeviation standardDeviation = new StandardDeviation();

    Double evaluatedStdDev = standardDeviation.evaluate(convertToPrimitives(attributeValues), mean);

    log.debug("standardDeviation( " + mean + " ) = " + evaluatedStdDev);

    return evaluatedStdDev;
}

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From source file:musite.prediction.feature.disorder.DisorderTest.java

@Test
public void extractMean() throws IOException {
    //         String xml = "testData/musite-test.xml";
    String xml = "data/Uniprot/uniprot_sprot.201009.ptm.musite.with.disorder.xml";

    ProteinsXMLReader reader = DisorderUtil.getDisorderXMLReader();
    Proteins proteins = MusiteIOUtil.read(reader, xml);

    TTest ttest = new TTestImpl();
    StandardDeviation std = new StandardDeviation();

    Map<AminoAcid, double[]> mapAAScores = new EnumMap<AminoAcid, double[]>(AminoAcid.class);
    for (AminoAcid aa : AminoAcid.values()) {
        List<Double> scores = new ArrayList<Double>();
        Iterator<Protein> it = proteins.proteinIterator();
        while (it.hasNext()) {
            Protein protein = it.next();
            List<Double> dis = DisorderUtil.extractDisorder(protein, aa);
            if (dis != null)
                scores.addAll(dis);// w  w  w  .jav a  2 s  . c  om
        }
        mapAAScores.put(aa, list2array(scores));
        //            System.out.print(aa.toString()+":");
        //            System.out.println(""+average(scores)+"("+scores.size()+")");
    }

    Map<String, AminoAcid> mapKeyAA = getMapKeywordAminoAcid();

    for (PTM ptm : PTM.values()) {
        Set<String> keywords = ptm.getUniprotKeywords();
        for (String keyword : keywords) {
            AnnotationFilter filter = ResidueAnnotationUtil.createAnnotationFilter("keyword",
                    Collections.singleton(keyword), true);

            double[] scores;
            {
                List<Double> list = new ArrayList<Double>();
                Iterator<Protein> it = proteins.proteinIterator();
                while (it.hasNext()) {
                    Protein protein = it.next();
                    List<Double> dis = DisorderUtil.extractDisorder(protein, ptm, filter);
                    if (dis != null)
                        list.addAll(dis);
                }
                scores = list2array(list);
            }

            System.out.print(ptm.toString());
            System.out.print("\t" + keyword);
            if (scores.length == 0)
                System.out.println("\tno_site");
            else {
                System.out.print("\t" + scores.length);
                double mean = StatUtils.mean(scores);
                System.out.print("\t" + mean);
                System.out.print("\t" + std.evaluate(scores, mean));

                AminoAcid aa = mapKeyAA.get(keyword);
                double[] bg = mapAAScores.get(aa);
                System.out.print("\t" + aa.toString());
                System.out.print("\t" + bg.length);
                mean = StatUtils.mean(bg);
                System.out.print("\t" + mean);
                System.out.print("\t" + std.evaluate(bg, mean));

                double pvalue = -1.0;
                try {
                    pvalue = ttest.tTest(scores, bg);
                } catch (Exception e) {
                    //                        e.printStackTrace();
                }

                if (pvalue != -1.0)
                    System.out.print("\t" + pvalue);

                System.out.println();
            }
        }
    }
}

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