Example usage for org.apache.commons.math.stat Frequency getCumPct

Introduction

In this page you can find the example usage for org.apache.commons.math.stat Frequency getCumPct.

Prototype

public double getCumPct(char v) 

Source Link

Document

Returns the cumulative percentage of values less than or equal to v (as a proportion between 0 and 1).

Usage

From source file:de.tum.bgu.msm.syntheticPopulationGenerator.capeTown.SyntheticPopCT.java

public void checkTripLengthDistribution(Frequency travelTimes, double alpha, double gamma, String fileName,
        double step) {
    //to obtain the trip length distribution
    int[] timeThresholds1 = new int[79];
    double[] frequencyTT1 = new double[79];
    for (int row = 0; row < timeThresholds1.length; row++) {
        timeThresholds1[row] = row + 1;/*  ww  w  .  java  2s  .  c om*/
        frequencyTT1[row] = travelTimes.getCumPct(timeThresholds1[row]);
        //logger.info("Time: " + timeThresholds1[row] + ", cummulated frequency:  " + frequencyTT1[row]);
    }
    writeVectorToCSV(timeThresholds1, frequencyTT1, fileName, alpha, gamma);

}

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From source file:org.broad.igv.renderer.SpliceJunctionRenderer.java

/**
 * Note:  assumption is that featureList is sorted by pStart position.
 *
 * @param featureList/*from www  .  j  a va 2  s.  c  om*/
 * @param context
 * @param trackRectangle
 * @param track
 */
@Override
public void render(List<IGVFeature> featureList, RenderContext context, Rectangle trackRectangle, Track track) {

    double origin = context.getOrigin();
    double locScale = context.getScale();

    // TODO -- use enum instead of string "Color"
    if ((featureList != null) && !featureList.isEmpty()) {

        // Create a graphics object to draw font names.  Graphics are not cached
        // by font, only by color, so its neccessary to create a new one to prevent
        // affecting other tracks.
        Font font = FontManager.getFont(track.getFontSize());
        Graphics2D fontGraphics = (Graphics2D) context.getGraphic2DForColor(Color.BLACK).create();

        if (PreferenceManager.getInstance().getAsBoolean(PreferenceManager.ENABLE_ANTIALISING)) {
            fontGraphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
                    RenderingHints.VALUE_TEXT_ANTIALIAS_ON);

        }
        fontGraphics.setFont(font);

        //determine whether to show flanking regions
        PreferenceManager prefs = PreferenceManager.getInstance();
        boolean shouldShowFlankingRegions = prefs
                .getAsBoolean(PreferenceManager.SAM_SHOW_JUNCTION_FLANKINGREGIONS);

        // Track coordinates
        double trackRectangleX = trackRectangle.getX();
        double trackRectangleMaxX = trackRectangle.getMaxX();

        SpliceJunctionFeature selectedFeature = (SpliceJunctionFeature) ((FeatureTrack) track)
                .getSelectedFeature();

        // Start of Roche-Tessella modification
        if (track.getAutoScale()) {
            Frequency f = new Frequency();
            List<Integer> scores = new ArrayList<Integer>();

            for (IGVFeature feature : featureList) {
                SpliceJunctionFeature junctionFeature = (SpliceJunctionFeature) feature;
                f.addValue(junctionFeature.getScore());
                scores.add((int) junctionFeature.getScore());
            }

            Collections.sort(scores);
            Collections.reverse(scores);
            for (int s : scores) {
                if (f.getCumPct(s) < 0.99) {
                    maxDepth = s;
                    break;
                }
            }

        }
        // End of Roche-Tessella modification

        for (IGVFeature feature : featureList) {
            SpliceJunctionFeature junctionFeature = (SpliceJunctionFeature) feature;
            //if same junction as selected feature, highlight
            boolean shouldHighlight = false;
            if (selectedFeature != null && selectedFeature.isSameJunction(junctionFeature)) {
                setHighlightFeature(junctionFeature);
                shouldHighlight = true;
            }

            // Get the pStart and pEnd of the entire feature.  at extreme zoom levels the
            // virtual pixel value can be too large for an int, so the computation is
            // done in double precision and cast to an int only when its confirmed its
            // within the field of view.
            int flankingStart = junctionFeature.getStart();
            int flankingEnd = junctionFeature.getEnd();

            int junctionStart = junctionFeature.getJunctionStart();
            int junctionEnd = junctionFeature.getJunctionEnd();

            double virtualPixelStart = Math.round((flankingStart - origin) / locScale);
            double virtualPixelEnd = Math.round((flankingEnd - origin) / locScale);

            double virtualPixelJunctionStart = Math.round((junctionStart - origin) / locScale);
            double virtualPixelJunctionEnd = Math.round((junctionEnd - origin) / locScale);

            // If the any part of the feature fits in the
            // Track rectangle draw it
            if ((virtualPixelEnd >= trackRectangleX) && (virtualPixelStart <= trackRectangleMaxX)) {

                //
                int displayPixelEnd = (int) Math.min(trackRectangleMaxX, virtualPixelEnd);
                int displayPixelStart = (int) Math.max(trackRectangleX, virtualPixelStart);

                float depth = junctionFeature.getJunctionDepth();
                Color color = feature.getColor();

                drawFeature((int) virtualPixelStart, (int) virtualPixelEnd, (int) virtualPixelJunctionStart,
                        (int) virtualPixelJunctionEnd, depth, trackRectangle, context, feature.getStrand(),
                        junctionFeature, shouldHighlight, color, shouldShowFlankingRegions);
            }
        }

        //draw a central horizontal line
        Graphics2D g2D = context.getGraphic2DForColor(COLOR_CENTERLINE);
        g2D.drawLine((int) trackRectangleX, (int) trackRectangle.getCenterY(), (int) trackRectangleMaxX,
                (int) trackRectangle.getCenterY());

    }
}

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