Package org.broad.igv.renderer

Examples of org.broad.igv.renderer.DataRange

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            }
            if (!Double.isInfinite(maxQValue) && score.getQValue() > maxQValue) {
                maxQValue = score.getQValue();
            }
        }
        setDataRange(new DataRange(0, 0, (float) maxQValue));
    }
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        super(locator);

        TDFReader reader = TDFReader.getReader(locator.getPath());
        scoreSource = new TDFDataSource(reader, 4, "Pi", genome);

        setDataRange(new DataRange(0, 0, 10));
        baseSources = new HashMap();
        for (int i = 0; i < 4; i++) {
            TDFDataSource src = new TDFDataSource(reader, i, Character.toString(nucleotides[i]), genome);
            baseSources.put(nucleotides[i], src);
        }
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            dataSource = new CachingMethylSource(new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome), resolutionThreshold);
            //dataSource = new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome);
        }

        loadedRange = new Range("", -1, -1, Collections.<MethylScore>emptyList());
        setDataRange(new DataRange(0, 100));
    }
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        PreferenceManager prefs = PreferenceManager.getInstance();

        // Set range from 0 to highest value rounded to greater integer
        int maxValue = (int) Math.ceil(gData.getMaxValue());
        super.setDataRange(new DataRange(0, (maxValue / 2), maxValue));


        // Get default values
        super.setHeight(prefs.getAsInt(PreferenceManager.GWAS_TRACK_HEIGHT));
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        double locScale = context.getScale();

        // Get the Y axis definition, consisting of minimum, maximum, and base value.  Often
        // the base value is == min value which is == 0.

        DataRange axisDefinition = this.getDataRange();
        float maxValue = axisDefinition.getMaximum();
        float minValue = axisDefinition.getMinimum();

        // Calculate the Y scale factor.
        double yScaleFactor = adjustedRect.getHeight() / (maxValue - minValue);

        //int lastPx = 0;
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            labelGraphics = context.getGraphic2DForColor(Color.black);
            labelGraphics.setFont(FontManager.getFont(11));


            Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);
            DataRange axisDefinition = getDataRange();
            float maxValue = axisDefinition.getMaximum();
            float minValue = axisDefinition.getMinimum();


            // Bottom (minimum tick mark)
            int pY = computeYPixelValue(drawingRect, axisDefinition, minValue);
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    private String setDataRange(String dataRangeString, String trackName) {
        List<Track> tracks = igv.getAllTracks();
        String[] tokens = dataRangeString.split(",");
        //Min,max or min,baseline,max
        DataRange range;
        try {
            if (tokens.length == 2) {
                range = new DataRange(Float.parseFloat(tokens[0]), Float.parseFloat(tokens[1]));
            } else if (tokens.length == 3) {
                range = new DataRange(Float.parseFloat(tokens[0]), Float.parseFloat(tokens[1]), Float.parseFloat(tokens[2]));
            } else {
                throw new IllegalArgumentException(String.format("ERROR: parsing %s for data range. \n" +
                        "String must be of form <min,max> or <min,baseline,max>", dataRangeString));
            }
        } catch (NumberFormatException e) {
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Related Classes of org.broad.igv.renderer.DataRange

  • org.broad.igv.batch.CommandExecutor
  • org.broad.igv.data.cufflinks.CufflinksTrack
  • org.broad.igv.gwas.GWASTrack
  • org.broad.igv.methyl.MethylTrack
  • org.broad.igv.sam.CoverageTrack
  • org.broad.igv.sam.CoverageTrack$IntervalRenderer
  • org.broad.igv.sam.EWigTrack
  • org.broad.igv.sam.SpliceJunctionFinderTrack
  • org.broad.igv.track.CNFreqTrack
  • org.broad.igv.track.DataSourceTrack
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