Examples with HotColdColourGradient uk.ac.babraham.SeqMonk.Gradients.HotColdColourGradient used on opensource projects

Example 11 with HotColdColourGradient

use of uk.ac.babraham.SeqMonk.Gradients.HotColdColourGradient in project SeqMonk by s-andrews.

the class ScatterPlotPanel method calculateNonredundantSet.

/**
 * This collapses individual points which are over the same
 * pixel when redrawing the plot at a different scale
 */
private synchronized void calculateNonredundantSet() {
    closestPoint = null;
    ProbePairValue[][] grid = new ProbePairValue[getWidth()][getHeight()];
    Probe[] probes = probeList.getAllProbes();
    try {
        for (int p = 0; p < probes.length; p++) {
            float xValue = xStore.getValueForProbe(probes[p]);
            float yValue = yStore.getValueForProbe(probes[p]);
            if (Float.isNaN(xValue) || Float.isInfinite(xValue) || Float.isNaN(yValue) || Float.isInfinite(yValue)) {
                continue;
            }
            int x = getX(xValue);
            int y = getY(yValue);
            if (grid[x][y] == null) {
                grid[x][y] = new ProbePairValue(xValue, yValue, x, y);
                grid[x][y].setProbe(probes[p]);
            } else {
                // belong to
                if (subLists == null)
                    grid[x][y].count++;
                // As we have multiple probes at this point we remove the
                // specific probe annotation.
                grid[x][y].setProbe(null);
            }
        }
        if (subLists != null) {
            for (int s = 0; s < subLists.length; s++) {
                Probe[] subListProbes = subLists[s].getAllProbes();
                for (int p = 0; p < subListProbes.length; p++) {
                    float xValue = xStore.getValueForProbe(subListProbes[p]);
                    float yValue = yStore.getValueForProbe(subListProbes[p]);
                    int x = getX(xValue);
                    int y = getY(yValue);
                    if (grid[x][y] == null) {
                        // This messes up where we catch it in the middle of a redraw
                        continue;
                    // throw new IllegalArgumentException("Found subList position not in main list");
                    }
                    // 1 = no list so 2 is the lowest sublist index
                    grid[x][y].count = s + 2;
                }
            }
        }
    } catch (SeqMonkException e) {
        throw new IllegalStateException(e);
    }
    // Now we need to put all of the ProbePairValues into
    // a single array;
    int count = 0;
    for (int x = 0; x < grid.length; x++) {
        for (int y = 0; y < grid[x].length; y++) {
            if (grid[x][y] != null)
                count++;
        }
    }
    ProbePairValue[] nonred = new ProbePairValue[count];
    count--;
    for (int x = 0; x < grid.length; x++) {
        for (int y = 0; y < grid[x].length; y++) {
            if (grid[x][y] != null) {
                nonred[count] = grid[x][y];
                count--;
            }
        }
    }
    Arrays.sort(nonred);
    // Work out the 95% percentile count
    int minCount = 1;
    int maxCount = 2;
    if (nonred.length > 0) {
        minCount = nonred[0].count;
        maxCount = nonred[((nonred.length - 1) * 95) / 100].count;
    }
    // Go through every nonred assigning a suitable colour
    ColourGradient gradient = new HotColdColourGradient();
    for (int i = 0; i < nonred.length; i++) {
        if (subLists == null) {
            nonred[i].color = gradient.getColor(nonred[i].count, minCount, maxCount);
        } else {
            if (nonred[i].count > subLists.length + 1) {
                throw new IllegalArgumentException("Count above threshold when showing sublists");
            }
            if (nonred[i].count == 1) {
                nonred[i].color = VERY_LIGHT_GREY;
            } else {
                nonred[i].color = ColourIndexSet.getColour(nonred[i].count - 2);
            }
        }
    }
    nonRedundantValues = nonred;
    lastNonredWidth = getWidth();
    lastNonredHeight = getHeight();
// System.out.println("Nonred was "+nonRedundantValues.length+" from "+probes.length);
}