Examples with AxisScale uk.ac.babraham.SeqMonk.Utilities.AxisScale used on opensource projects

Example 6 with AxisScale

use of uk.ac.babraham.SeqMonk.Utilities.AxisScale in project SeqMonk by s-andrews.

the class ZScoreScatterPlotPanel method paint.

/* (non-Javadoc)
	 * @see javax.swing.JComponent#paint(java.awt.Graphics)
	 */
public void paint(Graphics g) {
    super.paint(g);
    g.setColor(Color.WHITE);
    g.fillRect(0, 0, getWidth(), getHeight());
    FontMetrics metrics = getFontMetrics(g.getFont());
    if (!readyToDraw) {
        g.setColor(Color.GRAY);
        String message = "Calculating Plot";
        g.drawString(message, (getWidth() / 2) - (metrics.stringWidth(message) / 2), (getHeight() / 2 - 2));
        return;
    }
    // Check to see if we need to work out the counts for this size
    if (nonRedundantValues == null || lastNonredWidth != getWidth() || lastNonredHeight != getHeight()) {
        calculateNonredundantSet();
    }
    // If we're here then we can actually draw the graphs
    g.setColor(Color.BLACK);
    // X axis
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - 10, getHeight() - Y_AXIS_SPACE);
    AxisScale xAxisScale = new AxisScale(minValueX, maxValueX);
    double currentXValue = xAxisScale.getStartingValue();
    while (currentXValue < maxValueX) {
        g.drawString(xAxisScale.format(currentXValue), getX(currentXValue), getHeight() - (Y_AXIS_SPACE - (3 + g.getFontMetrics().getHeight())));
        g.drawLine(getX(currentXValue), getHeight() - Y_AXIS_SPACE, getX(currentXValue), getHeight() - (Y_AXIS_SPACE - 3));
        currentXValue += xAxisScale.getInterval();
    }
    // Y axis
    g.drawLine(X_AXIS_SPACE, 10, X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE);
    // 
    AxisScale yAxisScale = new AxisScale(minValueY, maxValueY);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < maxValueY) {
        g.drawString(yAxisScale.format(currentYValue), 5, getY(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.drawLine(X_AXIS_SPACE, getY(currentYValue), X_AXIS_SPACE - 3, getY(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // X label
    g.drawString("mean probe intensity", (getWidth() / 2) - (metrics.stringWidth("mean probe intensity") / 2), getHeight() - 3);
    // Y label
    g.drawString("z-score", X_AXIS_SPACE - metrics.stringWidth("z-score") - 3, 15);
    g.setColor(Color.BLUE);
    for (int p = 0; p < nonRedundantValues.length; p++) {
        if ((madeSelection || makingSelection) && nonRedundantValues[p].yValue >= Math.min(diffStart, diffEnd) && nonRedundantValues[p].yValue <= Math.max(diffStart, diffEnd)) {
            g.setColor(Color.BLACK);
        } else {
            g.setColor(nonRedundantValues[p].color);
        }
        g.fillRect(nonRedundantValues[p].x - (dotSize / 2), nonRedundantValues[p].y - (dotSize / 2), dotSize, dotSize);
    }
    // If we have a highlighted list, add the name
    if (subLists != null) {
        for (int s = 0; s < subLists.length; s++) {
            g.setColor(ColourIndexSet.getColour(s));
            g.drawString(subLists[s].name(), getWidth() - metrics.stringWidth(subLists[s].name()) - 5, 30 + (g.getFontMetrics().getHeight() * (s + 1)));
        }
        g.setColor(Color.BLACK);
    }
    // 0 line
    g.setColor(Color.GRAY);
    g.drawLine(X_AXIS_SPACE, getY(0), getWidth() - 10, getY(0));
    // label the datasets
    // the negative z-scores
    g.drawString(xStore.name(), X_AXIS_SPACE + 10, getHeight() - 50);
    // one with the positive z-scores
    g.drawString(yStore.name(), X_AXIS_SPACE + 10, 30);
    // Finally we draw the current measures if the mouse is inside the plot
    if (cursorX > 0) {
        g.setColor(Color.BLACK);
        // System.out.println("Drawing label at x="+cursorX+" y="+cursorY+" x*="+getValueFromX(cursorX)+" y*="+getValueFromY(cursorY));
        String label = "x=" + df.format(getValueFromX(cursorX)) + " y=" + df.format(getValueFromY(cursorY));
        int labelXPos = X_AXIS_SPACE + ((getWidth() - (X_AXIS_SPACE + 10)) / 2) - (g.getFontMetrics().stringWidth(label) / 2);
        g.drawString(label, labelXPos, getHeight() - (Y_AXIS_SPACE + 3));
        // We also draw the names on the closest point if there is one
        if (closestPoint != null && closestPoint.probe() != null) {
            g.drawString(closestPoint.probe().name(), closestPoint.x + 1, closestPoint.y - 1);
        }
    }
}

Example 7 with AxisScale

use of uk.ac.babraham.SeqMonk.Utilities.AxisScale in project SeqMonk by s-andrews.

the class CisTransScatterPlotPanel method paint.

/* (non-Javadoc)
	 * @see javax.swing.JComponent#paint(java.awt.Graphics)
	 */
public void paint(Graphics g) {
    super.paint(g);
    g.setColor(Color.WHITE);
    g.fillRect(0, 0, getWidth(), getHeight());
    FontMetrics metrics = getFontMetrics(g.getFont());
    if (!readyToDraw) {
        g.setColor(Color.GRAY);
        String message = "Calculating Plot";
        g.drawString(message, (getWidth() / 2) - (metrics.stringWidth(message) / 2), (getHeight() / 2 - 2));
        return;
    }
    // Check to see if we need to work out the counts for this size
    if (nonRedundantValues == null || lastNonredWidth != getWidth() || lastNonredHeight != getHeight()) {
        calculateNonredundantSet();
    }
    // If we're here then we can actually draw the graphs
    g.setColor(Color.BLACK);
    // X axis
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - 10, getHeight() - Y_AXIS_SPACE);
    AxisScale xAxisScale = new AxisScale(minValueX, maxValueX);
    double currentXValue = xAxisScale.getStartingValue();
    while (currentXValue < maxValueX) {
        g.drawString(xAxisScale.format(currentXValue), getX(currentXValue), getHeight() - (Y_AXIS_SPACE - (3 + g.getFontMetrics().getHeight())));
        g.drawLine(getX(currentXValue), getHeight() - Y_AXIS_SPACE, getX(currentXValue), getHeight() - (Y_AXIS_SPACE - 3));
        currentXValue += xAxisScale.getInterval();
    }
    // Y axis
    g.drawLine(X_AXIS_SPACE, 10, X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE);
    AxisScale yAxisScale = new AxisScale(minValueY, maxValueY);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < maxValueY) {
        g.drawString(yAxisScale.format(currentYValue), 5, getY(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.drawLine(X_AXIS_SPACE, getY(currentYValue), X_AXIS_SPACE - 3, getY(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // X label
    g.drawString("Cis", (getWidth() / 2) - (metrics.stringWidth("Cis") / 2), getHeight() - 3);
    // Y label
    g.drawString("Trans", X_AXIS_SPACE + 3, 15);
    // ProbeList
    g.drawString(probeList.name(), getWidth() - 10 - metrics.stringWidth(probeList.name()), 15);
    // 45 degree line
    g.setColor(Color.GRAY);
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - 10, 10);
    g.setColor(Color.BLUE);
    ColourGradient gradient = new HotColdColourGradient();
    for (int p = 0; p < nonRedundantValues.length; p++) {
        if ((madeSelection || makingSelection) && nonRedundantValues[p].difference() >= Math.min(diffStart, diffEnd) && nonRedundantValues[p].difference() <= Math.max(diffStart, diffEnd)) {
            g.setColor(Color.BLACK);
        } else {
            if (nonRedundantValues[p].color == null) {
                nonRedundantValues[p].color = gradient.getColor(Math.log(nonRedundantValues[p].count), 0, Math.log(maxPointCount));
            }
            g.setColor(nonRedundantValues[p].color);
        }
        g.fillRect(nonRedundantValues[p].x - (dotSize / 2), nonRedundantValues[p].y - (dotSize / 2), dotSize, dotSize);
    }
    // Finally we draw the current measures if the mouse is inside the plot
    if (cursorX > 0) {
        g.setColor(Color.BLACK);
        // System.out.println("Drawing label at x="+cursorX+" y="+cursorY+" x*="+getValueFromX(cursorX)+" y*="+getValueFromY(cursorY));
        String label = "x=" + df.format(getValueFromX(cursorX)) + " y=" + df.format(getValueFromY(cursorY)) + " diff=" + df.format(getValueFromX(cursorX) - getValueFromY(cursorY));
        int labelXPos = X_AXIS_SPACE + ((getWidth() - (X_AXIS_SPACE + 10)) / 2) - (g.getFontMetrics().stringWidth(label) / 2);
        g.drawString(label, labelXPos, getHeight() - (Y_AXIS_SPACE + 3));
        // We also draw the names on the closest point if there is one
        if (closestPoint != null && closestPoint.probe() != null) {
            g.drawString(closestPoint.probe().name(), closestPoint.x + 1, closestPoint.y - 1);
        }
    }
}

Example 8 with AxisScale

use of uk.ac.babraham.SeqMonk.Utilities.AxisScale in project SeqMonk by s-andrews.

the class CodonBiasPanel method paint.

public void paint(Graphics g) {
    super.paint(g);
    g.setColor(Color.WHITE);
    g.fillRect(0, 0, getWidth(), getHeight());
    if (!calculated)
        return;
    g.setColor(Color.BLACK);
    // Draw the axes
    // X-axis
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE);
    // Y-axis 1
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, X_AXIS_SPACE, 10);
    // Y-axis 2
    g.drawLine(getWidth() - X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - X_AXIS_SPACE, 10);
    // Draw the Y1 scale
    AxisScale yAxisScale = new AxisScale(0, 100);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < yAxisScale.getMax()) {
        g.drawString(yAxisScale.format(currentYValue), 5, getYPixels(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.drawLine(X_AXIS_SPACE, getYPixels(currentYValue), X_AXIS_SPACE - 3, getYPixels(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // Draw the Y2 scale (abundance)
    yAxisScale = new AxisScale(0, 100);
    currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < yAxisScale.getMax()) {
        g.drawString(yAxisScale.format(currentYValue), getWidth() - (X_AXIS_SPACE - 5), getYPixels(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.drawLine(getWidth() - X_AXIS_SPACE, getYPixels(currentYValue), getWidth() - (X_AXIS_SPACE - 3), getYPixels(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // Draw x axis
    AxisScale xAxisScale = new AxisScale(1, abundance.length);
    double currentXValue = xAxisScale.getStartingValue();
    while (currentXValue < xAxisScale.getMax()) {
        g.drawString(xAxisScale.format(currentXValue), getXPixels(currentXValue), getHeight() - (g.getFontMetrics().getAscent() / 2));
        g.drawLine(X_AXIS_SPACE, getYPixels(currentYValue), X_AXIS_SPACE - 3, getYPixels(currentYValue));
        currentXValue += xAxisScale.getInterval();
    }
    // Highlight the exons
    int lastExonEndX = getXPixels(0);
    for (int i = 1; i < exonBoundaries.length; i++) {
        int thisExonX = getXPixels(exonBoundaries[i]);
        if (i % 2 != 0) {
            g.setColor(GREY);
            g.fillRect(lastExonEndX, getYPixels(100), thisExonX - lastExonEndX, getYPixels(0) - getYPixels(100));
        }
        lastExonEndX = thisExonX;
    }
    if (exonBoundaries.length % 2 != 0) {
        int thisExonX = getXPixels(abundance.length);
        g.setColor(GREY);
        g.fillRect(lastExonEndX, getYPixels(100), thisExonX - lastExonEndX, getYPixels(0) - getYPixels(100));
    }
    // Draw the plots per codon
    // Work out the max count per codon
    int maxCountPerCodon = 0;
    for (int p = 0; p < abundance.length; p += 3) {
        // Get the total abundance for the codon
        int codon = abundance[p] + abundance[p + 1] + abundance[p + 2];
        if (codon > maxCountPerCodon)
            maxCountPerCodon = codon;
    }
    float lastY1 = -1;
    float lastY2 = -1;
    float lastY3 = -1;
    float lastYabundance = -1;
    for (int p = 0; p < abundance.length - 2; p += 3) {
        // Get the total abundance for the codon
        int codon = abundance[p] + abundance[p + 1] + abundance[p + 2];
        float codonPercent = (codon * 100f) / maxCountPerCodon;
        if (p > 0) {
            g.setColor(Color.GRAY);
            g.drawLine(getXPixels(p - 2), getYPixels(lastYabundance), getXPixels(p + 1), getYPixels(codonPercent));
        }
        lastYabundance = codonPercent;
        // Calculate percentages for each sub-position
        // Don't allow infinite values
        float c1percent = lastY1;
        float c2percent = lastY2;
        float c3percent = lastY3;
        if (maxCountPerCodon > 0) {
            c1percent = (abundance[p] * 100f) / maxCountPerCodon;
            c2percent = (abundance[p + 1] * 100f) / maxCountPerCodon;
            c3percent = (abundance[p + 2] * 100f) / maxCountPerCodon;
        }
        System.err.println("Codon at " + p + " 1=" + abundance[p] + " 2=" + abundance[p + 1] + " 3=" + abundance[p + 2] + " total=" + codon);
        System.err.println("Codon percentages " + p + " 1=" + c1percent + " 2=" + c2percent + " 3=" + c3percent);
        if (p > 0) {
            g.setColor(RED);
            g.drawLine(getXPixels(p - 3), getYPixels(lastY1), getXPixels(p), getYPixels(c1percent));
            g.setColor(GREEN);
            g.drawLine(getXPixels(p - 2), getYPixels(lastY2), getXPixels(p + 1), getYPixels(c2percent));
            g.setColor(BLUE);
            g.drawLine(getXPixels(p - 1), getYPixels(lastY3), getXPixels(p + 2), getYPixels(c3percent));
        }
        lastY1 = c1percent;
        lastY2 = c2percent;
        lastY3 = c3percent;
    }
}

Example 9 with AxisScale

use of uk.ac.babraham.SeqMonk.Utilities.AxisScale in project SeqMonk by s-andrews.

the class CumulativeDistributionPanel method paint.

public void paint(Graphics g) {
    super.paint(g);
    g.setColor(Color.WHITE);
    g.fillRect(0, 0, getWidth(), getHeight());
    g.setColor(Color.BLACK);
    // Draw the axes
    // X-axis
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - 10, getHeight() - Y_AXIS_SPACE);
    // Y-axis
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, X_AXIS_SPACE, 10);
    // Draw the Y scale
    AxisScale yAxisScale = new AxisScale(usedMin, usedMax);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < usedMax) {
        g.drawString(yAxisScale.format(currentYValue), 5, getYPixels(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.setColor(Color.LIGHT_GRAY);
        g.drawLine(X_AXIS_SPACE - 3, getYPixels(currentYValue), getWidth() - 10, getYPixels(currentYValue));
        g.drawLine(X_AXIS_SPACE, getYPixels(currentYValue), X_AXIS_SPACE - 3, getYPixels(currentYValue));
        g.setColor(Color.LIGHT_GRAY);
        g.drawLine(X_AXIS_SPACE + 1, getYPixels(currentYValue), getWidth() - 10, getYPixels(currentYValue));
        g.setColor(Color.BLACK);
        currentYValue += yAxisScale.getInterval();
    }
    // Draw x scale
    AxisScale xAxisScale = new AxisScale(0, 100);
    double currentXValue = xAxisScale.getStartingValue();
    while (currentXValue < 100) {
        g.drawString(xAxisScale.format(currentXValue), getXPixels(currentXValue), getHeight() - (Y_AXIS_SPACE - (g.getFontMetrics().getHeight() + 3)));
        g.drawLine(getXPixels(currentXValue), getHeight() - Y_AXIS_SPACE, getXPixels(currentXValue), getHeight() - (Y_AXIS_SPACE - 3));
        currentXValue += xAxisScale.getInterval();
    }
    // Mark the 50th percentile
    g.setColor(Color.LIGHT_GRAY);
    g.drawLine(getXPixels(50), getHeight() - Y_AXIS_SPACE, getXPixels(50), 10);
    g.setColor(Color.BLACK);
    // Put the probe list name at the top
    g.drawString(title, (getWidth() - 10) - (g.getFontMetrics().stringWidth(title)), g.getFontMetrics().getHeight());
    // Put the names on the right
    for (int n = 0; n < names.length; n++) {
        g.setColor(ColourIndexSet.getColour(n));
        g.drawString(names[n], X_AXIS_SPACE + 5, g.getFontMetrics().getHeight() * (n + 1));
    }
    // Now draw the lines
    for (int d = 0; d < distributions.length; d++) {
        g.setColor(ColourIndexSet.getColour(d));
        int lastY = 0;
        int lastX = 0;
        double width = getWidth() - (X_AXIS_SPACE + 10);
        for (int x = 0; x < distributions[d].length; x++) {
            double proportion = x / (double) distributions[d].length;
            int thisY = getYPixels(distributions[d][x]);
            int thisX = X_AXIS_SPACE;
            thisX += (int) (width * proportion);
            if (x > 0) {
                g.drawLine(lastX, lastY, thisX, thisY);
            }
            lastY = thisY;
            lastX = thisX;
        }
    }
}

Example 10 with AxisScale

use of uk.ac.babraham.SeqMonk.Utilities.AxisScale in project SeqMonk by s-andrews.

the class BeanPlotScaleBar method setLimits.

public void setLimits(double min, double max) {
    axisScale = new AxisScale(min, max);
    repaint();
}