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

Example 11 with AxisScale

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

the class BoxWhiskerScaleBar method setLimits.

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

Example 12 with AxisScale

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

the class ChromosomeScaleTrack method paintComponent.

/* (non-Javadoc)
	 * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
	 */
public void paintComponent(Graphics g) {
    super.paintComponent(g);
    DisplayPreferences dp = DisplayPreferences.getInstance();
    if (dp.getCurrentLocation() != lastLocation) {
        // We need to rescale the frequency with which we're drawing points
        scale = new AxisScale(0, SequenceRead.length(dp.getCurrentLocation()));
        lastLocation = dp.getCurrentLocation();
    }
    height = getHeight();
    width = getWidth();
    g.setColor(Color.WHITE);
    g.fillRect(0, 0, width, height);
    g.setColor(Color.DARK_GRAY);
    // Draw a line along the top
    g.drawLine(0, 3, width, 3);
    // Now go through all the scale positions figuring out whether they
    // need to be displayed
    int startBp = SequenceRead.start(lastLocation);
    int endBp = SequenceRead.end(lastLocation);
    int currentBase = 0;
    while (currentBase < endBp) {
        if (currentBase < startBp) {
            currentBase += scale.getInterval();
            continue;
        }
        String name = commify(currentBase);
        int nameWidth = g.getFontMetrics().stringWidth(name);
        int thisX = bpToPixel(currentBase);
        g.drawString(name, thisX - (nameWidth / 2), getHeight() - 2);
        g.drawLine(thisX, 3, thisX, height - (g.getFontMetrics().getAscent() + 3));
        currentBase += scale.getInterval();
    }
}

Example 13 with AxisScale

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

the class GradientScaleAxis method setLimits.

public void setLimits(double min, double max) {
    if (max < min)
        throw new IllegalArgumentException("Max cannot be <= min max=" + max + " min=" + min);
    axisScale = new AxisScale(min, max);
    maxX = getMaxWidth();
    repaint();
}

Example 14 with AxisScale

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

the class MAPlotPanel 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);
    // Centre line
    g.setColor(Color.GRAY);
    g.drawLine(X_AXIS_SPACE, getY(0), getWidth() - 10, getY(0));
    g.setColor(Color.BLACK);
    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
    String xLabel = "Average of " + xStore.name() + " and " + yStore.name();
    g.drawString(xLabel, (getWidth() / 2) - (metrics.stringWidth(xLabel) / 2), getHeight() - 3);
    // Y label
    String yLabel = "Difference " + xStore.name() + " - " + yStore.name();
    g.drawString(yLabel, X_AXIS_SPACE + 3, 15);
    // If we have sublists draw them below this in the right colours
    if (subLists != null) {
        for (int s = 0; s < subLists.length; s++) {
            g.setColor(ColourIndexSet.getColour(s));
            g.drawString(subLists[s].name(), X_AXIS_SPACE + 3, 15 + (g.getFontMetrics().getHeight() * (s + 1)));
        }
        g.setColor(Color.BLACK);
    }
    // ProbeList
    g.drawString(probeList.name(), getWidth() - 10 - metrics.stringWidth(probeList.name()), 15);
    g.setColor(Color.BLUE);
    for (int p = 0; p < nonRedundantValues.length; p++) {
        if ((madeSelection || makingSelection) && nonRedundantValues[p].yValue >= Math.min(ySelectionStart, ySelectionEnd) && nonRedundantValues[p].yValue <= Math.max(ySelectionStart, ySelectionEnd)) {
            g.setColor(Color.BLACK);
        } else {
            // if (nonRedundantValues[p].color == null) {
            // nonRedundantValues[p].color = Color.YELLOW;
            // }
            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));
        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 15 with AxisScale

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

the class PCAScatterPlotPanel 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
    String xLabel = data.getPCName(xIndex);
    g.drawString(xLabel, (getWidth() / 2) - (metrics.stringWidth(xLabel) / 2), getHeight() - 3);
    // Y label
    String yLabel = data.getPCName(yIndex);
    g.drawString(yLabel, X_AXIS_SPACE + 3, 15);
    // If we have sublists draw them below this in the right colours
    if (highlightedSets != null) {
        for (int s = 0; s < highlightedSets.length; s++) {
            g.setColor(ColourIndexSet.getColour(s));
            g.drawString(highlightedSets[s].name(), X_AXIS_SPACE + 3, 15 + (g.getFontMetrics().getHeight() * (s + 1)));
        }
        g.setColor(Color.BLACK);
    }
    // ProbeList
    g.drawString(data.probeListName(), getWidth() - 10 - metrics.stringWidth(data.probeListName()), 15);
    // 0 lines
    g.setColor(Color.GRAY);
    g.drawLine(getX(0), getHeight() - Y_AXIS_SPACE, getX(0), 10);
    g.drawLine(X_AXIS_SPACE, getY(0), getWidth() - 10, getY(0));
    g.setColor(Color.BLUE);
    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 = Color.YELLOW;
            // }
            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.store() != null) {
            int closestX = closestPoint.x + 1;
            if (closestX + g.getFontMetrics().stringWidth(closestPoint.store.name()) > getWidth()) {
                closestX = closestPoint.x - (1 + g.getFontMetrics().stringWidth(closestPoint.store.name()));
            }
            g.drawString(closestPoint.store().name(), closestX, closestPoint.y - 1);
        }
    }
    // Draw all the labels if we're asked to
    if (showLabels) {
        g.setColor(Color.BLACK);
        for (int i = 0; i < nonRedundantValues.length; i++) {
            ProbePairValue thisPoint = nonRedundantValues[i];
            if (thisPoint == null) {
                throw new IllegalStateException("Point was null when it should never be");
            }
            if (thisPoint.store == null) {
                throw new IllegalStateException("Store was null when it should never be");
            }
            int closestX = thisPoint.x + 1;
            if (closestX + g.getFontMetrics().stringWidth(thisPoint.store.name()) > getWidth()) {
                closestX = thisPoint.x - (1 + g.getFontMetrics().stringWidth(thisPoint.store.name()));
            }
            g.drawString(thisPoint.store().name(), closestX, thisPoint.y - 1);
        }
    }
}