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

Example 16 with AxisScale

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

the class VarianceLineGraphPanel 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.drawLine(X_AXIS_SPACE, getYPixels(currentYValue), X_AXIS_SPACE - 3, getYPixels(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // Draw x ticks
    for (int s = 0; s < values.length; s++) {
        int xTick = X_AXIS_SPACE + (s * ((getWidth() - (10 + X_AXIS_SPACE)) / (values.length - 1)));
        g.drawLine(xTick, getHeight() - Y_AXIS_SPACE, xTick, getHeight() - (Y_AXIS_SPACE - 3));
    }
    for (int s = 0; s < values.length; s++) {
        int xTick = X_AXIS_SPACE + (s * ((getWidth() - (10 + X_AXIS_SPACE)) / (values.length - 1)));
        int stringWidth = g.getFontMetrics().stringWidth("PC" + (s + 1));
        int xStart = xTick - (stringWidth / 2);
        if (xStart < 1)
            xStart = 1;
        if (xStart + stringWidth > (getWidth() - 1))
            xStart = (getWidth() - 1) - stringWidth;
        g.drawString("PC" + (s + 1), xStart, getHeight() - (Y_AXIS_SPACE - (g.getFontMetrics().getHeight() + 3)));
    }
    // Put the probe list name at the top
    String listName = "Variance";
    g.drawString(listName, X_AXIS_SPACE, 10);
    // Now draw the probes
    int lastX = 0;
    int lastY = 0;
    int thisX = 0;
    int thisY = 0;
    double value = 0;
    g.setColor(BLUE);
    for (int s = 0; s < values.length; s++) {
        thisX = getXPixels(s);
        value = values[s];
        if (value < usedMin)
            value = usedMin;
        if (value > usedMax)
            value = usedMax;
        thisY = getYPixels(value);
        if (s > 0) {
            g.drawLine(lastX, lastY, thisX, thisY);
        }
        g.fillOval(thisX - 4, thisY - 4, 8, 8);
        lastX = thisX;
        lastY = thisY;
    }
    // Now highlight the selected index
    thisX = getXPixels(selectedIndex);
    g.setColor(Color.BLACK);
    g.drawLine(thisX, getHeight() - Y_AXIS_SPACE, thisX, 10);
}

Example 17 with AxisScale

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

the class TrendOverProbePanel 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());
    // Don't draw anything if the calculation isn't done.
    if (counts == null) {
        return;
    }
    // First work out the amount of space we need to leave for the X axis
    int X_AXIS_SPACE = 0;
    AxisScale yAxisScale = new AxisScale(minCount, maxCount);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < maxCount) {
        int stringWidth = g.getFontMetrics().stringWidth(yAxisScale.format(currentYValue)) + 10;
        if (stringWidth > X_AXIS_SPACE) {
            X_AXIS_SPACE = stringWidth;
        }
        currentYValue += yAxisScale.getInterval();
    }
    if (Y_AXIS_SPACE == 0) {
        Y_AXIS_SPACE = g.getFontMetrics().getAscent() * 3;
    }
    // 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);
    // Y axis
    g.drawLine(X_AXIS_SPACE, 10, X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE);
    // X labels
    String xLabel;
    if (sameLength) {
        xLabel = "Bases 1 - " + fixedLength;
    } else {
        xLabel = "Relative distance across probe";
    }
    g.drawString(xLabel, (getWidth() / 2) - (metrics.stringWidth(xLabel) / 2), getHeight() - 5);
    if (sameLength) {
        AxisScale xAxisScale = new AxisScale(1, fixedLength);
        double currentXValue = xAxisScale.getStartingValue();
        while (currentXValue + xAxisScale.getInterval() < fixedLength) {
            int thisX = X_AXIS_SPACE;
            double xProportion = (double) currentXValue / fixedLength;
            thisX += (int) (xProportion * (getWidth() - (X_AXIS_SPACE + 10)));
            g.drawString(xAxisScale.format(currentXValue), thisX - (g.getFontMetrics().stringWidth(xAxisScale.format(currentXValue)) / 2), (int) ((getHeight() - Y_AXIS_SPACE) + 15));
            g.drawLine(thisX, getHeight() - Y_AXIS_SPACE, thisX, getHeight() - (Y_AXIS_SPACE - 3));
            currentXValue += xAxisScale.getInterval();
        }
    }
    // Labels on the y-axis
    currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < maxCount) {
        g.drawString(yAxisScale.format(currentYValue), 2, getY(currentYValue) + (g.getFontMetrics().getAscent() / 2));
        g.drawLine(X_AXIS_SPACE, getY(currentYValue), X_AXIS_SPACE - 3, getY(currentYValue));
        currentYValue += yAxisScale.getInterval();
    }
    // Now go through the various datastores
    for (int p = 0; p < probeLists.length; p++) {
        for (int s = 0; s < stores.length; s++) {
            int d = (p * stores.length) + s;
            g.setColor(ColourIndexSet.getColour(d));
            String name = probeLists[p].name() + " - " + stores[s].name();
            g.drawString(name, getWidth() - 10 - metrics.stringWidth(name), 15 + (15 * d));
            int lastX = X_AXIS_SPACE;
            int lastY = getY(counts[d][0]);
            boolean drawnCrossHair = false;
            for (int x = 1; x < counts[d].length; x++) {
                int thisX = X_AXIS_SPACE;
                double xProportion = (double) x / (counts[d].length - 1);
                thisX += (int) (xProportion * (getWidth() - (X_AXIS_SPACE + 10)));
                if (thisX == lastX)
                    continue;
                int thisY = getY(counts[d][x]);
                if (drawCrossHair && !drawnCrossHair && thisX >= mouseX) {
                    String label = df.format(counts[d][x]);
                    // Clean up the ends if we can
                    label = label.replaceAll("0+$", "");
                    label = label.replaceAll("\\.$", "");
                    g.drawString(label, thisX + 2, thisY);
                    drawnCrossHair = true;
                    if (d == 0) {
                        Color oldColor = g.getColor();
                        g.setColor(Color.GRAY);
                        g.drawLine(thisX, 10, thisX, getHeight() - 20);
                        g.drawString("" + x, thisX + 2, getHeight() - 27);
                        g.setColor(oldColor);
                    }
                }
                g.drawLine(lastX, lastY, thisX, thisY);
                lastX = thisX;
                lastY = thisY;
            }
        }
    }
}

Example 18 with AxisScale

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

the class ScatterPlotPanel 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(xStore.name(), (getWidth() / 2) - (metrics.stringWidth(xStore.name()) / 2), getHeight() - 3);
    // Y label
    g.drawString(yStore.name(), 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);
    // R-value
    g.drawString(rValue, getWidth() - 10 - metrics.stringWidth(rValue), getHeight() - (Y_AXIS_SPACE + 3));
    // 45 degree line
    g.setColor(Color.GRAY);
    g.drawLine(X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE, getWidth() - 10, 10);
    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.probe() != null) {
            g.drawString(closestPoint.probe().name(), closestPoint.x + 1, closestPoint.y - 1);
        }
    }
}

Example 19 with AxisScale

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

the class QuantitationTrendPlotPanel 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());
    // Don't draw anything if the calculation isn't done.
    if (counts == null) {
        return;
    }
    // First work out the amount of space we need to leave for the X axis
    int X_AXIS_SPACE = 0;
    AxisScale yAxisScale = new AxisScale(minCount, maxCount);
    double currentYValue = yAxisScale.getStartingValue();
    while (currentYValue < maxCount) {
        int stringWidth = g.getFontMetrics().stringWidth(yAxisScale.format(currentYValue)) + 10;
        if (stringWidth > X_AXIS_SPACE) {
            X_AXIS_SPACE = stringWidth;
        }
        currentYValue += yAxisScale.getInterval();
    }
    if (!leftMost) {
        X_AXIS_SPACE = 0;
    }
    if (Y_AXIS_SPACE == 0) {
        Y_AXIS_SPACE = g.getFontMetrics().getAscent() * 3;
    }
    // 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(), getHeight() - Y_AXIS_SPACE);
    // Y axis
    g.drawLine(X_AXIS_SPACE, 10, X_AXIS_SPACE, getHeight() - Y_AXIS_SPACE);
    // X labels
    String xLabel;
    if (sameLength) {
        xLabel = "Bases 1 - " + fixedLength;
    } else {
        xLabel = "Relative distance across " + featureName;
    }
    g.drawString(xLabel, (getWidth() / 2) - (metrics.stringWidth(xLabel) / 2), getHeight() - 5);
    if (sameLength) {
        AxisScale xAxisScale = new AxisScale(1, fixedLength);
        double currentXValue = xAxisScale.getStartingValue();
        double lastXLabelEnd = -1;
        while (currentXValue + xAxisScale.getInterval() <= fixedLength) {
            int thisX = X_AXIS_SPACE;
            double xProportion = (double) currentXValue / fixedLength;
            thisX += (int) (xProportion * (getWidth() - X_AXIS_SPACE));
            int thisHalfLabelWidth = (g.getFontMetrics().stringWidth(xAxisScale.format(currentXValue)) / 2);
            if (thisX - thisHalfLabelWidth <= lastXLabelEnd) {
                currentXValue += xAxisScale.getInterval();
                continue;
            }
            lastXLabelEnd = thisX + thisHalfLabelWidth;
            g.drawString(xAxisScale.format(currentXValue), thisX - thisHalfLabelWidth, (int) ((getHeight() - Y_AXIS_SPACE) + 15));
            g.drawLine(thisX, getHeight() - Y_AXIS_SPACE, thisX, getHeight() - (Y_AXIS_SPACE - 3));
        }
    }
    if (leftMost) {
        currentYValue = yAxisScale.getStartingValue();
        while (currentYValue < maxCount) {
            g.drawString(yAxisScale.format(currentYValue), 2, getY(currentYValue) + (g.getFontMetrics().getAscent() / 2));
            g.drawLine(X_AXIS_SPACE, getY(currentYValue), X_AXIS_SPACE - 3, getY(currentYValue));
            currentYValue += yAxisScale.getInterval();
        }
    }
    // Now go through the various datastores
    for (int d = 0; d < counts.length; d++) {
        g.setColor(ColourIndexSet.getColour(d));
        if (rightMost) {
            g.drawString(stores[d].name(), getWidth() - 10 - metrics.stringWidth(stores[d].name()), 15 + (15 * d));
        }
        int lastX = X_AXIS_SPACE;
        int lastY = getY(counts[d][0]);
        boolean drawnCrossHair = false;
        for (int x = 1; x < counts[d].length; x++) {
            int thisX = X_AXIS_SPACE;
            double xProportion = (double) x / (counts[d].length - 1);
            thisX += (int) (xProportion * (getWidth() - X_AXIS_SPACE));
            // Only draw something when we've moving somewhere.
            if (thisX == lastX)
                continue;
            int thisY = getY(counts[d][x]);
            if (drawCrossHair && !drawnCrossHair && thisX >= mouseX) {
                String label = df.format(counts[d][x]);
                // Clean up the ends if we can
                label = label.replaceAll("0+$", "");
                label = label.replaceAll("\\.$", "");
                g.drawString(label, thisX + 2, thisY);
                drawnCrossHair = true;
                if (d == 0) {
                    Color oldColor = g.getColor();
                    g.setColor(Color.GRAY);
                    g.drawLine(thisX, 10, thisX, getHeight() - 20);
                    g.drawString("" + x, thisX + 2, getHeight() - 27);
                    g.setColor(oldColor);
                }
            }
            g.drawLine(lastX, lastY, thisX, thisY);
            lastX = thisX;
            lastY = thisY;
        }
    }
}