Examples with Point2D java.awt.geom.Point2D used on opensource projects

Example 86 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class ReactionParticipantShape method paintSelf.

@Override
public void paintSelf(Graphics2D g2D, int parentOffsetX, int parentOffsetY) {
    if (startShape.isSelected()) {
        forgroundColor = Color.red.darker();
    } else {
        forgroundColor = Color.black;
    }
    if (isSelected()) {
        forgroundColor = Color.red;
    }
    // draw cubic spline with horizontal reactant-end (p' = 0) at reaction
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    CubicCurve2D.Double cubicCurve = getCurve();
    // render curve (make CatalystShapes draw with a dashed line)
    g2D.setColor(forgroundColor);
    if (getLineStyle() == LINE_STYLE_DASHED) {
        Stroke oldStroke = g2D.getStroke();
        g2D.setStroke(DASHED_STROKE);
        g2D.draw(cubicCurve);
        g2D.setStroke(oldStroke);
    } else {
        g2D.draw(cubicCurve);
    }
    int arrowDirection = 0;
    if (this instanceof ProductShape) {
        arrowDirection = 1;
    }
    if (this instanceof ReactantShape) {
        arrowDirection = -1;
    }
    if (arrowDirection == 1) {
        double arcLength = integrateArcLength(cubicCurve, 0.0, 1.0, 10);
        double centerT = getParameterAtArcLength(cubicCurve, 0.0, 1.0, arcLength / 2, 20);
        Point2D center = evaluate(cubicCurve, centerT);
        double backT = intersectWithCircle(cubicCurve, centerT, 1.0, center.getX(), center.getY(), 4);
        Point2D back = evaluate(cubicCurve, backT);
        double frontT = intersectWithCircle(cubicCurve, centerT, 0.0, center.getX(), center.getY(), 4);
        Point2D front = evaluate(cubicCurve, frontT);
        GeneralPath arrow = getArrow(front, back, 7);
        g2D.fill(arrow);
    }
    if (arrowDirection == -1) {
        double arcLength = integrateArcLength(cubicCurve, 0.0, 1.0, 10);
        double centerT = getParameterAtArcLength(cubicCurve, 0.0, 1.0, arcLength / 2 + 2, 20);
        Point2D center = evaluate(cubicCurve, centerT);
        double backT = intersectWithCircle(cubicCurve, centerT, 0.0, center.getX(), center.getY(), 4);
        Point2D back = evaluate(cubicCurve, backT);
        double frontT = intersectWithCircle(cubicCurve, centerT, 1.0, center.getX(), center.getY(), 4);
        Point2D front = evaluate(cubicCurve, frontT);
        GeneralPath arrow = getArrow(front, back, 7);
        g2D.fill(arrow);
    }
    // draw label
    if (getLabel() != null && getLabel().length() > 0) {
        int x = start.x + (int) (start.x * correctionFactor);
        int y = start.y + (int) (start.y * correctionFactor);
        g2D.drawString(getLabel(), (x + end.x) / 2, (y + end.y) / 2);
    }
    return;
}

Example 87 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class RuleParticipantEdgeDiagramShape method paintSelf.

@Override
public void paintSelf(Graphics2D g2D, int parentOffsetX, int parentOffsetY) {
    // draw cubic spline with horizontal reactant-end (p' = 0) at reaction
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    CubicCurve2D.Double cubicCurve = getCurve();
    // render curve (make CatalystShapes draw with a dashed line)
    g2D.setColor(forgroundColor);
    if (getLineStyle() == LINE_STYLE_DASHED) {
        Stroke oldStroke = g2D.getStroke();
        g2D.setStroke(DASHED_STROKE);
        g2D.draw(cubicCurve);
        g2D.setStroke(oldStroke);
    } else {
        g2D.draw(cubicCurve);
    }
    int arrowDirection = 0;
    if (this instanceof ProductPatternEdgeDiagramShape) {
        arrowDirection = 1;
    }
    if (this instanceof ReactantPatternEdgeDiagramShape) {
        arrowDirection = -1;
    }
    if (arrowDirection == 1) {
        double arcLength = integrateArcLength(cubicCurve, 0.0, 1.0, 10);
        double centerT = getParameterAtArcLength(cubicCurve, 0.0, 1.0, arcLength / 2, 20);
        Point2D center = evaluate(cubicCurve, centerT);
        double backT = intersectWithCircle(cubicCurve, centerT, 1.0, center.getX(), center.getY(), 4);
        Point2D back = evaluate(cubicCurve, backT);
        double frontT = intersectWithCircle(cubicCurve, centerT, 0.0, center.getX(), center.getY(), 4);
        Point2D front = evaluate(cubicCurve, frontT);
        GeneralPath arrow = getArrow(front, back, 7);
        g2D.fill(arrow);
    }
    if (arrowDirection == -1) {
        double arcLength = integrateArcLength(cubicCurve, 0.0, 1.0, 10);
        double centerT = getParameterAtArcLength(cubicCurve, 0.0, 1.0, arcLength / 2 + 2, 20);
        Point2D center = evaluate(cubicCurve, centerT);
        double backT = intersectWithCircle(cubicCurve, centerT, 0.0, center.getX(), center.getY(), 4);
        Point2D back = evaluate(cubicCurve, backT);
        double frontT = intersectWithCircle(cubicCurve, centerT, 1.0, center.getX(), center.getY(), 4);
        Point2D front = evaluate(cubicCurve, frontT);
        GeneralPath arrow = getArrow(front, back, 7);
        g2D.fill(arrow);
    }
    // draw label
    if (getLabel() != null && getLabel().length() > 0) {
        g2D.drawString(getLabel(), (start.x + end.x) / 2, (start.y + end.y) / 2);
    }
    return;
}

Example 88 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class RuleParticipantSignatureDiagramShape method paintSelf.

// TODO: Override ElipseShape::isInside()
// our shape here is rounded rectangle while IsInside thinks it's an ellipse, which means
// that clicking near the corners of a long shape (with many molecules) fails to select the shape
// TODO: the RoundRectangle2D contour below needs to be recalculated with updated width, using the
// species pattern in the RuleParticipantSignature
@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
    if (!bVisible) {
        return;
    }
    // we reserve space for at least 1 molecule
    int numMolecules = Math.max(1, ruleParticipantSignature.getSpeciesPattern().getMolecularTypePatterns().size());
    width = leftmargin + circleDiameter + displacement * (numMolecules - 1) + 1;
    getSpaceManager().setSize(width, height);
    int shapeHeight = getSpaceManager().getSize().height;
    int shapeWidth = getSpaceManager().getSize().width;
    Graphics2D g2D = g;
    Paint oldPaint = g2D.getPaint();
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    Color exterior;
    // draw the contour around the whole rule participant
    // no need to really draw it if the shapes of the molecules fill it perfectly, because it won't be visible anyway
    // however, the "isInside" function will need exactly this RoundRectangle2D to compute whether the point is inside the shape
    RoundRectangle2D contour = new RoundRectangle2D.Double(absPosX, absPosY, shapeWidth, shapeHeight, shapeHeight, shapeHeight);
    g2D.setPaint(isSelected() ? AbstractComponentShape.componentMediumPalePink : AbstractComponentShape.componentPaleGreen);
    g2D.fill(contour);
    exterior = isSelected() ? Color.red.darker().darker() : Color.darkGray;
    g.setColor(exterior);
    g2D.draw(contour);
    Model model = ((ReactionCartoon) graphModel).getModel();
    RbmModelContainer rbmmc = model.getRbmModelContainer();
    List<MolecularType> mtList = rbmmc.getMolecularTypeList();
    List<MolecularType> ruleSignatureMolecularTypes = ruleParticipantSignature.getMolecularTypes();
    // draw the molecules (they are properly drawn because we use the sp as it is in the associated RuleParticipantSignature object)
    for (int i = 0; i < ruleSignatureMolecularTypes.size(); i++) {
        double offsetx = leftmargin + i * displacement - 1.4;
        int offsety = getSpaceManager().getSize().height - circleDiameter - 2;
        Ellipse2D icon = new Ellipse2D.Double(absPosX + offsetx, absPosY + offsety, circleDiameter, circleDiameter);
        // int offsetx = leftmargin + i*displacement;
        // int offsety = 0;
        // Rectangle2D icon = new Rectangle2D.Double(absPosX + offsetx, absPosY + offsety, displacement, shapeHeight-1);
        MolecularType mt = ruleSignatureMolecularTypes.get(i);
        int index = mtList.indexOf(mt);
        index = index % 7;
        defaultBG = Color.lightGray;
        Color interior = Color.white;
        if (graphModel instanceof ReactionCartoonFull) {
            // take color from molecular type color selection
            defaultBG = MolecularTypeLargeShape.colorTable[index];
        }
        backgroundColor = defaultBG;
        // darkerBackground = backgroundColor.darker().darker();
        exterior = !isSelected() ? backgroundColor.darker().darker() : backgroundColor.darker();
        Color[] colors = { interior, exterior };
        g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
        Point2D center = new Point2D.Double(absPosX + offsetx + circleDiameter / 2, absPosY + offsety + circleDiameter / 2);
        float radius = circleDiameter * 0.5f;
        Point2D focus = new Point2D.Double(absPosX + offsetx + circleDiameter / 2 - 2, absPosY + offsety + circleDiameter / 2 - 2);
        float[] dist = { 0.1f, 1.0f };
        RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
        // Paint p = defaultBG.darker().darker();
        g2D.setPaint(p);
        g2D.fill(icon);
        g.setColor(forgroundColor);
        g2D.draw(icon);
    }
    // TODO: see if RefreshLabel below works properly, if it does make a similar call to refresh the width!!!
    if (getLabel() != null && getLabel().length() > 0) {
        if (isSelected()) {
            // clear background and outline to make selected label stand out
            Rectangle outlineRectangle = getLabelOutline(absPosX, absPosY);
            drawRaisedOutline(outlineRectangle.x, outlineRectangle.y, outlineRectangle.width, outlineRectangle.height, g, Color.white, forgroundColor, Color.gray);
        }
        if (bDisplayLabel || isSelected()) {
            g.setColor(forgroundColor);
            g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y - 2 + absPosY);
        }
    }
    if (linkText != null && linkText != "") {
        ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
    }
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
    g2D.setPaint(oldPaint);
}

Example 89 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class SpeciesContextShape method paintSelf.

@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
    boolean isBound = false;
    SpeciesContext sc = (SpeciesContext) getModelObject();
    boolean bHasPCLink = false;
    if (graphModel instanceof ModelCartoon) {
        ModelCartoon mc = (ModelCartoon) graphModel;
        // check if species has Pathway Commons link by querying VCMetadata : if it does, need to change color of speciesContext.
        try {
            MiriamManager miriamManager = mc.getModel().getVcMetaData().getMiriamManager();
            Map<MiriamRefGroup, MIRIAMQualifier> miriamRefGroups = miriamManager.getAllMiriamRefGroups(sc.getSpecies());
            if (miriamRefGroups != null && miriamRefGroups.size() > 0) {
                bHasPCLink = true;
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    if (sc.getSpecies().getDBSpecies() != null || bHasPCLink) {
        isBound = true;
    }
    int shapeHeight = getSpaceManager().getSize().height;
    int shapeWidth = getSpaceManager().getSize().width;
    int offsetX = (shapeWidth - circleDiameter) / 2;
    int offsetY = (shapeHeight - circleDiameter) / 2;
    Graphics2D g2D = g;
    // if (icon == null) {
    icon = new Area();
    icon.add(new Area(new Ellipse2D.Double(offsetX, offsetY, circleDiameter, circleDiameter)));
    // icon.add(new Area(new RoundRectangle2D.Double(offsetX, offsetY,circleDiameter,circleDiameter,circleDiameter/2,circleDiameter/2)));
    // }
    Area movedIcon = icon.createTransformedArea(AffineTransform.getTranslateInstance(absPosX, absPosY));
    if (sc.getSpeciesPattern() == null) {
        defaultBG = java.awt.Color.green;
    } else {
        defaultBG = java.awt.Color.blue;
    }
    if (isCatalyst == true) {
        defaultBG = java.awt.Color.magenta;
    }
    backgroundColor = defaultBG;
    darkerBackground = backgroundColor.darker().darker();
    // g.setColor((!isBound && !isSelected()?darkerBackground:backgroundColor));
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    Color exterior = !isBound && !isSelected() ? darkerBackground : backgroundColor;
    // Color interior = exterior.brighter().brighter();
    Point2D center = new Point2D.Float(absPosX + circleDiameter * 0.5f, absPosY + circleDiameter * 0.5f);
    float radius = circleDiameter * 0.5f;
    Point2D focus = new Point2D.Float(absPosX + circleDiameter * 0.4f, absPosY + circleDiameter * 0.4f);
    float[] dist = { 0.1f, 1.0f };
    Color[] colors = { Color.white, exterior };
    // Color[] colors = {interior, exterior};
    RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
    g2D.setPaint(p);
    g2D.fill(movedIcon);
    g.setColor(forgroundColor);
    g2D.draw(movedIcon);
    // draw label
    if (getLabel() != null && getLabel().length() > 0) {
        if (isSelected()) {
            // clear background and outline to make selected label stand out
            Rectangle outlineRectangle = getLabelOutline(absPosX, absPosY);
            drawRaisedOutline(outlineRectangle.x, outlineRectangle.y, outlineRectangle.width, outlineRectangle.height, g, Color.white, forgroundColor, Color.gray);
        }
        g.setColor(forgroundColor);
        g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y + absPosY);
    }
    if (linkText != null && linkText != "") {
        ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
    }
}

Example 90 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class FRAPData method createCircularBinaryKernel.

private KernelJAI createCircularBinaryKernel(int radius) {
    int enclosingBoxSideLength = radius * 2 + 1;
    float[] kernalData = new float[enclosingBoxSideLength * enclosingBoxSideLength];
    Point2D kernalPoint = new Point2D.Float(0f, 0f);
    int index = 0;
    for (int y = -radius; y <= radius; y++) {
        for (int x = -radius; x <= radius; x++) {
            if (kernalPoint.distance(x, y) <= radius) {
                kernalData[index] = 1.0f;
            }
            index++;
        }
    }
    return new KernelJAI(enclosingBoxSideLength, enclosingBoxSideLength, radius, radius, kernalData);
}