Examples with SpeciesContextShape cbit.vcell.graph.SpeciesContextShape used on opensource projects

Example 6 with SpeciesContextShape

use of cbit.vcell.graph.SpeciesContextShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method refreshLayoutChildrenFeatureShape.

public void refreshLayoutChildrenFeatureShape(FeatureShape shape) {
    // calculate total height and max width of speciesContext (column1)
    int scCount = 0;
    List<Shape> childShapeList = shape.getChildren();
    for (int i = 0; i < childShapeList.size(); i++) {
        Shape child = childShapeList.get(i);
        if (child instanceof SpeciesContextShape) {
            scCount++;
        }
    }
    // calculate total height and max width of Membranes (column2)
    int memCount = 0;
    int memHeight = 0;
    int memWidth = 0;
    for (int i = 0; i < childShapeList.size(); i++) {
        Shape child = childShapeList.get(i);
        if (child instanceof StructureShape) {
            memHeight += child.getSpaceManager().getSize().height;
            memWidth = Math.max(memWidth, child.getSpaceManager().getSize().width);
            memCount++;
        }
    }
    int centerX = shape.getSpaceManager().getSize().width / 2;
    int currentY = shape.getLabelSize().height;
    currentY += shape.getLabelSize().height;
    int totalSpacingY;
    int spacingY;
    int extraSpacingY;
    int currentX = shape.getSpaceManager().getSize().width / 2 - memWidth / 2;
    int spacingX = StructureShape.defaultSpacingX;
    // position column2 (membranes)
    totalSpacingY = (shape.getSpaceManager().getSize().height - currentY) - memHeight;
    if (totalSpacingY < 0) {
        LayoutErrorLog.logErrorMessage("unable to fit children within container");
    }
    spacingY = totalSpacingY / (memCount + 1);
    extraSpacingY = totalSpacingY % (memCount + 1);
    centerX = currentX + memWidth / 2;
    // position children (and label)
    int col2Y = currentY + spacingY + extraSpacingY;
    for (int i = 0; i < childShapeList.size(); i++) {
        Shape child = childShapeList.get(i);
        if (child instanceof StructureShape) {
            child.getSpaceManager().setRelPos(centerX - child.getSpaceManager().getSize().width / 2, col2Y);
            col2Y += child.getSpaceManager().getSize().height + spacingY;
        }
    }
    if (col2Y != shape.getSpaceManager().getSize().height) {
        LayoutErrorLog.logErrorMessage("layout for column2 incorrect (" + shape.getLabel() + "), currentY=" + currentY + ", screenSize.height=" + shape.getSpaceManager().getSize().height);
    }
    if (memCount > 0) {
        currentX += spacingX + memWidth;
    }
    if (scCount > 0) {
        // The following code attempts to position SpeciesContextShapes so that their
        // ovals and labels do not overlap other structures
        // Calculate Mask of valid area where SpeciesContextShape may render
        Area currentOval = new Area(new Ellipse2D.Double(shape.getSpaceManager().getRelX(), shape.getSpaceManager().getRelY(), shape.getSpaceManager().getSize().width, shape.getSpaceManager().getSize().height));
        for (int i = 0; i < childShapeList.size(); i++) {
            Shape child = childShapeList.get(i);
            if (child instanceof StructureShape) {
                Area childArea = new Area(new Ellipse2D.Double(child.getSpaceManager().getRelX() + shape.getSpaceManager().getRelX(), child.getSpaceManager().getRelY() + shape.getSpaceManager().getRelY(), child.getSpaceManager().getSize().width, child.getSpaceManager().getSize().height));
                currentOval.subtract(childArea);
            }
        }
        // 
        // Position SpeciesContextShapes so they and their labels don't overlap other structures.
        // If fail, try a few more times with reduced spacing between SpeciesContextShapes to see
        // if we can fit
        // 
        final int TOPOFFSET = 20;
        boolean bLayoutFailed = false;
        int layoutRetryCount = 0;
        final int MAX_LAYOUT_RETRY = 3;
        int boxSpacingX = 50;
        final int X_RETRY_SPACE_REDUCTION = 10;
        int boxSpacingY = 30;
        final int Y_RETRY_SPACE_REDUCTION = 5;
        final int XEND = currentOval.getBounds().x + currentOval.getBounds().width;
        final int YEND = currentOval.getBounds().y + currentOval.getBounds().height;
        while (true) {
            bLayoutFailed = false;
            int xCount = 0;
            int boxX = 0;
            int boxY = 0;
            for (int i = 0; i < childShapeList.size(); i++) {
                if (childShapeList.get(i) instanceof SpeciesContextShape) {
                    SpeciesContextShape child = (SpeciesContextShape) childShapeList.get(i);
                    final int XSTEP = child.getSpaceManager().getSize().width + boxSpacingX;
                    final int YSTEP = child.getSpaceManager().getSize().height + boxSpacingY;
                    while ((layoutRetryCount <= MAX_LAYOUT_RETRY && // If last try, don't check labels for overlap
                    (// away from structure label
                    boxY <= TOPOFFSET || !currentOval.contains(// SCS label not overlap other structures
                    boxX + child.getSmallLabelPos().x + currentOval.getBounds().getX(), boxY + child.getSmallLabelPos().y + currentOval.getBounds().getY() - child.getSmallLabelSize().height, child.getSmallLabelSize().width, child.getSmallLabelSize().height))) || !currentOval.contains(// SCS oval not overlap other structures
                    boxX + currentOval.getBounds().getX(), boxY + currentOval.getBounds().getY(), SpeciesContextShape.DIAMETER, SpeciesContextShape.DIAMETER)) {
                        if (boxY < YEND) {
                            boxY += YSTEP;
                        } else {
                            boxY = (xCount % 2 == 0 ? TOPOFFSET : TOPOFFSET + SpeciesContextShape.DIAMETER);
                            boxX += XSTEP;
                            xCount += 1;
                        }
                        if (boxX > XEND && boxY > YEND) {
                            bLayoutFailed = true;
                            break;
                        }
                    }
                    if (!bLayoutFailed) {
                        child.getSpaceManager().setRelPos(boxX, boxY);
                        boxY += YSTEP;
                    } else {
                        break;
                    }
                }
            }
            if (bLayoutFailed && layoutRetryCount <= MAX_LAYOUT_RETRY) {
                boxSpacingX -= X_RETRY_SPACE_REDUCTION;
                boxSpacingY -= Y_RETRY_SPACE_REDUCTION;
                layoutRetryCount += 1;
            } else {
                break;
            }
        }
    }
}

Example 7 with SpeciesContextShape

use of cbit.vcell.graph.SpeciesContextShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method refreshLayoutChildrenMembraneShape.

public void refreshLayoutChildrenMembraneShape(MembraneShape shape) {
    // this is like a row/column layout  (1 column)
    // find featureShape child
    FeatureShape featureShape = null;
    for (Shape child : shape.getChildren()) {
        if (child instanceof FeatureShape) {
            featureShape = (FeatureShape) child;
        }
    }
    // calculate total height of all children (not including label)
    // position featureShape (and label)
    int centerX = shape.getSpaceManager().getSize().width / 2;
    int currentY = MembraneShape.memSpacingY;
    if (featureShape != null) {
        featureShape.getSpaceManager().setRelPos(centerX - featureShape.getSpaceManager().getSize().width / 2, currentY);
        currentY += featureShape.getSpaceManager().getSize().height + MembraneShape.memSpacingY;
    }
    // position speciesContextShapes
    // angle = 0 at north pole and increases counter clockwise
    int numSpeciesContexts = shape.countChildren() - 1;
    if (numSpeciesContexts > 0) {
        double deltaAngle = MembraneShape.TotalAngle / (numSpeciesContexts + 1);
        double currentAngle = MembraneShape.BeginAngle + deltaAngle;
        for (Shape child : shape.getChildren()) {
            if (child instanceof SpeciesContextShape) {
                child.getSpaceManager().setRelPos(shape.getRadialPosition(currentAngle));
                currentAngle = (currentAngle + deltaAngle) % (2 * Math.PI);
            }
        }
    }
}

Example 8 with SpeciesContextShape

use of cbit.vcell.graph.SpeciesContextShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method getPreferedSizeReactionContainerShape.

public Dimension getPreferedSizeReactionContainerShape(ReactionContainerShape shape, Graphics2D g) {
    // get size when empty
    Font origFont = g.getFont();
    g.setFont(shape.getLabelFont(g));
    try {
        Dimension emptySize = shape.getPreferedSizeSelf(g);
        // make larger than empty size so that children fit
        for (Shape child : shape.getChildren()) {
            if (child instanceof ReactionStepShape || child instanceof SpeciesContextShape) {
                emptySize.width = Math.max(emptySize.width, child.getSpaceManager().getRelPos().x + child.getSpaceManager().getSize().width);
                emptySize.height = Math.max(emptySize.height, child.getSpaceManager().getRelPos().y + child.getSpaceManager().getSize().height);
            }
        }
        emptySize.width = emptySize.width + emptySize.width / 10;
        emptySize.height = emptySize.height + emptySize.height / 10;
        return emptySize;
    } finally {
        g.setFont(origFont);
    }
}

Example 9 with SpeciesContextShape

use of cbit.vcell.graph.SpeciesContextShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method getPreferedSizeFeatureShape.

public Dimension getPreferedSizeFeatureShape(FeatureShape shape, Graphics2D g) throws GraphModel.NotReadyException {
    Font origfont = g.getFont();
    g.setFont(shape.getLabelFont(g));
    FontMetrics fm = g.getFontMetrics();
    shape.setLabelSize(fm.stringWidth(shape.getLabel()), fm.getMaxAscent() + fm.getMaxDescent());
    shape.getLabelPos().x = shape.getSpaceManager().getSize().width / 2 - fm.stringWidth(shape.getLabel()) / 2;
    shape.getLabelPos().y = 5 + fm.getMaxAscent();
    try {
        if (shape.countChildren() > 0) {
            int structCount = 0;
            int childStructureTotalHeight = shape.getLabelSize().height;
            int childStructureMaxWidth = shape.getLabelSize().width;
            for (Shape child : shape.getChildren()) {
                if (child instanceof StructureShape) {
                    structCount += 1;
                    Dimension childDim = getPreferedSize(child, g);
                    childStructureTotalHeight += childDim.height + StructureShape.defaultSpacingY;
                    childStructureMaxWidth = Math.max(childStructureMaxWidth, childDim.width);
                }
            }
            int scsCount = 0;
            // int childSCTotalHeight = 0;
            int childSCMaxWidth = 0;
            int childSCMaxHeight = 0;
            for (Shape child : shape.getChildren()) {
                if (child instanceof SpeciesContextShape) {
                    scsCount += 1;
                    Dimension childDim = getPreferedSize(child, g);
                    childSCMaxHeight = Math.max(childSCMaxHeight, childDim.height + ((SpeciesContextShape) child).getSmallLabelSize().height);
                    childSCMaxWidth = Math.max(childSCMaxWidth, childDim.width);
                    childSCMaxWidth = Math.max(childSCMaxWidth, ((SpeciesContextShape) child).getSmallLabelSize().width);
                }
            }
            Dimension box = new Dimension();
            if (scsCount != 0) {
                int squareBoxX = (int) Math.ceil(Math.sqrt(scsCount));
                int squareBoxY = squareBoxX - (int) (((squareBoxX * squareBoxX) % scsCount) / (double) squareBoxX);
                int width1 = (squareBoxX * (childSCMaxWidth + 0));
                // + defaultSpacingX;
                int height1 = (squareBoxY * (childSCMaxHeight + 30));
                // + defaultSpacingY;
                box = new Dimension(width1, height1);
            }
            if (structCount == 0) {
                shape.getSpaceManager().setSizePreferred((box.width + StructureShape.defaultSpacingX * 2), (box.height + StructureShape.defaultSpacingY * 2));
            } else {
                shape.getSpaceManager().setSizePreferred((childStructureMaxWidth + box.width + StructureShape.defaultSpacingX * 2), (Math.max(childStructureTotalHeight, box.height) + StructureShape.defaultSpacingY * 2));
            }
        } else {
            shape.getSpaceManager().setSizePreferred((shape.getLabelSize().width + StructureShape.defaultSpacingX * 2), (shape.getLabelSize().height + StructureShape.defaultSpacingY * 2));
        }
        return shape.getSpaceManager().getSizePreferred();
    } finally {
        g.setFont(origfont);
    }
}

Example 10 with SpeciesContextShape

use of cbit.vcell.graph.SpeciesContextShape in project vcell by virtualcell.

the class GraphContainerLayoutReactions method getPreferedSizeReactionContainerShape.

public Dimension getPreferedSizeReactionContainerShape(ReactionContainerShape shape, Graphics2D g) {
    // get size when empty
    Font origFont = g.getFont();
    g.setFont(shape.getLabelFont(g));
    try {
        Dimension preferredSize = shape.getPreferedSizeSelf(g);
        // make larger than empty size so that children fit
        for (Shape child : shape.getChildren()) {
            if (child instanceof ReactionStepShape || child instanceof SpeciesContextShape || child instanceof RuleParticipantSignatureFullDiagramShape || child instanceof RuleParticipantSignatureShortDiagramShape || child instanceof ReactionRuleDiagramShape) {
                preferredSize.width = Math.max(preferredSize.width, child.getSpaceManager().getRelPos().x + child.getSpaceManager().getSize().width);
                preferredSize.height = Math.max(preferredSize.height, child.getSpaceManager().getRelPos().y + child.getSpaceManager().getSize().height);
            }
        }
        preferredSize.width = preferredSize.width + WIDTH_PADDING;
        preferredSize.height = preferredSize.height + HEIGHT_PADDING;
        Structure structure = shape.getStructure();
        int minWidthSum = 0;
        for (Structure structure2 : shape.getStructureSuite().getStructures()) {
            if (structure2 instanceof Feature) {
                minWidthSum += FEATURE_MIN_WIDTH;
            } else {
                minWidthSum += MEMBRANE_MIN_WIDTH;
            }
        }
        int compartmentMinWidth = 0;
        if (structure instanceof Feature) {
            compartmentMinWidth = FEATURE_MIN_WIDTH;
        } else {
            compartmentMinWidth = MEMBRANE_MIN_WIDTH;
        }
        int apportionedWidth = compartmentMinWidth * TOTAL_MIN_WIDTH / minWidthSum;
        if (preferredSize.width < compartmentMinWidth) {
            preferredSize.width = compartmentMinWidth;
        }
        if (preferredSize.width < apportionedWidth) {
            preferredSize.width = apportionedWidth;
        }
        if (preferredSize.height < MIN_HEIGHT) {
            preferredSize.height = MIN_HEIGHT;
        }
        return preferredSize;
    } finally {
        g.setFont(origFont);
    }
}