Examples with Shape cbit.gui.graph.Shape used on opensource projects

Example 41 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class BioPaxInteractionParticipantShape method getCurve.

// very similar with the code in ReactionParticipantShape
@Override
protected final CubicCurve2D.Double getCurve() {
    refreshLayoutSelf();
    // default behavior of control points is for direction at ends to follow secant between end-points.
    if (lastCurve_Start == null || !lastCurve_Start.equals(start) || lastCurve_End == null || !lastCurve_End.equals(end)) {
        lastp1ctrl = new Point2D.Double((1.0 - FRACT_WEIGHT) * start.getX() + FRACT_WEIGHT * end.getX(), (1.0 - FRACT_WEIGHT) * start.getY() + FRACT_WEIGHT * end.getY());
    }
    Point2D.Double p2ctrl = new Point2D.Double(FRACT_WEIGHT * start.getX() + (1.0 - FRACT_WEIGHT) * end.getX(), FRACT_WEIGHT * start.getY() + (1.0 - FRACT_WEIGHT) * end.getY());
    // check for siblings in the reaction (like a+a-> or a->a) and calculate a correction factor
    // so that the edges won't overlap
    correctionFactor = 0;
    if (endShape instanceof BioPaxInteractionShape) {
        // index in the array of siblings
        int myPosition = 0;
        // in total
        int numSiblings = 0;
        BioPaxInteractionShape reactionStepShape = (BioPaxInteractionShape) endShape;
        Interaction rs = reactionStepShape.getInteraction();
        for (InteractionParticipant rp : rs.getParticipants()) {
            if (rp == participant) {
                // myself
                if (rp.getType() == InteractionParticipant.Type.LEFT || rp.getType() == InteractionParticipant.Type.RIGHT) {
                    myPosition = numSiblings;
                    numSiblings++;
                }
            } else if (rp.getPhysicalEntity().getName().equals(participant.getPhysicalEntity().getName())) {
                if (rp.getType() == InteractionParticipant.Type.LEFT || rp.getType() == InteractionParticipant.Type.RIGHT) {
                    numSiblings++;
                }
            }
        }
        if (numSiblings > 1) {
            double offset = numSiblings / 2 - 0.5;
            correctionFactor = (myPosition - offset) * 0.08;
        }
    }
    // calculate tangent direction at interaction
    double tangentX = 0.0;
    double tangentY = 0.0;
    if (endShape instanceof BioPaxInteractionShape) {
        BioPaxInteractionShape reactionStepShape = (BioPaxInteractionShape) endShape;
        for (Shape shape : graphModel.getShapes()) {
            if (shape instanceof BioPaxInteractionParticipantShape && ((BioPaxInteractionParticipantShape) shape).endShape == reactionStepShape) {
                BioPaxInteractionParticipantShape rpShape = (BioPaxInteractionParticipantShape) shape;
                double dx = rpShape.start.getX() - rpShape.end.getX();
                double dy = rpShape.start.getY() - rpShape.end.getY();
                double len = dx * dx + dy * dy;
                if (rpShape.participant.getType() == InteractionParticipant.Type.LEFT) {
                    tangentX += (rpShape.start.getX() - rpShape.end.getX()) / len;
                    tangentY += (rpShape.start.getY() - rpShape.end.getY()) / len;
                } else if (rpShape.participant.getType() == InteractionParticipant.Type.RIGHT) {
                    tangentX -= (rpShape.start.getX() - rpShape.end.getX()) / len;
                    tangentY -= (rpShape.start.getY() - rpShape.end.getY()) / len;
                }
            }
        }
    }
    double tangentLength = Math.sqrt(tangentX * tangentX + tangentY * tangentY);
    if (tangentLength != 0) {
        tangentX = tangentX * CONTROL_WEIGHT / tangentLength;
        tangentY = tangentY * CONTROL_WEIGHT / tangentLength;
    }
    if (participant.getType() == InteractionParticipant.Type.CONTROLLER) {
        // choose side based on inner product with displacement vector between catalyst and reactionStep
        if (((start.getX() - end.getX()) * tangentY - (start.getY() - end.getY()) * tangentX) > 0) {
            p2ctrl.setLocation(end.getX() + tangentY, end.getY() - tangentX);
        } else {
            p2ctrl.setLocation(end.getX() - tangentY, end.getY() + tangentX);
        }
    } else if (participant.getType() == InteractionParticipant.Type.RIGHT) {
        p2ctrl.setLocation(end.getX() + tangentX, end.getY() + tangentY);
    } else if (participant.getType() == InteractionParticipant.Type.LEFT) {
        p2ctrl.setLocation(end.getX() - tangentX, end.getY() - tangentY);
    }
    if (lastCurve != null && lastCurve_Start != null && lastCurve_Start.equals(start) && lastCurve_End != null && lastCurve_End.equals(end) && lastp2ctrl != null && lastp2ctrl.equals(p2ctrl)) {
    // Do Nothing
    } else {
        lastCurve = new CubicCurve2D.Double(start.getX(), start.getY(), lastp1ctrl.getX() * (1 + correctionFactor), lastp1ctrl.getY() * (1 + correctionFactor), p2ctrl.getX(), p2ctrl.getY(), end.getX(), end.getY());
        lastCurve_Start = new Point(start);
        lastCurve_End = new Point(end);
        lastp2ctrl = p2ctrl;
    }
    return lastCurve;
}

Example 42 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class PathwayGraphModel method refreshParticipant.

private void refreshParticipant(BioPaxInteractionShape interactionShape, InteractionParticipant participant) {
    BioPaxInteractionParticipantShape edgeShape = (BioPaxInteractionParticipantShape) getShapeFromModelObject(participant);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxInteractionParticipantShape(participant, interactionShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, interactionShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 43 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class PathwayGraphModel method refreshAll.

@Override
public void refreshAll() {
    if (pathwayModel == null) {
        clearAllShapes();
        fireGraphChanged();
        return;
    }
    unwantedShapes = new HashSet<Shape>();
    unwantedShapes.addAll(getShapes());
    pathwayContainerShape = (PathwayContainerShape) getShapeFromModelObject(pathwayModel);
    if (pathwayContainerShape == null) {
        pathwayContainerShape = new PathwayContainerShape(this, pathwayModel);
        pathwayContainerShape.getSpaceManager().setSize(400, 300);
        addShape(pathwayContainerShape);
    }
    unwantedShapes.remove(pathwayContainerShape);
    Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(pathwayModel.getDisplayableBioPaxObjectList());
    for (BioPaxObject bpObject : bioPaxObjects) {
        BioPaxShape bpObjectShape = (BioPaxShape) getShapeFromModelObject(bpObject);
        if (bpObjectShape == null) {
            if (bpObject instanceof Conversion) {
                bpObjectShape = new BioPaxConversionShape((Conversion) bpObject, this);
            } else if (bpObject instanceof MolecularInteraction) {
                bpObjectShape = new BioPaxMolecularInteractionShape((MolecularInteraction) bpObject, this);
            } else if (bpObject instanceof Protein) {
                bpObjectShape = new BioPaxProteinShape((Protein) bpObject, this);
            } else if (bpObject instanceof Complex) {
                bpObjectShape = new BioPaxComplexShape((Complex) bpObject, this);
            } else if (bpObject instanceof SmallMolecule) {
                bpObjectShape = new BioPaxSmallMoleculeShape((SmallMolecule) bpObject, this);
            } else if (bpObject instanceof Dna) {
                bpObjectShape = new BioPaxDnaShape((Dna) bpObject, this);
            } else if (bpObject instanceof Rna) {
                bpObjectShape = new BioPaxRnaShape((Rna) bpObject, this);
            } else if (bpObject instanceof PhysicalEntity) {
                bpObjectShape = new BioPaxPhysicalEntityShape((PhysicalEntity) bpObject, this);
            } else if (bpObject instanceof GroupObject) {
                bpObjectShape = new BioPaxGroupShape((GroupObject) bpObject, this);
            } else {
                bpObjectShape = new BioPaxObjectShape(bpObject, this);
            }
            if (!(bpObject instanceof Control)) {
                // the Control objects will not be displayed on the diagram
                pathwayContainerShape.addChildShape(bpObjectShape);
                addShape(bpObjectShape);
            }
            Dimension shapeSize = bpObjectShape.getSpaceManager().getSize();
            Rectangle boundary = getContainerLayout().getBoundaryForAutomaticLayout(pathwayContainerShape);
            int xPos = boundary.x + random.nextInt(boundary.width - shapeSize.width);
            int yPos = boundary.y + random.nextInt(boundary.height - shapeSize.height);
            bpObjectShape.setAbsPos(xPos, yPos);
        }
        unwantedShapes.remove(bpObjectShape);
    }
    for (BioPaxObject bpObject : bioPaxObjects) {
        if (bpObject instanceof Conversion) {
            refreshInteraction((Conversion) bpObject);
        } else if (bpObject instanceof MolecularInteraction) {
            refreshInteraction((MolecularInteraction) bpObject);
        } else if (bpObject instanceof Control) {
            refreshControl((Control) bpObject);
        } else if (bpObject instanceof GroupObject) {
            refreshGroupObject((GroupObject) bpObject);
        }
    }
    for (Shape unwantedShape : unwantedShapes) {
        removeShape(unwantedShape);
    }
    refreshRelationshipInfo();
    fireGraphChanged();
}

Example 44 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class PathwayGraphModel method refreshGroupInteraction.

private void refreshGroupInteraction(GroupObject groupObject, InteractionParticipant participant) {
    BioPaxGroupShape groupShape = (BioPaxGroupShape) getShapeFromModelObject(groupObject);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    GroupNeighbor groupNeighbor = new GroupNeighbor(groupObject, physicalEntity, participant.getType());
    BioPaxGroupNeighborShape edgeShape = (BioPaxGroupNeighborShape) getShapeFromModelObject(groupNeighbor);
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxGroupNeighborShape(groupNeighbor, groupShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            // for grouped objects
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, groupShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 45 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class RuleParticipantEdgeDiagramShape method getCurve.

@Override
protected final CubicCurve2D.Double getCurve() {
    // TODO is this the best place for layout?
    refreshLayoutSelf();
    // default behavior of control points is for direction at ends to follow secant between end-points.
    if (lastCurve_Start == null || !lastCurve_Start.equals(start) || lastCurve_End == null || !lastCurve_End.equals(end)) {
        lastp1ctrl = new Point2D.Double((1.0 - FRACT_WEIGHT) * start.getX() + FRACT_WEIGHT * end.getX(), (1.0 - FRACT_WEIGHT) * start.getY() + FRACT_WEIGHT * end.getY());
    }
    Point2D.Double p2ctrl = new Point2D.Double(FRACT_WEIGHT * start.getX() + (1.0 - FRACT_WEIGHT) * end.getX(), FRACT_WEIGHT * start.getY() + (1.0 - FRACT_WEIGHT) * end.getY());
    // calculate tangent direction at "reactionStep"
    double tangentX = 0.0;
    double tangentY = 0.0;
    if (endShape instanceof ReactionRuleDiagramShape) {
        ReactionRuleDiagramShape reactionRuleDiagramShape = (ReactionRuleDiagramShape) endShape;
        for (Shape shape : graphModel.getShapes()) {
            if (shape instanceof RuleParticipantEdgeDiagramShape && ((RuleParticipantEdgeDiagramShape) shape).endShape == reactionRuleDiagramShape) {
                RuleParticipantEdgeDiagramShape rpShape = (RuleParticipantEdgeDiagramShape) shape;
                double dx = rpShape.start.getX() - rpShape.end.getX();
                double dy = rpShape.start.getY() - rpShape.end.getY();
                double len = dx * dx + dy * dy;
                if (shape instanceof ProductPatternEdgeDiagramShape) {
                    ProductPatternEdgeDiagramShape ps = (ProductPatternEdgeDiagramShape) shape;
                    tangentX += (ps.start.getX() - ps.end.getX()) / len;
                    tangentY += (ps.start.getY() - ps.end.getY()) / len;
                    if (bSibling) {
                        tangentX = 0.1;
                        tangentY = 0.1;
                    }
                } else if (shape instanceof ReactantPatternEdgeDiagramShape) {
                    ReactantPatternEdgeDiagramShape rs = (ReactantPatternEdgeDiagramShape) shape;
                    tangentX -= (rs.start.getX() - rs.end.getX()) / len;
                    tangentY -= (rs.start.getY() - rs.end.getY()) / len;
                    if (bSibling) {
                        tangentX = -0.1;
                        tangentY = -0.1;
                    }
                }
            }
        }
    }
    double tangentLength = Math.sqrt(tangentX * tangentX + tangentY * tangentY);
    if (tangentLength != 0) {
        tangentX = tangentX * CONTROL_WEIGHT / tangentLength;
        tangentY = tangentY * CONTROL_WEIGHT / tangentLength;
    }
    // } else
    if (this instanceof ProductPatternEdgeDiagramShape) {
        p2ctrl.setLocation(end.getX() + tangentX, end.getY() + tangentY);
    } else if (this instanceof ReactantPatternEdgeDiagramShape) {
        p2ctrl.setLocation(end.getX() - tangentX, end.getY() - tangentY);
    }
    if (lastCurve != null && lastCurve_Start != null && lastCurve_Start.equals(start) && lastCurve_End != null && lastCurve_End.equals(end) && lastp2ctrl != null && lastp2ctrl.equals(p2ctrl)) {
    // Do Nothing
    } else {
        lastCurve = new CubicCurve2D.Double(start.getX(), start.getY(), lastp1ctrl.getX(), lastp1ctrl.getY(), p2ctrl.getX(), p2ctrl.getY(), end.getX(), end.getY());
        lastCurve_Start = new Point(start);
        lastCurve_End = new Point(end);
        lastp2ctrl = p2ctrl;
    }
    return lastCurve;
}