[Demonstration 1]

[Buggy Method]
public Group draw(PannableCanvas canvas, NodeGestures nodeGestures) {
    CoordinateDetermination cdm = new CoordinateDetermination(dbm);
    Coordinate[] coords = cdm.calcCoords();
    ArrayList<Integer> from = dbm.getDBReader().getAllFromID();
    ArrayList<Integer> to = dbm.getDBReader().getAllToID();
    int maxX = getMaxX(coords);
    int maxY = getMaxY(coords);
    Group group = new Group();
    for (int i = 0; i < from.size(); i++) {
        int fromID = from.get(i);
        int toID = to.get(i);
        System.out.println(i);
        Path path = drawPath(coords[fromID - 1], coords[toID - 1], maxX, maxY);
        path.addEventFilter(MouseEvent.MOUSE_PRESSED, nodeGestures.getOnMousePressedEventHandler());
        path.addEventFilter(MouseEvent.MOUSE_DRAGGED, nodeGestures.getOnMouseDraggedEventHandler());
        path.setStrokeWidth(dbm.getDBReader().countGenomesInLink(fromID, toID));
        canvas.getChildren().add(path);
    }
    return group;
}

[Buggy Hunk]
path.setStrokeWidth(dbm.getDBReader().countGenomesInLink(fromID, toID));

[Patch]
path.setStrokeWidth(0.01 + 0.003 * dbm.getDBReader().countGenomesInLink(fromID, toID));

[Demonstration 2]

[Buggy Method]
private void setStoichiometryPosition() {
    if (stoichiometry.value > 1) {
        Segment segment;
        if (segments.size() > 0) {
            // First try to set the Stoichiometry Position in the segments
            // Place stoichiometry box in the first segment which is closer to the node
            segment = this.segments.get(0);
        } else {
            // If no segments are present then place the stoichiometry box on the backbone
            // of the edge. The backbone is also split in segments.
            switch(type) {
                case INPUT:
                    // Use the first segment of the backbone
                    segment = edge.segments.get(0);
                    break;
                case OUTPUT:
                    // Use the last segment of the backbone
                    segment = edge.segments.get(0);
                    break;
                default:
                    System.err.println(" >> Segment was not properly placed");
                    return;
            }
        }
        this.stoichiometry.shape = ShapeBuilder.createStoichiometryBox(setStoichiometryPosition(segment.from, segment.to), stoichiometry.value.toString());
    }
}

[Buggy Hunk]
segment = edge.segments.get(0);

[Patch]
segment = edge.segments.get(edge.segments.size()-1);

[Demonstration 3]

[Buggy Method]
public static Result service(String ownerName, String projectName, String service, boolean isAdvertise) throws IOException, UnsupportedOperationException, ServletException {
    if (!isSupportedService(service)) {
        return forbidden(String.format("Unsupported service: '%s'", service));
    }
    Project project = Project.findByOwnerAndProjectName(ownerName, projectName);
    if (project == null) {
        return notFound();
    }
    models.User user = UserApp.currentUser();
    if (!isAllowed(project, service)) {
        if (user.isAnonymous()) {
            return BasicAuthAction.unauthorized(response());
        } else {
            // If you want the Git client showing your custom message to
            // the user, the Content-Type should be exact "text/plain"
            // without any parameter. For more details, see the code at
            // https://github.com/git/git/commit/426e70d4a11ce3b4f70636d57c6a0ab16ae08a00#diff-eea0ad565ec5903a11b6023755d491cfR154
            response().setHeader("Content-Type", "text/plain");
            return forbidden(String.format("'%s' has no permission to '%s/%s'.", user.name, ownerName, projectName));
        }
    }
    if (isAdvertise) {
        return ok(RepositoryService.gitAdvertise(project, service, response()));
    } else {
        if (request().body().isMaxSizeExceeded()) {
            return status(REQUEST_ENTITY_TOO_LARGE);
        } else {
            user.visits(project);
            return ok(RepositoryService.gitRpc(project, service, request(), response()));
        }
    }
}

[Buggy Hunk]
user.name, ownerName, projectName));

[Patch]
user.loginId, ownerName, projectName));