GraphComponent ComposeRendering(GraphComponent component, Strand strand, double y0 = 0)
// We render a strand as a linear sequence of spring-separated particles.
// We initially lay things out in a linear line, either to the right (for
// normally oriented strands) or left (for reverse oriented strands).
{
if (null==component)
component = new GraphComponent(this);
//
// Compose edges for domains along the strand backbone
//
List<GraphVertex> strandVertices = new List<GraphVertex>();
List<GraphEdge> strandEdges = new List<GraphEdge>();
//
double count = strand.AllDomains().Count();
double length = strand.AllDomains().Sum(d => this.EdgeFromDomain(component, d).PreferredLength);
double radius = length / 2.0 / Math.PI;
//
radius /= 3; // hack -> otherwise the forces pulling the circle together overshoot
//
int i = 0;
foreach (Domain d in strand.AllDomains())
{
GraphEdge edge = this.EdgeFromDomain(component, d);
strandEdges.Add(edge);
//
// The first vertex in the strand needs to be explicitly positioned
//
double x,y;
//
if (strandVertices.IsEmpty())
{
strandVertices.Add(edge.A);
if (strand.IsCircular)
x = strand.Orientation==Strand.Direction.FiveToThree ? -radius : radius;
else
x = 0;
edge.A.SetLocation(x,y0);
}
//
// Position the B vertex of the edge
//
if (strand.IsCircular)
{
double theta = i / count * 2 * Math.PI;
x = radius * Math.Cos(theta);
y = radius * Math.Sin(theta);
if (strand.Orientation==Strand.Direction.FiveToThree)
{
x = -x;
y = -y;
}
}
else
{
y = y0;
x = edge.PreferredLength;
if (strand.Orientation == Strand.Direction.ThreeToFive)
x = -x;
x += strandVertices.Last().Location.X;
}
//
edge.B.SetLocation(x, y);
strandVertices.Add(edge.B);
//
i++;
}
//
// Make a spline for the strand as a whole
//
if (strandVertices.NotEmpty())
{
VisualStrand vStrand = new VisualStrand(strand, component, strandEdges, strandVertices);
this.mpStrandVisualization[strand] = vStrand;
//
// Place ticks at the ends of each of the interior domains in the strand
//
for (i = strand.IsCircular ? 0 : 1; i < strandVertices.Count-1; i++)
{
new VisualDomainEndTick(component, vStrand, i, Constants.DomainEndLength);
}
//
// Add domain labels and nucleotides
//
foreach (Domain d in strand.AllDomains())
{
i = d.StrandIndex;
//
VisualStrandLabel label = new VisualStrandLabel(component, vStrand, i, i+1, d.FullDisplayName, Constants.StyleDomainLabel);
label.LabelType = VisualStrandLabel.LABELTYPE.DOMAIN;
vStrand.NoteDomainLabel(i, label);
//
if (d.Nucleotides.Length > 0 && true)
{
label = new VisualStrandLabel(component, vStrand, i, i+1, d.Nucleotides, Constants.StyleNucleotides);
label.LabelType = VisualStrandLabel.LABELTYPE.NUCLEOTIDE;
label.FontVerticallyCentered = true;
label.AutoReverseText = true;
}
}
}
//
if (strandVertices.NotEmpty())
{
// Help a bit with initial placement: left align if we moved leftward
// from zero due to strand direction.
//
if (!strand.IsCircular && strand.Orientation == Strand.Direction.ThreeToFive)
{
double dx = -strandVertices.Last().Location.X;
foreach (GraphVertex v in strandVertices)
{
v.TranslateBy(dx, 0);
}
}
}
//
// Put in stiffness along the strand
//
foreach (Domain d in strand.AllDomains())
{
if (d.CircularNextTo5 != null)
{
GraphEdge curEdge = this.EdgeFromDomain(component, d);
GraphEdge prevEdge = this.EdgeFromDomain(component, d.CircularNextTo5);
//
new StraighteningForce(component, prevEdge.A, curEdge.A, curEdge.B, Constants.StraighteningStrength);
}
}
//
return component;
}
public void NoteDomainLabel(int iDomain, VisualStrandLabel label)
{
this.domainLabels[iDomain] = label;
}
