private void renderShapes() {
BioShapeCollection mps = (BioShapeCollection) shape;
for (int c = mps.bioShapes.length; --c >= 0; ) {
BioShape bioShape = mps.getBioShape(c);
if ((bioShape.modelVisibilityFlags & myVisibilityFlag) == 0) continue;
if (bioShape.monomerCount >= 2 && initializePolymer(bioShape)) {
bsRenderMesh.clearAll();
renderBioShape(bioShape);
renderMeshes();
freeTempArrays();
}
}
}
private boolean initializePolymer(BioShape bioShape) {
BS bsDeleted = vwr.getDeletedAtoms();
if (vwr.ms.isJmolDataFrameForModel(bioShape.modelIndex)) {
controlPoints = bioShape.bioPolymer.getControlPoints(true, 0, false);
} else {
controlPoints =
bioShape.bioPolymer.getControlPoints(isTraceAlpha, sheetSmoothing, invalidateSheets);
}
monomerCount = bioShape.monomerCount;
bsRenderMesh = BS.newN(monomerCount);
monomers = bioShape.monomers;
reversed = bioShape.bioPolymer.reversed;
leadAtomIndices = bioShape.bioPolymer.getLeadAtomIndices();
bsVisible.clearAll();
boolean haveVisible = false;
if (invalidateMesh) bioShape.falsifyMesh();
for (int i = monomerCount; --i >= 0; ) {
if ((monomers[i].shapeVisibilityFlags & myVisibilityFlag) == 0
|| ms.isAtomHidden(leadAtomIndices[i])
|| bsDeleted != null && bsDeleted.get(leadAtomIndices[i])) continue;
Atom lead = ms.at[leadAtomIndices[i]];
if (!g3d.isInDisplayRange(lead.sX, lead.sY)) continue;
bsVisible.set(i);
haveVisible = true;
}
if (!haveVisible) return false;
ribbonBorder = vwr.getBoolean(T.ribbonborder);
// note that we are not treating a PhosphorusPolymer
// as nucleic because we are not calculating the wing
// vector correctly.
// if/when we do that then this test will become
// isNucleic = bioShape.bioPolymer.isNucleic();
isNucleic = bioShape.bioPolymer instanceof NucleicPolymer;
isCarbohydrate = bioShape.bioPolymer instanceof CarbohydratePolymer;
haveControlPointScreens = false;
wingVectors = bioShape.wingVectors;
meshReady = bioShape.meshReady;
meshes = bioShape.meshes;
mads = bioShape.mads;
colixes = bioShape.colixes;
colixesBack = bioShape.colixesBack;
setStructureTypes();
return true;
}