Clazz.declarePackage ("J.renderbio");
Clazz.load (["J.renderbio.BioShapeRenderer"], "J.renderbio.BackboneRenderer", ["J.util.C"], function () {
c$ = Clazz.declareType (J.renderbio, "BackboneRenderer", J.renderbio.BioShapeRenderer);
$_V(c$, "renderBioShape", 
function (bioShape) {
var isDataFrame = this.viewer.isJmolDataFrameForModel (bioShape.modelIndex);
for (var i = this.bsVisible.nextSetBit (0); i >= 0; i = this.bsVisible.nextSetBit (i + 1)) {
var atomA = this.modelSet.atoms[this.leadAtomIndices[i]];
var atomB = this.modelSet.atoms[this.leadAtomIndices[i + 1]];
if (atomA.getNBackbonesDisplayed () == 0 || atomB.getNBackbonesDisplayed () == 0 || this.modelSet.isAtomHidden (atomB.getIndex ())) continue;
if (!isDataFrame && atomA.distance (atomB) > 10) continue;
var colixA = J.util.C.getColixInherited (this.colixes[i], atomA.getColix ());
var colixB = J.util.C.getColixInherited (this.colixes[i + 1], atomB.getColix ());
if (!this.isExport && !this.isPass2) {
var doA = !J.util.C.isColixTranslucent (colixA);
var doB = !J.util.C.isColixTranslucent (colixB);
if (!doA || !doB) {
if (!doA && !doB) continue;
this.needTranslucent = true;
}}var xA = atomA.sX;
var yA = atomA.sY;
var zA = atomA.sZ;
var xB = atomB.sX;
var yB = atomB.sY;
var zB = atomB.sZ;
this.mad = this.mads[i];
if (this.mad < 0) {
this.g3d.drawLine (colixA, colixB, xA, yA, zA, xB, yB, zB);
} else {
var width = Clazz.floatToInt (this.exportType == 1 ? this.mad : this.viewer.scaleToScreen (Clazz.doubleToInt ((zA + zB) / 2), this.mad));
this.g3d.fillCylinderXYZ (colixA, colixB, 3, width, xA, yA, zA, xB, yB, zB);
}}
}, "J.shapebio.BioShape");
});
