Clazz.declarePackage("J.jvxl.readers");
Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.CubeReader", ["JU.PT", "$.SB", "JU.Logger"], function(){
var c$ = Clazz.declareType(J.jvxl.readers, "CubeReader", J.jvxl.readers.VolumeFileReader);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.jvxl.readers.CubeReader, []);
});
Clazz.overrideMethod(c$, "init2", 
function(sg, br){
this.init2VFR(sg, br);
}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
Clazz.overrideMethod(c$, "readParameters", 
function(){
this.jvxlFileHeaderBuffer =  new JU.SB();
this.jvxlFileHeaderBuffer.append(this.rd()).appendC('\n');
this.jvxlFileHeaderBuffer.append(this.rd()).appendC('\n');
var atomLine = this.rd();
var tokens = JU.PT.getTokensAt(atomLine, 0);
this.ac = this.parseIntStr(tokens[0]);
this.negativeAtomCount = (this.ac < 0);
if (this.negativeAtomCount) this.ac = -this.ac;
this.volumetricOrigin.set(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
J.jvxl.readers.VolumeFileReader.checkAtomLine(this.isXLowToHigh, this.isAngstroms, tokens[0], atomLine, this.jvxlFileHeaderBuffer);
if (!this.isAngstroms) this.volumetricOrigin.scale(0.5291772);
for (var i = 0; i < 3; ++i) this.readVoxelVector(i);

for (var i = 0; i < this.ac; ++i) this.jvxlFileHeaderBuffer.append(this.rd() + "\n");

if (!this.negativeAtomCount) {
this.nSurfaces = 1;
} else {
this.rd();
JU.Logger.info("Reading extra CUBE information line: " + this.line);
this.nSurfaces = this.parseIntStr(this.line);
}});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
