Clazz.declarePackage("J.jvxl.readers");
Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.ApbsReader", ["JU.PT", "$.SB"], function(){
var c$ = Clazz.declareType(J.jvxl.readers, "ApbsReader", J.jvxl.readers.VolumeFileReader);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.jvxl.readers.ApbsReader, []);
});
Clazz.overrideMethod(c$, "init2", 
function(sg, br){
this.init2VFR(sg, br);
if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
this.isAngstroms = true;
this.nSurfaces = 1;
}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
Clazz.overrideMethod(c$, "readParameters", 
function(){
this.jvxlFileHeaderBuffer = JU.SB.newS(this.skipComments(false));
while (this.line != null && this.line.length == 0) this.rd();

this.jvxlFileHeaderBuffer.append("APBS OpenDx DATA ").append(this.line).append("\n");
this.jvxlFileHeaderBuffer.append("see http://apbs.sourceforge.net\n");
var atomLine = this.rd();
var tokens = JU.PT.getTokens(atomLine);
if (tokens.length >= 4) {
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);
this.readVoxelVector(0);
this.readVoxelVector(1);
this.readVoxelVector(2);
this.rd();
tokens = this.getTokens();
for (var i = 0; i < 3; i++) this.voxelCounts[i] = this.parseIntStr(tokens[i + 5]);

this.rd();
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
