/**
 * @author alteredq / http://alteredqualia.com/
 */

THREE.PDBLoader = function ( showStatus ) {

	THREE.Loader.call( this, showStatus );

};

THREE.PDBLoader.prototype = new THREE.Loader();
THREE.PDBLoader.prototype.constructor = THREE.PDBLoader;
THREE.PDBLoader.prototype.supr = THREE.Loader.prototype;

THREE.PDBLoader.prototype.load = function ( url, callback ) {

	var worker, scope = this;

	this.onLoadStart();
	this.loadAjaxPDB( this, url, callback );

};

THREE.PDBLoader.prototype.loadAjaxPDB = function ( context, url, callback, callbackProgress ) {

	var xhr = new XMLHttpRequest();

	var length = 0;

	xhr.onreadystatechange = function () {

		if ( xhr.readyState === xhr.DONE ) {

			if ( xhr.status === 200 || xhr.status === 0 ) {

				if ( xhr.responseText ) {

					var json = context.parsePDB( xhr.responseText );
					context.createModel( json, callback );

				} else {

					console.warn( "THREE.PDBLoader: [" + url + "] seems to be unreachable or file there is empty" );

				}

				// in context of more complex asset initialization
				// do not block on single failed file
				// maybe should go even one more level up

				context.onLoadComplete();

			} else {

				console.error( "THREE.PDBLoader: Couldn't load [" + url + "] [" + xhr.status + "]" );

			}

		} else if ( xhr.readyState === xhr.LOADING ) {

			if ( callbackProgress ) {

				if ( length === 0 ) {

					length = xhr.getResponseHeader( "Content-Length" );

				}

				callbackProgress( { total: length, loaded: xhr.responseText.length } );

			}

		} else if ( xhr.readyState === xhr.HEADERS_RECEIVED ) {

			length = xhr.getResponseHeader( "Content-Length" );

		}

	};

	xhr.open( "GET", url, true );
	if ( xhr.overrideMimeType ) xhr.overrideMimeType( "text/plain; charset=x-user-defined" );
	xhr.setRequestHeader( "Content-Type", "text/plain" );
	xhr.send( null );

};

// Based on CanvasMol PDB parser

THREE.PDBLoader.prototype.parsePDB = function ( text ) {

	function trim( text ) {

		return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');

	}

	function capitalize( text ) {

		return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();

	}

    function hash( s, e ) {

        return "s" + Math.min( s, e ) + "e" + Math.max( s, e );

    }

    function parseBond( start, length ) {

        var eatom = parseInt( lines[ i ].substr( start, length ) );

        if( eatom ) {

            var h = hash( satom, eatom );

            if ( bhash[ h ] == undefined ) {

                bonds.push( [ satom - 1, eatom - 1, 1 ] );
                bhash[ h ] = bonds.length - 1;

			} else {

                // doesn't really work as almost all PDBs
                // have just normal bonds appearing multiple
                // times instead of being double/triple bonds
                //bonds[bhash[h]][2] += 1;

            }

        }

    }

	var CPK = {"h":[255,255,255],"he":[217,255,255],"li":[204,128,255],"be":[194,255,0],"b":[255,181,181],"c":[144,144,144],"n":[48,80,248],"o":[255,13,13],"f":[144,224,80],"ne":[179,227,245],"na":[171,92,242],"mg":[138,255,0],"al":[191,166,166],"si":[240,200,160],"p":[255,128,0],"s":[255,255,48],"cl":[31,240,31],"ar":[128,209,227],"k":[143,64,212],"ca":[61,255,0],"sc":[230,230,230],"ti":[191,194,199],"v":[166,166,171],"cr":[138,153,199],"mn":[156,122,199],"fe":[224,102,51],"co":[240,144,160],"ni":[80,208,80],"cu":[200,128,51],"zn":[125,128,176],"ga":[194,143,143],"ge":[102,143,143],"as":[189,128,227],"se":[255,161,0],"br":[166,41,41],"kr":[92,184,209],"rb":[112,46,176],"sr":[0,255,0],"y":[148,255,255],"zr":[148,224,224],"nb":[115,194,201],"mo":[84,181,181],"tc":[59,158,158],"ru":[36,143,143],"rh":[10,125,140],"pd":[0,105,133],"ag":[192,192,192],"cd":[255,217,143],"in":[166,117,115],"sn":[102,128,128],"sb":[158,99,181],"te":[212,122,0],"i":[148,0,148],"xe":[66,158,176],"cs":[87,23,143],"ba":[0,201,0],"la":[112,212,255],"ce":[255,255,199],"pr":[217,255,199],"nd":[199,255,199],"pm":[163,255,199],"sm":[143,255,199],"eu":[97,255,199],"gd":[69,255,199],"tb":[48,255,199],"dy":[31,255,199],"ho":[0,255,156],"er":[0,230,117],"tm":[0,212,82],"yb":[0,191,56],"lu":[0,171,36],"hf":[77,194,255],"ta":[77,166,255],"w":[33,148,214],"re":[38,125,171],"os":[38,102,150],"ir":[23,84,135],"pt":[208,208,224],"au":[255,209,35],"hg":[184,184,208],"tl":[166,84,77],"pb":[87,89,97],"bi":[158,79,181],"po":[171,92,0],"at":[117,79,69],"rn":[66,130,150],"fr":[66,0,102],"ra":[0,125,0],"ac":[112,171,250],"th":[0,186,255],"pa":[0,161,255],"u":[0,143,255],"np":[0,128,255],"pu":[0,107,255],"am":[84,92,242],"cm":[120,92,227],"bk":[138,79,227],"cf":[161,54,212],"es":[179,31,212],"fm":[179,31,186],"md":[179,13,166],"no":[189,13,135],"lr":[199,0,102],"rf":[204,0,89],"db":[209,0,79],"sg":[217,0,69],"bh":[224,0,56],"hs":[230,0,46],"mt":[235,0,38],
           "ds":[235,0,38],"rg":[235,0,38],"cn":[235,0,38],"uut":[235,0,38],"uuq":[235,0,38],"uup":[235,0,38],"uuh":[235,0,38],"uus":[235,0,38],"uuo":[235,0,38]};


    var atoms = [];
    var bonds = [];
    var histogram = {};

    var bhash = {};

    var lines = text.split( "\n" );

    var x, y, z, e;

    for( var i = 0, il = lines.length; i < il; ++ i ) {

        if( lines[i].substr(0,4)=="ATOM" || lines[i].substr(0,6)=="HETATM" ) {

            x = parseFloat( lines[i].substr(30,7) );
            y = parseFloat( lines[i].substr(38,7) );
            z = parseFloat( lines[i].substr(46,7) );

            e = trim( lines[i].substr(76,2) ).toLowerCase();

            if ( e=="" ) e = trim(lines[i].substr(12,2)).toLowerCase();
            atoms.push( [ x,y,z, CPK[e], capitalize(e) ] );

            if (histogram[e]==undefined) histogram[e] = 1;
            else histogram[e] += 1;

        } else if(lines[i].substr(0,6)=="CONECT") {

            var satom = parseInt( lines[i].substr(6,5) );

            parseBond(11,5);
            parseBond(16,5);
            parseBond(21,5);
            parseBond(26,5);

        }

    }

    return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };

};

THREE.PDBLoader.prototype.createModel = function ( json, callback ) {

	var scope = this,
	geometryAtoms = new THREE.Geometry(),
	geometryBonds = new THREE.Geometry();

	geometryAtoms.elements = [];

	var atoms = json.atoms;
	var bonds = json.bonds;

	for ( var i = 0; i < atoms.length; i ++ ) {

		var atom = atoms[ i ];

		var x = atom[ 0 ];
		var y = atom[ 1 ];
		var z = atom[ 2 ];

		var position = new THREE.Vector3( x, y, z );
		geometryAtoms.vertices.push( position );

		var r = atom[ 3 ][ 0 ] / 255;
		var g = atom[ 3 ][ 1 ] / 255;
		var b = atom[ 3 ][ 2 ] / 255;
		var color = new THREE.Color();
		color.setRGB( r, g, b );

		geometryAtoms.colors.push( color );

		geometryAtoms.elements.push( atom[ 4 ] );

	}

	for ( var i = 0; i < bonds.length; i ++ ) {

		var bond = bonds[ i ];

		var start = bond[ 0 ];
		var end = bond[ 1 ];

		var vertex1 = geometryAtoms.vertices[ start ];
		var vertex2 = geometryAtoms.vertices[ end ];

		geometryBonds.vertices.push( vertex1.clone() );
		geometryBonds.vertices.push( vertex2.clone() );

	}


	callback( geometryAtoms, geometryBonds );

};

