io.js

// pedigree utils
(function (utils, $, undefined) {

	utils.isIE = function () {
		var ua = navigator.userAgent;
		/* MSIE used to detect old browsers and Trident used to newer ones*/
		return ua.indexOf("MSIE ") > -1 || ua.indexOf("Trident/") > -1;
	}

	utils.isEdge = function () {
		return navigator.userAgent.match(/Edge/g);
	}

	/**
	 *  Get formatted time or data & time
	 */
	utils.getFormattedDate = function (time) {
		var d = new Date();
		if (time)
			return ('0' + d.getHours()).slice(-2) + ":" + ('0' + d.getMinutes()).slice(-2) + ":" + ('0' + d.getSeconds()).slice(-2);
		else
			return d.getFullYear() + "-" + ('0' + (d.getMonth() + 1)).slice(-2) + "-" + ('0' + d.getDate()).slice(-2) + " " + ('0' + d.getHours()).slice(-2) + ":" + ('0' + d.getMinutes()).slice(-2) + ":" + ('0' + d.getSeconds()).slice(-2);
	}

	/**
	 * Show message or confirmation dialog.
	 * @param title     - dialog window title
	 * @param msg       - message to diasplay
	 * @param onConfirm - function to call in a confirmation dialog
	 * @param opts      - pedigreejs options
	 * @param dataset    - pedigree dataset
	 */
	utils.messages = function (title, msg, onConfirm, opts, dataset) {
		if (onConfirm) {
			$('<div id="msgDialog">' + msg + '</div>').dialog({
				modal: true,
				title: title,
				width: 350,
				buttons: {
					"Yes": function () {
						$(this).dialog('close');
						onConfirm(opts, dataset);
					},
					"No": function () {
						$(this).dialog('close');
					}
				}
			});
		} else {
			$('<div id="msgDialog">' + msg + '</div>').dialog({
				title: title,
				width: 350,
				buttons: [{
					text: "OK",
					click: function () { $(this).dialog("close"); }
				}]
			});
		}
	}

	/**
	 * Validate age and yob is consistent with current year. The sum of age and
	 * yob should not be greater than or equal to current year. If alive the
	 * absolute difference between the sum of age and year of birth and the
	 * current year should be <= 1.
	 * @param age    - age in years.
	 * @param yob    - year of birth.
	 * @param status - 0 = alive, 1 = dead.
	 * @return true if age and yob are consistent with current year otherwise false.
	 */
	utils.validate_age_yob = function (age, yob, status) {
		var year = new Date().getFullYear();
		var sum = parseInt(age) + parseInt(yob);
		if (status == 1) {   // deceased
			return year >= sum;
		}
		return Math.abs(year - sum) <= 1 && year >= sum;
	}

	utils.capitaliseFirstLetter = function (string) {
		return string.charAt(0).toUpperCase() + string.slice(1);
	}
}(window.utils = window.utils || {}, jQuery));


// pedigree I/O
(function (io, $, undefined) {

	// cancers, genetic & pathology tests
	io.cancers = {
		'breast_cancer': 'breast_cancer_diagnosis_age',
		'breast_cancer2': 'breast_cancer2_diagnosis_age',
		'ovarian_cancer': 'ovarian_cancer_diagnosis_age',
		'prostate_cancer': 'prostate_cancer_diagnosis_age',
		'pancreatic_cancer': 'pancreatic_cancer_diagnosis_age'
	};
	io.genetic_test = ['brca1', 'brca2', 'palb2', 'atm', 'chek2', 'rad51d', 'rad51c', 'brip1'];
	io.pathology_tests = ['er', 'pr', 'her2', 'ck14', 'ck56'];

	// get breast and ovarian PRS values
	io.get_prs_values = function () {
		var prs = {};
		if (io.hasInput("breast_prs_a") && io.hasInput("breast_prs_z")) {
			prs['breast_cancer_prs'] = {
				'alpha': parseFloat($('#breast_prs_a').val()),
				'zscore': parseFloat($('#breast_prs_z').val()),
				'percent': parseFloat($('#breast_prs_percent').val())
			};
		}
		if (io.hasInput("ovarian_prs_a") && io.hasInput("ovarian_prs_z")) {
			prs['ovarian_cancer_prs'] = {
				'alpha': parseFloat($('#ovarian_prs_a').val()),
				'zscore': parseFloat($('#ovarian_prs_z').val()),
				'percent': parseFloat($('#ovarian_prs_percent').val())
			};
		}
		console.log(prs);
		return (isEmpty(prs) ? 0 : prs);
	}

	// check if input has a value
	io.hasInput = function (id) {
		return $.trim($('#' + id).val()).length !== 0;
	}

	// return true if the object is empty
	var isEmpty = function (myObj) {
		for (var key in myObj) {
			if (myObj.hasOwnProperty(key)) {
				return false;
			}
		}
		return true;
	}

	io.get_surgical_ops = function () {
		var meta = "";
		if (!$('#A6_4_3_check').parent().hasClass("off")) {
			meta += ";OVARY2=y";
		}
		if (!$('#A6_4_7_check').parent().hasClass("off")) {
			meta += ";MAST2=y";
		}
		return meta;
	};

	io.add = function (opts) {
		$('#load').change(function (e) {
			io.load(e, opts);
		});

		$('#save').click(function (e) {
			io.save(opts, "pedigree.json");
		});

		$('#save_canrisk').click(function (e) {
			var meta = io.get_surgical_ops();
			try {
				var prs = io.get_prs_values();
				if (prs.breast_cancer_prs && prs.breast_cancer_prs.alpha !== 0 && prs.breast_cancer_prs.zscore !== 0) {
					meta += "\n##PRS_BC=alpha=" + prs.breast_cancer_prs.alpha + ",zscore=" + prs.breast_cancer_prs.zscore;
				}
				if (prs.ovarian_cancer_prs && prs.ovarian_cancer_prs.alpha !== 0 && prs.ovarian_cancer_prs.zscore !== 0) {
					meta += "\n##PRS_OC=alpha=" + prs.ovarian_cancer_prs.alpha + ",zscore=" + prs.ovarian_cancer_prs.zscore;
				}
			} catch (err) { console.warn("PRS", prs); }
			io.save_canrisk(opts, meta);
		});

		$('#saveBOADICEA').click(function (e) {
			io.save_boadicea(opts);
		});

		$('#print').click(function (e) {
			io.print(io.get_printable_svg(opts));
		});

		$('#svg_download').click(function (e) {
			io.svg_download(io.get_printable_svg(opts));
		});

		$('#png_download').click(function (e) {
			var deferred = io.svg2png($('svg'), "pedigree", utils.isEdge() || utils.isIE());
			$.when.apply($, [deferred]).done(function () {
				var obj = getByName(arguments, "pedigree");
				if (utils.isEdge() || utils.isIE()) {
					var html = "<img src='" + obj.img + "' alt='canvas image'/>";
					var newTab = window.open();
					newTab.document.write(html);
				} else {
					var a = document.createElement('a');
					a.href = obj.img;
					a.download = 'plot.png';
					a.target = '_blank';
					document.body.appendChild(a); a.click(); document.body.removeChild(a);
				}
			});
		});
	};

	/**
	 * Get object from array by the name attribute.
	 */
	function getByName(arr, name) {
		return $.grep(arr, function (o) { return o && o.name == name; })[0];
	}

	/**
	 * Given a SVG document element convert to PNG.
	 */
	io.svg2png = function (svg, deferred_name, iscanvg) {
		var deferred = $.Deferred();
		var svgStr;
		if (typeof window.XMLSerializer != "undefined") {
			svgStr = (new XMLSerializer()).serializeToString(svg.get(0));
		} else if (typeof svg.xml != "undefined") {
			svgStr = svg.get(0).xml;
		}

		var imgsrc = 'data:image/svg+xml;base64,' + btoa(unescape(encodeURIComponent(svgStr))); // convert SVG string to data URL
		var canvas = document.createElement("canvas");
		var context = canvas.getContext("2d");
		canvas.width = svg.width();
		canvas.height = svg.height();
		var img = document.createElement("img");
		img.onload = function () {
			if (utils.isIE() || iscanvg) {
				// change font so it isn't tiny
				svgStr = svgStr.replace(/ font-size="\d?.\d*em"/g, '');
				svgStr = svgStr.replace(/<text /g, '<text font-size="13px" ');
				canvg(canvas, svgStr, {
					scaleWidth: svg.width(),
					scaleHeight: svg.height(),
					ignoreDimensions: true
				});
				console.log(deferred_name, "use canvg to create PNG");
			} else {
				context.clearRect(0, 0, svg.width(), svg.height());
				context.drawImage(img, 0, 0, svg.width(), svg.height());
			}
			deferred.resolve({ 'name': deferred_name, 'img': canvas.toDataURL("image/png"), 'w': svg.width(), 'h': svg.height() });
		};
		img.src = imgsrc;
		return deferred.promise();
	}

	// return a copy pedigree svg
	io.copy_svg_html = function (opts) {
		var svg_html = io.get_printable_svg(opts).html();
		return io.copy_svg(svg_html);
	}

	// return a copy of svg html with unique url references (e.g. for clippath)
	io.copy_svg = function (svg_html) {
		// find all url's to make unique
		var myRegexp = /url\((&quot;|"|'){0,1}\#(.*?)(&quot;|"|'){0,1}\)/g;
		var matches = [];
		var match;
		var c = 0;
		myRegexp.lastIndex = 0;
		while (match = myRegexp.exec(svg_html)) {
			c++;
			if (c > 800) {
				console.error("io.copy_svg_html: counter exceeded 800");
				return "ERROR DISPLAYING PEDIGREE";
			}
			matches.push(match);
			if (myRegexp.lastIndex === match.index) {
				myRegexp.lastIndex++;
			}
		}

		for (var i = 0; i < matches.length; i++) {
			var quote = (matches[i][1] ? matches[i][1] : "");
			var val = matches[i][2];
			var m1 = "id=\"" + val + "\"";
			var m2 = "url\\(" + quote + "\#" + val + quote + "\\)";

			var newval = val + ptree.makeid(2);
			svg_html = svg_html.replace(new RegExp(m1, 'g'), "id=\"" + newval + "\"");
			svg_html = svg_html.replace(new RegExp(m2, 'g'), "url(#" + newval + ")");
		}
		return svg_html;
	};

	// get printable svg div, adjust size to tree dimensions and scale to fit
	io.get_printable_svg = function (opts) {
		var local_dataset = pedcache.current(opts); // get current dataset
		if (local_dataset !== undefined && local_dataset !== null) {
			opts.dataset = local_dataset;
		}

		var tree_dimensions = ptree.get_tree_dimensions(opts);
		var svg_div = $('#' + opts.targetDiv).find('svg').parent();
		if (opts.width < tree_dimensions.width || opts.height < tree_dimensions.height ||
			tree_dimensions.width > 595 || tree_dimensions.height > 842) {
			var wid = tree_dimensions.width;
			var hgt = tree_dimensions.height + 100;
			var scale = 1.0;

			if (tree_dimensions.width > 595 || tree_dimensions.height > 842) {   // scale to fit A4
				if (tree_dimensions.width > 595) wid = 595;
				if (tree_dimensions.height > 842) hgt = 842;
				var xscale = wid / tree_dimensions.width;
				var yscale = hgt / tree_dimensions.height;
				scale = (xscale < yscale ? xscale : yscale);
			}
			svg_div = $('<div></div>');  				// create a new div
			svg_div.append($('#' + opts.targetDiv).find('svg').parent().html());	// copy svg html to new div
			var svg = svg_div.find("svg");
			svg.attr('width', wid);		// adjust dimensions
			svg.attr('height', hgt);

			var ytransform = (-opts.symbol_size * 1.5 * scale);
			svg.find(".diagram").attr("transform", "translate(0, " + ytransform + ") scale(" + scale + ")");
		}
		return svg_div;
	};

	// download the SVG to a file
	io.svg_download = function (svg) {
		var a = document.createElement('a');
		a.href = 'data:image/svg+xml;base64,' + btoa(unescape(encodeURIComponent(svg.html())));
		a.download = 'plot.svg';
		a.target = '_blank';
		document.body.appendChild(a); a.click(); document.body.removeChild(a);
	};

	// open print window for a given element
	io.print = function (el, id) {
		if (el.constructor !== Array)
			el = [el];

		var width = $(window).width() * 0.9;
		var height = $(window).height() - 10;
		var cssFiles = [
			'/static/css/canrisk.css',
			'https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css'
		];
		var printWindow = window.open('', 'PrintMap', 'width=' + width + ',height=' + height);
		var headContent = '';
		for (var i = 0; i < cssFiles.length; i++)
			headContent += '<link href="' + cssFiles[i] + '" rel="stylesheet" type="text/css" media="all">';
		headContent += "<style>body {font-size: " + $("body").css('font-size') + ";}</style>";

		/*var headContent2 = '';
		var links = document.getElementsByTagName('link');
		for(var i=0;i<links.length; i++) {
			var html = links[i].outerHTML;
			if(html.indexOf('href="http') !== -1)
				headContent2 += html;
		}
		headContent2 += html;
		var scripts = document.getElementsByTagName('script');
		for(var i=0;i<scripts.length; i++) {
			var html = scripts[i].outerHTML;
			if(html.indexOf('src="http') !== -1)
				headContent += html;
		}*/

		html = "";
		for (i = 0; i < el.length; i++) {
			if (i === 0 && id)
				html += id;
			html += $(el[i]).html();
			if (i < el.length - 1)
				html += '<div style="page-break-before:always"> </div>';
		}

		printWindow.document.write(headContent);
		printWindow.document.write(html);
		printWindow.document.close();

		printWindow.focus();
		setTimeout(function () {
			printWindow.print();
			printWindow.close();
		}, 300);
	};

	// save content to a file
	io.save_file = function (opts, content, filename, type) {
		if (opts.DEBUG)
			console.log(content);
		if (!filename) filename = "ped.txt";
		if (!type) type = "text/plain";

		var file = new Blob([content], { type: type });
		if (window.navigator.msSaveOrOpenBlob) 	// IE10+
			window.navigator.msSaveOrOpenBlob(file, filename);
		else { 									// other browsers
			var a = document.createElement("a");
			var url = URL.createObjectURL(file);
			a.href = url;
			a.download = filename;
			document.body.appendChild(a);
			a.click();
			setTimeout(function () {
				document.body.removeChild(a);
				window.URL.revokeObjectURL(url);
			}, 0);
		}
	}

	io.save = function (opts, filename) {
		if (!filename) filename = "ped.txt";
		var content = JSON.stringify(pedcache.current(opts));
		io.save_file(opts, content, filename);
	};

	io.save_canrisk = function (opts, meta) {
		io.save_file(opts, run_prediction.get_non_anon_pedigree(pedcache.current(opts), meta), "canrisk.txt");
	};

	io.save_boadicea = function (opts) {
		var diseases_valid = true;
		var dis_names = $.map(opts.diseases, function (val, i) { return val.type; });
		for (var i = 0; i < DEFAULT_DISEASES.length; i++) {
			if ($.inArray(DEFAULT_DISEASES[i].type, dis_names) == -1) {
				diseases_valid = false;
			}
		}
		
		currentOpts = pedcache.current(opts);
		var targetDefined = false;
		for (var i = 0; i < currentOpts.length; i++) {
			var individual = currentOpts[i];
			targetDefined = targetDefined || individual['proband']
		}

		if (!diseases_valid) {
			$('#boadicea-error').dialog({
				autoOpen: false,
				title: 'Boadicea Format Error',
				height: 200,
				width: 400,
				dialogClass: 'boadicea-error-dialog',
				buttons: {
					Ok: function () {
						io.boadicea_to_file(opts);
						$(this).dialog("close");
					},
					Cancel: function () {
						$(this).dialog("close");
					}
				}
			});
			$('#boadicea-error').html("<p>It appears that not all diseases required for BOADICEA are present in" +
				" the disease configuration.</p><br><br><p>Proceed anyway?</p>");
			$('#boadicea-error').dialog('open');
		} if (!targetDefined) {
			$('#boadicea-error').dialog({
				autoOpen: false,
				title: 'Boadicea Format Error',
				height: 200,
				width: 400,
				dialogClass: 'boadicea-error-dialog',
				buttons: {
					Ok: function () {
						$(this).dialog("close");
					}
				}
			});
			$('#boadicea-error').html("<p>There is currently no proband defined. Please make sure that the pedigree features a proband for the risk calcualtion.</p>");
			$('#boadicea-error').dialog('open');
		} else {
			io.boadicea_to_file(opts);
		}
	}

	io.boadicea_to_file = function (opts) {
		var filetext = "BOADICEA import pedigree file format 4.0\n";
		filetext += "FamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob" +
			"\t1stBrCa\t2ndBrCa\tOvCa\tProCa\tPanCa" +
			"\tAshkn" +
			"\tBRCA1t\tBRCA1r\tBRCA2t\tBRCA2r\tPALB2t\tPALB2r\tATMt\tATMr\tCHEK2t\tCHEK2r" +
			"\tER\tPR\tHER2\tCK14\tCK56\n";
		currentOpts = pedcache.current(opts);
		var formatError = false;

		for (var i = 0; i < currentOpts.length; i++) {
			var nextline = "";
			var individual = currentOpts[i];
			// the ids of the possible information in the dataset (not everything gets read when loading a boadicea file)
			// 17 - 21 are dictionaries with [type] and [result]
			var infoID = ['famid', 'display_name', 'proband', 'name', 'father', 'mother',
				'sex', 'mztwin', 'status', 'age', 'yob', 'breast_cancer_diagnosis_age',
				'breast_cancer2_diagnosis_age', 'ovarian_cancer_diagnosis_age',
				'prostate_cancer_diagnosis_age', 'pancreatic_cancer_diagnosis_age',
				'ashkenazi', 'brca1_gene_test', 'brca2_gene_test', 'palb2_gene_test', 'atm_gene_test', 'chek2_gene_test',
				'er_bc_pathology', 'pr_bc_pathology', 'her2_bc_pathology', 'ck14_bc_pathology', 'ck56_bc_pathology'];

			for (var j = 0; j < infoID.length; j++) {
				if (individual[infoID[j]] && individual[infoID[j]] !== "") {
					if (j == 2) { // checks if individual is proband (saved as true or false, thus no extra checkup needed)
						nextline += "1\t";
					} else if (j==4 && individual['noparents'] &&  individual['noparents']==true) {
						nextline += "0\t";
					} else if (j==5 && individual['noparents'] &&  individual['noparents']==true) {
						nextline += "0\t";
					} else if (j == 6 && individual[infoID[j]] == 'U') { // prevents Default Gender 'Unknown'
						formatError = true;
						break;
					} else if (j > 16 && j < 22) { // saves the genetests
						if (individual[infoID[j]]['type'] == "" || individual[infoID[j]]['result'] == "") {
							nextline += "0\t0\t";
						} else {
							nextline += individual[infoID[j]]['type'] + "\t" + individual[infoID[j]]['result'] + "\t";
						}
					} else { // copies remaining values
						nextline += individual[infoID[j]] + "\t";
					}
				} else { // everything that wasn't selected/configured gets default value '0'
					if (j > 16 && j < 22) {
						nextline += "0\t0\t";
					} else {
						nextline += "0\t";
					}
				}
			}


			filetext += nextline + "\n";
		}

		if (formatError) {
			$('#boadicea-error').dialog({
				autoOpen: false,
				title: 'Boadicea Format Error',
				height: 175,
				width: 400,
				dialogClass: 'boadicea-error-dialog',
				buttons: {
					Ok: function () {
						$(this).dialog("close");
					}
				}
			});
			$('#boadicea-error').html("<p>The BOADICEA format requires a Gender that's either male or female. Please check for any unknown genders and try again.</p>");
			$('#boadicea-error').dialog('open');
		} else {
			io.save_file(opts, filetext, 'bodicea_ped.tsv');
		}
	}

	io.canrisk_validation = function (opts) {
		$.each(opts.dataset, function (idx, p) {
			if (!p.hidden && p.sex === 'M' && !pedigree_util.isProband(p)) {
				if (p[io.cancers['breast_cancer2']]) {
					var msg = 'Male family member (' + p.display_name + ') with contralateral breast cancer found. ' +
						'Please note that as the risk models do not take this into account the second ' +
						'breast cancer is ignored.'
					console.error(msg);
					delete p[io.cancers['breast_cancer2']];
					utils.messages("Warning", msg);
				}
			}
		});
	}

	io.setDiseases = function (opts) {
		var diseases = [];
		// get the diseases
		$.each(opts.dataset, function (k, v) {
			diseases = $.merge(diseases, $.map(Object.keys(this), function (val, i) {
				if (val.endsWith("_diagnosis_age"))
					return val.replace("_diagnosis_age", "");
			}))
		});
		// make correct format
		var disease_list = $.map([...new Set(diseases)], function (val, i) {
			return { 'type': val, 'colour': 'darkgrey' };
		});
		// check against defaults to split in default and additional
		var def_dis = $.map(DEFAULT_DISEASES, function (val, i) { return val.type; });
		opts.diseases = [];
		opts.additional_diseases = [];
		$.each(disease_list, function (k, v) {
			if (def_dis.includes(v.type)) {
				opts.diseases.push(v);
			} else {
				opts.additional_diseases.push(v);
			}
		});
		localStorage.setItem('diseases', JSON.stringify(opts.diseases));
		localStorage.setItem('additional_diseases', JSON.stringify(opts.additional_diseases));
	}

	io.load = function (e, opts) {
		var f = e.target.files[0];
		if (f) {
			var reader = new FileReader();
			reader.onload = function (e) {
				if (opts.DEBUG)
					console.log(e.target.result);
				try {
					if (e.target.result.startsWith("BOADICEA import pedigree file format 4.0")) {
						opts.dataset = io.readBoadiceaV4(opts, e.target.result, 4);
						io.canrisk_validation(opts);
					} else if (e.target.result.startsWith("BOADICEA import pedigree file format 2.0")) {
						opts.dataset = io.readBoadiceaV4(opts, e.target.result, 2);
						io.canrisk_validation(opts);
					} else if (e.target.result.startsWith("##") && e.target.result.indexOf("CanRisk") !== -1) {
						var canrisk_data = io.readCanRiskV1(e.target.result);
						var risk_factors = canrisk_data[0];
						opts.dataset = canrisk_data[1];
						io.canrisk_validation(opts);
					} else {
						try {
							opts.dataset = JSON.parse(e.target.result);
							io.setDiseases(opts);
						} catch (err) {
							opts.dataset = io.readLinkage(e.target.result);
						}
					}
					ptree.validate_pedigree(opts);
				} catch (err1) {
					console.error(err1, e.target.result);
					utils.messages("File Error", (err1.message ? err1.message : err1));
					return;
				}
				if (opts.DEBUG)
					console.log(opts.dataset);
				try {
					ptree.rebuild(opts);
					if (risk_factors !== undefined) {
						console.log(risk_factors);
						// load risk factors - fire riskfactorChange event
						$(document).trigger('riskfactorChange', [opts, risk_factors]);
					}
					$(document).trigger('fhChange', [opts]); 	// trigger fhChange event

					try {
						// update FH section
						acc_FamHist_ticked();
						acc_FamHist_Leave();
						RESULT.FLAG_FAMILY_MODAL = true;
					} catch (err3) { }
				} catch (err2) {
					utils.messages("File Error", (err2.message ? err2.message : err2));
				}
			};
			reader.onerror = function (event) {
				utils.messages("File Error", "File could not be read! Code " + event.target.error.code);
			};
			reader.readAsText(f);
		} else {
			console.error("File could not be read!");
		}
		$("#load")[0].value = ''; // reset value
	};

	//
	// https://www.cog-genomics.org/plink/1.9/formats#ped
	// https://www.cog-genomics.org/plink/1.9/formats#fam
	//	1. Family ID ('FID')
	//	2. Within-family ID ('IID'; cannot be '0')
	//	3. Within-family ID of father ('0' if father isn't in dataset)
	//	4. Within-family ID of mother ('0' if mother isn't in dataset)
	//	5. Sex code ('1' = male, '2' = female, '0' = unknown)
	//	6. Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)
	//  7. Genotypes (column 7 onwards);
	//     columns 7 & 8 are allele calls for first variant ('0' = no call); colummns 9 & 10 are calls for second variant etc.
	io.readLinkage = function (boadicea_lines) {
		var lines = boadicea_lines.trim().split('\n');
		var ped = [];
		var famid;
		for (var i = 0; i < lines.length; i++) {
			var attr = $.map(lines[i].trim().split(/\s+/), function (val, i) { return val.trim(); });
			if (attr.length < 5)
				throw ('unknown format');
			var sex = (attr[4] == '1' ? 'M' : (attr[4] == '2' ? 'F' : 'U'));
			var indi = {
				'famid': attr[0],
				'display_name': attr[1],
				'name': attr[1],
				'sex': sex
			};
			if (attr[2] !== "0") indi.father = attr[2];
			if (attr[3] !== "0") indi.mother = attr[3];

			if (typeof famid != 'undefined' && famid !== indi.famid) {
				console.error('multiple family IDs found only using famid = ' + famid);
				break;
			}
			if (attr[5] == "2") indi.affected = 2;
			// add genotype columns
			if (attr.length > 6) {
				indi.alleles = "";
				for (var j = 6; j < attr.length; j += 2) {
					indi.alleles += attr[j] + "/" + attr[j + 1] + ";";
				}
			}

			ped.unshift(indi);
			famid = attr[0];
		}
		return process_ped(ped);
	};

	io.readCanRiskV1 = function (boadicea_lines) {
		var lines = boadicea_lines.trim().split('\n');
		var ped = [];
		var hdr = [];  // collect risk factor header lines
		// assumes two line header
		for (var i = 0; i < lines.length; i++) {
			if (lines[i].startsWith("##")) {
				if (lines[i].startsWith("##CanRisk") && lines[i].indexOf(";") > -1) {   // contains surgical op data
					var ops = lines[i].split(";");
					for (var j = 1; j < ops.length; j++) {
						var opdata = ops[j].split("=");
						if (opdata.length === 2) {
							hdr.push(ops[j]);
						}
					}
				}
				if (lines[i].indexOf("CanRisk") === -1 && !lines[i].startsWith("##FamID")) {
					hdr.push(lines[i].replace("##", ""));
				}
				continue;
			}

			var delim = /\t/;
			if (lines[i].indexOf('\t') < 0) {
				delim = /\s+/;
				console.log("NOT TAB DELIM");
			}
			var attr = $.map(lines[i].trim().split(delim), function (val, i) { return val.trim(); });

			if (attr.length > 1) {
				var indi = {
					'famid': attr[0],
					'display_name': attr[1],
					'name': attr[3],
					'sex': attr[6],
					'status': attr[8]
				};
				if (attr[2] == 1) indi.proband = true;
				if (attr[4] !== "0") indi.father = attr[4];
				if (attr[5] !== "0") indi.mother = attr[5];
				if (attr[7] !== "0") indi.mztwin = attr[7];
				if (attr[9] !== "0") indi.age = attr[9];
				if (attr[10] !== "0") indi.yob = attr[10];

				var idx = 11;
				$.each(io.cancers, function (cancer, diagnosis_age) {
					// Age at 1st cancer or 0 = unaffected, AU = unknown age at diagnosis (affected unknown)
					if (attr[idx] !== "0") {
						indi[diagnosis_age] = attr[idx];
					}
					idx++;
				});

				if (attr[idx++] !== "0") indi.ashkenazi = 1;
				// BRCA1, BRCA2, PALB2, ATM, CHEK2, .... genetic tests
				// genetic test type, 0 = untested, S = mutation search, T = direct gene test
				// genetic test result, 0 = untested, P = positive, N = negative
				for (var j = 0; j < io.genetic_test.length; j++) {
					var gene_test = attr[idx].split(":");
					if (gene_test[0] !== '0') {
						if ((gene_test[0] === 'S' || gene_test[0] === 'T') && (gene_test[1] === 'P' || gene_test[1] === 'N'))
							indi[io.genetic_test[j] + '_gene_test'] = { 'type': gene_test[0], 'result': gene_test[1] };
						else
							console.warn('UNRECOGNISED GENE TEST ON LINE ' + (i + 1) + ": " + gene_test[0] + " " + gene_test[1]);
					}
					idx++;
				}
				// status, 0 = unspecified, N = negative, P = positive
				var path_test = attr[idx].split(":");
				for (j = 0; j < path_test.length; j++) {
					if (path_test[j] !== '0') {
						if (path_test[j] === 'N' || path_test[j] === 'P')
							indi[io.pathology_tests[j] + '_bc_pathology'] = path_test[j];
						else
							console.warn('UNRECOGNISED PATHOLOGY ON LINE ' + (i + 1) + ": " + io.pathology_tests[j] + " " + path_test[j]);
					}
				}
				ped.unshift(indi);
			}
		}

		try {
			return [hdr, process_ped(ped)];
		} catch (e) {
			console.error(e);
			return [hdr, ped];
		}
	};

	// read boadicea format v4 & v2
	io.readBoadiceaV4 = function (opts, boadicea_lines, version) {
		// set diseases accordingly
		opts.diseases = $.extend(true, [], DEFAULT_DISEASES);
		opts.additional_diseases = [];
		localStorage.setItem('diseases', JSON.stringify(opts.diseases));
		localStorage.setItem('additional_diseases', JSON.stringify(opts.additional_diseases));

		var lines = boadicea_lines.trim().split('\n');
		var ped = [];
		// assumes two line header
		for (var i = 2; i < lines.length; i++) {
			var attr = $.map(lines[i].trim().split(/\s+/), function (val, i) { return val.trim(); });
			if (attr.length > 1) {
				var indi = {
					'famid': attr[0],
					'display_name': attr[1],
					'name': attr[3],
					'sex': attr[6],
					'status': attr[8]
				};
				if (attr[2] == 1) indi.proband = true;
				if (attr[4] !== "0") indi.father = attr[4];
				if (attr[5] !== "0") indi.mother = attr[5];
				if (attr[7] !== "0") indi.mztwin = attr[7];
				if (attr[9] !== "0") indi.age = attr[9];
				if (attr[10] !== "0") indi.yob = attr[10];

				var idx = 11;
				$.each(io.cancers, function (cancer, diagnosis_age) {
					// Age at 1st cancer or 0 = unaffected, AU = unknown age at diagnosis (affected unknown)
					if (attr[idx] !== "0") {
						indi[diagnosis_age] = attr[idx];
					}
					idx++;
				});

				if (version === 4) {
					if (attr[idx++] !== "0") indi.ashkenazi = 1;
					// BRCA1, BRCA2, PALB2, ATM, CHEK2 genetic tests
					// genetic test type, 0 = untested, S = mutation search, T = direct gene test
					// genetic test result, 0 = untested, P = positive, N = negative
					for (var j = 0; j < 5; j++) {
						idx += 2;
						if (attr[idx - 2] !== '0') {
							if ((attr[idx - 2] === 'S' || attr[idx - 2] === 'T') && (attr[idx - 1] === 'P' || attr[idx - 1] === 'N'))
								indi[io.genetic_test[j] + '_gene_test'] = { 'type': attr[idx - 2], 'result': attr[idx - 1] };
							else
								console.warn('UNRECOGNISED GENE TEST ON LINE ' + (i + 1) + ": " + attr[idx - 2] + " " + attr[idx - 1]);
						}
					}
				} else if (version === 2) {
					// genetic test BRCA1, BRCA2
					// type, 0 = untested, S = mutation search, T = direct gene test
					// result, 0 = untested, N = no mutation, 1 = BRCA1 positive, 2 = BRCA2 positive, 3 = BRCA1/2 positive
					idx += 2; 	// gtest
					if (attr[idx - 2] !== '0') {
						if ((attr[idx - 2] === 'S' || attr[idx - 2] === 'T')) {
							if (attr[idx - 1] === 'N') {
								indi['brca1_gene_test'] = { 'type': attr[idx - 2], 'result': 'N' };
								indi['brca2_gene_test'] = { 'type': attr[idx - 2], 'result': 'N' };
							} else if (attr[idx - 1] === '1') {
								indi['brca1_gene_test'] = { 'type': attr[idx - 2], 'result': 'P' };
								indi['brca2_gene_test'] = { 'type': attr[idx - 2], 'result': 'N' };
							} else if (attr[idx - 1] === '2') {
								indi['brca1_gene_test'] = { 'type': attr[idx - 2], 'result': 'N' };
								indi['brca2_gene_test'] = { 'type': attr[idx - 2], 'result': 'P' };
							} else if (attr[idx - 1] === '3') {
								indi['brca1_gene_test'] = { 'type': attr[idx - 2], 'result': 'P' };
								indi['brca2_gene_test'] = { 'type': attr[idx - 2], 'result': 'P' };
							}
						} else {
							console.warn('UNRECOGNISED GENE TEST ON LINE ' + (i + 1) + ": " + attr[idx - 2] + " " + attr[idx - 1]);
						}
					}
					if (attr[idx++] !== "0") indi.ashkenazi = 1;
				}

				// status, 0 = unspecified, N = negative, P = positive
				for (j = 0; j < io.pathology_tests.length; j++) {
					if (attr[idx] !== '0') {
						if (attr[idx] === 'N' || attr[idx] === 'P')
							indi[io.pathology_tests[j] + '_bc_pathology'] = attr[idx];
						else
							console.warn('UNRECOGNISED PATHOLOGY ON LINE ' + (i + 1) + ": " + io.pathology_tests[j] + " " + attr[idx]);
					}
					idx++;
				}
				ped.unshift(indi);
			}
		}

		try {
			return process_ped(ped);
		} catch (e) {
			console.error(e);
			return ped;
		}
	};

	function process_ped(ped) {
		// find the level of individuals in the pedigree
		for (var j = 0; j < 2; j++) {
			for (var i = 0; i < ped.length; i++) {
				getLevel(ped, ped[i].name);
			}
		}

		// find the max level (i.e. top_level)
		var max_level = 0;
		for (i = 0; i < ped.length; i++) {
			if (ped[i].level && ped[i].level > max_level)
				max_level = ped[i].level;
		}

		// identify top_level and other nodes without parents
		for (i = 0; i < ped.length; i++) {
			if (pedigree_util.getDepth(ped, ped[i].name) == 1) {
				if (ped[i].level && ped[i].level == max_level) {
					ped[i].top_level = true;
				} else {
					ped[i].noparents = true;

					// 1. look for partners parents
					var pidx = getPartnerIdx(ped, ped[i]);
					if (pidx > -1) {
						if (ped[pidx].mother) {
							ped[i].mother = ped[pidx].mother;
							ped[i].father = ped[pidx].father;
						}
					}

					// 2. or adopt parents from level above
					if (!ped[i].mother) {
						for (var j = 0; j < ped.length; j++) {
							if (ped[i].level == (ped[j].level - 1)) {
								pidx = getPartnerIdx(ped, ped[j]);
								if (pidx > -1) {
									ped[i].mother = (ped[j].sex === 'F' ? ped[j].name : ped[pidx].name);
									ped[i].father = (ped[j].sex === 'M' ? ped[j].name : ped[pidx].name);
								}
							}
						}
					}
				}
			} else {
				delete ped[i].top_level;
			}
		}
		return ped;
	}

	// get the partners for a given node
	function getPartnerIdx(dataset, anode) {
		var ptrs = [];
		for (var i = 0; i < dataset.length; i++) {
			var bnode = dataset[i];
			if (anode.name === bnode.mother)
				return pedigree_util.getIdxByName(dataset, bnode.father);
			else if (anode.name === bnode.father)
				return pedigree_util.getIdxByName(dataset, bnode.mother);
		}
		return -1;
	}

	// for a given individual assign levels to a parents ancestors
	function getLevel(dataset, name) {
		var idx = pedigree_util.getIdxByName(dataset, name);
		var level = (dataset[idx].level ? dataset[idx].level : 0);
		update_parents_level(idx, level, dataset);
	}

	// recursively update parents levels
	function update_parents_level(idx, level, dataset) {
		var parents = ['mother', 'father'];
		level++;
		for (var i = 0; i < parents.length; i++) {
			var pidx = pedigree_util.getIdxByName(dataset, dataset[idx][parents[i]]);
			if (pidx >= 0) {
				var ma = dataset[pedigree_util.getIdxByName(dataset, dataset[idx].mother)];
				var pa = dataset[pedigree_util.getIdxByName(dataset, dataset[idx].father)];
				if (!dataset[pidx].level || dataset[pidx].level < level) {
					ma.level = level;
					pa.level = level;
				}

				if (ma.level < pa.level) {
					ma.level = pa.level;
				} else if (pa.level < ma.level) {
					pa.level = ma.level;
				}
				update_parents_level(pidx, level, dataset);
			}
		}
	}

}(window.io = window.io || {}, jQuery));