inline tooltips, maf summary

src/io/maf_file_reader.js

-morpheus.MafFileReader = function() {
+morpheus.MafFileReader = function () {
 	this.geneFilter = null;
 };
-morpheus.MafFileReader.summarizeMutations = function(dataset) {
-	var v = dataset.getRowMetadata().add('mutation_summary');
-	v.getProperties().set(
-			morpheus.VectorKeys.FIELDS,
-			[ 'Synonymous', 'In Frame Indel', 'Other Non-Synonymous',
-					'Missense', 'Splice Site', 'Frame Shift', 'Nonsense' ]);
-	v.getProperties().set(morpheus.VectorKeys.DATA_TYPE, '[number]');
-	v.getProperties().set(morpheus.VectorKeys.RECOMPUTE_FUNCTION, true);
-	v.getProperties().set(morpheus.VectorKeys.FUNCTION, function(view) {
-		var bins = new Int8Array(7); // 1-7
-		for (var i = 0, size = view.size(); i < size; i++) {
-			var value = view.getValue(i);
+morpheus.MafFileReader.summarizeMutations = function (dataset) {
+	var vector = dataset.getRowMetadata().add('mutation_summary');
+	vector.getProperties().set(
+		morpheus.VectorKeys.FIELDS,
+		['Synonymous', 'In Frame Indel', 'Other Non-Synonymous',
+			'Missense', 'Splice Site', 'Frame Shift', 'Nonsense']);
+	vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE, '[number]');
+
+	// v.getProperties().set(morpheus.VectorKeys.RECOMPUTE_FUNCTION, true);
+	// v.getProperties().set(morpheus.VectorKeys.FUNCTION, function (view) {
+	// 	var bins = new Int32Array(7); // 1-7
+	// 	for (var i = 0, size = view.size(); i < size; i++) {
+	// 		var value = view.getValue(i);
+	// 		if (value > 0) {
+	// 			bins[value - 1]++;
+	// 		}
+	// 	}
+	// 	return bins;
+	// });
+	// computing dynamically screws things up b/c summary is computed for other data types (e.g. CN)
+	for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) {
+		var bins = new Int32Array(7); // 1-7
+		for (var j = 0, ncols = dataset.getColumnCount(); j < ncols; j++) {
+			var value = dataset.getValue(i, j);
 			if (value > 0) {
 				bins[value - 1]++;
 			}
 		}
-		return bins;
-	});
-
+		vector.setValue(i, bins);
+	}
 };
 
-morpheus.MafFileReader.getField = function(fieldNames, fieldNameToIndex,
-		options) {
+morpheus.MafFileReader.getField = function (fieldNames, fieldNameToIndex,
+											options) {
 	options = $.extend({}, {
-		remove : true,
-		lc : false
+		remove: true,
+		lc: false
 	}, options);
 	var name;
 	var index;
@@ -53,8 +64,8 @@ morpheus.MafFileReader.getField = function(fieldNames, fieldNameToIndex,
 	}
 	if (index !== undefined) {
 		return {
-			name : name,
-			index : index
+			name: name,
+			index: index
 		};
 	}
 };
@@ -87,13 +98,13 @@ morpheus.MafFileReader.VARIANT_MAP.set('Frame_Shift_Ins', 6);
 // non-sense
 morpheus.MafFileReader.VARIANT_MAP.set('Nonsense_Mutation', 7);
 morpheus.MafFileReader.prototype = {
-	setGeneFilter : function(geneFilter) {
+	setGeneFilter: function (geneFilter) {
 		this.geneFilter = geneFilter;
 	},
-	getFormatName : function() {
+	getFormatName: function () {
 		return 'maf';
 	},
-	_getGeneLevelDataset : function(datasetName, reader) {
+	_getGeneLevelDataset: function (datasetName, reader) {
 		var _this = this;
 		var tab = /\t/;
 		var header = reader.readLine().split(tab);
@@ -105,11 +116,11 @@ morpheus.MafFileReader.prototype = {
 		// TODO six classes of base substitution—C>A, C>G, C>T, T>A, T>C, T>G
 		// (all substitutions are referred to by the pyrimidine of the mutated
 		// Watson–Crick base pair)
-		var fields = [ 'Hugo_Symbol', 'Chromosome', 'Start_position',
-				'Reference_Allele', 'Tumor_Seq_Allele2',
-				'Variant_Classification', 'Protein_Change', 'ccf_hat',
-				'tumor_f', 'i_tumor_f', 'Tumor_Sample_Barcode', 'tumor_name',
-				'Tumor_Sample_UUID' ];
+		var fields = ['Hugo_Symbol', 'Chromosome', 'Start_position',
+			'Reference_Allele', 'Tumor_Seq_Allele2',
+			'Variant_Classification', 'Protein_Change', 'ccf_hat',
+			'tumor_f', 'i_tumor_f', 'Tumor_Sample_Barcode', 'tumor_name',
+			'Tumor_Sample_UUID'];
 		var fieldNameToIndex = {};
 
 		for (var i = 0, length = fields.length; i < length; i++) {
@@ -119,17 +130,17 @@ morpheus.MafFileReader.prototype = {
 			}
 		}
 		var sampleField = morpheus.MafFileReader.getField([
-				'Tumor_Sample_Barcode', 'tumor_name', 'Tumor_Sample_UUID' ],
-				fieldNameToIndex, {
-					lc : true,
-					remove : true
-				});
+				'Tumor_Sample_Barcode', 'tumor_name', 'Tumor_Sample_UUID'],
+			fieldNameToIndex, {
+				lc: true,
+				remove: true
+			});
 		var sampleColumnName = sampleField.name;
 		var sampleIdColumnIndex = sampleField.index;
-		var tumorFractionField = morpheus.MafFileReader.getField([ 'ccf_hat',
-				'tumor_f', 'i_tumor_f' ], fieldNameToIndex, {
-			lc : true,
-			remove : true
+		var tumorFractionField = morpheus.MafFileReader.getField(['ccf_hat',
+			'tumor_f', 'i_tumor_f'], fieldNameToIndex, {
+			lc: true,
+			remove: true
 		});
 		var ccfColumnName;
 		var ccfColumnIndex;
@@ -139,28 +150,28 @@ morpheus.MafFileReader.prototype = {
 		}
 		var chromosomeColumn = fieldNameToIndex['Chromosome'.toLowerCase()];
 		var startPositionColumn = fieldNameToIndex['Start_position'
-				.toLowerCase()];
+		.toLowerCase()];
 		var refAlleleColumn = fieldNameToIndex['Reference_Allele'.toLowerCase()];
 		var tumorAllelColumn = fieldNameToIndex['Tumor_Seq_Allele2'
-				.toLowerCase()];
+		.toLowerCase()];
 		var proteinChangeColumn = fieldNameToIndex['Protein_Change'
-				.toLowerCase()];
+		.toLowerCase()];
 		var geneSymbolColumn = fieldNameToIndex['Hugo_Symbol'.toLowerCase()];
 		var variantColumnIndex = headerToIndex['Variant_Classification'
-				.toLowerCase()];
+		.toLowerCase()];
 		if (variantColumnIndex === undefined) {
 			throw new Error('Variant_Classification not found');
 		}
 		// keep fields that are in file only
 		fields = [];
 		var geneFields = [];
-		for ( var key in fieldNameToIndex) {
+		for (var key in fieldNameToIndex) {
 			if (key !== sampleColumnName && key !== ccfColumnName) {
 				geneFields.push(key);
 			}
 			fields.push(key);
 		}
-		var geneColumnIndices = geneFields.map(function(field) {
+		var geneColumnIndices = geneFields.map(function (field) {
 			return fieldNameToIndex[field];
 		});
 		var nGeneFields = geneColumnIndices.length;
@@ -182,7 +193,7 @@ morpheus.MafFileReader.prototype = {
 				continue;
 			}
 			if (this.geneFilter == null
-					|| this.geneFilter.has(tokens[geneSymbolColumn])) {
+				|| this.geneFilter.has(tokens[geneSymbolColumn])) {
 				var rowIndex = geneSymbolToIndex.get(gene);
 				if (rowIndex === undefined) {
 					rowIndex = geneSymbolToIndex.size();
@@ -201,11 +212,11 @@ morpheus.MafFileReader.prototype = {
 				variantObject.__v = variantCode;
 				variantObject.Variant = value;
 				variantObject.Mutation = String(tokens[chromosomeColumn]) + ':'
-						+ String(tokens[startPositionColumn]) + ' '
-						+ String(tokens[refAlleleColumn]) + ' > '
-						+ String(tokens[tumorAllelColumn]);
+					+ String(tokens[startPositionColumn]) + ' '
+					+ String(tokens[refAlleleColumn]) + ' > '
+					+ String(tokens[tumorAllelColumn]);
 				var wrappedVariant = morpheus.Util.wrapNumber(variantCode,
-						variantObject);
+					variantObject);
 				var variantRow = variantMatrix[rowIndex];
 				if (variantRow === undefined) {
 					variantRow = [];
@@ -235,22 +246,22 @@ morpheus.MafFileReader.prototype = {
 			}
 		}
 		var dataset = new morpheus.Dataset({
-			name : datasetName,
-			array : variantMatrix,
-			dataType : 'object',
-			rows : geneSymbolToIndex.size(),
-			columns : sampleIdToIndex.size()
+			name: datasetName,
+			array: variantMatrix,
+			dataType: 'object',
+			rows: geneSymbolToIndex.size(),
+			columns: sampleIdToIndex.size()
 		});
 		var columnIds = dataset.getColumnMetadata().add('id');
-		sampleIdToIndex.forEach(function(index, id) {
+		sampleIdToIndex.forEach(function (index, id) {
 			columnIds.setValue(index, id);
 		});
 		var rowIds = dataset.getRowMetadata().add('id');
-		geneSymbolToIndex.forEach(function(index, id) {
+		geneSymbolToIndex.forEach(function (index, id) {
 			rowIds.setValue(index, id);
 		});
 		for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset
-				.getColumnCount(); i < nrows; i++) {
+		.getColumnCount(); i < nrows; i++) {
 			for (var j = 0; j < ncols; j++) {
 				if (variantMatrix[i][j] === undefined) {
 					variantMatrix[i][j] = 0;
@@ -259,9 +270,9 @@ morpheus.MafFileReader.prototype = {
 		}
 		if (ccfColumnIndex !== undefined) {
 			dataset.addSeries({
-				dataType : 'object',
-				name : 'allelic_fraction',
-				array : ccfMatrix
+				dataType: 'object',
+				name: 'allelic_fraction',
+				array: ccfMatrix
 			});
 		}
 		if (this.geneFilter) {
@@ -272,58 +283,58 @@ morpheus.MafFileReader.prototype = {
 				orderVector.setValue(i, order);
 			}
 			var project = new morpheus.Project(dataset);
-			project.setRowSortKeys([ new morpheus.SortKey('order',
-					morpheus.SortKey.SortOrder.ASCENDING) ], true); // sort
+			project.setRowSortKeys([new morpheus.SortKey('order',
+				morpheus.SortKey.SortOrder.ASCENDING)], true); // sort
 			// collapsed
 			// dataset
 			var tmp = project.getSortedFilteredDataset();
 			project = new morpheus.Project(tmp);
 			var columnIndices = morpheus.Util.seq(tmp.getColumnCount());
 			columnIndices
-					.sort(function(a, b) {
-						for (var i = 0, nrows = tmp.getRowCount(); i < nrows; i++) {
-							for (var seriesIndex = 0, nseries = tmp
-									.getSeriesCount(); seriesIndex < nseries; seriesIndex++) {
-								var f1 = tmp.getValue(i, a, seriesIndex);
-								if (isNaN(f1)) {
-									f1 = Number.NEGATIVE_INFINITY;
-								}
-								f1 = f1.valueOf();
-								var f2 = tmp.getValue(i, b, seriesIndex);
-								if (isNaN(f2)) {
-									f2 = Number.NEGATIVE_INFINITY;
-								}
-								f2 = f2.valueOf();
-								var returnVal = (f1 === f2 ? 0 : (f1 < f2 ? 1
-										: -1));
-								if (returnVal !== 0) {
-									return returnVal;
-								}
-							}
+			.sort(function (a, b) {
+				for (var i = 0, nrows = tmp.getRowCount(); i < nrows; i++) {
+					for (var seriesIndex = 0, nseries = tmp
+					.getSeriesCount(); seriesIndex < nseries; seriesIndex++) {
+						var f1 = tmp.getValue(i, a, seriesIndex);
+						if (isNaN(f1)) {
+							f1 = Number.NEGATIVE_INFINITY;
+						}
+						f1 = f1.valueOf();
+						var f2 = tmp.getValue(i, b, seriesIndex);
+						if (isNaN(f2)) {
+							f2 = Number.NEGATIVE_INFINITY;
 						}
-						return 0;
-					});
+						f2 = f2.valueOf();
+						var returnVal = (f1 === f2 ? 0 : (f1 < f2 ? 1
+							: -1));
+						if (returnVal !== 0) {
+							return returnVal;
+						}
+					}
+				}
+				return 0;
+			});
 			dataset = new morpheus.SlicedDatasetView(dataset, null,
-					columnIndices);
+				columnIndices);
 		}
 		morpheus.MafFileReader.summarizeMutations(dataset);
 		morpheus.MafFileReader
-				.summarizeMutations(new morpheus.TransposedDatasetView(dataset));
+		.summarizeMutations(new morpheus.TransposedDatasetView(dataset));
 		return dataset;
 	},
-	read : function(fileOrUrl, callback) {
+	read: function (fileOrUrl, callback) {
 		var _this = this;
 		var name = morpheus.Util.getBaseFileName(morpheus.Util
-				.getFileName(fileOrUrl));
-		morpheus.BufferedReader.getArrayBuffer(fileOrUrl, function(err,
-				arrayBuffer) {
+		.getFileName(fileOrUrl));
+		morpheus.BufferedReader.getArrayBuffer(fileOrUrl, function (err,
+																	arrayBuffer) {
 			if (err) {
 				callback(err);
 			} else {
 				try {
 					callback(null, _this._getGeneLevelDataset(name,
-							new morpheus.BufferedReader(new Uint8Array(
-									arrayBuffer))));
+						new morpheus.BufferedReader(new Uint8Array(
+							arrayBuffer))));
 				} catch (err) {
 					callback(err);
 				}

src/sample_datasets.js

@@ -376,7 +376,7 @@ morpheus.SampleDatasets.prototype = {
 			}],
 			columns: [{
 				field: 'id',
-				display: 'text'
+				display: 'text,tooltip'
 			}, {
 				field: 'mutation_summary',
 				display: 'stacked_bar'

src/ui/heat_map_tooltip_provider.js

@@ -33,36 +33,22 @@ morpheus.HeatMapTooltipProvider = function (heatMap, rowIndex, columnIndex,
 			var quickRowTracks = heatMap.rowTracks.filter(function (t) {
 				return t.settings.inlineTooltip;
 			});
-			morpheus.HeatMapTooltipProvider._tracksToString(options,
-				quickRowTracks, dataset.getRowMetadata(), rowIndex,
-				tipText, separator);
-
-			// if (quickRowTracks.length > 0) {
-			// tipText
-			// .push('<div
-			// style="height:1px;background-color:LightGrey;"></div>');
-			// }
-			morpheus.HeatMapTooltipProvider._tracksToString(options,
-				heatMap.columnTracks.filter(function (t) {
-					return t.settings.inlineTooltip;
-				}), dataset.getColumnMetadata(), columnIndex, tipText,
-				separator);
+			morpheus.HeatMapTooltipProvider._tracksToString(quickRowTracks, dataset.getRowMetadata(), rowIndex, tipText, separator);
+			morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function (t) {
+				return t.settings.inlineTooltip;
+			}), dataset.getColumnMetadata(), columnIndex, tipText, separator);
 
 		}
 	} else if (quick) {
 		if (rowIndex !== -1) {
-			morpheus.HeatMapTooltipProvider._tracksToString(options,
-				heatMap.rowTracks.filter(function (t) {
-					return t.settings.inlineTooltip;
-				}), dataset.getRowMetadata(), rowIndex, tipText,
-				separator);
+			morpheus.HeatMapTooltipProvider._tracksToString(heatMap.rowTracks.filter(function (t) {
+				return t.settings.inlineTooltip && options.name !== t.getName();
+			}), dataset.getRowMetadata(), rowIndex, tipText, separator);
 		}
 		if (columnIndex !== -1) {
-			morpheus.HeatMapTooltipProvider._tracksToString(options,
-				heatMap.columnTracks.filter(function (t) {
-					return t.settings.inlineTooltip;
-				}), dataset.getColumnMetadata(), columnIndex, tipText,
-				separator);
+			morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function (t) {
+				return t.settings.inlineTooltip && options.name !== t.getName();
+			}), dataset.getColumnMetadata(), columnIndex, tipText, separator);
 		}
 	}
 
@@ -286,7 +272,7 @@ morpheus.HeatMapTooltipProvider.vectorToString = function (vector, index,
 		}
 	}
 };
-morpheus.HeatMapTooltipProvider._tracksToString = function (options, tracks, metadata, index, tipText, separator) {
+morpheus.HeatMapTooltipProvider._tracksToString = function (tracks, metadata, index, tipText, separator) {
 	for (var i = 0; i < tracks.length; i++) {
 		morpheus.HeatMapTooltipProvider.vectorToString(metadata.getByName(tracks[i].name), index, tipText,
 			separator);
@@ -299,7 +285,7 @@ morpheus.HeatMapTooltipProvider._metadataToString = function (options, tracks,
 	for (var i = 0, ntracks = tracks.length; i < ntracks; i++) {
 		var track = tracks[i];
 		if ((track.isVisible() && track.isShowTooltip())) {
-			if (tracks[i].name === options.name) {
+			if (tracks[i].name === options.name) { // show the vector that we're mousing over 1st
 				filtered.splice(0, 0, track);
 			} else {
 				filtered.push(track);
@@ -307,9 +293,7 @@ morpheus.HeatMapTooltipProvider._metadataToString = function (options, tracks,
 		}
 	}
 
-	// show the vector that we're mousing over 1st
-	morpheus.HeatMapTooltipProvider._tracksToString(options, filtered,
-		metadata, index, tipText, separator);
+	morpheus.HeatMapTooltipProvider._tracksToString(filtered, metadata, index, tipText, separator);
 
 };
 morpheus.HeatMapTooltipProvider._nodesToString = function (tipText, nodes,