morpheus.HeatMapToolBar = function (controller) {
	this.controller = controller;
	this.rowSearchResultModelIndices = [];
	this.columnSearchResultModelIndices = [];
	var _this = this;
	var $el = $('<div style="white-space:nowrap;" class="hidden-print container-fluid">'
		+ '<div class="row"><div class="col-xs-12"><div data-name="lineOneColumn"></div></div></div>'
		+ '<div class="row"><div class="col-xs-12"><div data-name="lineTwoColumn" style="border-bottom: 1px solid #e7e7e7;margin-bottom:10px;"></div></div></div>'
		+ '</div>');
	var searchHtml = [];
	var $search = $('<form name="searchForm" class="form form-inline form-compact" role="search"></form>');
	$search.on('submit', function (e) {
		e.preventDefault();
	});
	// search rows
	if (controller.options.toolbar.searchRows) {
		searchHtml.push('<div class="form-group">');
		searchHtml.push('<div class="input-group">');
		searchHtml.push('<div class="input-group-btn">');
		searchHtml
		.push('<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span data-toggle="tooltip" title="Search rows. Quote search term for exact match. Narrow search with field: modifier. Exclude matches using - modifier. Use min..max to perform a range search.">Rows</span> <span class="caret"></span></button>');
		searchHtml.push('<ul data-name="rowSearchOptions" class="dropdown-menu">');
		searchHtml.push('<li><a data-name="exact" href="#">Exact Match</a></li>');
		searchHtml
		.push('<li class="active"><a data-name="contains" href="#">Contains</a></li>');
		searchHtml.push('</ul>');
		searchHtml.push('</div>'); // input-group-btn
		searchHtml
		.push('<input type="text" style="border-top:3px solid rgb(127,127,127);width:240px;padding-right:25px;" class="form-control input-sm" autocomplete="off" name="searchRows">');
		searchHtml.push('</div>');
		searchHtml.push('</div>');
		searchHtml.push('<div class="form-group">');
		searchHtml.push('<span data-name="rowSearchDiv" style="display:none;">');
		searchHtml
		.push('<span data-name="searchResultsRows"></span>');
		searchHtml
		.push('<button name="previousRowMatch" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Previous"><i class="fa fa-chevron-up"></i></button>');
		searchHtml
		.push('<button name="nextRowMatch" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Next"><i class="fa fa-chevron-down"></i></button>');
		searchHtml
		.push('<button name="rowMatchesToTop" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Matches To Top"><i class="fa fa-level-up"></i></button>');
		searchHtml.push('</span>');
		searchHtml.push('</div>');

	}
	if (controller.options.toolbar.searchColumns) {
		searchHtml
		.push('<div class="form-group" style="margin-right:10px;"></div>'); // spacer
		// search columns
		searchHtml.push('<div class="form-group">');
		searchHtml.push('<div class="input-group">'); // group
		searchHtml.push('<div class="input-group-btn">');
		searchHtml
		.push('<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span data-toggle="tooltip" title="Search columns. Quote search term for exact match. Narrow search with field: modifier. Exclude matches using - modifier. Use min..max to perform a range search.">Columns</span> <span class="caret"></span></button>');
		searchHtml
		.push('<ul data-name="columnSearchOptions" class="dropdown-menu">');
		searchHtml.push('<li><a data-name="exact" href="#">Exact Match</a></li>');
		searchHtml
		.push('<li class="active"><a data-name="contains" href="#">Contains</a></li>');
		searchHtml.push('</ul>');
		searchHtml.push('</div>'); // input-group-btn

		searchHtml
		.push('<input type="text" style="border-right:4px solid rgb(127,127,127);width:240px;padding-right:25px;" class="form-control input-sm" autocomplete="off" name="searchColumns"></div>');
		searchHtml.push('</div>');
		searchHtml.push('</div>');
		searchHtml.push('<div class="form-group" style="margin-left:4px;">');
		searchHtml
		.push('<span data-name="searchResultsColumns"></span>');
		searchHtml.push('<span data-name="columnSearchDiv" style="display:none;">');
		searchHtml
		.push('<button name="previousColumnMatch" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Previous"><i class="fa fa-chevron-up"></i></button>');
		searchHtml
		.push('<button name="nextColumnMatch" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Next"><i class="fa fa-chevron-down"></i></button>');
		searchHtml
		.push('<button name="columnMatchesToTop" type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Matches To Top"><i class="fa fa-level-up"></i></button>');
		searchHtml.push('</span>');
		searchHtml.push('</div>');
	}

	// search values
	searchHtml
	.push('<div data-name="searchValuesDiv" class="form-group" style="margin-left:10px;">');
	searchHtml
	.push('<div class="input-group"><span class="input-group-addon">Values</span><input type="text" style="width:240px;padding-right:25px;" class="form-control input-sm" autocomplete="off" name="searchValues"></div>');
	searchHtml.push('</div>');
	searchHtml.push('<div class="form-group" style="margin-left:4px;">');
	searchHtml
	.push('<h6 data-name="searchResultsValues" style="display: inline;"></h6>');
	searchHtml.push('</div>');

	// row dendrogram
	searchHtml
	.push('<div style="display: none;  margin-left:10px;" data-name="searchRowDendrogramWrapper"' +
		' class="form-group">');
	searchHtml
	.push('<div class="input-group"><span class="input-group-addon">Row Dendrogram</span><input type="text" style="width:240px;" class="form-control input-sm" autocomplete="off" name="searchRowDendrogram"></div>');
	searchHtml
	.push('<h6 data-name="searchResultsRowDendrogram" style="display: inline;"></h6>');
	searchHtml.push('</div>');
	// column dendrogram
	searchHtml
	.push('<div style="display: none; margin-left:10px;"' +
		' data-name="searchColumnDendrogramWrapper" class="form-group">');
	searchHtml
	.push('<div class="input-group"><span class="input-group-addon">Column Dendrogram</span><input type="text" style="width:240px;" class="form-control input-sm" autocomplete="off" name="searchColumnDendrogram"></div>');
	searchHtml
	.push('<h6 data-name="searchResultsColumnDendrogram" style="display: inline;"></h6>');
	searchHtml.push('</div>');
	// dimensions
	searchHtml.push('<div class="form-group">');
	searchHtml
	.push('<h6 style="display: inline; margin-left:10px;" data-name="dim"></h6>');
	searchHtml
	.push('<h6 style="display: inline; margin-left:10px; background-color:rgb(182,213,253);"' +
		' data-name="selection"></h6>');
	searchHtml.push('</div>');
	searchHtml.push('<div data-name="buttons" style="margin-left:10px;" class="form-group"></div>');

	$(searchHtml.join('')).appendTo($search);
	if (!controller.options.toolbar.searchValues) {
		$search.find('[data-name=searchValuesDiv]').css('display', 'none');
	}
	var $buttons = $search.find('[data-name=buttons]');

	var $tools = $('<form name="tools" class="form-inline" role="form"></form>');
	$tools.on('submit', function (e) {
		e.preventDefault();
	});

	var toolbarHtml = [];
	// zoom
	if (controller.options.toolbar.zoom) {
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Zoom Out (-)" name="out"><span class="fa fa-minus"></span></button>');
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Zoom In (+)" name="in"><span class="fa fa-plus"></span></button>');
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Fit To Window" name="fit"><span class="fa fa-compress"></span></button>');
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Reset Zoom" name="resetZoom">100%</button>');
	}




	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
	if (controller.options.toolbar.sort) {
		toolbarHtml
		.push('<button data-toggle="tooltip" title="Sort" name="sort" type="button" class="btn btn-default btn-xs"><span class="fa fa-sort-alpha-asc"></span></button>');
	}
	if (controller.options.toolbar.options) {
		toolbarHtml
		.push('<button name="options" data-toggle="tooltip" title="Options" type="button" class="btn btn-default btn-xs"><span class="fa fa-cog"></span></button>');

	}

	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
	if (controller.options.toolbar.saveImage) {
		toolbarHtml
		.push('<button name="saveImage" data-toggle="tooltip" title="Save Image ('
			+ morpheus.Util.COMMAND_KEY
			+ 'S)" type="button" class="btn btn-default btn-xs"><span class="fa fa-file-image-o"></span></button>');
	}
	if (controller.options.toolbar.saveDataset) {
		toolbarHtml
		.push('<button name="saveDataset" data-toggle="tooltip" title="Save Dataset ('
			+ morpheus.Util.COMMAND_KEY
			+ 'Shift+S)" type="button" class="btn btn-default btn-xs"><span class="fa fa-floppy-o"></span></button>');
	}
	if (controller.options.toolbar.openFile) {
		toolbarHtml
		.push('<button name="openFile" data-toggle="tooltip" title="Open File ('
			+ morpheus.Util.COMMAND_KEY
			+ 'O)" type="button" class="btn btn-default btn-xs"><span class="fa fa-folder-open-o"></span></button>');
	}
	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
	if (controller.options.toolbar.filter) {
		toolbarHtml
		.push('<button name="filterButton" data-toggle="tooltip" title="Filter" type="button" class="btn btn-default btn-xs"><span class="fa fa-filter"></span></button>');
	}
	if (typeof Plotly !== 'undefined') {
		toolbarHtml
		.push('<button name="chart" data-toggle="tooltip" title="Chart" type="button" class="btn btn-default btn-xs"><span class="fa fa-line-chart"></span></button>');

	}
	var tools = [{
		tool: new morpheus.HClusterTool()
	}, {
		tool: new morpheus.MarkerSelection()
	}, {
		tool: new morpheus.NearestNeighbors()
	}, {
		tool: new morpheus.NewHeatMapTool(),
	}, null, {
		tool: new morpheus.AdjustDataTool()
	}, {
		tool: new morpheus.CollapseDatasetTool()
	}, {
		tool: new morpheus.CreateAnnotation()
	}, {
		tool: new morpheus.SimilarityMatrixTool()
	}, {
		tool: new morpheus.TransposeTool()
	}, {
		tool: new morpheus.WordCloudTool()
	}]; // DevAPI, {
	this.getToolByName = function (name) {
		for (var i = 0; i < tools.length; i++) {
			if (tools[i] && tools[i].tool.toString
				&& tools[i].tool.toString() === name) {
				return tools[i].tool;
			}
		}
		throw name + ' not found';
	};
	if (controller.options.toolbar.tools) {
		toolbarHtml.push('<div class="btn-group">');
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown"><span title="Tools" data-toggle="tooltip" class="fa fa-wrench"></span> <span class="caret"></span></button>');
		toolbarHtml.push('<ul data-name="tools" class="dropdown-menu" role="menu">');

		for (var i = 0; i < tools.length; i++) {
			if (tools[i] == null) {
				toolbarHtml
				.push('<li role="presentation" class="divider"></li>');
			} else if (tools[i].action) {
				toolbarHtml.push('<li><a data-name="' + i + '" href="#">'
					+ tools[i].name + '</a></li>');
			} else {
				toolbarHtml.push('<li><a data-name="' + i + '" href="#">'
					+ tools[i].tool.toString() + '</a></li>');
			}
		}
		toolbarHtml.push('</ul></div>');
	}

	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
	// legend
	if (controller.options.toolbar.colorKey) {
		toolbarHtml.push('<div class="btn-group">');
		toolbarHtml
		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="dropdown"><span title="Color Key" data-toggle="tooltip" class="fa fa-key"></span></button>');
		toolbarHtml.push('<ul data-name="key" class="dropdown-menu" role="menu">');
		toolbarHtml.push('<li data-name="keyContent"></li>');
		toolbarHtml.push('</ul>');
		toolbarHtml.push('</div>');
	}

	toolbarHtml.push('<div class="morpheus-button-divider"></div>');

	toolbarHtml.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="PCAPlot" name="pca">PCA</button>');

	$buttons.on('click', '[name=pca]', function () {
		console.log("test button clicked");
		new morpheus.PcaPlotTool({project : controller.getProject()});

	});

	var $lineOneColumn = $el.find('[data-name=lineOneColumn]');
	$search.appendTo($lineOneColumn);
	var $toolbarForm = $(toolbarHtml.join(''));
	$toolbarForm.appendTo($buttons);
	if (controller.options.$help) {
		controller.options.$help.appendTo($buttons);
	}
	$('<div data-name="tip" style="height: 14px; font-size: 12px;overflow:hidden;"></div>').appendTo($el.find('[data-name=lineTwoColumn]'));

	// $hide.appendTo($el.find('[data-name=toggleEl]'));
	$el.prependTo(controller.$content);
	var $tools = $el.find('[data-name=tools]');
	this.$tip = $el.find('[data-name=tip]');
	$tools.on('click', 'li > a', function (e) {
		e.preventDefault();
		var index = parseInt($(this).attr('data-name'));
		if (tools[index].tool) {
			morpheus.HeatMap.showTool(tools[index].tool, controller);
		} else {
			tools[index].action();
		}
	});
	this.defaultRowMatchMode = 'contains';
	this.defaultColumnMatchMode = 'contains';
	var $rowSearchOptions = $el.find('[data-name=rowSearchOptions]');
	$rowSearchOptions.on('click', 'li > a', function (e) {
		e.preventDefault();
		_this.defaultRowMatchMode = $(this).attr('data-name');
		$rowSearchOptions.find('li').removeClass('active');
		$(this).parent('li').addClass('active');
		_this.search(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'rowSearchMatchMode'
		});
	});
	var $columnSearchOptions = $el.find('[data-name=columnSearchOptions]');
	$columnSearchOptions.on('click', 'li > a', function (e) {
		e.preventDefault();
		_this.defaultColumnMatchMode = $(this).attr('data-name');
		$columnSearchOptions.find('li').removeClass('active');
		$(this).parent('li').addClass('active');
		_this.search(false);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'columnSearchMatchMode'
		});
	});

	var filterModal = [];
	var filterLabelId = _.uniqueId('morpheus');
	filterModal
	.push('<div class="modal fade" tabindex="1" role="dialog" aria-labelledby="'
		+ filterLabelId + '">');
	filterModal.push('<div class="modal-dialog" role="document">');
	filterModal.push('<div class="modal-content">');
	filterModal.push('<div class="modal-header">');
	filterModal
	.push('<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>');
	filterModal.push('<h4 class="modal-title" id="' + filterLabelId
		+ '">Filter</h4>');
	filterModal.push('</div>');
	filterModal.push('<div class="modal-body">');
	filterModal.push('');
	filterModal.push('</div>');
	filterModal.push('</div>');
	filterModal.push('</div>');
	filterModal.push('</div>');
	var $filterModal = $(filterModal.join(''));
	$filterModal.on('mousewheel', function (e) {
		e.stopPropagation();
	});
	var $filter = $('<div></div>');
	$filter.appendTo($filterModal.find('.modal-body'));
	$filterModal.appendTo($el);
	var filterHtml = [];
	filterHtml
	.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="rows" checked>Rows</label></div> ');
	filterHtml
	.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="columns">Columns</label></div>');

	var $filterChooser = $(filterHtml.join(''));
	$filterChooser.appendTo($filter);
	var columnFilterUI = new morpheus.FilterUI(controller.getProject(), true);
	var rowFilterUI = new morpheus.FilterUI(controller.getProject(), false);
	controller.getProject().getRowFilter().on('focus', function (e) {
		$filterChooser.find('[value=rows]').prop('checked', true);
		columnFilterUI.$div.hide();
		rowFilterUI.$div.show();
		$filterModal.modal('show');
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'rowFilter'
		});

	});
	controller.getProject().getColumnFilter().on('focus', function (e) {
		$filterChooser.find('[value=columns]').prop('checked', true);
		columnFilterUI.$div.show();
		rowFilterUI.$div.hide();
		$filterModal.modal('show');
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'columnFilter'
		});
	});
	rowFilterUI.$div.appendTo($filter);
	columnFilterUI.$div.appendTo($filter);
	columnFilterUI.$div.css('display', 'none');
	var $filterRadio = $filterChooser.find('[name=rowsOrColumns]');
	$filterRadio.on('change', function (e) {
		var val = $filterRadio.filter(':checked').val();
		if (val === 'columns') {
			columnFilterUI.$div.show();
			rowFilterUI.$div.hide();
		} else {
			columnFilterUI.$div.hide();
			rowFilterUI.$div.show();
		}
		e.preventDefault();
	});
	$el.find('[name=filterButton]').on('click', function () {
		$filterModal.modal('show');
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'filter'
		});
	});
	$el.find('[data-toggle="tooltip"]').tooltip({
		placement: 'bottom',
		container: 'body',
		trigger: 'hover'
	}).on('click', function () {
		$(this).tooltip('hide');
	});
	var $key = $el.find('[data-name=key]');
	var $keyContent = $el.find('[data-name=keyContent]');
	$key.dropdown().parent().on('show.bs.dropdown', function () {
		new morpheus.HeatMapColorSchemeLegend(controller, $keyContent);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'colorKey'
		});
	});
	$el.find('[name=openFile]').on('click', function () {
		morpheus.HeatMap.showTool(new morpheus.OpenFileTool({
			customUrls: controller._customUrls
		}), controller);
	});
	$el.find('[name=saveImage]').on('click', function () {
		morpheus.HeatMap.showTool(new morpheus.SaveImageTool(), controller);
	});
	$el.find('[name=saveDataset]').on('click', function () {
		morpheus.HeatMap.showTool(new morpheus.SaveDatasetTool(), controller);
	});
	$el.find('[name=chart]').on(
		'click',
		function () {
			new morpheus.ChartTool({
				project: controller.getProject(),
				getVisibleTrackNames: _.bind(
					controller.getVisibleTrackNames, controller)
			});
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'chart'
			});
		});

	var _this = this;
	$el
	.find('[name=tutorial]')
	.on(
		'click',
		function () {
			window
			.open('http://www.broadinstitute.org/cancer/software/morpheus/tutorial.html');
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'tutorial'
			});
		});

	this.$previousColumnMatch = $el.find('[name=previousColumnMatch]');
	this.$nextColumnMatch = $el.find('[name=nextColumnMatch]');
	this.$previousRowMatch = $el.find('[name=previousRowMatch]');
	this.$nextRowMatch = $el.find('[name=nextRowMatch]');
	this.$dimensionsLabel = $el.find('[data-name=dim]');
	this.$columnTextField = $el.find('[name=searchColumns]');
	this.$valueTextField = $el.find('[name=searchValues]');
	this.$selectionLabel = $el.find('[data-name=selection]');
	this.$rowTextField = $el.find('[name=searchRows]');
	this.$columnMatchesToTop = $el.find('[name=columnMatchesToTop]');
	this.$rowMatchesToTop = $el.find('[name=rowMatchesToTop]');
	this.$rowSearchDiv = $el.find('[data-name=rowSearchDiv]');
	this.$columnSearchDiv = $el.find('[data-name=columnSearchDiv]');
	this.$searchRowDendrogramWrapper = $el
	.find('[data-name=searchRowDendrogramWrapper]');
	this.$searchRowDendrogram = $el.find('[name=searchRowDendrogram]');
	this.$searchResultsRowDendrogram = $el
	.find('[data-name=searchResultsRowDendrogram]');
	this.$searchColumnDendrogramWrapper = $el
	.find('[data-name=searchColumnDendrogramWrapper]');
	this.$searchColumnDendrogram = $el.find('[name=searchColumnDendrogram]');
	this.$searchResultsColumnDendrogram = $el
	.find('[data-name=searchResultsColumnDendrogram]');
	controller.on('dendrogramAnnotated', function (e) {
		(e.isColumns ? _this.$searchColumnDendrogramWrapper
			: _this.$searchRowDendrogramWrapper).show();
	});
	controller.on('dendrogramChanged', function (e) {
		(e.isColumns ? _this.$searchColumnDendrogramWrapper
			: _this.$searchRowDendrogramWrapper).hide();
	});
	var project = controller.getProject();

	morpheus.Util.autosuggest({
		$el: this.$rowTextField,
		filter: function (terms, cb) {
			var indices = [];
			var meta = project.getSortedFilteredDataset().getRowMetadata();
			controller.getVisibleTrackNames(false).forEach(function (name) {
				indices.push(morpheus.MetadataUtil.indexOf(meta, name));
			});
			meta = new morpheus.MetadataModelColumnView(meta, indices);
			morpheus.MetadataUtil.autocomplete(meta)(terms, cb);
		},
		select: function () {
			_this.search(true);
		}
	});

	this.$rowTextField.on('keyup', _.debounce(function (e) {
		if (e.which === 13) {
			e.preventDefault();
		}
		_this.search(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'searchRows'
		});
	}, 500));
	morpheus.Util.autosuggest({
		$el: this.$columnTextField,
		filter: function (terms, cb) {
			var indices = [];
			var meta = project.getSortedFilteredDataset().getColumnMetadata();
			controller.getVisibleTrackNames(true).forEach(function (name) {
				indices.push(morpheus.MetadataUtil.indexOf(meta, name));
			});
			meta = new morpheus.MetadataModelColumnView(meta, indices);
			morpheus.MetadataUtil.autocomplete(meta)(terms, cb);
		},
		select: function () {
			_this.search(false);
		}
	});
	this.$columnTextField.on('keyup', _.debounce(function (e) {
		if (e.which === 13) {
			e.preventDefault();
		}
		_this.search(false);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'searchColumns'
		});
	}, 500));

	// TODO combine search with autocomplete
	this.$searchRowDendrogram.on('keyup', _.debounce(function (e) {
		if (e.which === 13) {
			// _this.$searchRowDendrogram.autocomplete('close');
			e.preventDefault();
		}
		_this.searchDendrogram(false);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'searchRowDendrogram'
		});
	}, 500));
	this.$searchColumnDendrogram.on('keyup', _.debounce(function (e) {
		if (e.which === 13) {
			// _this.$searchColumnDendrogram.autocomplete('close');
			e.preventDefault();
		}
		_this.searchDendrogram(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'searchColumnDendrogram'
		});
	}, 500));

	function searchValues() {
		var $searchResultsLabel = _this.$el.find('[data-name=searchResultsValues]');
		var text = $.trim(_this.$valueTextField.val());
		if (text === '') {
			$searchResultsLabel.html('');
			project.getElementSelectionModel().setViewIndices(null);
		} else {
			var viewIndices = new morpheus.Set();
			morpheus.DatasetUtil.searchValues(project
			.getSortedFilteredDataset(), text, function (value, i, j) {
				viewIndices.add(new morpheus.Identifier([i, j]));
			});
			project.getElementSelectionModel().setViewIndices(viewIndices);
			$searchResultsLabel.html(viewIndices.size() + ' match'
				+ (viewIndices.size() === 1 ? '' : 'es'));
		}
	}

	morpheus.Util.autosuggest({
		$el: this.$valueTextField,
		filter: function (terms, cb) {
			morpheus.DatasetUtil.autocompleteValues(
				project.getSortedFilteredDataset())(terms, cb);
		},
		select: function () {
			searchValues();
		}
	});

	this.$valueTextField.on('keyup', _.debounce(function (e) {
		if (e.which === 13) {
			_this.$valueTextField.autocomplete('close');
			e.preventDefault();
		}
		searchValues();
	}, 500));

	$toolbarForm.on('submit', function (e) {
		e.preventDefault();
	});
	$buttons.on('click', '[name=in]', function (e) {
		e.preventDefault();
		controller.zoom(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'zoomIn'
		});
	});
	$buttons.on('click', '[name=out]', function (e) {
		e.preventDefault();
		controller.zoom(false);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'zoomOut'
		});
	});
	$buttons.on('click', '[name=options]', function (e) {
		e.preventDefault();
		controller.showOptions();
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'options'
		});
	});
	$buttons.on('click', '[name=sort]', function (e) {
		e.preventDefault();
		new morpheus.SortDialog(project);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'sort'
		});
	});
	$buttons.on('click', '[name=fit]', function (e) {
		e.preventDefault();
		controller.fitToWindow(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'fit'
		});
	});
	$buttons.on('click', '[name=resetZoom]', function (e) {
		e.preventDefault();
		controller.resetZoom();
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'resetZoom'
		});
	});
	this.toggleMenu = function () {
		if ($lineOneColumn.css('display') === 'none') {
			$lineOneColumn.css('display', '');
			_this.$rowTextField.focus();
		} else {
			$lineOneColumn.css('display', 'none');
			$(_this.controller.heatmap.canvas).focus();
		}
	};
	this.$el = $el;
	var updateFilterStatus = function () {
		if (controller.getProject().getRowFilter().isEnabled()
			|| controller.getProject().getColumnFilter().isEnabled()) {
			_this.$el.find('[name=filterButton]').addClass('btn-primary');
		} else {
			_this.$el.find('[name=filterButton]').removeClass('btn-primary');
		}

	};
	updateFilterStatus();

	this.$columnMatchesToTop
	.on(
		'click',
		function (e) {
			e.preventDefault();
			var $this = $(this);
			$this.toggleClass('btn-primary');
			_this.setSelectionOnTop({
				isColumns: true,
				isOnTop: $this.hasClass('btn-primary'),
				updateButtonStatus: false
			});
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'columnMatchesToTop'
			});
		});
	this.$rowMatchesToTop
	.on(
		'click',
		function (e) {
			e.preventDefault();
			var $this = $(this);
			$this.toggleClass('btn-primary');
			_this.setSelectionOnTop({
				isColumns: false,
				isOnTop: $this.hasClass('btn-primary'),
				updateButtonStatus: false
			});
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'rowMatchesToTop'
			});
		});
	project.on('rowSortOrderChanged.morpheus', function (e) {
		if (_this.searching) {
			return;
		}
		_this._updateSearchIndices(false);
		_this.$rowMatchesToTop.removeClass('btn-primary');
	});

	project.on('columnSortOrderChanged.morpheus', function (e) {
		if (_this.searching) {
			return;
		}
		_this._updateSearchIndices(true);
		_this.$columnMatchesToTop.removeClass('btn-primary');
	});

	controller.getProject().on('rowFilterChanged.morpheus', function (e) {
		_this.search(true);
		updateFilterStatus();
	});
	controller.getProject().on('columnFilterChanged.morpheus', function (e) {
		_this.search(false);
		updateFilterStatus();
	});
	controller.getProject().on('datasetChanged.morpheus', function () {
		_this.search(true);
		_this.search(false);
		updateFilterStatus();
	});
	controller.getProject().getRowSelectionModel().on(
		'selectionChanged.morpheus', function () {
			_this.updateSelectionLabel();
		});
	controller.getProject().getColumnSelectionModel().on(
		'selectionChanged.morpheus', function () {
			_this.updateSelectionLabel();
		});
	this.rowSearchResultViewIndicesSorted = null;
	this.currentRowSearchIndex = 0;
	this.columnSearchResultViewIndicesSorted = null;
	this.currentColumnSearchIndex = -1;
	this.$previousColumnMatch
	.on(
		'click',
		function () {
			_this.currentColumnSearchIndex--;
			if (_this.currentColumnSearchIndex < 0) {
				_this.currentColumnSearchIndex = _this.columnSearchResultViewIndicesSorted.length - 1;
			}
			controller
			.scrollLeft(controller
			.getHeatMapElementComponent()
			.getColumnPositions()
			.getPosition(
				_this.columnSearchResultViewIndicesSorted[_this.currentColumnSearchIndex]));
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'previousColumnMatch'
			});
		});
	this.$previousRowMatch
	.on(
		'click',
		function () {
			_this.currentRowSearchIndex--;
			if (_this.currentRowSearchIndex < 0) {
				_this.currentRowSearchIndex = _this.rowSearchResultViewIndicesSorted.length - 1;
			}
			controller
			.scrollTop(controller
			.getHeatMapElementComponent()
			.getRowPositions()
			.getPosition(
				_this.rowSearchResultViewIndicesSorted[_this.currentRowSearchIndex]));
			morpheus.Util.trackEvent({
				eventCategory: 'ToolBar',
				eventAction: 'previousRowMatch'
			});
		});
	this.$nextColumnMatch.on('click', function () {
		_this.next(true);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'nextColumnMatch'
		});

	});
	this.$nextRowMatch.on('click', function () {
		_this.next(false);
		morpheus.Util.trackEvent({
			eventCategory: 'ToolBar',
			eventAction: 'nextRowMatch'
		});
	});
	this.updateDimensionsLabel();
	this.updateSelectionLabel();
};
morpheus.HeatMapToolBar.HIGHLIGHT_SEARCH_MODE = 0;
morpheus.HeatMapToolBar.FILTER_SEARCH_MODE = 1;
morpheus.HeatMapToolBar.MATCHES_TO_TOP_SEARCH_MODE = 2;
morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE = 3;
morpheus.HeatMapToolBar.prototype = {
	quickColumnFilter: false,
	searching: false,
	rowSearchMode: morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,
	columnSearchMode: morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,
	_updateSearchIndices: function (isColumns) {
		var project = this.controller.getProject();
		if (isColumns) {
			var viewIndices = [];
			var modelIndices = this.columnSearchResultModelIndices;
			for (var i = 0, length = modelIndices.length; i < length; i++) {
				var index = project
				.convertModelColumnIndexToView(modelIndices[i]);
				if (index !== -1) {
					viewIndices.push(index);
				}
			}
			viewIndices.sort(function (a, b) {
				return a < b ? -1 : 1;
			});
			this.columnSearchResultViewIndicesSorted = viewIndices;
			this.currentColumnSearchIndex = -1;
		} else {
			var viewIndices = [];
			var modelIndices = this.rowSearchResultModelIndices;
			for (var i = 0, length = modelIndices.length; i < length; i++) {
				var index = project.convertModelRowIndexToView(modelIndices[i]);
				if (index !== -1) {
					viewIndices.push(index);
				}
			}
			viewIndices.sort(function (a, b) {
				return a < b ? -1 : 1;
			});
			this.rowSearchResultViewIndicesSorted = viewIndices;
			this.currentRowSearchIndex = -1;
		}
	},
	next: function (isColumns) {
		var controller = this.controller;
		if (isColumns) {
			this.currentColumnSearchIndex++;
			if (this.currentColumnSearchIndex >= this.columnSearchResultViewIndicesSorted.length) {
				this.currentColumnSearchIndex = 0;
			}
			controller
			.scrollLeft(controller
			.getHeatMapElementComponent()
			.getColumnPositions()
			.getPosition(
				this.columnSearchResultViewIndicesSorted[this.currentColumnSearchIndex]));
		} else {
			this.currentRowSearchIndex++;
			if (this.currentRowSearchIndex >= this.rowSearchResultViewIndicesSorted.length) {
				this.currentRowSearchIndex = 0;
			}
			controller
			.scrollTop(controller
			.getHeatMapElementComponent()
			.getRowPositions()
			.getPosition(
				this.rowSearchResultViewIndicesSorted[this.currentRowSearchIndex]));
		}
	},
	setSearchText: function (options) {
		var $tf = options.isColumns ? this.$columnTextField
			: this.$rowTextField;
		var existing = options.append ? $.trim($tf.val()) : '';
		if (existing !== '') {
			existing += ' ';
		}
		if (options.onTop) {
			options.isColumns ? this.$columnMatchesToTop
			.addClass('btn-primary') : this.$rowMatchesToTop
			.addClass('btn-primary');

		}
		$tf.val(existing + options.text);
		this.search(!options.isColumns);
		if (options.scrollTo) {
			this.next(options.isColumns);
			// click next
		}
	},
	updateDimensionsLabel: function () {
		var p = this.controller.getProject();
		var d = p.getFullDataset();
		var f = p.getSortedFilteredDataset();
		var text = 'showing ' + morpheus.Util.intFormat(f.getRowCount())
			+ '/' + morpheus.Util.intFormat(d.getRowCount()) + ' rows, '
			+ morpheus.Util.intFormat(f.getColumnCount()) + '/'
			+ morpheus.Util.intFormat(d.getColumnCount()) + ' columns';
		this.$dimensionsLabel.html(text);
	},
	updateSelectionLabel: function () {
		var nc = this.controller.getProject().getColumnSelectionModel().count();
		var nr = this.controller.getProject().getRowSelectionModel().count();
		var text = [];
		text.push(morpheus.Util.intFormat(nr) + ' row');
		if (nr !== 1) {
			text.push('s');
		}
		text.push(', ');
		text.push(morpheus.Util.intFormat(nc) + ' column');
		if (nc !== 1) {
			text.push('s');
		}
		text.push(' selected');
		this.$selectionLabel.html(text.join(''));
	},
	searchDendrogram: function (isColumns) {
		var text = $.trim(isColumns ? this.$searchColumnDendrogram.val()
			: this.$searchRowDendrogram.val());
		var dendrogram = isColumns ? this.controller.columnDendrogram
			: this.controller.rowDendrogram;
		var $searchResults = isColumns ? this.$searchResultsColumnDendrogram
			: this.$searchResultsRowDendrogram;
		var matches = morpheus.AbstractDendrogram.search(
			dendrogram.tree.rootNode, text);
		if (matches === -1) {
			$searchResults.html('');
		} else {
			$searchResults.html(matches + ' match'
				+ (matches === 1 ? '' : 'es'));
		}
		if (matches <= 0) {
			var positions = isColumns ? this.controller
			.getHeatMapElementComponent().getColumnPositions()
				: this.controller.getHeatMapElementComponent()
			.getRowPositions();
			positions.setSquishedIndices(null);
			if (isColumns) {
				this.controller.getProject().setGroupColumns([], true);
			} else {
				this.controller.getProject().setGroupRows([], true);
			}
			positions.setSize(isColumns ? this.controller.getFitColumnSize()
				: this.controller.getFitRowSize());
		} else {
			morpheus.AbstractDendrogram.squishNonSearchedNodes(this.controller,
				isColumns);
		}
		this.controller.updateDataset(); // need to update spaces for group
		// by
		this.controller.revalidate();
	},
	search: function (isRows) {
		this.searching = true;
		var isMatchesOnTop = isRows ? this.$rowMatchesToTop
		.hasClass('btn-primary') : this.$columnMatchesToTop
		.hasClass('btn-primary');
		var controller = this.controller;
		var project = controller.getProject();

		var sortKeys = isRows ? project.getRowSortKeys() : project
		.getColumnSortKeys();
		var keyIndex = -1;
		for (var i = 0; i < sortKeys.length; i++) {
			if (sortKeys[i].toString() === 'matches on top') {
				keyIndex = i;
				break;
			}
		}
		if (keyIndex !== -1) {
			sortKeys.splice(keyIndex, 1);
		}

		var dataset = project.getSortedFilteredDataset();
		var $searchResultsLabel = this.$el.find('[data-name=searchResults'
			+ (isRows ? 'Rows' : 'Columns') + ']');
		var searchText = !isRows ? $.trim(this.$columnTextField.val()) : $
		.trim(this.$rowTextField.val());

		var metadata = isRows ? dataset.getRowMetadata() : dataset
		.getColumnMetadata();
		var visibleIndices = [];
		controller.getVisibleTrackNames(!isRows).forEach(function (name) {
			visibleIndices.push(morpheus.MetadataUtil.indexOf(metadata, name));
		});
		metadata = new morpheus.MetadataModelColumnView(metadata,
			visibleIndices);

		var searchResultViewIndices = morpheus.MetadataUtil.search({
			model: metadata,
			text: searchText,
			isColumns: !isRows,
			defaultMatchMode: isRows ? this.defaultRowMatchMode
				: this.defaultColumnMatchMode
		});
		if (searchText === '') {
			$searchResultsLabel.html('');
			if (isRows) {
				this.$rowSearchDiv.hide();
			} else {
				this.$columnSearchDiv.hide();
			}

		} else {
			$searchResultsLabel.html(searchResultViewIndices.length + ' match'
				+ (searchResultViewIndices.length === 1 ? '' : 'es'));
			if (isRows) {
				this.$rowSearchDiv.show();
			} else {
				this.$columnSearchDiv.show();
			}

		}

		var searchResultsModelIndices = [];
		if (searchResultViewIndices != null) {
			for (var i = 0, length = searchResultViewIndices.length; i < length; i++) {
				var viewIndex = searchResultViewIndices[i];
				searchResultsModelIndices.push(isRows ? project
				.convertViewRowIndexToModel(viewIndex) : project
				.convertViewColumnIndexToModel(viewIndex));
			}
		}

		if (searchResultViewIndices !== null && isMatchesOnTop) {
			var key = new morpheus.MatchesOnTopSortKey(project,
				searchResultsModelIndices, 'matches on top');
			sortKeys = sortKeys.filter(function (key) {
				return !(key instanceof morpheus.MatchesOnTopSortKey);
			});
			searchResultViewIndices = key.indices; // matching indices
			// are now on top
			// add to beginning of sort keys
			sortKeys.splice(0, 0, key);
			if (isRows) {
				project.setRowSortKeys(sortKeys, false);
			} else {
				project.setColumnSortKeys(sortKeys, false);
			}
		}
		var searchResultsViewIndicesSet = new morpheus.Set();
		if (searchResultViewIndices != null) {
			for (var i = 0, length = searchResultViewIndices.length; i < length; i++) {
				var viewIndex = searchResultViewIndices[i];
				searchResultsViewIndicesSet.add(viewIndex);
			}
		}
		if (searchResultViewIndices == null) {
			searchResultViewIndices = [];
		}

		if (isRows) {
			this.rowSearchResultModelIndices = searchResultsModelIndices;
			this.rowSearchResultViewIndicesSorted = searchResultViewIndices
			.sort(function (a, b) {
				return a < b ? -1 : 1;
			});
			this.currentRowSearchIndex = -1;

		} else {
			this.columnSearchResultModelIndices = searchResultsModelIndices;
			this.columnSearchResultViewIndicesSorted = searchResultViewIndices
			.sort(function (a, b) {
				return a < b ? -1 : 1;
			});
			this.currentColumnSearchIndex = -1;

		}
		// update selection
		(!isRows ? project.getColumnSelectionModel() : project
		.getRowSelectionModel()).setViewIndices(
			searchResultsViewIndicesSet, true);

		if (isMatchesOnTop) { // resort
			if (isRows) {
				project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(
					sortKeys, project.getRowSortKeys()), true);
			} else {
				project.setColumnSortKeys(morpheus.SortKey
				.keepExistingSortKeys(sortKeys, project
				.getColumnSortKeys()), true);
			}
		}
		this.updateDimensionsLabel();
		this.updateSelectionLabel();
		this.searching = false;

	},
	isSelectionOnTop: function (isColumns) {
		var $btn = isColumns ? this.$columnMatchesToTop : this.$rowMatchesToTop;
		return $btn.hasClass('btn-primary');
	},
	setSelectionOnTop: function (options) {
		if (options.updateButtonStatus) {
			var $btn = options.isColumns ? this.$columnMatchesToTop : this.$rowMatchesToTop;
			if (options.isOnTop) {
				$btn.addClass('btn-primary');
			} else {
				$btn.removeClass('btn-primary');
			}
		}
		var project = this.controller.getProject();
		var sortKeys = options.isColumns ? project.getColumnSortKeys() : project.getRowSortKeys();
		// clear existing sort keys except dendrogram
		sortKeys = sortKeys
		.filter(function (key) {
			return (key instanceof morpheus.SpecifiedModelSortOrder && key.name === 'dendrogram');
		});
		if (options.isOnTop) { // bring to top
			var key = new morpheus.MatchesOnTopSortKey(project,
				options.isColumns ? this.columnSearchResultModelIndices : this.rowSearchResultModelIndices,
				'matches on top');
			sortKeys.splice(0, 0, key);
			if (options.isColumns) {
				this.controller.scrollLeft(0);
			} else {
				this.controller.scrollTop(0);
			}
		}
		this.searching = true;
		if (options.isColumns) {
			project.setColumnSortKeys(sortKeys, true);
		} else {
			project.setRowSortKeys(sortKeys, true);
		}
		this._updateSearchIndices(options.isColumns);
		this.searching = false;

	}
};