/client/galaxy/scripts/viz/trackster/tracks.js

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define( ["libs/underscore", "viz/visualization", "viz/viz_views", "viz/trackster/util", 
         "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters",
         "mvc/data", "mvc/tools", "utils/config" ], 
         function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod) {

var extend = _.extend;

// ---- Web UI specific utilities ----

/**
 * Dictionary of HTML element-JavaScript object relationships.
 */
// TODO: probably should separate moveable objects from containers.
var html_elt_js_obj_dict = {};

/**
 * Designates an HTML as a container.
 */
var is_container = function(element, obj) {
    html_elt_js_obj_dict[element.attr("id")] = obj;
};

/** 
 * Make `element` moveable within parent and sibling elements by dragging `handle` (a selector).
 * Function manages JS objects, containers as well.
 *
 * @param element HTML element to make moveable
 * @param handle_class classname that denotes HTML element to be used as handle
 * @param container_selector selector used to identify possible containers for this element
 * @param element_js_obj JavaScript object associated with element; used 
 */
var moveable = function(element, handle_class, container_selector, element_js_obj) {
    // HACK: set default value for container selector.
    container_selector = ".group";
    
    // Register element with its object.
    html_elt_js_obj_dict[element.attr("id")] = element_js_obj;
    
    // Need to provide selector for handle, not class.
    element.bind( "drag", { handle: "." + handle_class, relative: true }, function ( e, d ) {
        var element = $(this),
            parent = $(this).parent(),
            // Only sorting amongst tracks and groups.
            children = parent.children('.track,.group'),
            this_obj = html_elt_js_obj_dict[$(this).attr("id")],
            child,
            container,
            top,
            bottom,
            i;
            
        //
        // Enable three types of dragging: (a) out of container; (b) into container; 
        // (c) sibling movement, aka sorting. Handle in this order for simplicity.
        //
        
        // Handle dragging out of container.
        container = $(this).parents(container_selector);
        if (container.length !== 0) {
            top = container.position().top;
            bottom = top + container.outerHeight();
            var cur_container = html_elt_js_obj_dict[container.attr("id")];
            if (d.offsetY < top) {
                // Moving above container.
                $(this).insertBefore(container);
                cur_container.remove_drawable(this_obj);
                cur_container.container.add_drawable_before(this_obj, cur_container);
                return;
            }
            else if (d.offsetY > bottom) {
                // Moving below container.
                $(this).insertAfter(container);
                cur_container.remove_drawable(this_obj);
                cur_container.container.add_drawable(this_obj);
                return;
            }            
        }
        
        // Handle dragging into container. Child is appended to container's content_div.
        container = null;
        for ( i = 0; i < children.length; i++ ) {
            child = $(children.get(i));
            top = child.position().top;
            bottom = top + child.outerHeight();
            // Dragging into container if child is a container and offset is inside container.
            if ( child.is(container_selector) && this !== child.get(0) && 
                 d.offsetY >= top && d.offsetY <= bottom ) {
                // Append/prepend based on where offsetY is closest to and return.
                if (d.offsetY - top < bottom - d.offsetY) {
                    child.find(".content-div").prepend(this);
                }
                else {
                    child.find(".content-div").append(this);
                }
                // Update containers. Object may not have container if it is being moved quickly.
                if (this_obj.container) {
                    this_obj.container.remove_drawable(this_obj);                    
                }
                html_elt_js_obj_dict[child.attr("id")].add_drawable(this_obj);
                return;
            }
        }

        // Handle sibling movement, aka sorting.
        
        // Determine new position
        for ( i = 0; i < children.length; i++ ) {
            child = $(children.get(i));
            if ( d.offsetY < child.position().top &&
                 // Cannot move tracks above reference track or intro div.
                 !(child.hasClass("reference-track") || child.hasClass("intro")) ) {
                break;
            }
        }
                
        // If not already in the right place, move. Need 
        // to handle the end specially since we don't have 
        // insert at index
        if ( i === children.length ) {
            if ( this !== children.get(i - 1) ) {
                parent.append(this);
                html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, i);
            }
        }
        else if ( this !== children.get(i) ) {
            $(this).insertBefore( children.get(i) );
            // Need to adjust insert position if moving down because move is changing 
            // indices of all list items.
            html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, (d.deltaY > 0 ? i-1 : i) );
        }
    }).bind("dragstart", function() {
        $(this).addClass('dragging');
    }).bind("dragend", function() {
        $(this).removeClass('dragging');
    });
};

/**
 * Init constants & functions used throughout trackster.
 */
var 
    // Padding at the top of tracks for error messages
    ERROR_PADDING = 20,
    // Maximum number of rows un a slotted track
    MAX_FEATURE_DEPTH = 100,
    // Minimum width for window for squish to be used.
    MIN_SQUISH_VIEW_WIDTH = 12000,
    // Number of pixels per tile, not including left offset.
    TILE_SIZE = 400,
    DEFAULT_DATA_QUERY_WAIT = 5000,
    // Maximum number of chromosomes that are selectable at any one time.
    MAX_CHROMS_SELECTABLE = 100,
    DATA_ERROR = "Cannot display dataset due to an error. ",
    DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",
    DATA_NONE = "No data for this chrom/contig.",
    DATA_PENDING = "Preparing data. This can take a while for a large dataset. " + 
                   "If the visualization is saved and closed, preparation will continue in the background.",
    DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ",
    DATA_LOADING = "Loading data...",
    DATA_OK = "Ready for display",
    TILE_CACHE_SIZE = 10,
    DATA_CACHE_SIZE = 20,

    // Numerical/continuous data display modes.
    CONTINUOUS_DATA_MODES = ["Histogram", "Line", "Filled", "Intensity"];
    
/**
 * Round a number to a given number of decimal places.
 */
function round(num, places) {
    // Default rounding is to integer.
    if (!places) {
        places = 0;
    }
    
    var val = Math.pow(10, places);
    return Math.round(num * val) / val;
}

/**
 * Drawables hierarchy:
 *
 * Drawable
 *    --> DrawableCollection
 *        --> DrawableGroup
 *        --> View
 *    --> Track
 */

/**
 * Base class for all drawable objects. Drawable objects are associated with a view and live in a 
 * container. They have the following HTML elements and structure:
 *  <container_div>
 *      <header_div>
 *      <content_div>
 *
 * They optionally have a drag handle class. 
 */
var Drawable = function(view, container, obj_dict) {
    if (!Drawable.id_counter) { Drawable.id_counter = 0; }
    this.id = Drawable.id_counter++;
    this.view = view;
    this.container = container;
    this.drag_handle_class = obj_dict.drag_handle_class;
    this.is_overview = false;
    this.action_icons = {};
    
    // -- Set up drawable configuration. --

    this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(this.config_params, obj_dict.prefs);
    
    // If there's no saved name, use object name.
    if (!this.config.get_value('name')) {
        this.config.set_value('name', obj_dict.name);
    }
    if (this.config_onchange) {
        this.config.on('change', this.config_onchange, this);
    }
    
    // Build Drawable HTML and behaviors.
    this.container_div = this.build_container_div();
    this.header_div = null;

    // Use opt-out policy on header creation because this is the more frequent approach: 
    // unless flag set, create header.
    if (obj_dict.header !== false) {
        var header_view = new viz_views.TrackHeaderView({
            model: this,
            id: this.id
        });
            
        this.header_div = header_view.$el;
        this.container_div.append(this.header_div);

        // Show icons when users is hovering over track.
        var icons_div = header_view.icons_div;
        this.action_icons = header_view.action_icons;
        this.container_div.hover(
            function() { icons_div.show(); }, function() { icons_div.hide(); }
        );
    }
};

Drawable.prototype.action_icons_def = [
    // Hide/show drawable content.
    // FIXME: make this an odict for easier lookup.
    {
        name: "toggle_icon",
        title: "Hide/show content",
        css_class: "toggle",
        on_click_fn: function(drawable) {
            if ( drawable.config.get_value('content_visible') ) {
                drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
                drawable.hide_contents();
                drawable.config.set_value('content_visible', false);
            }
            else {
                drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");
                drawable.config.set_value('content_visible', true);
                drawable.show_contents();
            }
        }
    },
    // Edit settings.
    {
        name: "settings_icon",
        title: "Edit settings",
        css_class: "gear",
        on_click_fn: function(drawable) {
            var view = new config_mod.ConfigSettingCollectionView({
                collection: drawable.config
            });
            view.render_in_modal('Configure Track');
        }
    },
    // Remove.
    {
        name: "remove_icon",
        title: "Remove",
        css_class: "remove-icon",
        on_click_fn: function(drawable) {
            // Tooltip for remove icon must be deleted when drawable is deleted.
            $(".tooltip").remove();
            drawable.remove();
        }
    }
];

extend(Drawable.prototype, {
    config_params: [
        { key: 'name', label: 'Name', type: 'text', default_value: '' },
        { key: 'content_visible', type: 'bool', default_value: true, hidden: true }
    ],

    config_onchange: function() {},
    
    init: function() {},

    changed: function() {
        this.view.changed();
    },

    can_draw: function() {
        if (this.enabled && this.config.get_value('content_visible')) {
            return true;
        }
        
        return false;
    },

    request_draw: function() {},

    _draw: function(options) {},

    /** 
     * Returns representation of object in a dictionary for easy saving. 
     * Use from_dict to recreate object.
     */
    to_dict: function() {},

    /**
     * Set drawable name.
     */
    set_name: function(new_name) {
        this.old_name = this.config.get_value('name');
        this.config.set_value('name', new_name);
    },

    /**
     * Revert track name; currently name can be reverted only once.
     */
    revert_name: function() {
        if (this.old_name) {
            this.config.set_value('name', this.old_name);
        }
    },

    /**
     * Remove drawable (a) from its container and (b) from the HTML.
     */
    remove: function() {
        this.changed();
        
        this.container.remove_drawable(this);
        var view = this.view;
        this.container_div.hide(0, function() {
            $(this).remove();
            // HACK: is there a better way to update the view?
            view.update_intro_div();
        });
    },

    /**
     * Build drawable's container div; this is the parent div for all drawable's elements.
     */
    build_container_div: function() {},
    
    /**
     * Update icons.
     */
    update_icons: function() {},
    
    /**
     * Hide drawable's contents.
     */
    hide_contents: function () {},
    
    /**
     * Show drawable's contents.
     */
    show_contents: function() {},

    /**
     * Returns a shallow copy of all drawables in this drawable.
     */
    get_drawables: function() {}
});

/**
 * A collection of drawable objects.
 */
var DrawableCollection = function(view, container, obj_dict) {
    Drawable.call(this, view, container, obj_dict);
    
    // Attribute init.
    this.obj_type = obj_dict.obj_type;
    this.drawables = [];
};

extend(DrawableCollection.prototype, Drawable.prototype, {
    /**
     * Unpack and add drawables to the collection.
     */
    unpack_drawables: function(drawables_array) {
        // Add drawables to collection.
        this.drawables = [];
        var drawable;
        for (var i = 0; i < drawables_array.length; i++) {
            drawable = object_from_template(drawables_array[i], this.view, this);
            this.add_drawable(drawable);
        }
    },
    
    /**
     * Init each drawable in the collection.
     */
    init: function() {
        for (var i = 0; i < this.drawables.length; i++) {
            this.drawables[i].init();
        }
    },    
    
    /**
     * Draw each drawable in the collection.
     */
    _draw: function(options) {
        for (var i = 0; i < this.drawables.length; i++) {
            this.drawables[i]._draw(options);
        }
    },
    
    /** 
     * Returns representation of object in a dictionary for easy saving. 
     * Use from_dict to recreate object.
     */
    to_dict: function() {
        var dictified_drawables = [];
        for (var i = 0; i < this.drawables.length; i++) {
            dictified_drawables.push(this.drawables[i].to_dict());
        }
        return {
            prefs: this.config.to_key_value_dict(),
            obj_type: this.obj_type,
            drawables: dictified_drawables
        };
    },
    
    /**
     * Add a drawable to the end of the collection.
     */
    add_drawable: function(drawable) {
        this.drawables.push(drawable);
        drawable.container = this;
        this.changed();
    },
    
    /**
     * Add a drawable before another drawable.
     */
    add_drawable_before: function(drawable, other) {
        this.changed();
        var index = this.drawables.indexOf(other);
        if (index !== -1) {
            this.drawables.splice(index, 0, drawable);
            return true;
        }
        return false;
    },
    
    /**
     * Replace one drawable with another.
     */
    replace_drawable: function(old_drawable, new_drawable, update_html) {
        var index = this.drawables.indexOf(old_drawable);
        if (index !== -1) {
            this.drawables[index] = new_drawable;
            if (update_html) {
                old_drawable.container_div.replaceWith(new_drawable.container_div);
            }
            this.changed();
        }
        return index;
    },
    
    /**
     * Remove drawable from this collection.
     */
    remove_drawable: function(drawable) {
        var index = this.drawables.indexOf(drawable);
        if (index !== -1) {
            // Found drawable to remove.
            this.drawables.splice(index, 1);
            drawable.container = null;
            this.changed();
            return true;        
        }
        return false;
    },
    
    /**
     * Move drawable to another location in collection.
     */
    move_drawable: function(drawable, new_position) {
        var index = this.drawables.indexOf(drawable);
        if (index !== -1) {
            // Remove from current position:
            this.drawables.splice(index, 1);
            // insert into new position:
            this.drawables.splice(new_position, 0, drawable);
            this.changed();
            return true;
        }
        return false;
    },

    /**
     * Returns all drawables in this drawable.
     */
    get_drawables: function() {
        return this.drawables;
    },

    /**
     * Returns all <track_type> tracks in collection.
     */
    get_tracks: function(track_type) {
        // Initialize queue with copy of drawables array.
        var queue = this.drawables.slice(0),
            tracks = [],
            drawable;
        while (queue.length !== 0) {
            drawable = queue.shift();
            if (drawable instanceof track_type) {
                tracks.push(drawable);
            }
            else if (drawable.drawables) {
                queue = queue.concat(drawable.drawables);
            }
        }
        return tracks;
    }
});

/**
 * A group of drawables that are moveable, visible.
 */
var DrawableGroup = function(view, container, obj_dict) {
    extend(obj_dict, {
        obj_type: "DrawableGroup",
        drag_handle_class: "group-handle" 
    });
    DrawableCollection.call(this, view, container, obj_dict);
        
    // Set up containers/moving for group: register both container_div and content div as container
    // because both are used as containers (container div to recognize container, content_div to 
    // store elements). Group can be moved.
    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div);
    is_container(this.container_div, this);
    is_container(this.content_div, this);
    moveable(this.container_div, this.drag_handle_class, ".group", this);
    
    // Set up filters.
    this.filters_manager = new filters_mod.FiltersManager(this);
    this.header_div.after(this.filters_manager.parent_div);

    // HACK: add div to clear floating elements.
    this.filters_manager.parent_div.after( $("<div style='clear: both'/>") );

    // For saving drawables' filter managers when group-level filtering is done:
    this.saved_filters_managers = [];
    
    // Add drawables.
    if ('drawables' in obj_dict) {
        this.unpack_drawables(obj_dict.drawables);
    }
    
    // Restore filters.
    if ('filters' in obj_dict) {
        // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier.
        var old_manager = this.filters_manager;
        this.filters_manager = new filters_mod.FiltersManager(this, obj_dict.filters);
        old_manager.parent_div.replaceWith(this.filters_manager.parent_div);
    
        if (obj_dict.filters.visible) {
            this.setup_multitrack_filtering();
        }
    }
};

extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
    action_icons_def: [
        Drawable.prototype.action_icons_def[0],
        Drawable.prototype.action_icons_def[1],
        // Replace group with composite track.
        {
            name: "composite_icon",
            title: "Show composite track",
            css_class: "layers-stack",
            on_click_fn: function(group) {
                $(".tooltip").remove();
                group.show_composite_track();
            }
        },
        // Toggle track filters.
        {
            name: "filters_icon",
            title: "Filters",
            css_class: "ui-slider-050",
            on_click_fn: function(group) {
                // TODO: update Tooltip text.
                if (group.filters_manager.visible()) {
                    // Hiding filters.
                    group.filters_manager.clear_filters();
                    group._restore_filter_managers();
                    // TODO: maintain current filter by restoring and setting saved manager's 
                    // settings to current/shared manager's settings.
                    // TODO: need to restore filter managers when moving drawable outside group.             
                }
                else {
                    // Showing filters.
                    group.setup_multitrack_filtering();
                    group.request_draw({ clear_tile_cache: true });
                }
                group.filters_manager.toggle();
            }
        },
        Drawable.prototype.action_icons_def[2]
    ],

    build_container_div: function() {
        var container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id);
        if (this.container) {
            this.container.content_div.append(container_div);
        }
        return container_div;
    },

    hide_contents: function () {
        this.tiles_div.hide();
    },

    show_contents: function() {
        // Show the contents div and labels (if present)
        this.tiles_div.show();
        // Request a redraw of the content
        this.request_draw();
    },

    update_icons: function() {
        //
        // Handle update when there are no tracks.
        //
        var num_drawables = this.drawables.length;
        if (num_drawables === 0) {
            this.action_icons.composite_icon.hide();
            this.action_icons.filters_icon.hide();
        }
        else if (num_drawables === 1) {
            this.action_icons.composite_icon.toggle(this.drawables[0] instanceof CompositeTrack);
            this.action_icons.filters_icon.hide();
        }
        else { // There are 2 or more tracks.

            //
            // Determine if a composite track can be created. Current criteria:
            // (a) all tracks are line tracks;
            //      OR
            // FIXME: this is not enabled right now because it has not been well tested:
            // (b) there is a single FeatureTrack.
            //

            // All tracks the same?
            var i, j, drawable,
                same_type = true,
                a_type = this.drawables[0].get_type(),
                num_feature_tracks = 0;
            for (i = 0; i < num_drawables; i++) {
                drawable = this.drawables[i];
                if (drawable.get_type() !== a_type) {
                    can_composite = false;
                    break;
                }
                if (drawable instanceof FeatureTrack) {
                    num_feature_tracks++;
                }
            }
        
            if (same_type && this.drawables[0] instanceof LineTrack) {
                this.action_icons.composite_icon.show();
            }
            else {
                this.action_icons.composite_icon.hide();
                $(".tooltip").remove();
            }

            //
            // Set up group-level filtering and update filter icon.
            //
            if (num_feature_tracks > 1 && num_feature_tracks === this.drawables.length) {
                //
                // Find shared filters.
                //
                var shared_filters = {},
                    filter;
            
                // Init shared filters with filters from first drawable.
                drawable = this.drawables[0];
                for (j = 0; j < drawable.filters_manager.filters.length; j++) {
                    filter = drawable.filters_manager.filters[j];
                    shared_filters[filter.name] = [filter];
                }
            
                // Create lists of shared filters.
                for (i = 1; i < this.drawables.length; i++) {
                    drawable = this.drawables[i];
                    for (j = 0; j < drawable.filters_manager.filters.length; j++) {
                        filter = drawable.filters_manager.filters[j];
                        if (filter.name in shared_filters) {
                            shared_filters[filter.name].push(filter);
                        }
                    }
                }
            
                //
                // Create filters for shared filters manager. Shared filters manager is group's
                // manager.
                //
                this.filters_manager.remove_all();
                var 
                    filters,
                    new_filter,
                    min,
                    max;
                for (var filter_name in shared_filters) {
                    filters = shared_filters[filter_name];
                    if (filters.length === num_feature_tracks) {
                        // Add new filter.
                        // FIXME: can filter.copy() be used?
                        new_filter = new filters_mod.NumberFilter( {
                                        name: filters[0].name, 
                                        index: filters[0].index
                                        } );
                        this.filters_manager.add_filter(new_filter);
                    }
                }
            
                // Show/hide icon based on filter availability.
                this.action_icons.filters_icon.toggle(this.filters_manager.filters.length > 0);
            }
            else {
                this.action_icons.filters_icon.hide();
            }
        }
    },

    /**
     * Restore individual track filter managers.
     */
    _restore_filter_managers: function() {
        for (var i = 0; i < this.drawables.length; i++) {
            this.drawables[i].filters_manager = this.saved_filters_managers[i];
        }
        this.saved_filters_managers = [];
    },

    /**
     *
     */
    setup_multitrack_filtering: function() {
        // Save tracks' managers and set up shared manager.
        if (this.filters_manager.filters.length > 0) {
            // For all tracks, save current filter manager and set manager to shared (this object's) manager.
            this.saved_filters_managers = [];
            for (var i = 0; i < this.drawables.length; i++) {
                drawable = this.drawables[i];
                this.saved_filters_managers.push(drawable.filters_manager);
                drawable.filters_manager = this.filters_manager;
            }

            //TODO: hide filters icons for each drawable?
        }
        this.filters_manager.init_filters();
    },

    /**
     * Replace group with a single composite track that includes all group's tracks.
     */
    show_composite_track: function() {
        var composite_track = new CompositeTrack(this.view, this.view, {
            name: this.config.get_value('name'),
            drawables: this.drawables
        });
        var index = this.container.replace_drawable(this, composite_track, true);
        composite_track.request_draw();
    },
    
    add_drawable: function(drawable) {
        DrawableCollection.prototype.add_drawable.call(this, drawable);
        this.update_icons();
    },
    
    remove_drawable: function(drawable) {
        DrawableCollection.prototype.remove_drawable.call(this, drawable);
        this.update_icons();
    },
    
    to_dict: function() {
        // If filters are visible, need to restore original filter managers before converting to dict.        
        if (this.filters_manager.visible()) {
            this._restore_filter_managers();
        }

        var obj_dict = extend(DrawableCollection.prototype.to_dict.call(this), { "filters": this.filters_manager.to_dict() });
        
        // Setup multi-track filtering again.
        if (this.filters_manager.visible()) {
            this.setup_multitrack_filtering();
        }
        
        return obj_dict;
    },

    request_draw: function(options) {
        _.each(this.drawables, function(d) {
            d.request_draw(options);
        });
    }
});

/**
 * View object manages a trackster visualization, including tracks and user interactions.
 * Events triggered:
 *      navigate: when browser view changes to a new locations
 */
var TracksterView = Backbone.View.extend({

    initialize: function(obj_dict) {
        extend(obj_dict, {
            obj_type: "View"
        });
        DrawableCollection.call(this, "View", obj_dict.container, obj_dict);
        this.chrom = null;
        this.vis_id = obj_dict.vis_id;
        this.dbkey = obj_dict.dbkey;
        this.stand_alone = (obj_dict.stand_alone !== undefined ? obj_dict.stand_alone : true);
        this.label_tracks = [];
        this.tracks_to_be_redrawn = [];
        this.max_low = 0;
        this.max_high = 0;
        this.zoom_factor = 3;
        this.min_separation = 30;
        this.has_changes = false;
        // Deferred object that indicates when view's chrom data has been loaded.
        this.load_chroms_deferred = null;
        this.render();
        this.canvas_manager = new visualization.CanvasManager( this.container.get(0).ownerDocument );
        this.reset();

        // Define track configuration
        this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values( [
                { key: 'name', label: 'Name', type: 'text', default_value: '' },
                { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" },
                { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" },
                { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" },
                { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" },
                { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" }
            ], { name: obj_dict.name });
    },

    render: function() {
        // Attribute init.
        this.requested_redraw = false;
        
        // Create DOM elements
        var parent_element = this.container,
            view = this;
        // Top container for things that are fixed at the top
        this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element);
        // Browser content, primary tracks are contained in here
        this.browser_content_div = $("<div/>").addClass("content").appendTo(parent_element);
        // Bottom container for things that are fixed at the bottom
        this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element);
        // Label track fixed at top 
        this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container);        
        // Viewport for dragging tracks in center    
        this.viewport_container = $("<div/>").addClass("viewport-container").attr("id", "viewport-container").appendTo(this.browser_content_div);
        // Alias viewport_container as content_div so that it matches function of DrawableCollection/Group content_div.
        this.content_div = this.viewport_container;
        is_container(this.viewport_container, view);
        // Introduction div shown when there are no tracks.
        this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container);
        var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
            visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
                _.each(tracks, function(track) {
                    view.add_drawable( object_from_template(track, view, view) );  
                });
            });
        });

        // Navigation at top
        this.nav_container = $("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);
        this.nav = $("<div/>").addClass("trackster-nav").appendTo(this.nav_container);

        if (this.stand_alone) {
            this.nav_container.addClass("stand-alone");
            this.nav.addClass("stand-alone");
        }

        // Overview (scrollbar and overview plot) at bottom
        this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container);
        this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
        this.overview_close = $("<a/>").attr("title", "Close overview")
                                       .addClass("icon-button overview-close tooltip")
                                       .hide()
                                       .appendTo(this.overview_viewport);
        this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
        this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);
        this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport);
        this.default_overview_height = this.overview_box.height();
        
        this.nav_controls = $("<div/>").addClass("nav-controls").appendTo(this.nav);
        this.chrom_select = $("<select/>").attr({ "name": "chrom"}).addClass('chrom-nav').append("<option value=''>Loading</option>").appendTo(this.nav_controls);
        var submit_nav = function(e) {
            if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27 ) {
                if ((e.keyCode || e.which) !== 27) { // Not escape key
                    view.go_to( $(this).val() );
                }
                $(this).hide();
                $(this).val('');
                view.location_span.show();
                view.chrom_select.show();
            }

            // Suppress key presses so that they do impact viz.
            e.stopPropagation();
        };
        this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls);
        this.location_span = $("<span/>").addClass("location").attr('title', 'Click to change location').tooltip( { placement: 'bottom' } ).appendTo(this.nav_controls);
        this.location_span.click(function() {
            view.location_span.hide();
            view.chrom_select.hide();
            view.nav_input.val(view.chrom + ":" + view.low + "-" + view.high);
            view.nav_input.css("display", "inline-block");
            view.nav_input.select();
            view.nav_input.focus();
            // Set up autocomplete for tracks' features.
            view.nav_input.autocomplete({
                source: function(request, response) {
                    // Using current text, query each track and create list of all matching features.
                    var all_features = [],
                        feature_search_deferreds = $.map(view.get_tracks(FeatureTrack), function(t) {
                        return t.data_manager.search_features(request.term).success(function(dataset_features) {
                            all_features = all_features.concat(dataset_features);
                        });
                    });

                    // When all searching is done, fill autocomplete.
                    $.when.apply($, feature_search_deferreds).done(function() {
                        response($.map(all_features, function(feature) {
                            return { 
                                label: feature[0],
                                value: feature[1]
                            };
                        }));
                    });
                },
                minLength: 2
            });
        });
        if (this.vis_id !== undefined) {
            this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls);
        }
        
        this.zo_link = $("<a/>").attr("id", "zoom-out").attr("title", "Zoom out").tooltip( {placement: 'bottom'} )
                                .click(function() { view.zoom_out(); }).appendTo(this.nav_controls);
        this.zi_link = $("<a/>").attr("id", "zoom-in").attr("title", "Zoom in").tooltip( {placement: 'bottom'} )
                                .click(function() { view.zoom_in(); }).appendTo(this.nav_controls);      
        
        // Get initial set of chroms.
        this.load_chroms_deferred = this.load_chroms({low: 0});
        this.chrom_select.bind("change", function() {
            view.change_chrom(view.chrom_select.val());
        });
                
        /*
        this.browser_content_div.bind("mousewheel", function( e, delta ) {
            if (Math.abs(delta) < 0.5) {
                return;
            }
            if (delta > 0) {
                view.zoom_in(e.pageX, this.viewport_container);
            } else {
                view.zoom_out();
            }
            e.preventDefault();
        });
        */
        
        // Blur tool/filter inputs when user clicks on content div.
        this.browser_content_div.click(function( e ) {
            $(this).find("input").trigger("blur"); 
        });

        // Double clicking zooms in
        this.browser_content_div.bind("dblclick", function( e ) {
            view.zoom_in(e.pageX, this.viewport_container);
        });

        // Dragging the overview box (~ horizontal scroll bar)
        this.overview_box.bind("dragstart", function( e, d ) {
            this.current_x = d.offsetX;
        }).bind("drag", function( e, d ) {
            var delta = d.offsetX - this.current_x;
            this.current_x = d.offsetX;
            var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.max_high - view.max_low) );
            view.move_delta(-delta_chrom);
        });
        
        this.overview_close.click(function() {
            view.reset_overview();
        });
        
        // Dragging in the viewport scrolls
        this.viewport_container.bind( "draginit", function( e, d ) {
            // Disable interaction if started in scrollbar (for webkit)
            if ( e.clientX > view.viewport_container.width() - 16 ) {
                return false;
            }
        }).bind( "dragstart", function( e, d ) {
            d.original_low = view.low;
            d.current_height = e.clientY;
            d.current_x = d.offsetX;
        }).bind( "drag", function( e, d ) {
            var container = $(this);
            var delta = d.offsetX - d.current_x;
            var new_scroll = container.scrollTop() - (e.clientY - d.current_height);
            container.scrollTop(new_scroll);
            d.current_height = e.clientY;
            d.current_x = d.offsetX;
            var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low));
            view.move_delta(delta_chrom);
        });
        /*
        FIXME: Do not do this for now because it's too jittery. Some kind of gravity approach is 
        needed here because moving left/right should be difficult.

        // Also capture mouse wheel for left/right scrolling
        }).bind( 'mousewheel', function( e, d, dx, dy ) {
            // Only handle x axis scrolling; y axis scrolling is
            // handled by the browser when the event bubbles up.
            if (dx) {
                var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );
                view.move_delta( delta_chrom );
            }
        });
        */
       
        // Dragging in the top label track allows selecting a region to zoom in on selected region.
        this.top_labeltrack.bind( "dragstart", function( e, d ) {
            return $("<div/>").addClass('zoom-area').css(
                "height", view.browser_content_div.height() + view.top_labeltrack.height() + 1
            ).appendTo( $(this) );
        }).bind( "drag", function( e, d ) {
            $( d.proxy ).css({ left: Math.min( e.pageX, d.startX ) - view.container.offset().left, width: Math.abs( e.pageX - d.startX ) });
            var min = Math.min(e.pageX, d.startX ) - view.container.offset().left,
                max = Math.max(e.pageX, d.startX ) - view.container.offset().left,
                span = (view.high - view.low),
                width = view.viewport_container.width();
            view.update_location( Math.round(min / width * span) + view.low, 
                                  Math.round(max / width * span) + view.low );
        }).bind( "dragend", function( e, d ) {
            var min = Math.min(e.pageX, d.startX),
                max = Math.max(e.pageX, d.startX),
                span = (view.high - view.low),
                width = view.viewport_container.width(),
                old_low = view.low;
            view.low = Math.round(min / width * span) + old_low;
            view.high = Math.round(max / width * span) + old_low;
            $(d.proxy).remove();
            view.request_redraw();
        });

        // FIXME: this is still wonky for embedded visualizations.
        /*
        // For vertical alignment, track mouse with simple line.
        var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element);

        // Show tracker only when hovering over view.
        parent_element.hover(
            function() {
                mouse_tracker_div.show();
                parent_element.mousemove(function(e) {
                    mouse_tracker_div.css({
                        // -1 makes line appear next to the mouse w/o preventing mouse actions.
                        left: e.pageX - parent_element.offset().left - 1
                    });
                });
            },
            function() {
                parent_element.off('mousemove');
                mouse_tracker_div.hide();
            }
        );
        */
        
        this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) );
        
        $(window).bind("resize", function() {
            // Stop previous timer.
            if (this.resize_timer) {
                clearTimeout(this.resize_timer);
            }
            
            // When function activated, resize window and redraw.
            this.resize_timer = setTimeout(function () {
                view.resize_window();
            }, 500 );
        });
        $(document).bind("redraw", function() { view.redraw(); });
        
        this.reset();
        $(window).trigger("resize");
    },

    get_base_color: function(base) {
        return this.config.get_value(base.toLowerCase() + '_color') || 
               this.config.get_value('n_color');
    }

});

// FIXME: need to use this approach to enable inheritance of DrawableCollection functions.
extend( TracksterView.prototype, DrawableCollection.prototype, {

    changed: function() {
        this.has_changes = true;  
    },

    /** Add or remove intro div depending on view state. */
    update_intro_div: function() {
        this.intro_div.toggle(this.drawables.length === 0);
    },

    /**
     * Triggers navigate events as needed. If there is a delay,
     * then event is triggered only after navigation has stopped.
     */
    trigger_navigate: function(new_chrom, new_low, new_high, delay) {
        // Stop previous timer.
        if (this.timer) {
            clearTimeout(this.timer);
        }
        
        if (delay) {
            // To aggregate calls, use timer and only navigate once
            // location has stabilized.
            var self = this;
            this.timer = setTimeout(function () {
                self.trigger("navigate", new_chrom + ":" + new_low + "-" + new_high);
            }, 500 );
        }
        else {
            view.trigger("navigate", new_chrom + ":" + new_low + "-" + new_high);
        }
    },

    update_location: function(low, high) {
        this.location_span.text( commatize(low) + ' - ' + commatize(high) );
        this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) );
        
        // Update location. Only update when there is a valid chrom; when loading vis, there may 
        // not be a valid chrom.
        var chrom = this.chrom_select.val();
        if (chrom !== "") {
            this.trigger_navigate(chrom, this.low, this.high, true);
        }
    },

    /**
     * Load chrom data for the view. Returns a jQuery Deferred.
     */
    // FIXME: instead of loading chrom data, should load and store genome object.
    load_chroms: function(url_parms) {
        url_parms.num = MAX_CHROMS_SELECTABLE;

        var
            view = this,
            chrom_data = $.Deferred();
        $.ajax({
            url: galaxy_config.root + "api/genomes/" + this.dbkey,
            data: url_parms,
            dataType: "json",
            success: function (result) {
                // Do nothing if could not load chroms.
                if (result.chrom_info.length === 0) {
                    return;
                }
                
                // Load chroms.
                if (result.reference) {
                    var ref_track = new ReferenceTrack(view);
                    view.add_label_track(ref_track);
                    view.reference_track = ref_track;
                }
                view.chrom_data = result.chrom_info;
                var chrom_options = '<option value="">Select Chrom/Contig</option>';
                for (var i = 0, len = view.chrom_data.length; i < len; i++) {
                    var chrom = view.chrom_data[i].chrom;
                    chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
                }
                if (result.prev_chroms) {
                    chrom_options += '<option value="previous">Previous ' + MAX_CHROMS_SELECTABLE + '</option>';
                }
                if (result.next_chroms) {
                    chrom_options += '<option value="next">Next ' + MAX_CHROMS_SELECTABLE + '</option>';
                }
                view.chrom_select.html(chrom_options);
                view.chrom_start_index = result.start_index;
                
                chrom_data.resolve(result.chrom_info);
            },
            error: function() {
                alert("Could not load chroms for this dbkey: " + view.dbkey);
            }
        });
        return chrom_data;
    },
    
    change_chrom: function(chrom, low, high) {
        var view = this;
        // If chrom data is still loading, wait for it.
        if (!view.chrom_data) {
            view.load_chroms_deferred.then(function() {
                view.change_chrom(chrom, low, high);
            });
            return;
        }
        
        // Don't do anything if chrom is "None" (hackish but some browsers already have this set), or null/blank
        if (!chrom || chrom === "None") {
            return;
        }
        
        //
        // If user is navigating to previous/next set of chroms, load new chrom set and return.
        //
        if (chrom === "previous") {
            view.load_chroms({low: this.chrom_start_index - MAX_CHROMS_SELECTABLE});
            return;
        }
        if (chrom === "next") {
            view.load_chroms({low: this.chrom_start_index + MAX_CHROMS_SELECTABLE});
            return;
        }
    
        //
        // User is loading a particular chrom. Look first in current set; if not in current set, load new
        // chrom set.
        //
        var found = $.grep(view.chrom_data, function(v, i) {
            return v.chrom === chrom;
        })[0];
        if (found === undefined) {
            // Try to load chrom and then change to chrom.
            view.load_chroms({'chrom': chrom}, function() { view.change_chrom(chrom, low, high); });
            return;
        }
        else {
            // Switching to local chrom.
            if (chrom !== view.chrom) {
                view.chrom = chrom;
                view.chrom_select.val(view.chrom);
                view.max_high = found.len-1; // -1 because we're using 0-based indexing.
                view.reset();
                
                for (var i = 0, len = view.drawables.length; i < len; i++) {
                    var drawable = view.drawables[i];
                    if (drawable.init) {
                        drawable.init();
                    }
                }
                if (view.reference_track) {
                    view.reference_track.init();
                }
            }

            // Resolve low, high.
            if (low === undefined && high === undefined) {
                // Both are undefined, so view is whole chromosome.
                view.low = 0;
                view.high = view.max_high;
            }
            else {
                // Low and/or high is defined.
                view.low = (low !== undefined ? Math.max(low, 0) : 0);
                if (high === undefined) {
                    // Center visualization around low.
                    // HACK: max resolution is currently 30 bases.
                    view.low = Math.max(view.low - 15, 0);
                    view.high = view.low + 30;
                }
                else {
                    // High is defined.
                    view.high = Math.min(high, view.max_high);
                }
            }

            view.request_redraw();
        }
    },

    /**
     * Change viewing region to that denoted by string. General format of string is:
     *
     * <chrom>[ {separator}<start>[-<end>] ]
     *
     * where separator can be whitespace or a colon. Examples:
     *
     * chr22
     * chr1:100-200
     * chr7 89999
     * chr8 90000 990000
     */
    go_to: function(str) {
        // Remove commas.
        str = str.replace(/,/g, '');

        // Replace colons and hyphens with space for easy parsing.
        str = str.replace(/:|\-/g, ' ');

        // Parse new location.
        var chrom_pos = str.split(/\s+/),
            chrom = chrom_pos[0],
            new_low = (chrom_pos[1] ? parseInt(chrom_pos[1], 10) : undefined),
            new_high = (chrom_pos[2] ? parseInt(chrom_pos[2], 10) : undefined);

        this.change_chrom(chrom, new_low, new_high);
 …