[galaxy-commits] commit/galaxy-central: jgoecks: Place track filters in their own file.

21 Sep 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/cd739bd3dca4/
changeset:   cd739bd3dca4
user:        jgoecks
date:        2012-09-21 17:14:56
summary:     Place track filters in their own file.
affected #:  2 files

diff -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 -r cd739bd3dca4859fecfe499fc976b0e0b6478238 static/scripts/viz/trackster/filters.js

--- /dev/null
+++ b/static/scripts/viz/trackster/filters.js
@@ -0,0 +1,623 @@
+define( ["libs/underscore"], function(_) {
+
+var extend = _.extend;
+
+/**
+ * Filters that enable users to show/hide data points dynamically.
+ */
+var Filter = function(obj_dict) {
+    this.manager = null;
+    this.name = obj_dict.name;
+    // Index into payload to filter.
+    this.index = obj_dict.index;
+    this.tool_id = obj_dict.tool_id;
+    // Name to use for filter when building expression for tool.
+    this.tool_exp_name = obj_dict.tool_exp_name;
+};
+
+extend(Filter.prototype, {
+    /**
+     * Convert filter to dictionary.
+     */
+    to_dict: function() {
+        return {
+            name: this.name,
+            index: this.index,
+            tool_id: this.tool_id,
+            tool_exp_name: this.tool_exp_name
+        };
+    } 
+});
+
+/**
+ * Creates an action icon.
+ */
+var create_action_icon =  function(title, css_class, on_click_fn) {
+    return $("<a/>").attr("href", "javascript:void(0);").attr("title", title)
+                    .addClass("icon-button").addClass(css_class).tooltip()
+                    .click(on_click_fn);
+};
+
+/**
+ * Number filters have a min, max as well as a low, high; low and high are used 
+ */
+var NumberFilter = function(obj_dict) {
+    //
+    // Attribute init.
+    //
+    Filter.call(this, obj_dict);
+    // Filter low/high. These values are used to filter elements.
+    this.low = ('low' in obj_dict ? obj_dict.low : -Number.MAX_VALUE);
+    this.high = ('high' in obj_dict ? obj_dict.high : Number.MAX_VALUE);
+    // Slide min/max. These values are used to set/update slider.
+    this.min = ('min' in obj_dict ? obj_dict.min : Number.MAX_VALUE);
+    this.max = ('max' in obj_dict ? obj_dict.max : -Number.MAX_VALUE);
+    // UI elements associated with filter.
+    this.container = null;
+    this.slider = null;
+    this.slider_label = null;
+    
+    //
+    // Create HTML.
+    //
+    
+    // Function that supports inline text editing of slider values.
+    // Enable users to edit parameter's value via a text box.
+    var edit_slider_values = function(container, span, slider) {
+        container.click(function() {
+            var cur_value = span.text(),
+                max = parseFloat(slider.slider("option", "max")),
+                input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6),
+                multi_value = false,
+                slider_row = $(this).parents(".slider-row");
+                
+            // Row now has input.
+            slider_row.addClass("input");
+                
+            // Increase input size if there are two values.
+            if (slider.slider("option", "values")) {
+                input_size = 2*input_size + 1;
+                multi_value = true;
+            }
+            span.text("");
+            // Temporary input for changing value.
+            $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size)
+                                     .attr("value", cur_value).appendTo(span).focus().select()
+                                     .click(function(e) {
+                // Don't want click to propogate up to values_span and restart everything.
+                e.stopPropagation();
+            }).blur(function() {
+                $(this).remove();
+                span.text(cur_value);
+                slider_row.removeClass("input");
+            }).keyup(function(e) {
+                if (e.keyCode === 27) {
+                    // Escape key.
+                    $(this).trigger("blur");
+                } else if (e.keyCode === 13) {
+                    //
+                    // Enter/return key initiates callback. If new value(s) are in slider range, 
+                    // change value (which calls slider's change() function).
+                    //
+                    var slider_min = slider.slider("option", "min"),
+                        slider_max = slider.slider("option", "max"),
+                        invalid = function(a_val) {
+                            return (isNaN(a_val) || a_val > slider_max || a_val < slider_min);
+                        },
+                        new_value = $(this).val();
+                    if (!multi_value) {
+                        new_value = parseFloat(new_value);
+                        if (invalid(new_value)) {
+                            alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]");
+                            return $(this);
+                        }
+                    }
+                    else { // Multi value.
+                        new_value = new_value.split("-");
+                        new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])];
+                        if (invalid(new_value[0]) || invalid(new_value[1])) {
+                            alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]");
+                            return $(this);
+                        }
+                    }
+                    
+                    // Updating the slider also updates slider values and removes input. 
+                    slider.slider((multi_value ? "values" : "value"), new_value);
+                    slider_row.removeClass("input");
+                }
+            });
+        });
+    };
+    
+    var filter = this;
+    
+    filter.parent_div = $("<div/>").addClass("filter-row slider-row");
+    
+    // Set up filter label (name, values).
+    var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.parent_div),
+        name_span = $("<span/>").addClass("slider-name").text(filter.name + "  ").appendTo(filter_label),
+        values_span = $("<span/>").text(this.low + "-" + this.high),
+        values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]");
+    filter.values_span = values_span;
+            
+    // Set up slider for filter.
+    var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div);
+    filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div);
+    filter.control_element.slider({
+        range: true,
+        min: this.min,
+        max: this.max,
+        step: this.get_slider_step(this.min, this.max),
+        values: [this.low, this.high],
+        slide: function(event, ui) { 
+            filter.slide(event, ui); 
+        },
+        change: function(event, ui) {
+            filter.control_element.slider("option", "slide").call(filter.control_element, event, ui);
+        }
+    });
+    filter.slider = filter.control_element;
+    filter.slider_label = values_span;
+    
+    // Enable users to edit slider values via text box.
+    edit_slider_values(values_span_container, values_span, filter.control_element);
+    
+    // Set up filter display controls.
+    var display_controls_div = $("<div/>").addClass("display-controls").appendTo(filter.parent_div);
+    this.transparency_icon = create_action_icon("Use filter for data transparency", "layer-transparent", 
+                                                function() {
+                                                    if (filter.manager.alpha_filter !== filter) {
+                                                        // Setting this filter as the alpha filter.
+                                                        filter.manager.alpha_filter = filter;
+                                                        // Update UI for new filter.
+                                                        filter.manager.parent_div.find(".layer-transparent").removeClass("active").hide();
+                                                        filter.transparency_icon.addClass("active").show();
+                                                    }
+                                                    else {
+                                                        // Clearing filter as alpha filter.
+                                                        filter.manager.alpha_filter = null;
+                                                        filter.transparency_icon.removeClass("active");
+                                                    }
+                                                    filter.manager.track.request_draw(true, true);
+                                                } )
+                                                .appendTo(display_controls_div).hide();
+    this.height_icon = create_action_icon("Use filter for data height", "arrow-resize-090", 
+                                                function() {
+                                                    if (filter.manager.height_filter !== filter) {
+                                                        // Setting this filter as the height filter.
+                                                        filter.manager.height_filter = filter;
+                                                        // Update UI for new filter.
+                                                        filter.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();
+                                                        filter.height_icon.addClass("active").show();
+                                                    }
+                                                    else {
+                                                        // Clearing filter as alpha filter.
+                                                        filter.manager.height_filter = null;
+                                                        filter.height_icon.removeClass("active");
+                                                    }
+                                                    filter.manager.track.request_draw(true, true);
+                                                } )
+                                                .appendTo(display_controls_div).hide();
+    filter.parent_div.hover( function() { 
+                                filter.transparency_icon.show();
+                                filter.height_icon.show(); 
+                            },
+                            function() {
+                                if (filter.manager.alpha_filter !== filter) {
+                                    filter.transparency_icon.hide();
+                                }
+                                if (filter.manager.height_filter !== filter) {
+                                    filter.height_icon.hide();
+                                }
+                            } );
+    
+    // Add to clear floating layout.
+    $("<div style='clear: both;'/>").appendTo(filter.parent_div);
+};
+extend(NumberFilter.prototype, {
+    /**
+     * Convert filter to dictionary.
+     */
+    to_dict: function() {
+        var obj_dict = Filter.prototype.to_dict.call(this);
+        return extend(obj_dict, {
+            type: 'number',
+            min: this.min,
+            max: this.max,
+            low: this.low,
+            high: this.high
+        });
+    },
+    /**
+     * Return a copy of filter.
+     */
+    copy: function() {
+        return new NumberFilter( 
+            {
+                name: this.name, 
+                index: this.index, 
+                tool_id: this.tool_id, 
+                tool_exp_name: this.tool_exp_name
+            });
+    },
+    /**
+     * Get step for slider.
+     */
+    // FIXME: make this a "static" function.
+    get_slider_step: function(min, max) {
+        var range = max - min;
+        return (range <= 2 ? 0.01 : 1);
+    },
+    /**
+     * Handle slide events.
+     */
+    slide: function(event, ui) {
+        var values = ui.values;
+
+        // Set new values in UI.
+        this.values_span.text(values[0] + "-" + values[1]);
+
+        // Set new values in filter.
+        this.low = values[0];
+        this.high = values[1];
+         
+        // Set timeout to update if filter low, high are stable.
+        var self = this;
+        setTimeout(function() {
+            if (values[0] === self.low && values[1] === self.high) {
+                self.manager.track.request_draw(true, true);
+            }
+        }, 25);
+         
+     },
+    /** 
+     * Returns true if filter can be applied to element.
+     */
+    applies_to: function(element) {
+        if (element.length > this.index) {
+            return true;
+        }
+        return false;
+    },
+    /**
+     * Helper function: returns true if value in in filter's [low, high] range.
+     */
+    _keep_val: function(val) {
+        return (isNaN(val) || (val >= this.low && val <= this.high));
+    },    
+    /**
+     * Returns true if (a) element's value(s) is in [low, high] (range is inclusive) 
+     * or (b) if value is non-numeric and hence unfilterable.
+     */
+    keep: function(element) {
+        if ( !this.applies_to( element ) ) {
+            // No element to filter on.
+            return true;
+        }
+
+        // Keep value function.
+        var filter = this;
+
+        // Do filtering.
+        var to_filter = element[this.index];
+        if (to_filter instanceof Array) {
+            var returnVal = true;
+            for (var i = 0; i < to_filter.length; i++) {
+                if (!this._keep_val(to_filter[i])) {
+                    // Exclude element.
+                    returnVal = false;
+                    break;
+                }
+            }
+            return returnVal;
+        }
+        else {
+            return this._keep_val(element[this.index]);
+        }
+    },
+    /**
+     * Update filter's min and max values based on element's values.
+     */
+    update_attrs: function(element) {
+        var updated = false;
+        if (!this.applies_to(element) ) {
+            return updated;
+        }
+        
+        //
+        // Update filter's min, max based on element values.
+        //
+        
+        // Make value(s) into an Array.
+        var values = element[this.index];
+        if (!(values instanceof Array)) {
+            values = [values];
+        }
+        
+        // Loop through values and update min, max.
+        for (var i = 0; i < values.length; i++) {
+            var value = values[i];
+            if (value < this.min) {
+                this.min = Math.floor(value);
+                updated = true;
+            }
+            if (value > this.max) {
+                this.max = Math.ceil(value);
+                updated = true;
+            }
+        }
+        return updated;
+    },
+    /**
+     * Update filter's slider.
+     */
+    update_ui_elt: function () {
+        // Only show filter if min < max because filter is not useful otherwise. This
+        // covers all corner cases, such as when min, max have not been defined and
+        // when min == max.
+        if (this.min < this.max) {
+            this.parent_div.show();
+        }
+        else {
+            this.parent_div.hide();
+        }
+        
+        var 
+            slider_min = this.slider.slider("option", "min"),
+            slider_max = this.slider.slider("option", "max");
+        if (this.min < slider_min || this.max > slider_max) {
+            // Update slider min, max, step.
+            this.slider.slider("option", "min", this.min);
+            this.slider.slider("option", "max", this.max);
+            this.slider.slider("option", "step", this.get_slider_step(this.min, this.max));
+            // Refresh slider:
+            // TODO: do we want to keep current values or reset to min/max?
+            // Currently we reset values:
+            this.slider.slider("option", "values", [this.min, this.max]);
+            // To use the current values.
+            //var values = this.slider.slider( "option", "values" );
+            //this.slider.slider( "option", "values", values );
+        }
+    }
+});
+ 
+/**
+ * Manages a set of filters.
+ */
+var FiltersManager = function(track, obj_dict) {
+    this.track = track;
+    this.alpha_filter = null;
+    this.height_filter = null;
+    this.filters = [];
+    
+    //
+    // Create HTML.
+    //
+        
+    //
+    // Create parent div.
+    //
+    this.parent_div = $("<div/>").addClass("filters").hide();
+    // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz.
+    this.parent_div.bind("drag", function(e) {
+        e.stopPropagation();
+    }).click(function(e) {
+        e.stopPropagation();
+    }).bind("dblclick", function(e) {
+        e.stopPropagation();
+    }).bind("keydown", function(e) {
+        e.stopPropagation();
+    });
+    
+    //
+    // Restore state from dict.
+    //
+    if (obj_dict && 'filters' in obj_dict) { // Second condition needed for backward compatibility.
+        var 
+            alpha_filter_name = ('alpha_filter' in obj_dict ? obj_dict.alpha_filter : null),
+            height_filter_name = ('height_filter' in obj_dict ? obj_dict.height_filter : null),            
+            filters_dict = obj_dict.filters,
+            filter;
+        for (var i = 0; i < filters_dict.length; i++) {
+            if (filters_dict[i].type === 'number') {
+                filter = new NumberFilter(filters_dict[i]);
+                this.add_filter(filter);
+                if (filter.name === alpha_filter_name) {
+                    this.alpha_filter = filter;
+                    filter.transparency_icon.addClass("active").show();
+                }
+                if (filter.name === height_filter_name) {
+                    this.height_filter = filter;
+                    filter.height_icon.addClass("active").show();
+                }
+            } 
+            else {
+                console.log("ERROR: unsupported filter: ", name, type);
+            }
+        }
+        
+        
+        if ('visible' in obj_dict && obj_dict.visible) {
+            this.parent_div.show();
+        }
+    }
+    
+    // Add button to filter complete dataset.
+    if (this.filters.length !== 0) {
+        var run_buttons_row = $("<div/>").addClass("param-row").appendTo(this.parent_div);
+        var run_on_dataset_button = $("<input type='submit'/>").attr("value", "Run on complete dataset").appendTo(run_buttons_row);
+        var filter_manager = this;
+        run_on_dataset_button.click( function() {
+            filter_manager.run_on_dataset();
+        });
+    }
+        
+};
+
+extend(FiltersManager.prototype, {
+    // HTML manipulation and inspection.
+    show: function() { this.parent_div.show(); },
+    hide: function() { this.parent_div.hide(); },
+    toggle: function() { this.parent_div.toggle(); },
+    visible: function() { return this.parent_div.is(":visible"); },
+    /**
+     * Returns dictionary for manager.
+     */
+    to_dict: function() {
+        var obj_dict = {},
+            filter_dicts = [],
+            filter;
+            
+        // Include individual filter states.
+        for (var i = 0; i < this.filters.length; i++) {
+            filter = this.filters[i];
+            filter_dicts.push(filter.to_dict());
+        }
+        obj_dict.filters = filter_dicts;
+        
+        // Include transparency, height filters.
+        obj_dict.alpha_filter = (this.alpha_filter ? this.alpha_filter.name : null);
+        obj_dict.height_filter = (this.height_filter ? this.height_filter.name : null);
+        
+        // Include visibility.
+        obj_dict.visible = this.parent_div.is(":visible");
+        
+        return obj_dict;
+    },
+    /**
+     * Return a copy of the manager.
+     */
+    copy: function(new_track) {
+        var copy = new FiltersManager(new_track);
+        for (var i = 0; i < this.filters.length; i++) {
+            copy.add_filter(this.filters[i].copy());
+        }
+        return copy;
+    },
+    /**
+     * Add a filter to the manager.
+     */
+    add_filter: function(filter) {
+        filter.manager = this;
+        this.parent_div.append(filter.parent_div);
+        this.filters.push(filter);  
+    },
+    /**
+     * Remove all filters from manager.
+     */
+    remove_all: function() {
+        this.filters = [];
+        this.parent_div.children().remove();
+    },
+    /**
+     * Initialize filters.
+     */ 
+    init_filters: function() {
+        for (var i = 0; i < this.filters.length; i++) {
+            var filter = this.filters[i];
+            filter.update_ui_elt();
+        }
+    },
+    /**
+     * Clear filters so that they do not impact track display.
+     */
+    clear_filters: function() {
+        for (var i = 0; i < this.filters.length; i++) {
+            var filter = this.filters[i];
+            filter.slider.slider("option", "values", [filter.min, filter.max]);
+        }
+        this.alpha_filter = null;
+        this.height_filter = null;
+        
+        // Hide icons for setting filters.
+        this.parent_div.find(".icon-button").hide();
+    },
+    run_on_dataset: function() {
+        // Get or create dictionary item.
+        var get_or_create_dict_item = function(dict, key, new_item) {
+            // Add new item to dict if 
+            if (!(key in dict)) {
+                dict[key] = new_item;
+            }
+            return dict[key];
+        };
+        
+        //
+        // Find and group active filters. Active filters are those being used to hide data.
+        // Filters with the same tool id are grouped.
+        //
+        var active_filters = {},
+            filter, 
+            tool_filter_conditions;
+        for (var i = 0; i < this.filters.length; i++) {
+            filter = this.filters[i];
+            if (filter.tool_id) {
+                // Add filtering conditions if filter low/high are set.
+                if (filter.min !== filter.low) {
+                    tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []);
+                    tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " >= " + filter.low;
+                }
+                if (filter.max !== filter.high) {
+                    tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []);
+                    tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " <= " + filter.high;
+                }
+            }
+        }
+        
+        //
+        // Use tools to run filters.
+        //
+        
+        // Create list of (tool_id, tool_filters) tuples.
+        var active_filters_list = [];
+        for (var tool_id in active_filters) {
+            active_filters_list[active_filters_list.length] = [tool_id, active_filters[tool_id]];
+        }
+        
+        // Invoke recursive function to run filters; this enables chaining of filters via
+        // iteratively application.
+        (function run_filter(input_dataset_id, filters) {
+            var 
+                // Set up filtering info and params.
+                filter_tuple = filters[0],
+                tool_id = filter_tuple[0],
+                tool_filters = filter_tuple[1],
+                tool_filter_str = "(" + tool_filters.join(") and (") + ")",
+                url_params = {
+                    cond: tool_filter_str,
+                    input: input_dataset_id,
+                    target_dataset_id: input_dataset_id,
+                    tool_id: tool_id
+                };
+
+            // Remove current filter.
+            filters = filters.slice(1);
+                
+            $.getJSON(run_tool_url, url_params, function(response) {
+                if (response.error) {
+                    // General error.
+                    show_modal("Filter Dataset",
+                               "Error running tool " + tool_id,
+                               { "Close" : hide_modal } );
+                }
+                else if (filters.length === 0) {
+                    // No more filters to run.
+                    show_modal("Filtering Dataset", 
+                               "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", 
+                               { "Close" : hide_modal } );
+                }
+                else {
+                    // More filters to run.
+                    run_filter(response.dataset_id, filters);
+                }
+            });
+              
+        })(this.track.dataset_id, active_filters_list);        
+    }
+});
+
+return {
+    FiltersManager: FiltersManager
+};
+
+});


diff -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 -r cd739bd3dca4859fecfe499fc976b0e0b6478238 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1,6 +1,7 @@
 define( ["libs/underscore", "viz/visualization", "viz/trackster/util", 
-         "viz/trackster/slotting", "viz/trackster/painters", "mvc/data" ], 
-         function( _, visualization, util, slotting, painters, data ) {
+         "viz/trackster/slotting", "viz/trackster/painters", "mvc/data",
+         "viz/trackster/filters" ], 
+         function( _, visualization, util, slotting, painters, data, filters ) {
 
 var extend = _.extend;
 var get_random_color = util.get_random_color;
@@ -586,7 +587,7 @@
     moveable(this.container_div, this.drag_handle_class, ".group", this);
     
     // Set up filters.
-    this.filters_manager = new FiltersManager(this);
+    this.filters_manager = new filters.FiltersManager(this);
     this.header_div.after(this.filters_manager.parent_div);
     // For saving drawables' filter managers when group-level filtering is done:
     this.saved_filters_managers = [];
@@ -600,7 +601,7 @@
     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 FiltersManager(this, obj_dict.filters);
+        this.filters_manager = new filters.FiltersManager(this, obj_dict.filters);
         old_manager.parent_div.replaceWith(this.filters_manager.parent_div);
     
         if (obj_dict.filters.visible) {
@@ -1831,619 +1832,6 @@
 });
 
 /**
- * Filters that enable users to show/hide data points dynamically.
- */
-var Filter = function(obj_dict) {
-    this.manager = null;
-    this.name = obj_dict.name;
-    // Index into payload to filter.
-    this.index = obj_dict.index;
-    this.tool_id = obj_dict.tool_id;
-    // Name to use for filter when building expression for tool.
-    this.tool_exp_name = obj_dict.tool_exp_name;
-};
-
-extend(Filter.prototype, {
-    /**
-     * Convert filter to dictionary.
-     */
-    to_dict: function() {
-        return {
-            name: this.name,
-            index: this.index,
-            tool_id: this.tool_id,
-            tool_exp_name: this.tool_exp_name
-        };
-    } 
-});
-
-/**
- * Creates an action icon.
- */
-var create_action_icon =  function(title, css_class, on_click_fn) {
-    return $("<a/>").attr("href", "javascript:void(0);").attr("title", title)
-                    .addClass("icon-button").addClass(css_class).tooltip()
-                    .click(on_click_fn);
-};
-
-/**
- * Number filters have a min, max as well as a low, high; low and high are used 
- */
-var NumberFilter = function(obj_dict) {
-    //
-    // Attribute init.
-    //
-    Filter.call(this, obj_dict);
-    // Filter low/high. These values are used to filter elements.
-    this.low = ('low' in obj_dict ? obj_dict.low : -Number.MAX_VALUE);
-    this.high = ('high' in obj_dict ? obj_dict.high : Number.MAX_VALUE);
-    // Slide min/max. These values are used to set/update slider.
-    this.min = ('min' in obj_dict ? obj_dict.min : Number.MAX_VALUE);
-    this.max = ('max' in obj_dict ? obj_dict.max : -Number.MAX_VALUE);
-    // UI elements associated with filter.
-    this.container = null;
-    this.slider = null;
-    this.slider_label = null;
-    
-    //
-    // Create HTML.
-    //
-    
-    // Function that supports inline text editing of slider values.
-    // Enable users to edit parameter's value via a text box.
-    var edit_slider_values = function(container, span, slider) {
-        container.click(function() {
-            var cur_value = span.text(),
-                max = parseFloat(slider.slider("option", "max")),
-                input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6),
-                multi_value = false,
-                slider_row = $(this).parents(".slider-row");
-                
-            // Row now has input.
-            slider_row.addClass("input");
-                
-            // Increase input size if there are two values.
-            if (slider.slider("option", "values")) {
-                input_size = 2*input_size + 1;
-                multi_value = true;
-            }
-            span.text("");
-            // Temporary input for changing value.
-            $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size)
-                                     .attr("value", cur_value).appendTo(span).focus().select()
-                                     .click(function(e) {
-                // Don't want click to propogate up to values_span and restart everything.
-                e.stopPropagation();
-            }).blur(function() {
-                $(this).remove();
-                span.text(cur_value);
-                slider_row.removeClass("input");
-            }).keyup(function(e) {
-                if (e.keyCode === 27) {
-                    // Escape key.
-                    $(this).trigger("blur");
-                } else if (e.keyCode === 13) {
-                    //
-                    // Enter/return key initiates callback. If new value(s) are in slider range, 
-                    // change value (which calls slider's change() function).
-                    //
-                    var slider_min = slider.slider("option", "min"),
-                        slider_max = slider.slider("option", "max"),
-                        invalid = function(a_val) {
-                            return (isNaN(a_val) || a_val > slider_max || a_val < slider_min);
-                        },
-                        new_value = $(this).val();
-                    if (!multi_value) {
-                        new_value = parseFloat(new_value);
-                        if (invalid(new_value)) {
-                            alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]");
-                            return $(this);
-                        }
-                    }
-                    else { // Multi value.
-                        new_value = new_value.split("-");
-                        new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])];
-                        if (invalid(new_value[0]) || invalid(new_value[1])) {
-                            alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]");
-                            return $(this);
-                        }
-                    }
-                    
-                    // Updating the slider also updates slider values and removes input. 
-                    slider.slider((multi_value ? "values" : "value"), new_value);
-                    slider_row.removeClass("input");
-                }
-            });
-        });
-    };
-    
-    var filter = this;
-    
-    filter.parent_div = $("<div/>").addClass("filter-row slider-row");
-    
-    // Set up filter label (name, values).
-    var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.parent_div),
-        name_span = $("<span/>").addClass("slider-name").text(filter.name + "  ").appendTo(filter_label),
-        values_span = $("<span/>").text(this.low + "-" + this.high),
-        values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]");
-    filter.values_span = values_span;
-            
-    // Set up slider for filter.
-    var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div);
-    filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div);
-    filter.control_element.slider({
-        range: true,
-        min: this.min,
-        max: this.max,
-        step: this.get_slider_step(this.min, this.max),
-        values: [this.low, this.high],
-        slide: function(event, ui) { 
-            filter.slide(event, ui); 
-        },
-        change: function(event, ui) {
-            filter.control_element.slider("option", "slide").call(filter.control_element, event, ui);
-        }
-    });
-    filter.slider = filter.control_element;
-    filter.slider_label = values_span;
-    
-    // Enable users to edit slider values via text box.
-    edit_slider_values(values_span_container, values_span, filter.control_element);
-    
-    // Set up filter display controls.
-    var display_controls_div = $("<div/>").addClass("display-controls").appendTo(filter.parent_div);
-    this.transparency_icon = create_action_icon("Use filter for data transparency", "layer-transparent", 
-                                                function() {
-                                                    if (filter.manager.alpha_filter !== filter) {
-                                                        // Setting this filter as the alpha filter.
-                                                        filter.manager.alpha_filter = filter;
-                                                        // Update UI for new filter.
-                                                        filter.manager.parent_div.find(".layer-transparent").removeClass("active").hide();
-                                                        filter.transparency_icon.addClass("active").show();
-                                                    }
-                                                    else {
-                                                        // Clearing filter as alpha filter.
-                                                        filter.manager.alpha_filter = null;
-                                                        filter.transparency_icon.removeClass("active");
-                                                    }
-                                                    filter.manager.track.request_draw(true, true);
-                                                } )
-                                                .appendTo(display_controls_div).hide();
-    this.height_icon = create_action_icon("Use filter for data height", "arrow-resize-090", 
-                                                function() {
-                                                    if (filter.manager.height_filter !== filter) {
-                                                        // Setting this filter as the height filter.
-                                                        filter.manager.height_filter = filter;
-                                                        // Update UI for new filter.
-                                                        filter.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();
-                                                        filter.height_icon.addClass("active").show();
-                                                    }
-                                                    else {
-                                                        // Clearing filter as alpha filter.
-                                                        filter.manager.height_filter = null;
-                                                        filter.height_icon.removeClass("active");
-                                                    }
-                                                    filter.manager.track.request_draw(true, true);
-                                                } )
-                                                .appendTo(display_controls_div).hide();
-    filter.parent_div.hover( function() { 
-                                filter.transparency_icon.show();
-                                filter.height_icon.show(); 
-                            },
-                            function() {
-                                if (filter.manager.alpha_filter !== filter) {
-                                    filter.transparency_icon.hide();
-                                }
-                                if (filter.manager.height_filter !== filter) {
-                                    filter.height_icon.hide();
-                                }
-                            } );
-    
-    // Add to clear floating layout.
-    $("<div style='clear: both;'/>").appendTo(filter.parent_div);
-};
-extend(NumberFilter.prototype, {
-    /**
-     * Convert filter to dictionary.
-     */
-    to_dict: function() {
-        var obj_dict = Filter.prototype.to_dict.call(this);
-        return extend(obj_dict, {
-            type: 'number',
-            min: this.min,
-            max: this.max,
-            low: this.low,
-            high: this.high
-        });
-    },
-    /**
-     * Return a copy of filter.
-     */
-    copy: function() {
-        return new NumberFilter( 
-            {
-                name: this.name, 
-                index: this.index, 
-                tool_id: this.tool_id, 
-                tool_exp_name: this.tool_exp_name
-            });
-    },
-    /**
-     * Get step for slider.
-     */
-    // FIXME: make this a "static" function.
-    get_slider_step: function(min, max) {
-        var range = max - min;
-        return (range <= 2 ? 0.01 : 1);
-    },
-    /**
-     * Handle slide events.
-     */
-    slide: function(event, ui) {
-        var values = ui.values;
-
-        // Set new values in UI.
-        this.values_span.text(values[0] + "-" + values[1]);
-
-        // Set new values in filter.
-        this.low = values[0];
-        this.high = values[1];
-         
-        // Set timeout to update if filter low, high are stable.
-        var self = this;
-        setTimeout(function() {
-            if (values[0] === self.low && values[1] === self.high) {
-                self.manager.track.request_draw(true, true);
-            }
-        }, 25);
-         
-     },
-    /** 
-     * Returns true if filter can be applied to element.
-     */
-    applies_to: function(element) {
-        if (element.length > this.index) {
-            return true;
-        }
-        return false;
-    },
-    /**
-     * Helper function: returns true if value in in filter's [low, high] range.
-     */
-    _keep_val: function(val) {
-        return (isNaN(val) || (val >= this.low && val <= this.high));
-    },    
-    /**
-     * Returns true if (a) element's value(s) is in [low, high] (range is inclusive) 
-     * or (b) if value is non-numeric and hence unfilterable.
-     */
-    keep: function(element) {
-        if ( !this.applies_to( element ) ) {
-            // No element to filter on.
-            return true;
-        }
-
-        // Keep value function.
-        var filter = this;
-
-        // Do filtering.
-        var to_filter = element[this.index];
-        if (to_filter instanceof Array) {
-            var returnVal = true;
-            for (var i = 0; i < to_filter.length; i++) {
-                if (!this._keep_val(to_filter[i])) {
-                    // Exclude element.
-                    returnVal = false;
-                    break;
-                }
-            }
-            return returnVal;
-        }
-        else {
-            return this._keep_val(element[this.index]);
-        }
-    },
-    /**
-     * Update filter's min and max values based on element's values.
-     */
-    update_attrs: function(element) {
-        var updated = false;
-        if (!this.applies_to(element) ) {
-            return updated;
-        }
-        
-        //
-        // Update filter's min, max based on element values.
-        //
-        
-        // Make value(s) into an Array.
-        var values = element[this.index];
-        if (!(values instanceof Array)) {
-            values = [values];
-        }
-        
-        // Loop through values and update min, max.
-        for (var i = 0; i < values.length; i++) {
-            var value = values[i];
-            if (value < this.min) {
-                this.min = Math.floor(value);
-                updated = true;
-            }
-            if (value > this.max) {
-                this.max = Math.ceil(value);
-                updated = true;
-            }
-        }
-        return updated;
-    },
-    /**
-     * Update filter's slider.
-     */
-    update_ui_elt: function () {
-        // Only show filter if min < max because filter is not useful otherwise. This
-        // covers all corner cases, such as when min, max have not been defined and
-        // when min == max.
-        if (this.min < this.max) {
-            this.parent_div.show();
-        }
-        else {
-            this.parent_div.hide();
-        }
-        
-        var 
-            slider_min = this.slider.slider("option", "min"),
-            slider_max = this.slider.slider("option", "max");
-        if (this.min < slider_min || this.max > slider_max) {
-            // Update slider min, max, step.
-            this.slider.slider("option", "min", this.min);
-            this.slider.slider("option", "max", this.max);
-            this.slider.slider("option", "step", this.get_slider_step(this.min, this.max));
-            // Refresh slider:
-            // TODO: do we want to keep current values or reset to min/max?
-            // Currently we reset values:
-            this.slider.slider("option", "values", [this.min, this.max]);
-            // To use the current values.
-            //var values = this.slider.slider( "option", "values" );
-            //this.slider.slider( "option", "values", values );
-        }
-    }
-});
- 
-/**
- * Manages a set of filters.
- */
-var FiltersManager = function(track, obj_dict) {
-    this.track = track;
-    this.alpha_filter = null;
-    this.height_filter = null;
-    this.filters = [];
-    
-    //
-    // Create HTML.
-    //
-        
-    //
-    // Create parent div.
-    //
-    this.parent_div = $("<div/>").addClass("filters").hide();
-    // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz.
-    this.parent_div.bind("drag", function(e) {
-        e.stopPropagation();
-    }).click(function(e) {
-        e.stopPropagation();
-    }).bind("dblclick", function(e) {
-        e.stopPropagation();
-    }).bind("keydown", function(e) {
-        e.stopPropagation();
-    });
-    
-    //
-    // Restore state from dict.
-    //
-    if (obj_dict && 'filters' in obj_dict) { // Second condition needed for backward compatibility.
-        var 
-            alpha_filter_name = ('alpha_filter' in obj_dict ? obj_dict.alpha_filter : null),
-            height_filter_name = ('height_filter' in obj_dict ? obj_dict.height_filter : null),            
-            filters_dict = obj_dict.filters,
-            filter;
-        for (var i = 0; i < filters_dict.length; i++) {
-            if (filters_dict[i].type === 'number') {
-                filter = new NumberFilter(filters_dict[i]);
-                this.add_filter(filter);
-                if (filter.name === alpha_filter_name) {
-                    this.alpha_filter = filter;
-                    filter.transparency_icon.addClass("active").show();
-                }
-                if (filter.name === height_filter_name) {
-                    this.height_filter = filter;
-                    filter.height_icon.addClass("active").show();
-                }
-            } 
-            else {
-                console.log("ERROR: unsupported filter: ", name, type);
-            }
-        }
-        
-        
-        if ('visible' in obj_dict && obj_dict.visible) {
-            this.parent_div.show();
-        }
-    }
-    
-    // Add button to filter complete dataset.
-    if (this.filters.length !== 0) {
-        var run_buttons_row = $("<div/>").addClass("param-row").appendTo(this.parent_div);
-        var run_on_dataset_button = $("<input type='submit'/>").attr("value", "Run on complete dataset").appendTo(run_buttons_row);
-        var filter_manager = this;
-        run_on_dataset_button.click( function() {
-            filter_manager.run_on_dataset();
-        });
-    }
-        
-};
-
-extend(FiltersManager.prototype, {
-    // HTML manipulation and inspection.
-    show: function() { this.parent_div.show(); },
-    hide: function() { this.parent_div.hide(); },
-    toggle: function() { this.parent_div.toggle(); },
-    visible: function() { return this.parent_div.is(":visible"); },
-    /**
-     * Returns dictionary for manager.
-     */
-    to_dict: function() {
-        var obj_dict = {},
-            filter_dicts = [],
-            filter;
-            
-        // Include individual filter states.
-        for (var i = 0; i < this.filters.length; i++) {
-            filter = this.filters[i];
-            filter_dicts.push(filter.to_dict());
-        }
-        obj_dict.filters = filter_dicts;
-        
-        // Include transparency, height filters.
-        obj_dict.alpha_filter = (this.alpha_filter ? this.alpha_filter.name : null);
-        obj_dict.height_filter = (this.height_filter ? this.height_filter.name : null);
-        
-        // Include visibility.
-        obj_dict.visible = this.parent_div.is(":visible");
-        
-        return obj_dict;
-    },
-    /**
-     * Return a copy of the manager.
-     */
-    copy: function(new_track) {
-        var copy = new FiltersManager(new_track);
-        for (var i = 0; i < this.filters.length; i++) {
-            copy.add_filter(this.filters[i].copy());
-        }
-        return copy;
-    },
-    /**
-     * Add a filter to the manager.
-     */
-    add_filter: function(filter) {
-        filter.manager = this;
-        this.parent_div.append(filter.parent_div);
-        this.filters.push(filter);  
-    },
-    /**
-     * Remove all filters from manager.
-     */
-    remove_all: function() {
-        this.filters = [];
-        this.parent_div.children().remove();
-    },
-    /**
-     * Initialize filters.
-     */ 
-    init_filters: function() {
-        for (var i = 0; i < this.filters.length; i++) {
-            var filter = this.filters[i];
-            filter.update_ui_elt();
-        }
-    },
-    /**
-     * Clear filters so that they do not impact track display.
-     */
-    clear_filters: function() {
-        for (var i = 0; i < this.filters.length; i++) {
-            var filter = this.filters[i];
-            filter.slider.slider("option", "values", [filter.min, filter.max]);
-        }
-        this.alpha_filter = null;
-        this.height_filter = null;
-        
-        // Hide icons for setting filters.
-        this.parent_div.find(".icon-button").hide();
-    },
-    run_on_dataset: function() {
-        // Get or create dictionary item.
-        var get_or_create_dict_item = function(dict, key, new_item) {
-            // Add new item to dict if 
-            if (!(key in dict)) {
-                dict[key] = new_item;
-            }
-            return dict[key];
-        };
-        
-        //
-        // Find and group active filters. Active filters are those being used to hide data.
-        // Filters with the same tool id are grouped.
-        //
-        var active_filters = {},
-            filter, 
-            tool_filter_conditions;
-        for (var i = 0; i < this.filters.length; i++) {
-            filter = this.filters[i];
-            if (filter.tool_id) {
-                // Add filtering conditions if filter low/high are set.
-                if (filter.min !== filter.low) {
-                    tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []);
-                    tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " >= " + filter.low;
-                }
-                if (filter.max !== filter.high) {
-                    tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []);
-                    tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " <= " + filter.high;
-                }
-            }
-        }
-        
-        //
-        // Use tools to run filters.
-        //
-        
-        // Create list of (tool_id, tool_filters) tuples.
-        var active_filters_list = [];
-        for (var tool_id in active_filters) {
-            active_filters_list[active_filters_list.length] = [tool_id, active_filters[tool_id]];
-        }
-        
-        // Invoke recursive function to run filters; this enables chaining of filters via
-        // iteratively application.
-        (function run_filter(input_dataset_id, filters) {
-            var 
-                // Set up filtering info and params.
-                filter_tuple = filters[0],
-                tool_id = filter_tuple[0],
-                tool_filters = filter_tuple[1],
-                tool_filter_str = "(" + tool_filters.join(") and (") + ")",
-                url_params = {
-                    cond: tool_filter_str,
-                    input: input_dataset_id,
-                    target_dataset_id: input_dataset_id,
-                    tool_id: tool_id
-                },
-                // Remove current filter.
-                filters = filters.slice(1);
-                
-            $.getJSON(run_tool_url, url_params, function(response) {
-                if (response.error) {
-                    // General error.
-                    show_modal("Filter Dataset",
-                               "Error running tool " + tool_id,
-                               { "Close" : hide_modal } );
-                }
-                else if (filters.length === 0) {
-                    // No more filters to run.
-                    show_modal("Filtering Dataset", 
-                               "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", 
-                               { "Close" : hide_modal } );
-                }
-                else {
-                    // More filters to run.
-                    run_filter(response.dataset_id, filters);
-                }
-            });
-              
-        })(this.track.dataset_id, active_filters_list);        
-    }
-});
-
-/**
  * Generates scale values based on filter and feature's value for filter.
  */
 var FilterScaler = function(filter, default_val) {
@@ -3224,7 +2612,7 @@
     moveable(track.container_div, track.drag_handle_class, ".group", track);
     
     // Attribute init.
-    this.filters_manager = new FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null));
+    this.filters_manager = new filters.FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null));
     // HACK: set filters manager for data manager.
     // FIXME: prolly need function to set filters and update data_manager reference.
     this.data_manager.set('filters_manager', this.filters_manager);

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: jgoecks: Place track filters in their own file.

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