[galaxy-commits] commit/galaxy-central: jgoecks: Move workflows JavaScript code to its own file for modularity and bundling purposes. Pack scripts.

26 Aug 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d51946b4a19f/
Changeset:   d51946b4a19f
User:        jgoecks
Date:        2013-08-26 16:32:07
Summary:     Move workflows JavaScript code to its own file for modularity and bundling purposes. Pack scripts.
Affected #:  6 files

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f static/scripts/galaxy.workflows.js

--- /dev/null
+++ b/static/scripts/galaxy.workflows.js
@@ -0,0 +1,617 @@
+$( function() {
+
+    if ( window.lt_ie_7 ) {
+            show_modal(
+                "Browser not supported",
+                "Sorry, the workflow editor is not supported for IE6 and below."
+            );
+            return;
+    }
+
+    // Init searching.
+    $("#tool-search-query").click( function (){
+        $(this).focus();
+        $(this).select();
+    })
+    .keyup( function () {
+        // Remove italics.
+        $(this).css("font-style", "normal");
+        // Don't update if same value as last time
+        if ( this.value.length < 3 ) {
+            reset_tool_search(false);
+        } else if ( this.value != this.lastValue ) {
+            // Add class to denote that searching is active.
+            $(this).addClass("search_active");
+            // input.addClass(config.loadingClass);
+            // Add '*' to facilitate partial matching.
+            var q = this.value + '*';
+            // Stop previous ajax-request
+            if (this.timer) {
+                clearTimeout(this.timer);
+            }
+            // Start a new ajax-request in X ms
+            $("#search-spinner").show();
+            this.timer = setTimeout(function () {
+                $.get(tool_search_url, { query: q }, function (data) {
+                    // input.removeClass(config.loadingClass);
+                    // Show live-search if results and search-term aren't empty
+                    $("#search-no-results").hide();
+                    // Hide all tool sections.
+                    $(".toolSectionWrapper").hide();
+                    // This hides all tools but not workflows link (which is in a .toolTitle div).
+                    $(".toolSectionWrapper").find(".toolTitle").hide();
+                    if ( data.length != 0 ) {
+                        // Map tool ids to element ids and join them.
+                        var s = $.map( data, function( n, i ) { return "link-" + n; } );
+                        // First pass to show matching tools and their parents.
+                        $(s).each( function(index,id) {
+                            // Add class to denote match.
+                            $("[id='"+id+"']").parent().addClass("search_match");
+                            $("[id='"+id+"']").parent().show().parent().parent().show().parent().show();
+                        });
+                        // Hide labels that have no visible children.
+                        $(".toolPanelLabel").each( function() {
+                           var this_label = $(this);
+                           var next = this_label.next();
+                           var no_visible_tools = true;
+                           // Look through tools following label and, if none are visible, hide label.
+                           while (next.length !== 0 && next.hasClass("toolTitle")) {
+                               if (next.is(":visible")) {
+                                   no_visible_tools = false;
+                                   break;
+                               } else {
+                                   next = next.next();
+                               }
+                            }
+                            if (no_visible_tools) {
+                                this_label.hide();
+                            }
+                        });
+                    } else {
+                        $("#search-no-results").show();
+                    }
+                    $("#search-spinner").hide();
+                }, "json" );
+            }, 200 );
+        }
+        this.lastValue = this.value;
+    });
+
+    // Canvas overview management
+    canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") );
+
+    // Initialize workflow state
+    reset();
+    // Load the datatype info
+    $.ajax( {
+        url: get_datatypes_url,
+        dataType: "json",
+        cache: false,
+        success: function( data ) {
+            populate_datatype_info( data );
+            // Load workflow definition
+            $.ajax( {
+                url: load_workflow_url,
+                data: { id: workflow_id, "_": "true" },
+                dataType: 'json',
+                cache: false,
+                success: function( data ) {
+                     reset();
+                     workflow.from_simple( data );
+                     workflow.has_changes = false;
+                     workflow.fit_canvas_to_nodes();
+                     scroll_to_nodes();
+                     canvas_manager.draw_overview();
+                     // Determine if any parameters were 'upgraded' and provide message
+                     upgrade_message = "";
+                     $.each( data.upgrade_messages, function( k, v ) {
+                        upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + "<ul>");
+                        $.each( v, function( i, vv ) {
+                            upgrade_message += "<li>" + vv +"</li>";
+                        });
+                        upgrade_message += "</ul></li>";
+                     });
+                     if ( upgrade_message ) {
+                        show_modal( "Workflow loaded with changes",
+                                    "Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>" + upgrade_message + "</ul>",
+                                    { "Continue" : hide_modal } );
+                     } else {
+                        hide_modal();
+                     }
+                     show_workflow_parameters();
+                 },
+                 beforeSubmit: function( data ) {
+                     show_message( "Loading workflow", "progress" );
+                 }
+            });
+        }
+    });
+
+    // For autosave purposes
+    $(document).ajaxStart( function() {
+        active_ajax_call = true;
+        $(document).bind( "ajaxStop.global", function() {
+            active_ajax_call = false;
+        });
+    });
+
+    $(document).ajaxError( function ( e, x ) {
+        // console.log( e, x );
+        var message = x.responseText || x.statusText || "Could not connect to server";
+        show_modal( "Server error", message, { "Ignore error" : hide_modal } );
+        return false;
+    });
+
+    make_popupmenu( $("#workflow-options-button"), {
+        "Save" : save_current_workflow,
+        "Run": function() {
+            window.location = run_workflow_url;
+        },
+        //"Create New" : create_new_workflow_dialog,
+        "Edit Attributes" : edit_workflow_attributes,
+        //"Edit Workflow Outputs": edit_workflow_outputs,
+        "Auto Re-layout": layout_editor,
+        //"Load a Workflow" : load_workflow,
+        "Close": close_editor
+    });
+
+    function edit_workflow_outputs(){
+        workflow.clear_active_node();
+        $('.right-content').hide();
+        var new_content = "";
+        for (var node_key in workflow.nodes){
+            var node = workflow.nodes[node_key];
+            if(node.type == 'tool'){
+                new_content += "<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step " + node.id + " - " + node.name + "</div>";
+                for (var ot_key in node.output_terminals){
+                    var output = node.output_terminals[ot_key];
+                    // if (node.workflow_outputs[node.id + "|" + output.name]){
+                    if ($.inArray(output.name, node.workflow_outputs) != -1){
+                        new_content += "<p>"+output.name +"<input type='checkbox' name='"+ node.id + "|" + output.name +"' checked /></p>";
+                    }
+                    else{
+                        new_content += "<p>"+output.name +"<input type='checkbox' name='"+ node.id + "|" + output.name +"' /></p>";
+                    }
+                }
+                new_content += "</div>";
+            }
+        }
+        $("#output-fill-area").html(new_content);
+        $("#output-fill-area input").bind('click', function(){
+            var node_id = this.name.split('|')[0];
+            var output_name = this.name.split('|')[1];
+            if (this.checked){
+                if($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) == -1){
+                    workflow.nodes[node_id].workflow_outputs.push(output_name);
+                }//else it's already in the array.  Shouldn't happen, but forget it.
+            }else{
+                while ($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) != -1){
+                    var ia = $.inArray(output_name, workflow.nodes[node_id].workflow_outputs);
+                    workflow.nodes[node_id].workflow_outputs = workflow.nodes[node_id].workflow_outputs.slice(0,ia).concat( workflow.nodes[node_id].workflow_outputs.slice(ia+1) );
+                }
+            }
+            workflow.has_changes = true;
+        });
+        $('#workflow-output-area').show();
+    }
+
+    function layout_editor() {
+        workflow.layout();
+        workflow.fit_canvas_to_nodes();
+        scroll_to_nodes();
+        canvas_manager.draw_overview();
+    }
+
+    function edit_workflow_attributes() {
+        workflow.clear_active_node();
+        $('.right-content').hide();
+        $('#edit-attributes').show();
+
+    }
+
+    // On load, set the size to the pref stored in local storage if it exists
+    overview_size = $.jStorage.get("overview-size");
+    if (overview_size !== undefined) {
+        $("#overview-border").css( {
+            width: overview_size,
+            height: overview_size
+        });
+    }
+
+    // Show viewport on load unless pref says it's off
+    if ($.jStorage.get("overview-off")) {
+        hide_overview();
+    } else {
+        show_overview();
+    }
+
+    // Stores the size of the overview into local storage when it's resized
+    $("#overview-border").bind( "dragend", function( e, d ) {
+        var op = $(this).offsetParent();
+        var opo = op.offset();
+        var new_size = Math.max( op.width() - ( d.offsetX - opo.left ),
+                                 op.height() - ( d.offsetY - opo.top ) );
+        $.jStorage.set("overview-size", new_size + "px");
+    });
+
+    function show_overview() {
+        $.jStorage.set("overview-off", false);
+        $("#overview-border").css("right", "0px");
+        $("#close-viewport").css("background-position", "0px 0px");
+    }
+
+    function hide_overview() {
+        $.jStorage.set("overview-off", true);
+        $("#overview-border").css("right", "20000px");
+        $("#close-viewport").css("background-position", "12px 0px");
+    }
+
+    // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly
+    $("#close-viewport").click( function() {
+        if ( $("#overview-border").css("right") === "0px" ) {
+            hide_overview();
+        } else {
+            show_overview();
+        }
+    });
+
+    // Unload handler
+    window.onbeforeunload = function() {
+        if ( workflow && workflow.has_changes ) {
+            return "There are unsaved changes to your workflow which will be lost.";
+        }
+    };
+
+    // Tool menu
+    $( "div.toolSectionBody" ).hide();
+    $( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" );
+    var last_expanded = null;
+    $( "div.toolSectionTitle" ).each( function() {
+       var body = $(this).next( "div.toolSectionBody" );
+       $(this).click( function() {
+           if ( body.is( ":hidden" ) ) {
+               if ( last_expanded ) last_expanded.slideUp( "fast" );
+               last_expanded = body;
+               body.slideDown( "fast" );
+           }
+           else {
+               body.slideUp( "fast" );
+               last_expanded = null;
+           }
+       });
+    });
+
+    // Rename async.
+    async_save_text("workflow-name", "workflow-name", rename_async_url, "new_name");
+
+    // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.
+    $('#workflow-tag').click( function() {
+        $('.tag-area').click();
+        return false;
+    });
+    // Annotate async.
+    async_save_text("workflow-annotation", "workflow-annotation", annotate_async_url, "new_annotation", 25, true, 4);
+});
+
+// Global state for the whole workflow
+function reset() {
+    if ( workflow ) {
+        workflow.remove_all();
+    }
+    workflow = new Workflow( $("#canvas-container") );
+}
+
+function scroll_to_nodes() {
+    var cv = $("#canvas-viewport");
+    var cc = $("#canvas-container");
+    var top, left;
+    if ( cc.width() < cv.width() ) {
+        left = ( cv.width() - cc.width() ) / 2;
+    } else {
+        left = 0;
+    }
+    if ( cc.height() < cv.height() ) {
+        top = ( cv.height() - cc.height() ) / 2;
+    } else {
+        top = 0;
+    }
+    cc.css( { left: left, top: top } );
+}
+
+// Add a new step to the workflow by tool id
+function add_node_for_tool( id, title ) {
+    var node = prebuild_node( 'tool', title, id );
+    workflow.add_node( node );
+    workflow.fit_canvas_to_nodes();
+    canvas_manager.draw_overview();
+    workflow.activate_node( node );
+    $.ajax( {
+        url: get_new_module_info_url,
+        data: { type: "tool", tool_id: id, "_": "true" },
+        global: false,
+        dataType: "json",
+        success: function( data ) {
+            node.init_field_data( data );
+        },
+        error: function( x, e ) {
+            var m = "error loading field data";
+            if ( x.status === 0 ) {
+                m += ", server unavailable";
+            }
+            node.error( m );
+        }
+    });
+}
+
+function add_node_for_module( type, title ) {
+    node = prebuild_node( type, title );
+    workflow.add_node( node );
+    workflow.fit_canvas_to_nodes();
+    canvas_manager.draw_overview();
+    workflow.activate_node( node );
+    $.ajax( {
+        url: get_new_module_info_url,
+        data: { type: type, "_": "true" },
+        dataType: "json",
+        success: function( data ) {
+            node.init_field_data( data );
+        },
+        error: function( x, e ) {
+            var m = "error loading field data"
+            if ( x.status == 0 ) {
+                m += ", server unavailable"
+            }
+            node.error( m );
+        }
+    });
+}
+
+// This function preloads how to display known pja's.
+function display_pja(pja, node) {
+    // DBTODO SANITIZE INPUTS.
+    $("#pja_container").append( get_pja_form(pja) );
+    $("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
+        action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
+        $(this).closest(".toolForm").remove();
+        delete workflow.active_node.post_job_actions[action_to_rem];
+        workflow.active_form_has_changes = true;
+    });
+}
+
+function display_pja_list(){
+    return pja_list;
+}
+
+function display_file_list(node){
+    addlist = "<select id='node_data_list' name='node_data_list'>";
+    for (var out_terminal in node.output_terminals){
+        addlist += "<option value='" + out_terminal + "'>"+ out_terminal +"</option>";
+    }
+    addlist += "</select>";
+    return addlist;
+}
+
+function new_pja(action_type, target, node){
+    if (node.post_job_actions === undefined){
+        //New tool node, set up dict.
+        node.post_job_actions = {};
+    }
+    if (node.post_job_actions[action_type+target] === undefined){
+        var new_pja = {};
+        new_pja.action_type = action_type;
+        new_pja.output_name = target;
+        node.post_job_actions[action_type+target] = null;
+        node.post_job_actions[action_type+target] =  new_pja;
+        display_pja(new_pja, node);
+        workflow.active_form_has_changes = true;
+        return true;
+    } else {
+        return false;
+    }
+}
+
+function show_workflow_parameters(){
+    var parameter_re = /\$\{.+?\}/g;
+    var workflow_parameters = [];
+    var wf_parm_container = $("#workflow-parameters-container");
+    var wf_parm_box = $("#workflow-parameters-box");
+    var new_parameter_content = "";
+    var matches = [];
+    $.each(workflow.nodes, function (k, node){
+        var form_matches = node.form_html.match(parameter_re);
+        if (form_matches){
+            matches = matches.concat(form_matches);
+        }
+        if (node.post_job_actions){
+            $.each(node.post_job_actions, function(k, pja){
+                if (pja.action_arguments){
+                    $.each(pja.action_arguments, function(k, action_argument){
+                        var arg_matches = action_argument.match(parameter_re);
+                        if (arg_matches){
+                            matches = matches.concat(arg_matches);
+                        }
+                    });
+                }
+            });
+            if (matches){
+                $.each(matches, function(k, element){
+                    if ($.inArray(element, workflow_parameters) === -1){
+                        workflow_parameters.push(element);
+                    }
+                });
+            }
+        }
+    });
+    if (workflow_parameters && workflow_parameters.length !== 0){
+        $.each(workflow_parameters, function(k, element){
+            new_parameter_content += "<div>" + element.substring(2, element.length -1) + "</div>";
+        });
+        wf_parm_container.html(new_parameter_content);
+        wf_parm_box.show();
+    }else{
+        wf_parm_container.html(new_parameter_content);
+        wf_parm_box.hide();
+    }
+}
+
+function show_form_for_tool( text, node ) {
+    $('.right-content').hide();
+    $("#right-content").show().html( text );
+    // Add metadata form to tool.
+    if (node) {
+        $("#right-content").find(".toolForm:first").after( "<p><div class='metadataForm'> \
+            <div class='metadataFormTitle'>Edit Step Attributes</div> \
+            <div class='form-row'> \
+            <label>Annotation / Notes:</label> \
+                    <div style='margin-right: 10px;'> \
+                    <textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \
+                        <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \
+                    </div> \
+            </div> \
+            </div>" );
+    }
+    // Add step actions.
+    if (node && node.type=='tool'){
+        pjastr = "<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> \
+            " + display_pja_list() + " <br/> "+ display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\
+            </div><div class='form-row'>\
+            <div style='margin-right: 10px;'><span id='pja_container'></span>";
+        pjastr += "<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";
+        $("#right-content").find(".toolForm").after( pjastr );
+        for (var key in node.post_job_actions){
+            if (key != "undefined"){ //To make sure we haven't just deleted it.
+                display_pja(node.post_job_actions[key], node);
+            }
+        }
+        $("#add_pja").click(function (){
+            new_pja($("#new_pja_list").val(),$("#node_data_list").val(), node);
+        });
+    }
+    $("#right-content").find( "form" ).ajaxForm( {
+        type: 'POST',
+        dataType: 'json',
+        success: function( data ) {
+            workflow.active_form_has_changes = false;
+            node.update_field_data( data );
+            show_workflow_parameters();
+        },
+        beforeSubmit: function( data ) {
+            data.push( { name: 'tool_state', value: node.tool_state } );
+            data.push( { name: '_', value: "true" } );
+        }
+    }).each( function() {
+        var form = this;
+        $(this).find( "select[refresh_on_change='true']").change( function() {
+            $(form).submit();
+        });
+        $(this).find( ".popupmenu" ).each( function() {
+            var id = $(this).parents( "div.form-row" ).attr( 'id' );
+            var b = $('<a class="popup-arrow" id="popup-arrow-for-' + id + '">▼</a>');
+            var options = {};
+            $(this).find( "button" ).each( function() {
+                var name = $(this).attr( 'name' );
+                var value = $(this).attr( 'value' );
+                options[ $(this).text() ] = function() {
+                    $(form).append( "<input type='hidden' name='"+name+"' value='"+value+"' />" ).submit();
+                };
+            });
+            b.insertAfter( this );
+            $(this).remove();
+            make_popupmenu( b, options );
+        });
+        // Implements auto-saving based on whether the inputs change. We consider
+        // "changed" to be when a field is accessed and not necessarily modified
+        // because of an issue where "onchange" is not triggered when activating
+        // another node, or saving the workflow.
+        $(this).find("input,textarea,select").each( function() {
+            $(this).bind("focus click", function() {
+                workflow.active_form_has_changes = true;
+            });
+        });
+    });
+}
+
+var close_editor = function() {
+    workflow.check_changes_in_active_form();
+    if ( workflow && workflow.has_changes ) {
+        do_close = function() {
+            window.onbeforeunload = undefined;
+            window.document.location = workflow_index_url;
+        };
+        show_modal( "Close workflow editor",
+                    "There are unsaved changes to your workflow which will be lost.",
+                    {
+                        "Cancel" : hide_modal,
+                        "Save Changes" : function() {
+                            save_current_workflow( null, do_close );
+                        }
+                    }, {
+                        "Don't Save": do_close
+                    } );
+    } else {
+        window.document.location = workflow_index_url;
+    }
+};
+
+var save_current_workflow = function ( eventObj, success_callback ) {
+    show_message( "Saving workflow", "progress" );
+    workflow.check_changes_in_active_form();
+    if (!workflow.has_changes) {
+        hide_modal();
+        if ( success_callback ) {
+            success_callback();
+        }
+        return;
+    }
+    workflow.rectify_workflow_outputs();
+    var savefn = function(callback) {
+        $.ajax( {
+            url: save_workflow_url,
+            type: "POST",
+            data: {
+                id: workflow_id,
+                workflow_data: function() { return JSON.stringify( workflow.to_simple() ); },
+                "_": "true"
+            },
+            dataType: 'json',
+            success: function( data ) {
+                var body = $("<div></div>").text( data.message );
+                if ( data.errors ) {
+                    body.addClass( "warningmark" );
+                    var errlist = $( "<ul/>" );
+                    $.each( data.errors, function( i, v ) {
+                        $("<li></li>").text( v ).appendTo( errlist );
+                    });
+                    body.append( errlist );
+                } else {
+                    body.addClass( "donemark" );
+                }
+                workflow.name = data.name;
+                workflow.has_changes = false;
+                workflow.stored = true;
+                show_workflow_parameters();
+                if ( data.errors ) {
+                    show_modal( "Saving workflow", body, { "Ok" : hide_modal } );
+                } else {
+                    if (callback) {
+                        callback();
+                    }
+                    hide_modal();
+                }
+            }
+        });
+    };
+
+    // We bind to ajaxStop because of auto-saving, since the form submission ajax
+    // call needs to be completed so that the new data is saved
+    if (active_ajax_call) {
+        $(document).bind('ajaxStop.save_workflow', function() {
+            $(document).unbind('ajaxStop.save_workflow');
+            savefn();
+            $(document).unbind('ajaxStop.save_workflow'); // IE7 needs it here
+            active_ajax_call = false;
+        });
+    } else {
+        savefn(success_callback);
+    }
+};

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f static/scripts/packed/galaxy.workflows.js
--- /dev/null
+++ b/static/scripts/packed/galaxy.workflows.js
@@ -0,0 +1,1 @@
+$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(c,b){var a=prebuild_node("tool",b,c);workflow.add_node(a);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(a);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:c,_:"true"},global:false,dataType:"json",success:function(d){a.init_field_data(d)},error:function(f,g){var d="error loading field data";if(f.status===0){d+=", server unavailable"}a.error(d)}})}function add_node_for_module(a,b){node=prebuild_node(a,b);workflow.add_node(node);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(node);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var o=n.match(c);if(o){d=d.concat(o)}})}});if(d){$.each(d,function(j,l){if($.inArray(l,b)===-1){b.push(l)}})}}});if(b&&b.length!==0){$.each(b,function(g,h){a+="<div>"+h.substring(2,h.length-1)+"</div>"});f.html(a);e.show()}else{f.html(a);e.hide()}}function show_form_for_tool(c,b){$(".right-content").hide();$("#right-content").show().html(c);if(b){$("#right-content").find(".toolForm:first").after("<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Attributes</div><div class='form-row'><label>Annotation / Notes:</label><div style='margin-right: 10px;'><textarea name='annotation' rows='3' style='width: 100%'>"+b.annotation+"</textarea><div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div></div>")}if(b&&b.type=="tool"){pjastr="<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'>             "+display_pja_list()+" <br/> "+display_file_list(b)+" <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div></div><div class='form-row'><div style='margin-right: 10px;'><span id='pja_container'></span>";pjastr+="<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";$("#right-content").find(".toolForm").after(pjastr);for(var a in b.post_job_actions){if(a!="undefined"){display_pja(b.post_job_actions[a],b)}}$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(d){workflow.active_form_has_changes=false;b.update_field_data(d);show_workflow_parameters()},beforeSubmit:function(d){d.push({name:"tool_state",value:b.tool_state});d.push({name:"_",value:"true"})}}).each(function(){var d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var f={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:d},create:function(v){var w=e.TYPE_DICT[v.type]||e;return new w(v)}});var d=e.extend({defaults:t.extend({},e.prototype.defaults,{min:null,max:null}),initialize:function(){e.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return e.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,f);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var r=Backbone.Model.extend(f);var i=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof r){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(i.prototype,f);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(c.prototype,f);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.model_class;if(z.indexOf("Tool")===z.length-4){return v.attributes.tools.get(A.id)}else{if(z==="ToolSection"){var y=t.map(A.elems,x);A.elems=y;return new i(A)}else{if(z==="ToolSectionLabel"){return new r(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof i){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof r){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var b=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var o=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof r){var y=new b({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof i){var x=new o({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof r){var A=new b({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,Tool:h,ToolCollection:k,ToolSearch:c,ToolPanel:l,ToolPanelView:s,ToolFormView:q}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},subModelTypes:{integer:"IntegerToolParameter","float":"FloatToolParameter",data:"DataToolParameter",select:"SelectToolParameter"},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var o={};Backbone.Relational.store.addModelScope(o);var j=o.DataToolParameter=e.extend({});var d=o.IntegerToolParameter=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=o.FloatToolParameter=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=o.SelectToolParameter=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});var i=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:e}],urlRoot:galaxy_config.root+"api/tools",remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new i(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(i.prototype,g);var q=Backbone.View.extend({});var m=Backbone.Collection.extend({model:i});var v=Backbone.Model.extend(g);var k=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof i){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(k.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var n=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new k(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof k){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof i){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var l=s.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof i){var B=new l({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof k){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof i){var D=new l({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:i,ToolCollection:m,ToolSearch:c,ToolPanel:n,ToolPanelView:w,ToolFormView:u}});
\ No newline at end of file

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f static/scripts/packed/viz/sweepster.js
--- a/static/scripts/packed/viz/sweepster.js
+++ b/static/scripts/packed/viz/sweepster.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){if(!t.get_samples()){return}t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion}],initialize:function(r){if(r.track){var s=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(r){var s=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",s);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".bs-tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(w==="number"){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(w==="select"){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},G.first().get("track_config")),F=h.object_from_template(H,r,null);F.data_manager.set("data_type","raw_data");F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}});
\ No newline at end of file
+define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion}],initialize:function(r){if(r.track){var s=m.extend({data_url:galaxy_config.root+"dummy1",converted_datasets_state_url:galaxy_config.root+"dummy2"},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(r){var s=this.get("tool");this.set("tool_with_samplable_inputs",s);s.remove_inputs(["data","hidden_data","conditional"]);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".bs-tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_config.root+"images/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(s instanceof g.IntegerToolParameter){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(s instanceof g.SelectToolParameter){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=G.first(),I=H.get("track_config");I.dataset=H;I.tool=null;var F=h.object_from_template(I,r,null);F.init_for_tool_data();F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}});
\ No newline at end of file

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;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;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{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"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}],initialize:function(ae){var ad=this.get("tool"),af=ad.get("inputs").filter(function(ag){return(["data","hidden_data","group"].indexOf(ag.get("type"))!==-1)});ad.get("inputs").remove(af)}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;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;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{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"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});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(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}],initialize:function(ad){this.get("tool").remove_inputs(["data","hidden_data","conditional"])}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:new X.Dataset(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file

diff -r 89813e684db6ba8582aabc7cd045894d2021c872 -r d51946b4a19f41ebb77e79774c01b89357aa007f templates/webapps/galaxy/workflow/editor.mako
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -32,7 +32,8 @@
             "libs/jquery/jstorage",
             "galaxy.workflow_editor.canvas",
             "libs/jquery/jquery.autocomplete",
-            "galaxy.autocom_tagging")}
+            "galaxy.autocom_tagging",
+            "galaxy.workflows" )}
 
     <!--[if lt IE 7]><script type='text/javascript'>
@@ -41,639 +42,37 @@
     <![endif]--><script type='text/javascript'>
-    // Globals
-    workflow = null;
-    canvas_manager = null;
-    active_ajax_call = false;
-    var galaxy_async = new GalaxyAsync();
-    galaxy_async.set_func_url(galaxy_async.set_user_pref, "${h.url_for( controller='user', action='set_user_pref_async' )}");
+        // Globals
+        workflow = null;
+        canvas_manager = null;
+        active_ajax_call = false;
 
-    // jQuery onReady
-    $( function() {
+        var workflow_id = "${trans.security.encode_id( stored.id ) }";
 
-        if ( window.lt_ie_7 ) {
-            show_modal(
-                "Browser not supported",
-                "Sorry, the workflow editor is not supported for IE6 and below."
-            );
-            return;
-        }
+        // URLs used by galaxy.workflows.js
+        var tool_search_url = "${h.url_for( controller='root', action='tool_search' )}",
+            get_datatypes_url = "${h.url_for( controller='workflow', action='get_datatypes' )}",
+            load_workflow_url = "${h.url_for( controller='workflow', action='load_workflow' )}",
+            run_workflow_url = "${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id))}",
+            rename_async_url = "${h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) )}",
+            annotate_async_url = "${h.url_for( controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id) )}",
+            get_new_module_info_url = "${h.url_for(controller='workflow', action='get_new_module_info' )}",
+            workflow_index_url = "${h.url_for( controller='workflow', action='index' )}",
+            save_workflow_url = "${h.url_for(controller='workflow', action='save_workflow' )}";
 
-        // Init searching.
-        $("#tool-search-query").click( function (){
-            $(this).focus();
-            $(this).select();
-        })
-        .keyup( function () {
-            // Remove italics.
-            $(this).css("font-style", "normal");
-            // Don't update if same value as last time
-            if ( this.value.length < 3 ) {
-                reset_tool_search(false);
-            } else if ( this.value != this.lastValue ) {
-                // Add class to denote that searching is active.
-                $(this).addClass("search_active");
-                // input.addClass(config.loadingClass);
-                // Add '*' to facilitate partial matching.
-                var q = this.value + '*';
-                // Stop previous ajax-request
-                if (this.timer) {
-                    clearTimeout(this.timer);
-                }
-                // Start a new ajax-request in X ms
-                $("#search-spinner").show();
-                this.timer = setTimeout(function () {
-                    $.get("${h.url_for( controller='root', action='tool_search' )}", { query: q }, function (data) {
-                        // input.removeClass(config.loadingClass);
-                        // Show live-search if results and search-term aren't empty
-                        $("#search-no-results").hide();
-                        // Hide all tool sections.
-                        $(".toolSectionWrapper").hide();
-                        // This hides all tools but not workflows link (which is in a .toolTitle div).
-                        $(".toolSectionWrapper").find(".toolTitle").hide();
-                        if ( data.length != 0 ) {
-                            // Map tool ids to element ids and join them.
-                            var s = $.map( data, function( n, i ) { return "link-" + n; } );
-                            // First pass to show matching tools and their parents.
-                            $(s).each( function(index,id) {
-                                // Add class to denote match.
-                                $("[id='"+id+"']").parent().addClass("search_match");
-                                $("[id='"+id+"']").parent().show().parent().parent().show().parent().show();
-                            });
-                            // Hide labels that have no visible children.
-                            $(".toolPanelLabel").each( function() {
-                               var this_label = $(this);
-                               var next = this_label.next();
-                               var no_visible_tools = true;
-                               // Look through tools following label and, if none are visible, hide label.
-                               while (next.length !== 0 && next.hasClass("toolTitle")) {
-                                   if (next.is(":visible")) {
-                                       no_visible_tools = false;
-                                       break;
-                                   } else {
-                                       next = next.next();
-                                   }
-                                }
-                                if (no_visible_tools) {
-                                    this_label.hide();
-                                }
-                            });
-                        } else {
-                            $("#search-no-results").show();
-                        }
-                        $("#search-spinner").hide();
-                    }, "json" );
-                }, 200 );
-            }
-            this.lastValue = this.value;
-        });
+    <%
+        from galaxy.jobs.actions.post import ActionBox
+    %>
+        // Post-job action vars.
+        var pja_list = "${ActionBox.get_add_list()}",
+            get_pja_form = function(pja) {
+                var p_str = '';
+                // FIXME: this writes JS code; this logic should be codified in galaxy.workflows.js
+                ${ActionBox.get_forms(trans)}
+                return p_str;
+            };
 
-        // Canvas overview management
-        canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") );
-
-        // Initialize workflow state
-        reset();
-        // Load the datatype info
-        $.ajax( {
-            url: "${h.url_for( controller='workflow', action='get_datatypes' )}",
-            dataType: "json",
-            cache: false,
-            success: function( data ) {
-                populate_datatype_info( data );
-                // Load workflow definition
-                $.ajax( {
-                    url: "${h.url_for( controller='workflow', action='load_workflow' )}",
-                    data: { id: "${trans.security.encode_id( stored.id )}", "_": "true" },
-                    dataType: 'json',
-                    cache: false,
-                    success: function( data ) {
-                         reset();
-                         workflow.from_simple( data );
-                         workflow.has_changes = false;
-                         workflow.fit_canvas_to_nodes();
-                         scroll_to_nodes();
-                         canvas_manager.draw_overview();
-                         // Determine if any parameters were 'upgraded' and provide message
-                         upgrade_message = "";
-                         $.each( data.upgrade_messages, function( k, v ) {
-                            upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + "<ul>");
-                            $.each( v, function( i, vv ) {
-                                upgrade_message += "<li>" + vv +"</li>";
-                            });
-                            upgrade_message += "</ul></li>";
-                         });
-                         if ( upgrade_message ) {
-                            show_modal( "Workflow loaded with changes",
-                                        "Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>" + upgrade_message + "</ul>",
-                                        { "Continue" : hide_modal } );
-                         } else {
-                            hide_modal();
-                         }
-                         show_workflow_parameters();
-                     },
-                     beforeSubmit: function( data ) {
-                         show_message( "Loading workflow", "progress" );
-                     }
-                });
-            }
-        });
-
-        // For autosave purposes
-        $(document).ajaxStart( function() {
-            active_ajax_call = true;
-            $(document).bind( "ajaxStop.global", function() {
-                active_ajax_call = false;
-            });
-        });
-
-        $(document).ajaxError( function ( e, x ) {
-            // console.log( e, x );
-            var message = x.responseText || x.statusText || "Could not connect to server";
-            show_modal( "Server error", message, { "Ignore error" : hide_modal } );
-            return false;
-        });
-
-        make_popupmenu( $("#workflow-options-button"), {
-            "Save" : save_current_workflow,
-            "Run": function() {
-                window.location = "${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id))}";
-            },
-            ##"Create New" : create_new_workflow_dialog,
-            "Edit Attributes" : edit_workflow_attributes,
-            ##"Edit Workflow Outputs": edit_workflow_outputs,
-            "Auto Re-layout": layout_editor,
-            ##"Load a Workflow" : load_workflow,
-            "Close": close_editor
-        });
-
-        function edit_workflow_outputs(){
-            workflow.clear_active_node();
-            $('.right-content').hide();
-            var new_content = "";
-            for (var node_key in workflow.nodes){
-                var node = workflow.nodes[node_key];
-                if(node.type == 'tool'){
-                    new_content += "<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step " + node.id + " - " + node.name + "</div>";
-                    for (var ot_key in node.output_terminals){
-                        var output = node.output_terminals[ot_key];
-                        // if (node.workflow_outputs[node.id + "|" + output.name]){
-                        if ($.inArray(output.name, node.workflow_outputs) != -1){
-                            new_content += "<p>"+output.name +"<input type='checkbox' name='"+ node.id + "|" + output.name +"' checked /></p>";
-                        }
-                        else{
-                            new_content += "<p>"+output.name +"<input type='checkbox' name='"+ node.id + "|" + output.name +"' /></p>";
-                        }
-                    }
-                    new_content += "</div>";
-                }
-            }
-            $("#output-fill-area").html(new_content);
-            $("#output-fill-area input").bind('click', function(){
-                var node_id = this.name.split('|')[0];
-                var output_name = this.name.split('|')[1];
-                if (this.checked){
-                    if($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) == -1){
-                        workflow.nodes[node_id].workflow_outputs.push(output_name);
-                    }//else it's already in the array.  Shouldn't happen, but forget it.
-                }else{
-                    while ($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) != -1){
-                        var ia = $.inArray(output_name, workflow.nodes[node_id].workflow_outputs);
-                        workflow.nodes[node_id].workflow_outputs = workflow.nodes[node_id].workflow_outputs.slice(0,ia).concat( workflow.nodes[node_id].workflow_outputs.slice(ia+1) );
-                    }
-                }
-                workflow.has_changes = true;
-            });
-            $('#workflow-output-area').show();
-        }
-
-        function layout_editor() {
-            workflow.layout();
-            workflow.fit_canvas_to_nodes();
-            scroll_to_nodes();
-            canvas_manager.draw_overview();
-        }
-
-        function edit_workflow_attributes() {
-            workflow.clear_active_node();
-            $('.right-content').hide();
-            $('#edit-attributes').show();
-
-        }
-
-        // On load, set the size to the pref stored in local storage if it exists
-        overview_size = $.jStorage.get("overview-size");
-        if (overview_size !== undefined) {
-            $("#overview-border").css( {
-                width: overview_size,
-                height: overview_size
-            });
-        }
-
-        // Show viewport on load unless pref says it's off
-        if ($.jStorage.get("overview-off")) {
-            hide_overview();
-        } else {
-            show_overview();
-        }
-
-        // Stores the size of the overview into local storage when it's resized
-        $("#overview-border").bind( "dragend", function( e, d ) {
-            var op = $(this).offsetParent();
-            var opo = op.offset();
-            var new_size = Math.max( op.width() - ( d.offsetX - opo.left ),
-                                     op.height() - ( d.offsetY - opo.top ) );
-            $.jStorage.set("overview-size", new_size + "px");
-        });
-
-        function show_overview() {
-            $.jStorage.set("overview-off", false);
-            $("#overview-border").css("right", "0px");
-            $("#close-viewport").css("background-position", "0px 0px");
-        }
-
-        function hide_overview() {
-            $.jStorage.set("overview-off", true);
-            $("#overview-border").css("right", "20000px");
-            $("#close-viewport").css("background-position", "12px 0px");
-        }
-
-        // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly
-        $("#close-viewport").click( function() {
-            if ( $("#overview-border").css("right") === "0px" ) {
-                hide_overview();
-            } else {
-                show_overview();
-            }
-        });
-
-        // Unload handler
-        window.onbeforeunload = function() {
-            if ( workflow && workflow.has_changes ) {
-                return "There are unsaved changes to your workflow which will be lost.";
-            }
-        };
-
-        // Tool menu
-        $( "div.toolSectionBody" ).hide();
-        $( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" );
-        var last_expanded = null;
-        $( "div.toolSectionTitle" ).each( function() {
-           var body = $(this).next( "div.toolSectionBody" );
-           $(this).click( function() {
-               if ( body.is( ":hidden" ) ) {
-                   if ( last_expanded ) last_expanded.slideUp( "fast" );
-                   last_expanded = body;
-                   body.slideDown( "fast" );
-               }
-               else {
-                   body.slideUp( "fast" );
-                   last_expanded = null;
-               }
-           });
-        });
-
-        // Rename async.
-        async_save_text("workflow-name", "workflow-name", "${h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) )}", "new_name");
-
-        // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.
-        $('#workflow-tag').click( function() {
-            $('.tag-area').click();
-            return false;
-        });
-        // Annotate async.
-        async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4);
-    });
-
-    // Global state for the whole workflow
-    function reset() {
-        if ( workflow ) {
-            workflow.remove_all();
-        }
-        workflow = new Workflow( $("#canvas-container") );
-    }
-
-    function scroll_to_nodes() {
-        var cv = $("#canvas-viewport");
-        var cc = $("#canvas-container");
-        var top, left;
-        if ( cc.width() < cv.width() ) {
-            left = ( cv.width() - cc.width() ) / 2;
-        } else {
-            left = 0;
-        }
-        if ( cc.height() < cv.height() ) {
-            top = ( cv.height() - cc.height() ) / 2;
-        } else {
-            top = 0;
-        }
-        cc.css( { left: left, top: top } );
-    }
-
-    // Add a new step to the workflow by tool id
-    function add_node_for_tool( id, title ) {
-        var node = prebuild_node( 'tool', title, id );
-        workflow.add_node( node );
-        workflow.fit_canvas_to_nodes();
-        canvas_manager.draw_overview();
-        workflow.activate_node( node );
-        $.ajax( {
-            url: "${h.url_for(controller='workflow', action='get_new_module_info' )}",
-            data: { type: "tool", tool_id: id, "_": "true" },
-            global: false,
-            dataType: "json",
-            success: function( data ) {
-                node.init_field_data( data );
-            },
-            error: function( x, e ) {
-                var m = "error loading field data";
-                if ( x.status === 0 ) {
-                    m += ", server unavailable";
-                }
-                node.error( m );
-            }
-        });
-    }
-
-    function add_node_for_module( type, title ) {
-        node = prebuild_node( type, title );
-        workflow.add_node( node );
-        workflow.fit_canvas_to_nodes();
-        canvas_manager.draw_overview();
-        workflow.activate_node( node );
-        $.ajax( {
-            url: "${h.url_for(controller='workflow', action='get_new_module_info' )}",
-            data: { type: type, "_": "true" },
-            dataType: "json",
-            success: function( data ) {
-                node.init_field_data( data );
-            },
-            error: function( x, e ) {
-                var m = "error loading field data"
-                if ( x.status == 0 ) {
-                    m += ", server unavailable"
-                }
-                node.error( m );
-            }
-        });
-    }
-
-<%
-    from galaxy.jobs.actions.post import ActionBox
-%>
-
-    // This function preloads how to display known pja's.
-    function display_pja(pja, node){
-        // DBTODO SANITIZE INPUTS.
-        p_str = '';
-        ${ActionBox.get_forms(trans)}
-        $("#pja_container").append(p_str);
-        $("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
-            action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
-            $(this).closest(".toolForm").remove();
-            delete workflow.active_node.post_job_actions[action_to_rem];
-            workflow.active_form_has_changes = true;
-        });
-    }
-
-    function display_pja_list(){
-        return "${ActionBox.get_add_list()}";
-    }
-
-    function display_file_list(node){
-        addlist = "<select id='node_data_list' name='node_data_list'>";
-        for (var out_terminal in node.output_terminals){
-            addlist += "<option value='" + out_terminal + "'>"+ out_terminal +"</option>";
-        }
-        addlist += "</select>";
-        return addlist;
-    }
-
-    function new_pja(action_type, target, node){
-        if (node.post_job_actions === undefined){
-            //New tool node, set up dict.
-            node.post_job_actions = {};
-        }
-        if (node.post_job_actions[action_type+target] === undefined){
-            var new_pja = {};
-            new_pja.action_type = action_type;
-            new_pja.output_name = target;
-            node.post_job_actions[action_type+target] = null;
-            node.post_job_actions[action_type+target] =  new_pja;
-            display_pja(new_pja, node);
-            workflow.active_form_has_changes = true;
-            return true;
-        } else {
-            return false;
-        }
-    }
-
-    function show_workflow_parameters(){
-        var parameter_re = /\$\{.+?\}/g;
-        var workflow_parameters = [];
-        var wf_parm_container = $("#workflow-parameters-container");
-        var wf_parm_box = $("#workflow-parameters-box");
-        var new_parameter_content = "";
-        var matches = [];
-        $.each(workflow.nodes, function (k, node){
-            var form_matches = node.form_html.match(parameter_re);
-            if (form_matches){
-                matches = matches.concat(form_matches);
-            }
-            if (node.post_job_actions){
-                $.each(node.post_job_actions, function(k, pja){
-                    if (pja.action_arguments){
-                        $.each(pja.action_arguments, function(k, action_argument){
-                            var arg_matches = action_argument.match(parameter_re);
-                            if (arg_matches){
-                                matches = matches.concat(arg_matches);
-                            }
-                        });
-                    }
-                });
-                if (matches){
-                    $.each(matches, function(k, element){
-                        if ($.inArray(element, workflow_parameters) === -1){
-                            workflow_parameters.push(element);
-                        }
-                    });
-                }
-            }
-        });
-        if (workflow_parameters && workflow_parameters.length !== 0){
-            $.each(workflow_parameters, function(k, element){
-                new_parameter_content += "<div>" + element.substring(2, element.length -1) + "</div>";
-            });
-            wf_parm_container.html(new_parameter_content);
-            wf_parm_box.show();
-        }else{
-            wf_parm_container.html(new_parameter_content);
-            wf_parm_box.hide();
-        }
-    }
-
-    function show_form_for_tool( text, node ) {
-        $('.right-content').hide();
-        $("#right-content").show().html( text );
-        // Add metadata form to tool.
-        if (node) {
-            $("#right-content").find(".toolForm:first").after( "<p><div class='metadataForm'> \
-                <div class='metadataFormTitle'>Edit Step Attributes</div> \
-                <div class='form-row'> \
-                <label>Annotation / Notes:</label> \
-                        <div style='margin-right: 10px;'> \
-                        <textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \
-                            <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \
-                        </div> \
-                </div> \
-                </div>" );
-        }
-        // Add step actions.
-        if (node && node.type=='tool'){
-            pjastr = "<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> \
-                " + display_pja_list() + " <br/> "+ display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\
-                </div><div class='form-row'>\
-                <div style='margin-right: 10px;'><span id='pja_container'></span>";
-            pjastr += "<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";
-            $("#right-content").find(".toolForm").after( pjastr );
-            for (var key in node.post_job_actions){
-                if (key != "undefined"){ //To make sure we haven't just deleted it.
-                    display_pja(node.post_job_actions[key], node);
-                }
-            }
-            $("#add_pja").click(function (){
-                new_pja($("#new_pja_list").val(),$("#node_data_list").val(), node);
-            });
-        }
-        $("#right-content").find( "form" ).ajaxForm( {
-            type: 'POST',
-            dataType: 'json',
-            success: function( data ) {
-                workflow.active_form_has_changes = false;
-                node.update_field_data( data );
-                show_workflow_parameters();
-            },
-            beforeSubmit: function( data ) {
-                data.push( { name: 'tool_state', value: node.tool_state } );
-                data.push( { name: '_', value: "true" } );
-            }
-        }).each( function() {
-            var form = this;
-            $(this).find( "select[refresh_on_change='true']").change( function() {
-                $(form).submit();
-            });
-            $(this).find( ".popupmenu" ).each( function() {
-                var id = $(this).parents( "div.form-row" ).attr( 'id' );
-                var b = $('<a class="popup-arrow" id="popup-arrow-for-' + id + '">▼</a>');
-                var options = {};
-                $(this).find( "button" ).each( function() {
-                    var name = $(this).attr( 'name' );
-                    var value = $(this).attr( 'value' );
-                    options[ $(this).text() ] = function() {
-                        $(form).append( "<input type='hidden' name='"+name+"' value='"+value+"' />" ).submit();
-                    };
-                });
-                b.insertAfter( this );
-                $(this).remove();
-                make_popupmenu( b, options );
-            });
-            // Implements auto-saving based on whether the inputs change. We consider
-            // "changed" to be when a field is accessed and not necessarily modified
-            // because of an issue where "onchange" is not triggered when activating
-            // another node, or saving the workflow.
-            $(this).find("input,textarea,select").each( function() {
-                $(this).bind("focus click", function() {
-                    workflow.active_form_has_changes = true;
-                });
-            });
-        });
-    }
-
-    var close_editor = function() {
-        <% next_url = h.url_for( controller='workflow', action='index' ) %>
-        workflow.check_changes_in_active_form();
-        if ( workflow && workflow.has_changes ) {
-            do_close = function() {
-                window.onbeforeunload = undefined;
-                window.document.location = "${next_url}"
-            };
-            show_modal( "Close workflow editor",
-                        "There are unsaved changes to your workflow which will be lost.",
-                        {
-                            "Cancel" : hide_modal,
-                            "Save Changes" : function() {
-                                save_current_workflow( null, do_close );
-                            }
-                        }, {
-                            "Don't Save": do_close
-                        } );
-        } else {
-            window.document.location = "${next_url}";
-        }
-    };
-
-    var save_current_workflow = function ( eventObj, success_callback ) {
-        show_message( "Saving workflow", "progress" );
-        workflow.check_changes_in_active_form();
-        if (!workflow.has_changes) {
-            hide_modal();
-            if ( success_callback ) {
-                success_callback();
-            }
-            return;
-        }
-        workflow.rectify_workflow_outputs();
-        var savefn = function(callback) {
-            $.ajax( {
-                url: "${h.url_for(controller='workflow', action='save_workflow' )}",
-                type: "POST",
-                data: {
-                    id: "${trans.security.encode_id( stored.id )}",
-                    workflow_data: function() { return JSON.stringify( workflow.to_simple() ); },
-                    "_": "true"
-                },
-                dataType: 'json',
-                success: function( data ) {
-                    var body = $("<div></div>").text( data.message );
-                    if ( data.errors ) {
-                        body.addClass( "warningmark" );
-                        var errlist = $( "<ul/>" );
-                        $.each( data.errors, function( i, v ) {
-                            $("<li></li>").text( v ).appendTo( errlist );
-                        });
-                        body.append( errlist );
-                    } else {
-                        body.addClass( "donemark" );
-                    }
-                    workflow.name = data.name;
-                    workflow.has_changes = false;
-                    workflow.stored = true;
-                    show_workflow_parameters();
-                    if ( data.errors ) {
-                        show_modal( "Saving workflow", body, { "Ok" : hide_modal } );
-                    } else {
-                        if (callback) {
-                            callback();
-                        }
-                        hide_modal();
-                    }
-                }
-            });
-        };
-
-        // We bind to ajaxStop because of auto-saving, since the form submission ajax
-        // call needs to be completed so that the new data is saved
-        if (active_ajax_call) {
-            $(document).bind('ajaxStop.save_workflow', function() {
-                $(document).unbind('ajaxStop.save_workflow');
-                savefn();
-                $(document).unbind('ajaxStop.save_workflow'); // IE7 needs it here
-                active_ajax_call = false;
-            });
-        } else {
-            savefn(success_callback);
-        }
-    };
-
+        // NOTE: code to initialize and edit workflows is in galaxy.workflows.js
     </script></%def>

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

--

This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.

    

[galaxy-commits] commit/galaxy-central: jgoecks: Move workflows JavaScript code to its own file for modularity and bundling purposes. Pack scripts.

commits-noreply＠bitbucket.org