allow javascript for analyses

ui/nG6/pi1/analyzes/MothurClassifyAnalyse.js

+/***************************************************************
+*  Copyright notice
+*
+*  (c) 2009 PF bioinformatique de Toulouse <>
+*  All rights reserved
+*
+*  This script is part of the TYPO3 project. The TYPO3 project is
+*  free software; you can redistribute it and/or modify
+*  it under the terms of the GNU General Public License as published by
+*  the Free Software Foundation; either version 2 of the License, or
+*  (at your option) any later version.
+*
+*  The GNU General Public License can be found at
+*  http://www.gnu.org/copyleft/gpl.html.
+*
+*  This script is distributed in the hope that it will be useful,
+*  but WITHOUT ANY WARRANTY; without even the implied warranty of
+*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*  GNU General Public License for more details.
+*
+*  This copyright notice MUST APPEAR in all copies of the script!
+***************************************************************/
+/**
+ * Plugin 'nG6' for the 'nG6' extension.
+ *
+ * @author	PF bioinformatique de Toulouse <>
+ */
+
+$(function () {
+    /* 
+     * Define functions in charge to visualize phylogenic bar charts
+     */
+    $(".phylogeny-bar-view-btn").click(function() {
+    	if ($(":checked[id^=chk_sample_]").size() == 0) {
+    		$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
+    		$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_zero_check").val() + "</div>").dialog("open");
+    		var buttons = {};
+	    	buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }
+	    	$("#user_information_dialog").dialog('option', 'buttons', buttons);
+    	} else if ($(":checked[id^=chk_sample_]").size() == 1) {
+	       	$("#img_dialog").dialog("option", "title", "nG6 - " + $("#analyse_name").val());
+	       	$("#img_dialog").html('<div id="highcharts_container"></div>').dialog("open");
+	       	$("#img_dialog").dialog("option", "width", 850);
+	       	var index = $(":checked[id^=chk_sample_]").attr("id").split("_")[2];
+	        $.get($("#phylogeny_file_"+index).val(), function(data) {
+	        	// First convert mothur_phylo to hash table
+	        	var lines = data.split("\n");
+	        	var current_level = 0;
+	        	var full_phylo = "";
+	        	var taxonomy = new Array(); 
+	        	level_1_keys = new Array();
+	        	level_1_values = new Array();
+	        	for (i=0; i<lines.length; i++) {
+	        		parts = lines[i].split("\t");
+	        		if (parts[0] != "taxlevel" && parts[0] != "0") {
+	        			// If this is a 1st level
+	        			if (parts[0] == "1") {
+	        				level_1_keys.push(parts[2]);
+	        				level_1_values.push(parseInt(parts[4]));
+	        			}
+	        			// If it's a sub level: children
+	        			if (parseInt(parts[0]) > current_level) {
+	        				// If it's a leaf
+	                        if (parseInt(parts[3]) == 0) {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        // It's a node 
+	                        } else {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        }
+		        		// If it's the same level: siblings
+		        		} else if (parseInt(parts[0]) == current_level) {
+		        			var phylo_tab = full_phylo.split(";");
+		        			full_phylo = "";
+		        			var indice = phylo_tab.length-2;
+		        			for (j=0;j<indice;j++) {
+		        				full_phylo += phylo_tab[j] + ";";
+		        			}
+	        				// If it's a leaf
+	                        if (parseInt(parts[3]) == 0) {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        // It's a node 
+	                        } else {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        }
+		        		// If it's a higher level
+		        		} else {
+		        			var phylo_tab = full_phylo.split(";");
+		        			full_phylo = "";
+		        			var indice = phylo_tab.length-(current_level-parseInt(parts[0]))-2;
+		        			for (j=0;j<indice;j++) {
+		        				full_phylo += phylo_tab[j] + ";";
+		        			}
+	        				// If it's a leaf
+	                        if (parseInt(parts[3]) == 0) {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        // It's a node 
+	                        } else {
+	                        	full_phylo += parts[2];
+	                        	taxonomy.push(full_phylo+"\t"+parts[3]+"\t"+parts[4]);
+	                        	full_phylo +=  ";";
+	                        }
+		        		}
+	        			current_level = parseInt(parts[0]);
+	        		}
+	        	}
+	        	
+	        	var colors = new Array("#4572A7","#AA4643","#89A54E","#80699B","#3D96AE","#DB843D","#92A8CD","#A47D7C","#B5CA92", "#FFF718", "#ED00D4", "#D5B0FF", "#91E2F9", "#FFB87E", "#FFFCA3", "#FFA0F5");//Highcharts.getOptions().colors;
+	        	var categories = level_1_keys;
+	        	var name = '';
+	        	data = []
+	        	for (i=0; i<level_1_keys.length; i++) {
+	        		var sub_taxonomy = new Array();
+	        		for (j=0; j<taxonomy.length; j++){
+	        			// Produce the sub table
+	        			var value = taxonomy[j].split("\t")[0];
+	        			if (taxonomy[j].indexOf(level_1_keys[i]) === 0 && level_1_keys[i] != value) {
+	        				sub_taxonomy.push(taxonomy[j]);
+	        			}
+	        		}
+	        		data.push({
+	        			y: level_1_values[i],
+	        			color: colors[i],
+	        			drilldown: {
+	        				name: level_1_keys[i],
+	        				categories: get_categories(sub_taxonomy, 1),
+	        				data: get_data(sub_taxonomy, 1, colors),
+	        				color: colors[i]
+	        			}
+	        		});
+	        	}
+	
+	        	function setChart(name, categories, data, color) {
+					chart.xAxis[0].setCategories(categories);
+					chart.series[0].remove();
+					chart.addSeries({
+						name: name,
+						data: data,
+						color: 'white'
+					});
+				}
+
+				chart = new Highcharts.Chart({
+					chart: {
+						renderTo: 'highcharts_container', 
+						type: 'column'
+					},
+					title: {
+						text: $("#bar_title").val().replace("###DB_NAME###", $("#phylogeny_file_"+index).val().split(".").slice(-3)[0])
+					},
+					subtitle: {
+						text: ''
+					},
+					xAxis: {
+						categories: categories,
+						labels: {
+							rotation: -45,
+							align: 'right'
+						}
+					},
+					yAxis: {
+						title: {
+							text: $("#nb_sequences").val()
+						}
+					},
+                    legend: {
+                        enabled: true
+					},
+					credits: { enabled: false },
+					plotOptions: {
+						column: {
+							cursor: 'pointer',
+							point: {
+								events: {
+									click: function() {
+										var drilldown = this.drilldown;
+										if (drilldown) { // drill down
+											setChart(drilldown.name, drilldown.categories, drilldown.data, drilldown.color);
+										} else { // restore
+											setChart(name, categories, data);
+										}
+									}
+								}
+							},
+							dataLabels: {
+								enabled: true,
+								color: colors[0],
+								style: {
+									fontWeight: 'bold'
+								},
+								formatter: function() {
+									return this.y;
+								}
+							}					
+						}
+					},
+					tooltip: {
+						formatter: function() {
+							var point = this.point,
+								s = this.x +':<b>'+ this.y +' ' + $("#sequences").val() + '</b><br/>';
+							if (point.drilldown) {
+								s += $("#click_to_view").val().replace("###CATEGORY###", point.category);
+							} else {
+								s += $("#click_to_return").val();
+							}
+							return s;
+						}
+					},
+					series: [{
+						name: name,
+						data: data,
+						color: 'white'
+					}]
+				});
+	        });
+    	} else {
+    		/* Function in charge to create the chart */
+            function updateChart(rankid) {
+            	var ajax = new Array();
+                var samples = new Array();
+                var index = "";
+                $(":checked[id^=chk_sample_]").each(function(){
+    	            index = $(this).attr("id").split("_")[2];
+    	            ajax.push($.ajax($("#phylogeny_file_"+index).val()));
+    	            samples.push($("#sample_id_"+index).html());
+        		});
+                $.when.apply($, ajax).done(function(){
+                	var taxonomy = new Array();
+                	var taxonomy_val = new Array();
+                	var samples_taxonomy = new Array();
+                	var taxlevel = rankid.split(".").length - 1;
+                	// for each taxonomy files
+                    for( var i = 0; i < arguments.length; i++ ) {
+                    	samples_taxonomy.push(new Array());
+                    	var rank_found = false;
+                    	var lines = arguments[i][0].split("\n");
+        	        	for (j=0; j<lines.length; j++) {
+        	        		parts = lines[j].split("\t");
+        	        		if (rank_found && parseInt(parts[0]) == taxlevel) {
+        	        			break;
+        	        		}
+        	        		if (rank_found && parseInt(parts[0]) == taxlevel + 1) {
+        	        			if (taxonomy.indexOf(parts[2].replace(/"/g, '')) === -1) {
+        	        				taxonomy.push(parts[2].replace(/"/g, ''));
+        	        				taxonomy_val.push(parts[1]);
+        	        			}
+        	        			samples_taxonomy[i][parts[1]] = parts[4];
+        	        		}
+        	        		if (parts[1] == rankid) {
+        	        			rank_found = true;
+        	        		}
+        	        	}
+                    }
+                    var series_table = new Array();
+                    for (i in samples) {
+                    	data_table = new Array();
+                    	for (j in taxonomy_val) {
+                    		if (taxonomy_val[j] in samples_taxonomy[i]) {
+                    			data_table.push(parseInt(samples_taxonomy[i][taxonomy_val[j]]))
+                    		} else {
+                    			data_table.push(0);
+                    		}
+                    	}
+                    	series_table.push({name:samples[i], data:data_table});
+                    }
+                    chart = new Highcharts.Chart({
+    					chart: {
+    						renderTo: 'highcharts_container',
+    						defaultSeriesType: 'column'
+    					},
+    					credits: { enabled: false },
+    					title: {
+    						text: $("#bar_title").val().replace("###DB_NAME###", $("#phylogeny_file_"+index).val().split(".").slice(-3)[0])
+    					},
+    					subtitle: {
+    						text: ''
+    					},
+    					xAxis: {
+    						categories: taxonomy,
+    						labels: {
+    							rotation: -45,
+    							align: 'right'
+    						}
+    					},
+    					yAxis: {
+    						min: 0,
+    						title: {
+    							text: $("#nb_sequences").val()
+    						}
+    					},
+    					legend: {
+    						layout: 'vertical',
+    						backgroundColor: '#FFFFFF',
+    						align: 'left',
+    						verticalAlign: 'top',
+    						x: 100,
+    						y: 70,
+    						floating: true,
+    						shadow: true
+    					},
+    					tooltip: {
+    						formatter: function() {
+    							return ''+
+    								this.x +': '+ this.y +' '+ $("#sequences").val();
+    						}
+    					},
+    					plotOptions: {
+    						column: {
+    							pointPadding: 0.2,
+    							borderWidth: 0
+    						}
+    					},
+    				        series: series_table
+    				});
+                });
+            }
+            
+            $("#img_dialog").dialog("option", "title", "nG6 - " + $("#analyse_name").val());
+            $("#img_dialog").dialog("option", "width", 1200);
+            $("#img_dialog").html('<div id="navigation_container" style="float: left; width: 280px;"></div><div id="highcharts_container" style="width: 900px;"></div>').dialog("open");
+        	var ajax = new Array();
+            var samples = new Array();
+            $(":checked[id^=chk_sample_]").each(function(){
+	            var index = $(this).attr("id").split("_")[2];
+	            ajax.push($.ajax($("#phylogeny_file_"+index).val()));
+	            samples.push($("#phylogeny_file_"+index).val());
+    		});            
+            // Init the navigation
+            $.when.apply($, ajax).done(function(){
+               	$("#navigation_container").html('<p class="information">'+$("#navigation_txt").val() + '</p><div class="underline"> </div><br /><div id="jstree_navigation"></div>');
+                var html_data = $("<ul></ul>");
+                var current_level = -1;
+                var parentl = ""
+                for( var i = 0; i < arguments.length; i++ ) {
+                	var lines = arguments[i][0].split("\n");
+    	        	for (j=0; j<lines.length; j++) {
+    	        		if (lines[j] != "") {
+        	        		mparts = lines[j].split("\t");
+        	        		if (mparts[0] != "taxlevel" && mparts[0] != "9") {
+        	        			// If this guy doesnt exist yet
+        	        			if (html_data.find("#li_"+mparts[1].replace(/\./g, '_')).length == 0) {
+        	        				parentl = mparts[1].split(".").slice(0,-1).join("_");
+	        	        			// If no parent yet, this is the root
+	        	        			if (html_data.find("#li_"+parentl).length == 0) {
+	        	        				html_data.append('<li id=li_'+mparts[1].replace(/\./g, '_')+'><a class="taxonomy_click" id="'+mparts[1].replace(/\./g, '_')+'">'+mparts[2]+'</a><ul></ul></li>');
+	        	        			// Otherwise append it to the parent
+	        	        			} else {
+	        	        				if (mparts[0] != "8") {
+	        	        					html_data.find("#li_"+parentl+" > ul").append('<li id=li_'+mparts[1].replace(/\./g, '_')+'><a class="taxonomy_click" id="'+mparts[1].replace(/\./g, '_')+'">'+mparts[2]+'</a><ul></ul></li>');
+	        	        				} else {
+	        	        					html_data.find("#li_"+parentl+" > ul").append('<li id=li_'+mparts[1].replace(/\./g, '_')+'><a class="taxonomy_click" id="'+mparts[1].replace(/\./g, '_')+'">'+mparts[2]+'</a></li>');
+	        	        				}
+	        	        			}
+        	        			}
+
+        	        		}
+    	        		}
+    	        	}
+                }
+                $("#jstree_navigation").jstree({
+            		"themes" : {
+            			"theme" : "default",
+            			"icons" : false
+            		},
+            		"ui" : {
+            			"select_limit" : 1,
+            			"selected_parent_close" : "select_parent",
+            			"initially_select" : [ "li_0" ]
+            		},
+                    "html_data" : {
+                        "data" : html_data
+                    },
+                    "plugins" : [ "themes", "html_data", "ui" ]
+                });
+                
+                $("a.taxonomy_click").click(function(){
+                	updateChart($(this).attr("id").replace(/_/g, '.'));
+                });                    
+            });
+            // Init the chart
+            updateChart("0");
+    	}
+    });
+    function get_categories(lines, depth) {
+    	var cathegories = new Array();
+    	for (var x=0;x<lines.length;x++) {
+    		parts = lines[x].split(";");
+    		// If this is the right depth
+    		if (depth+1 == parts.length) {
+    			var values = lines[x].split("\t");
+    			var final_value = values[0].split(";");
+    			cathegories.push(final_value[final_value.length-1].replace(/"/g, ''));
+    		}
+    	}
+    	return cathegories;
+    }
+    function get_data(lines, depth, colors) {
+    	var data = new Array(); 
+    	var current_level = new Array();
+    	for (var i=0;i<lines.length;i++) {
+    		parts = lines[i].split(";");
+    		// If this is the right depth
+    		if (depth+1 == parts.length) {
+    			current_level.push(lines[i]);
+    		}
+    	}
+    	for (var i=0;i<current_level.length;i++) {
+    		parts = current_level[i].split("\t");
+    		// If it's a leaf
+    		if (parts[1] == "0") {
+    			data.push({y:parseInt(parts[2]), color: colors[i]});			
+    		// It's a node
+    		} else {
+        		var sub_taxonomy = new Array();
+        		for (j=0; j<lines.length; j++){
+        			// Produce the sub table
+        			var value = lines[j].split("\t")[0];
+        			if (lines[j].indexOf(parts[0]) === 0 && parts[0] != value) {
+        				sub_taxonomy.push(lines[j]);
+        			}
+        		}
+        		var final_name = parts[0].replace(/"/g, '');
+        		data.push({y:parseInt(parts[2]), color: colors[i], drilldown:{name:final_name, categories:get_categories(sub_taxonomy, depth+1), data:get_data(sub_taxonomy, depth+1, colors)}});
+    		}
+    	}
+    	return data;
+    }
+    
+    /*$(".phylogeny-tree-view-btn").click(function() {
+	if ($(":checked[id^=chk_sample_]").size() == 0) {
+		$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
+		$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_zero_check").val() + "</div>").dialog("open");
+		var buttons = {};
+    	buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }
+    	$("#user_information_dialog").dialog('option', 'buttons', buttons);
+	} else if ($(":checked[id^=chk_sample_]").size() == 1) {
+       	$("#img_dialog").dialog("option", "title", "nG6 - " + $("#analyse_name").val());
+       	var init_control = false;
+       	if ($("#svgCanvas_control").html() == "") {init_control=true;}
+       	$("#img_dialog").html('<div id="svgCanvas_control" class="tx-nG6-wait"></div><div id="svgCanvas"></div>').dialog("open");
+       	var index = $(":checked[id^=chk_sample_]").attr("id").split("_")[2];
+       	$.ajax({
+       		url: $("#phylogeny_file_"+index).val(),
+       		success: function(data){
+       			var xml_data = '<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">';
+	        	xml_data += '<phylogeny rooted="false">';
+	        	xml_data += '<render>';
+	        	xml_data += '    <parameters>';
+	        	xml_data += '        <circular>';
+	        	xml_data += '            <bufferRadius>0.5</bufferRadius>';
+	        	xml_data += '        </circular>';
+	        	xml_data += '        <rectangular>';
+	        	xml_data += '            <alignRight>1</alignRight>';
+	        	xml_data += '            <bufferX>300</bufferX>';
+	        	xml_data += '        </rectangular>';
+	        	xml_data += '    </parameters>';
+	        	xml_data += '    <charts>';
+	        	xml_data += '        <content type="bar" fill="#666" width="0.2" />';
+	        	xml_data += '    </charts>';
+	        	xml_data += '    <styles>';
+	        	xml_data += '        <barChart fill="#333" stroke-width="0" />';
+	        	xml_data += '    </styles>';
+	        	xml_data += '</render>';
+	        	xml_data += '<clade>';
+	        	var current_level = 0;
+	        	var annot = '';
+	        	var lines = data.split("\n");
+	        	var lists = new Array();
+	        	for (i=0; i<lines.length; i++) {
+	        		parts = lines[i].split("\t");
+	        		if (lines[i] != "" && parts[0] != "taxlevel" && parts[0] != "0") {
+	        			var indent = Array(parseInt(parts[0])*4).join(" ");
+	        			// If it's a sub level: children
+	                    if (parseInt(parts[0]) >= current_level) {
+	                        // If it's a leaf
+	                        if (parseInt(parts[3]) == 0) {
+	                            annot += parts[2];
+	                            xml_data += indent + '<clade>';
+	        					xml_data += indent + '    <name>'+parts[2]+'</name>';
+								xml_data += indent + '    <branch_length>1.0</branch_length>';
+								xml_data += indent + '    <annotation>';
+								xml_data += indent + '        <desc>'+annot+'</desc>';
+								xml_data += indent + '    </annotation>';
+								xml_data += indent + '    <chart>';
+								xml_data += indent + '        <content>'+parts[4]+'</content>';
+								xml_data += indent + '    </chart>';
+								xml_data += indent + '</clade>';
+								var annot_parts = annot.split(";");
+								annot_parts.pop();
+	                            annot = annot_parts.join(";");
+	                        // It's a node
+	                        } else {
+	                            annot += parts[2] + ";";
+	                            xml_data += indent + '    <clade>';
+	                            xml_data += indent + '        <branch_length>1.0</branch_length>';
+	                        }
+	                    // If it's a higher level
+	                    } else {
+	                    	for (j=0; j<current_level-parseInt(parts[0]);j++) {
+	                    		var ind = Array((current_level-j-1)*4).join(" ");
+	                    		xml_data += ind + '</clade>';
+								var annot_parts = annot.split(";");
+								annot_parts.pop();
+	                            annot = annot_parts.join(";");
+	                    	}
+	                        // If it's a leaf
+	                        if (parseInt(parts[3]) == 0) {
+	                            annot += parts[2];
+	                            xml_data += indent + '<clade>';
+	        					xml_data += indent + '    <name>'+parts[2]+'</name>';
+								xml_data += indent + '    <branch_length>1.0</branch_length>';
+								xml_data += indent + '    <annotation>';
+								xml_data += indent + '        <desc>'+annot+'</desc>';
+								xml_data += indent + '    </annotation>';
+								xml_data += indent + '    <chart>';
+								xml_data += indent + '        <content>'+parts[4]+'</content>';
+								xml_data += indent + '    </chart>';
+								xml_data += indent + '</clade>';
+								var annot_parts = annot.split(";");
+								annot_parts.pop();
+	                            annot = annot_parts.join(";");
+	                        // It's a node
+	                        } else {
+	                            annot += parts[2] + ';';
+	                            xml_data += indent + '    <clade>';
+	                            xml_data += indent + '        <branch_length>1.0</branch_length>';
+	                        }
+	                    }
+	                    current_level = parseInt(parts[0]);
+	        		}
+	        	}
+            	for (j=0; j<current_level-1;j++) {
+            		var ind = Array((current_level-1)*4).join(" ");
+            		xml_data += ind + '</clade>';
+            	}
+	        	xml_data += '</clade>';
+	        	xml_data += '</phylogeny>';
+	        	xml_data += '</phyloxml>';
+	        	
+	        	
+	        	var lists = new Array();
+	        	lists[] = new Array("Bacteria")
+	        	
+	        	var controler_html = 'Display tree for ';
+	        	controler_html += '<select>';
+	        	
+	        	
+	        	
+				var dataObject = {
+					xml: xml_data,
+					fileSource: false
+				};		
+				phylocanvas = new Smits.PhyloCanvas(
+					dataObject,
+					'svgCanvas', 
+					800, 800,
+					'linear'
+				);
+				$("#svgCanvas_control").removeClass("tx-nG6-wait");
+				$("#svgCanvas_control").html(controler_html);
+		        init(); //unitip
+       	  	}
+       	});
+       	
+	} else {
+		alert("no more than 1");
+	}
+});*/
+
+});

ui/nG6/pi1/analyzes/MothurOTUAnalyse.js

+/***************************************************************