Fixed additive effect for lodchart

Made some more changes/improvements to various tables throughout the site

16 files changed, 1176 insertions, 1279 deletions

diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 672a9401..79cb1481 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -53,6 +53,9 @@ class IntervalMapping(object):
  
         self.set_options(start_vars)
  
+        self.score_type = "LRS"
+        self.cutoff = 3
+
         self.json_data = {}
         self.json_data['lodnames'] = ['lod.hk']
         self.gen_reaper_results(tempdata)
@@ -65,22 +68,17 @@ class IntervalMapping(object):
             
             chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
         
-        #print("self.qtl_results:", self.qtl_results)
-        
         print("JSON DATA:", self.json_data)
         
-        #os.chdir(webqtlConfig.TMPDIR)
         json_filename = webqtlUtil.genRandStr(prefix="intmap_")
         json.dumps(self.json_data, webqtlConfig.TMPDIR + json_filename)
         
         self.js_data = dict(
-            result_score_type = "LRS",
+            result_score_type = self.score_type,
             manhattan_plot = self.manhattan_plot,
-            additive = self.additive,
             chromosomes = chromosome_mb_lengths,
             qtl_results = self.qtl_results,
             json_data = self.json_data
-            #lrs_lod = self.lrs_lod,
         )
 
     def set_options(self, start_vars):
@@ -158,7 +156,6 @@ class IntervalMapping(object):
         self.json_data['chr'] = []
         self.json_data['pos'] = []
         self.json_data['lod.hk'] = []
-        self.json_data['additive'] = []
         self.json_data['markernames'] = []
         for qtl in reaper_results:
             reaper_locus = qtl.locus
@@ -166,6 +163,7 @@ class IntervalMapping(object):
             self.json_data['lod.hk'].append(qtl.lrs)
             self.json_data['markernames'].append(reaper_locus.name)
             if self.additive:
+                self.json_data['additive'] = []
                 self.json_data['additive'].append(qtl.additive)
             locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
             qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive}
@@ -206,8 +204,9 @@ class IntervalMapping(object):
         self.json_data['chr'] = []
         self.json_data['pos'] = []
         self.json_data['lod.hk'] = []
-        self.json_data['additive'] = []
         self.json_data['markernames'] = []
+        if self.additive:
+            self.json_data['additive'] = []
 
         #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
         self.qtl_results = []
@@ -223,37 +222,6 @@ class IntervalMapping(object):
             qtl = {"lrs_value": qtl.lrs, "chr":reaper_locus.chr, "Mb":reaper_locus.Mb,
                    "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive}
             self.qtl_results.append(qtl)
-            
-
-    def gen_qtl_results_2(self, tempdata):
-        """Generates qtl results for plotting interval map"""
-    
-        self.dataset.group.get_markers()
-        self.dataset.read_genotype_file()
-    
-        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
-    
-        #if self.dataset.group.species == "human":
-        #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
-        #else:
-        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-        
-        no_val_samples = self.identify_empty_samples()
-        trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-        
-        genotype_matrix = np.array(trimmed_genotype_data).T
-        
-        t_stats, p_values = lmm.run(
-            pheno_vector,
-            genotype_matrix,
-            restricted_max_likelihood=True,
-            refit=False,
-            temp_data=tempdata
-        )
-        
-        self.dataset.group.markers.add_pvalues(p_values)
-        
-        self.qtl_results = self.dataset.group.markers.markers
 
 
     def identify_empty_samples(self):
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c003f5e8..850dfc7f 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -79,9 +79,9 @@ class MarkerRegression(object):
             included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
             self.dataset.group.get_specified_markers(markers = included_markers)
             self.dataset.group.markers.add_pvalues(p_values)
-            qtl_results = self.dataset.group.markers.markers
+            results = self.dataset.group.markers.markers
         elif self.mapping_method == "rqtl_plink":
-            qtl_results = self.run_rqtl_plink()
+            results = self.run_rqtl_plink()
         elif self.mapping_method == "rqtl_geno":
             if start_vars['num_perm'] == "":
                 self.num_perm = 0
@@ -95,32 +95,32 @@ class MarkerRegression(object):
             if start_vars['pair_scan'] == "true":
                 self.pair_scan = True
 
-            qtl_results = self.run_rqtl_geno()
-            print("qtl_results:", qtl_results)
+            results = self.run_rqtl_geno()
+            print("qtl_results:", results)
         elif self.mapping_method == "plink":
-            qtl_results = self.run_plink()
-            #print("qtl_results:", pf(qtl_results))
+            results = self.run_plink()
+            #print("qtl_results:", pf(results))
         elif self.mapping_method == "pylmm":
             print("RUNNING PYLMM")
             self.num_perm = start_vars['num_perm']
             if self.num_perm != "":
                 if int(self.num_perm) > 0:
 	             self.run_permutations(str(temp_uuid))
-            qtl_results = self.gen_data(str(temp_uuid))
+            results = self.gen_data(str(temp_uuid))
         else:
             print("RUNNING NOTHING")
             
         if self.pair_scan == True:  
-            self.filtered_markers = []
+            self.qtl_results = []
             highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
-            for marker in qtl_results:
+            for marker in results:
                 if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                     if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                         highest_chr = marker['chr1']
                     if 'lod_score' in marker:
-                        self.filtered_markers.append(marker)
+                        self.qtl_results.append(marker)
 
-            for qtl in enumerate(self.filtered_markers):
+            for qtl in enumerate(self.qtl_results):
                 self.json_data['chr1'].append(str(qtl['chr1']))
                 self.json_data['chr2'].append(str(qtl['chr2']))
                 self.json_data['Mb'].append(qtl['Mb'])
@@ -132,19 +132,20 @@ class MarkerRegression(object):
                 data_set = self.dataset.name,
                 maf = self.maf,
                 manhattan_plot = self.manhattan_plot,
-                qtl_results = self.filtered_markers,
+                qtl_results = self.qtl_results,
             )
 
         else:
-            self.lod_cutoff = 2    
-            self.filtered_markers = []
+            self.score_type = "LRS"
+            self.cutoff = 2    
+            self.qtl_results = []
             highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
-            for marker in qtl_results:
+            for marker in results:
                 if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
                     if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
                         highest_chr = marker['chr']
                     if 'lod_score' in marker:
-                        self.filtered_markers.append(marker)
+                        self.qtl_results.append(marker)
 
             self.json_data['chr'] = []
             self.json_data['pos'] = []
@@ -155,8 +156,7 @@ class MarkerRegression(object):
             self.json_data['significant'] = self.significant
 
             #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-            self.qtl_results = []
-            for index, qtl in enumerate(self.filtered_markers):
+            for index, qtl in enumerate(self.qtl_results):
                 if index<40:
                     print("lod score is:", qtl['lod_score'])
                 if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
@@ -179,14 +179,14 @@ class MarkerRegression(object):
         
 
             self.js_data = dict(
-                result_score_type = "LOD",
+                result_score_type = self.score_type,
                 json_data = self.json_data,
                 this_trait = self.this_trait.name,
                 data_set = self.dataset.name,
                 maf = self.maf,
                 manhattan_plot = self.manhattan_plot,
                 chromosomes = chromosome_mb_lengths,
-                qtl_results = self.filtered_markers,
+                qtl_results = self.qtl_results,
             )
         
 
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 631d8632..35b37070 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -20,7 +20,6 @@ lodchart = function() {
   };
   titlepos = 20;
   manhattanPlot = false;
-  additive = false;
   ylim = null;
   additive_ylim = null;
   nyticks = 5;
@@ -70,7 +69,8 @@ lodchart = function() {
         return results;
       })();
       ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
-      if (additive) {
+
+      if ('additive' in data) {
         data['additive'] = (function() {
           var j, len, ref, results;
           ref = data['additive'];
@@ -91,7 +91,7 @@ lodchart = function() {
       g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
       yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
       yticks = yticks != null ? yticks : yscale.ticks(nyticks);
-      if (additive) {
+      if ('additive' in data) {
         additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
         additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
       }
@@ -147,7 +147,7 @@ lodchart = function() {
         return formatAxis(yticks)(d);
       });
       yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
-      if (additive) {
+      if ('additive' in data) {
         rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
         additive_yaxis = g.append("g").attr("class", "y axis");
         additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
@@ -186,12 +186,12 @@ lodchart = function() {
             return yscale(data.lodByChr[chr][i][lodcolumn]);
           });
         };
-        if (additive) {
+        if ('additive' in data) {
           additivecurve = function(chr, lodcolumn) {
             return d3.svg.line().x(function(d) {
               return xscale[chr](d);
             }).y(function(d, i) {
-              return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
+              return additive_yscale(data.additiveByChr[chr][i]);
             });
           };
         }
@@ -203,7 +203,7 @@ lodchart = function() {
             curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
           }
         }
-        if (additive) {
+        if ('additive' in data) {
           ref1 = data.chrnames;
           for (k = 0, len1 = ref1.length; k < len1; k++) {
             chr = ref1[k];
@@ -430,9 +430,6 @@ lodchart = function() {
   chart.yscale = function() {
     return yscale;
   };
-  chart.additive = function() {
-    return additive;
-  };
   chart.additive_yscale = function() {
     return additive_yscale;
   };
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js
index 7c14f4de..113512b4 100644
--- a/wqflask/wqflask/static/new/javascript/panelutil.js
+++ b/wqflask/wqflask/static/new/javascript/panelutil.js
@@ -47,12 +47,19 @@ reorgLodData = function(data, lodvarname) {
   }
   data.posByChr = {};
   data.lodByChr = {};
+  if ('additive' in data){
+    data.additiveByChr = {};
+  }
   _ref = data.chrnames;
   for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
     chr = _ref[i];
     data.posByChr[chr[0]] = [];
     data.lodByChr[chr[0]] = [];
+    if ('additive' in data){
+      data.additiveByChr[chr[0]] = [];
+    }
     _ref1 = data.pos;
+
     for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
       pos = _ref1[j];
       if (data.chr[j].toString() === chr[0]) {
@@ -71,6 +78,12 @@ reorgLodData = function(data, lodvarname) {
           return _results;
         })();
         data.lodByChr[chr[0]].push(lodval);
+
+        if ('additive' in data){
+          addval = data['additive'][j]
+          data.additiveByChr[chr[0]].push(addval);            
+        }
+
       }
     }
   }
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 16ca1886..d14fb98c 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -112,6 +112,11 @@ open_mapping_results = (data) ->
               form.submit()
      )
 
+outlier_text = "One or more outliers exist in this data set. Please review values before mapping. \
+                  Including outliers when mapping may lead to misleading results. \
+                  We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
+                  or simply deleting them."
+
 showalert = (message,alerttype) ->
     $('#alert_placeholder').append('<div id="alertdiv" class="alert ' +  alerttype + '"><a class="close" data-dismiss="alert">×</a><span>'+message+'</span></div>')
     
@@ -126,6 +131,11 @@ $('input[name=display_all]').change(() =>
             $('#suggestive').hide()
 )
 
+$("#pylmm_mapping_compute").on("mouseover", =>
+        if ( $(".outlier").length and $(".outlier-alert").length < 1 ) 
+            showalert(outlier_text, "alert-success outlier-alert")
+)
+
 $("#pylmm_compute").on("click", =>
         $("#progress_bar_container").modal()
         url = "/marker_regression"
@@ -140,8 +150,7 @@ $("#pylmm_compute").on("click", =>
         #    block_outliers()
         do_ajax_post(url, form_data)
 )
-    
-    
+
     
 $("#rqtl_geno_compute").on("click", =>
         $("#progress_bar_container").modal()
@@ -187,11 +196,12 @@ $("#gemma_compute").on("click", =>
         do_ajax_post(url, form_data)
 )
 
+$("#interval_mapping_compute").on("mouseover", =>
+        if ( $(".outlier").length and $(".outlier-alert").length < 1 ) 
+            showalert(outlier_text, "alert-success outlier-alert")
+)
+
 $("#interval_mapping_compute").on("click", =>
-        showalert("One or more outliers exist in this data set. Please review values before mapping. \
-                  Including outliers when mapping may lead to misleading results. \
-                  We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
-                  or simply deleting them.", "alert-success")
         console.log("In interval mapping")
         $("#progress_bar_container").modal()
         url = "/interval_mapping"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index d6f4ba89..3be40a57 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,249 +1,269 @@
-// Generated by CoffeeScript 1.9.2
-var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining;
-
-submit_special = function() {
-  var url;
-  console.log("In submit_special");
-  console.log("this is:", this);
-  console.log("$(this) is:", $(this));
-  url = $(this).data("url");
-  console.log("url is:", url);
-  $("#trait_data_form").attr("action", url);
-  return $("#trait_data_form").submit();
-};
-
-update_time_remaining = function(percent_complete) {
-  var minutes_remaining, now, period, total_seconds_remaining;
-  now = new Date();
-  period = now.getTime() - root.start_time;
-  console.log("period is:", period);
-  if (period > 8000) {
-    total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
-    minutes_remaining = Math.round(total_seconds_remaining / 60);
-    if (minutes_remaining < 3) {
-      return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
-    } else {
-      return $('#time_remaining').text(minutes_remaining + " minutes remaining");
+// Generated by CoffeeScript 1.8.0
+(function() {
+  var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+
+  submit_special = function() {
+    var url;
+    console.log("In submit_special");
+    console.log("this is:", this);
+    console.log("$(this) is:", $(this));
+    url = $(this).data("url");
+    console.log("url is:", url);
+    $("#trait_data_form").attr("action", url);
+    return $("#trait_data_form").submit();
+  };
+
+  update_time_remaining = function(percent_complete) {
+    var minutes_remaining, now, period, total_seconds_remaining;
+    now = new Date();
+    period = now.getTime() - root.start_time;
+    console.log("period is:", period);
+    if (period > 8000) {
+      total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+      minutes_remaining = Math.round(total_seconds_remaining / 60);
+      if (minutes_remaining < 3) {
+        return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+      } else {
+        return $('#time_remaining').text(minutes_remaining + " minutes remaining");
+      }
     }
-  }
-};
-
-get_progress = function() {
-  var params, params_str, temp_uuid, url;
-  console.log("temp_uuid:", $("#temp_uuid").val());
-  temp_uuid = $("#temp_uuid").val();
-  params = {
-    key: temp_uuid
   };
-  params_str = $.param(params);
-  url = "/get_temp_data?" + params_str;
-  console.log("url:", url);
-  $.ajax({
-    type: "GET",
-    url: url,
-    success: (function(_this) {
-      return function(progress_data) {
-        var percent_complete;
-        percent_complete = progress_data['percent_complete'];
-        console.log("in get_progress data:", progress_data);
-        $('#marker_regression_progress').css("width", percent_complete + "%");
-        if (root.start_time) {
-          if (!isNaN(percent_complete)) {
-            return update_time_remaining(percent_complete);
-          }
-        } else {
-          return root.start_time = new Date().getTime();
-        }
-      };
-    })(this)
-  });
-  return false;
-};
 
-block_outliers = function() {
-  return $('.outlier').each((function(_this) {
-    return function(_index, element) {
-      return $(element).find('.trait_value_input').val('x');
+  get_progress = function() {
+    var params, params_str, temp_uuid, url;
+    console.log("temp_uuid:", $("#temp_uuid").val());
+    temp_uuid = $("#temp_uuid").val();
+    params = {
+      key: temp_uuid
     };
-  })(this));
-};
-
-do_ajax_post = function(url, form_data) {
-  $.ajax({
-    type: "POST",
-    url: url,
-    data: form_data,
-    error: (function(_this) {
-      return function(xhr, ajaxOptions, thrownError) {
-        alert("Sorry, an error occurred");
-        console.log(xhr);
-        clearInterval(_this.my_timer);
-        $('#progress_bar_container').modal('hide');
-        $('#static_progress_bar_container').modal('hide');
-        return $("body").html("We got an error.");
-      };
-    })(this),
-    success: (function(_this) {
-      return function(data) {
-        clearInterval(_this.my_timer);
-        $('#progress_bar_container').modal('hide');
-        $('#static_progress_bar_container').modal('hide');
-        return open_mapping_results(data);
-      };
-    })(this)
-  });
-  console.log("settingInterval");
-  this.my_timer = setInterval(get_progress, 1000);
-  return false;
-};
-
-open_mapping_results = function(data) {
-  return $.colorbox({
-    html: data,
-    href: "#mapping_results_holder",
-    height: "90%",
-    width: "90%",
-    onComplete: (function(_this) {
-      return function() {
-        var filename, getSvgXml;
-        root.create_lod_chart();
-        filename = "lod_chart_" + js_data.this_trait;
-        getSvgXml = function() {
-          var svg;
-          svg = $("#topchart").find("svg")[0];
-          return (new XMLSerializer).serializeToString(svg);
+    params_str = $.param(params);
+    url = "/get_temp_data?" + params_str;
+    console.log("url:", url);
+    $.ajax({
+      type: "GET",
+      url: url,
+      success: (function(_this) {
+        return function(progress_data) {
+          var percent_complete;
+          percent_complete = progress_data['percent_complete'];
+          console.log("in get_progress data:", progress_data);
+          $('#marker_regression_progress').css("width", percent_complete + "%");
+          if (root.start_time) {
+            if (!isNaN(percent_complete)) {
+              return update_time_remaining(percent_complete);
+            }
+          } else {
+            return root.start_time = new Date().getTime();
+          }
         };
-        $("#exportform > #export").click(function() {
-          var form, svg_xml;
-          svg_xml = getSvgXml();
-          form = $("#exportform");
-          form.find("#data").val(svg_xml);
-          form.find("#filename").val(filename);
-          return form.submit();
-        });
-        return $("#exportpdfform > #export_pdf").click(function() {
-          var form, svg_xml;
-          svg_xml = getSvgXml();
-          form = $("#exportpdfform");
-          form.find("#data").val(svg_xml);
-          form.find("#filename").val(filename);
-          return form.submit();
-        });
-      };
-    })(this)
-  });
-};
-
-showalert = function(message, alerttype) {
-  return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
-};
-
-$('#suggestive').hide();
-
-$('input[name=display_all]').change((function(_this) {
-  return function() {
-    console.log("check");
-    if ($('input[name=display_all]:checked').val() === "False") {
-      return $('#suggestive').show();
-    } else {
-      return $('#suggestive').hide();
-    }
+      })(this)
+    });
+    return false;
   };
-})(this));
-
-$("#pylmm_compute").on("click", (function(_this) {
-  return function() {
-    var form_data, url;
-    $("#progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("pylmm");
-    $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  block_outliers = function() {
+    return $('.outlier').each((function(_this) {
+      return function(_index, element) {
+        return $(element).find('.trait_value_input').val('x');
+      };
+    })(this));
   };
-})(this));
-
-$("#rqtl_geno_compute").on("click", (function(_this) {
-  return function() {
-    var form_data, url;
-    $("#progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("rqtl_geno");
-    $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
-    $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  do_ajax_post = function(url, form_data) {
+    $.ajax({
+      type: "POST",
+      url: url,
+      data: form_data,
+      error: (function(_this) {
+        return function(xhr, ajaxOptions, thrownError) {
+          alert("Sorry, an error occurred");
+          console.log(xhr);
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          $('#static_progress_bar_container').modal('hide');
+          return $("body").html("We got an error.");
+        };
+      })(this),
+      success: (function(_this) {
+        return function(data) {
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          $('#static_progress_bar_container').modal('hide');
+          return open_mapping_results(data);
+        };
+      })(this)
+    });
+    console.log("settingInterval");
+    this.my_timer = setInterval(get_progress, 1000);
+    return false;
   };
-})(this));
-
-$("#plink_compute").on("click", (function(_this) {
-  return function() {
-    var form_data, url;
-    $("#static_progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("plink");
-    $('input[name=maf]').val($('input[name=maf_plink]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  open_mapping_results = function(data) {
+    return $.colorbox({
+      html: data,
+      href: "#mapping_results_holder",
+      height: "90%",
+      width: "90%",
+      onComplete: (function(_this) {
+        return function() {
+          var filename, getSvgXml;
+          root.create_lod_chart();
+          filename = "lod_chart_" + js_data.this_trait;
+          getSvgXml = function() {
+            var svg;
+            svg = $("#topchart").find("svg")[0];
+            return (new XMLSerializer).serializeToString(svg);
+          };
+          $("#exportform > #export").click(function() {
+            var form, svg_xml;
+            svg_xml = getSvgXml();
+            form = $("#exportform");
+            form.find("#data").val(svg_xml);
+            form.find("#filename").val(filename);
+            return form.submit();
+          });
+          return $("#exportpdfform > #export_pdf").click(function() {
+            var form, svg_xml;
+            svg_xml = getSvgXml();
+            form = $("#exportpdfform");
+            form.find("#data").val(svg_xml);
+            form.find("#filename").val(filename);
+            return form.submit();
+          });
+        };
+      })(this)
+    });
   };
-})(this));
-
-$("#gemma_compute").on("click", (function(_this) {
-  return function() {
-    var form_data, url;
-    console.log("RUNNING GEMMA");
-    $("#static_progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("gemma");
-    $('input[name=maf]').val($('input[name=maf_gemma]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.";
+
+  showalert = function(message, alerttype) {
+    return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
   };
-})(this));
-
-$("#interval_mapping_compute").on("click", (function(_this) {
-  return function() {
-    var form_data, url;
-    showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
-    console.log("In interval mapping");
-    $("#progress_bar_container").modal();
-    url = "/interval_mapping";
-    $('input[name=method]').val("reaper");
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
-    $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
-    $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  $('#suggestive').hide();
+
+  $('input[name=display_all]').change((function(_this) {
+    return function() {
+      console.log("check");
+      if ($('input[name=display_all]:checked').val() === "False") {
+        return $('#suggestive').show();
+      } else {
+        return $('#suggestive').hide();
+      }
+    };
+  })(this));
+
+  $("#pylmm_mapping_compute").on("mouseover", (function(_this) {
+    return function() {
+      if ($(".outlier").length && $(".outlier-alert").length < 1) {
+        return showalert(outlier_text, "alert-success outlier-alert");
+      }
+    };
+  })(this));
+
+  $("#pylmm_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      $("#progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("pylmm");
+      $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#rqtl_geno_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      $("#progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("rqtl_geno");
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#plink_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      $("#static_progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("plink");
+      $('input[name=maf]').val($('input[name=maf_plink]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#gemma_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      console.log("RUNNING GEMMA");
+      $("#static_progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("gemma");
+      $('input[name=maf]').val($('input[name=maf_gemma]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#interval_mapping_compute").on("mouseover", (function(_this) {
+    return function() {
+      if ($(".outlier").length && $(".outlier-alert").length < 1) {
+        return showalert(outlier_text, "alert-success outlier-alert");
+      }
+    };
+  })(this));
+
+  $("#interval_mapping_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      console.log("In interval mapping");
+      $("#progress_bar_container").modal();
+      url = "/interval_mapping";
+      $('input[name=method]').val("reaper");
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+      $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  composite_mapping_fields = function() {
+    return $(".composite_fields").toggle();
   };
-})(this));
 
-composite_mapping_fields = function() {
-  return $(".composite_fields").toggle();
-};
+  mapping_method_fields = function() {
+    return $(".mapping_method_fields").toggle();
+  };
 
-mapping_method_fields = function() {
-  return $(".mapping_method_fields").toggle();
-};
+  $("#use_composite_choice").change(composite_mapping_fields);
 
-$("#use_composite_choice").change(composite_mapping_fields);
+  $("#mapping_method_choice").change(mapping_method_fields);
 
-$("#mapping_method_choice").change(mapping_method_fields);
+  toggle_enable_disable = function(elem) {
+    return $(elem).prop("disabled", !$(elem).prop("disabled"));
+  };
 
-toggle_enable_disable = function(elem) {
-  return $(elem).prop("disabled", !$(elem).prop("disabled"));
-};
+  $("#choose_closet_control").change(function() {
+    return toggle_enable_disable("#control_locus");
+  });
 
-$("#choose_closet_control").change(function() {
-  return toggle_enable_disable("#control_locus");
-});
+  $("#display_all_lrs").change(function() {
+    return toggle_enable_disable("#suggestive_lrs");
+  });
 
-$("#display_all_lrs").change(function() {
-  return toggle_enable_disable("#suggestive_lrs");
-});
+}).call(this);
diff --git a/wqflask/wqflask/static/new/packages/DataTables/extensions/dataTables.colResize.js b/wqflask/wqflask/static/new/packages/DataTables/extensions/dataTables.colResize.js
index 6ef9907a..2712750a 100644
--- a/wqflask/wqflask/static/new/packages/DataTables/extensions/dataTables.colResize.js
+++ b/wqflask/wqflask/static/new/packages/DataTables/extensions/dataTables.colResize.js
@@ -1,943 +1,846 @@
-var dt;
-(function (dt) {
-    var ColResize = (function () {
-        function ColResize($, api, settings) {
-            this.$ = $;
-            this.tableSize = -1;
-            this.initialized = false;
-            this.dt = {};
-            this.dom = {
-                fixedLayout: false,
-                fixedHeader: null,
-                winResizeTimer: null,
-                mouse: {
-                    startX: -1,
-                    startWidth: null
-                },
-                table: {
-                    prevWidth: null
-                },
-                origState: true,
-                resize: false,
-                scrollHead: null,
-                scrollHeadTable: null,
-                scrollFoot: null,
-                scrollFootTable: null,
-                scrollFootInner: null,
-                scrollBody: null,
-                scrollBodyTable: null,
-                scrollX: false,
-                scrollY: false
-            };
-            this.settings = this.$.extend(true, {}, dt.ColResize.defaultSettings, settings);
-            this.dt.settings = api.settings()[0];
-            this.dt.api = api;
-            this.dt.settings.colResize = this;
-            this.registerCallbacks();
-        }
-        ColResize.prototype.initialize = function () {
-            var _this = this;
-            this.$.each(this.dt.settings.aoColumns, function (i, col) {
-                return _this.setupColumn(col);
-            });
-
-            //Initialize fixedHeader if specified
-            if (this.settings.fixedHeader)
-                this.setupFixedHeader();
-
-            //Save scroll head and body if found
-            this.dom.scrollHead = this.$('div.' + this.dt.settings.oClasses.sScrollHead, this.dt.settings.nTableWrapper);
-            this.dom.scrollHeadInner = this.$('div.' + this.dt.settings.oClasses.sScrollHeadInner, this.dom.scrollHead);
-            this.dom.scrollHeadTable = this.$('div.' + this.dt.settings.oClasses.sScrollHeadInner + ' > table', this.dom.scrollHead);
-
-            this.dom.scrollFoot = this.$('div.' + this.dt.settings.oClasses.sScrollFoot, this.dt.settings.nTableWrapper);
-            this.dom.scrollFootInner = this.$('div.' + this.dt.settings.oClasses.sScrollFootInner, this.dom.scrollFoot);
-            this.dom.scrollFootTable = this.$('div.' + this.dt.settings.oClasses.sScrollFootInner + ' > table', this.dom.scrollFoot);
-
-            this.dom.scrollBody = this.$('div.' + this.dt.settings.oClasses.sScrollBody, this.dt.settings.nTableWrapper);
-            this.dom.scrollBodyTable = this.$('> table', this.dom.scrollBody);
-            this.dt.api.on('draw.dt', this.onDraw.bind(this));
-            if (this.dom.scrollFootTable) {
-                this.dt.api.on('colPinFcDraw.dt', function (e, colPin, data) {
-                    if (data.leftClone.header)
-                        _this.$('tfoot', data.leftClone.header).remove();
-                    if (data.leftClone.footer)
-                        _this.$('thead', data.leftClone.footer).remove();
-                    if (data.rightClone.header)
-                        _this.$('tfoot', data.rightClone.header).remove();
-                    if (data.rightClone.footer)
-                        _this.$('thead', data.rightClone.footer).remove();
-                });
-            }
-
-            this.dom.scrollX = this.dt.settings.oInit.sScrollX === undefined ? false : true;
-            this.dom.scrollY = this.dt.settings.oInit.sScrollY === undefined ? false : true;
-
-            //SaveTableWidth
-            this.dt.settings.sTableWidthOrig = this.$(this.dt.settings.nTable).width();
-            this.updateTableSize();
-
-            this.dt.settings.oFeatures.bAutoWidthOrig = this.dt.settings.oFeatures.bAutoWidth;
-            this.dt.settings.oFeatures.bAutoWidth = false;
-
-            if (this.dt.settings.oInit.bStateSave && this.dt.settings.oLoadedState) {
-                this.loadState(this.dt.settings.oLoadedState);
+/*! ColResize 0.0.10
+ */
+
+/**
+ * @summary     ColResize
+ * @description Provide the ability to resize columns in a DataTable
+ * @version     0.0.10
+ * @file        dataTables.colResize.js
+ * @author      Silvacom Ltd.
+ *
+ * For details please refer to: http://www.datatables.net
+ *
+ * Special thank to everyone who has contributed to this plug in
+ * - dykstrad
+ * - tdillan (for 0.0.3 and 0.0.5 bug fixes)
+ * - kylealonius (for 0.0.8 bug fix)
+ * - the86freak (for 0.0.9 bug fix)
+ */
+
+(function (window, document, undefined) {
+
+    /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+     * DataTables plug-in API functions test
+     *
+     * This are required by ColResize in order to perform the tasks required, and also keep this
+     * code portable, to be used for other column resize projects with DataTables, if needed.
+     * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+    var factory = function ($, DataTable) {
+        "use strict";
+
+        /**
+         * Plug-in for DataTables which will resize the columns depending on the handle clicked
+         *  @method  $.fn.dataTableExt.oApi.fnColResize
+         *  @param   object oSettings DataTables settings object - automatically added by DataTables!
+         *  @param   int iCol Take the column to be resized
+         *  @returns void
+         */
+        $.fn.dataTableExt.oApi.fnColResize = function (oSettings, iCol) {
+            var v110 = $.fn.dataTable.Api ? true : false;
+
+            /*
+             * Update DataTables' event handlers
+             */
+
+            /* Fire an event so other plug-ins can update */
+            $(oSettings.oInstance).trigger('column-resize', [ oSettings, {
+                "iCol": iCol
+            } ]);
+        };
+
+        /**
+         * ColResize provides column resize control for DataTables
+         * @class ColResize
+         * @constructor
+         * @param {object} dt DataTables settings object
+         * @param {object} opts ColResize options
+         */
+        var ColResize = function (dt, opts) {
+            var oDTSettings;
+
+            if ($.fn.dataTable.Api) {
+                oDTSettings = new $.fn.dataTable.Api(dt).settings()[0];
+            }
+            // 1.9 compatibility
+            else if (dt.fnSettings) {
+                // DataTables object, convert to the settings object
+                oDTSettings = dt.fnSettings();
+            }
+            else if (typeof dt === 'string') {
+                // jQuery selector
+                if ($.fn.dataTable.fnIsDataTable($(dt)[0])) {
+                    oDTSettings = $(dt).eq(0).dataTable().fnSettings();
+                }
             }
-
-            this.onDraw();
-            this.dom.table.preWidth = parseFloat(this.dom.scrollBodyTable.css('width'));
-
-            if (!this.dom.scrollX && this.dom.scrollY && this.settings.fixedLayout && this.dt.settings._reszEvt) {
-                //We have to manually resize columns on window resize
-                var eventName = 'resize.DT-' + this.dt.settings.sInstance;
-                this.$(window).off(eventName);
-                this.$(window).on(eventName, function () {
-                    _this.proportionallyColumnSizing();
-                    //api._fnAdjustColumnSizing(this.dt.settings);
-                });
+            else if (dt.nodeName && dt.nodeName.toLowerCase() === 'table') {
+                // Table node
+                if ($.fn.dataTable.fnIsDataTable(dt.nodeName)) {
+                    oDTSettings = $(dt.nodeName).dataTable().fnSettings();
+                }
             }
-
-            if (this.dom.scrollX || this.dom.scrollY) {
-                this.dt.api.on('column-sizing.dt', this.fixFootAndHeadTables.bind(this));
-                this.dt.api.on('column-visibility.dt', this.fixFootAndHeadTables.bind(this));
+            else if (dt instanceof jQuery) {
+                // jQuery object
+                if ($.fn.dataTable.fnIsDataTable(dt[0])) {
+                    oDTSettings = dt.eq(0).dataTable().fnSettings();
+                }
             }
+            else {
+                // DataTables settings object
+                oDTSettings = dt;
+            }
+
+            // Convert from camelCase to Hungarian, just as DataTables does
+            if ($.fn.dataTable.camelToHungarian) {
+                $.fn.dataTable.camelToHungarian(ColResize.defaults, opts || {});
+            }
+
+
+            /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+             * Public class variables
+             * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+            /**
+             * @namespace Settings object which contains customizable information for ColResize instance
+             */
+            this.s = {
+                /**
+                 * DataTables settings object
+                 *  @property dt
+                 *  @type     Object
+                 *  @default  null
+                 */
+                "dt": null,
+
+                /**
+                 * Initialisation object used for this instance
+                 *  @property init
+                 *  @type     object
+                 *  @default  {}
+                 */
+                "init": $.extend(true, {}, ColResize.defaults, opts),
+
+                /**
+                 * @namespace Information used for the mouse drag
+                 */
+                "mouse": {
+                    "startX": -1,
+                    "startY": -1,
+                    "targetIndex": -1,
+                    "targetColumn": -1,
+                    "neighbourIndex": -1,
+                    "neighbourColumn": -1
+                },
 
-            this.initialized = true;
-            this.dt.settings.oApi._fnCallbackFire(this.dt.settings, 'colResizeInitCompleted', 'colResizeInitCompleted', [this]);
-        };
-
-        ColResize.prototype.setupColumn = function (col) {
-            var _this = this;
-            var $th = this.$(col.nTh);
-            if (col.resizable === false)
-                return;
-
-            // listen to mousemove event for resize
-            $th.on('mousemove.ColResize', function (e) {
-                if (_this.dom.resize || col.resizable === false)
-                    return;
-
-                /* Store information about the mouse position */
-                var $thTarget = e.target.nodeName.toUpperCase() == 'TH' ? _this.$(e.target) : _this.$(e.target).closest('TH');
-                var offset = $thTarget.offset();
-                var nLength = $thTarget.innerWidth();
-
-                /* are we on the col border (if so, resize col) */
-                if (Math.abs(e.pageX - Math.round(offset.left + nLength)) <= 5) {
-                    $thTarget.css({ 'cursor': 'col-resize' });
-                } else
-                    $thTarget.css({ 'cursor': 'pointer' });
-            });
-
-            //Save the original width
-            col._ColResize_sWidthOrig = col.sWidthOrig;
-            col.initWidth = $th.width();
-            col.minWidthOrig = col.minWidth;
-
-            $th.on('dblclick.ColResize', function (e) {
-                _this.onDblClick(e, $th, col);
-            });
-
-            $th.off('mousedown.ColReorder');
-
-            // listen to mousedown event
-            $th.on('mousedown.ColResize', function (e) {
-                return _this.onMouseDown(e, col);
-            });
-        };
-
-        ColResize.prototype.setupFixedHeader = function () {
-            var fhSettings = this.settings.fixedHeader === true ? undefined : this.settings.fixedHeader;
-
-            //If left or right option was set to true disable resizing for the first or last column
-            if (this.$.isPlainObject(fhSettings)) {
-                var columns = this.dt.settings.aoColumns;
-                if (fhSettings.left === true)
-                    columns[0].resizable = false;
-                if (fhSettings.right === true)
-                    columns[columns.length - 1].resizable = false;
-            }
+                /**
+                 * Status variable keeping track of mouse down status
+                 *  @property isMousedown
+                 *  @type     boolean
+                 *  @default  false
+                 */
+                "isMousedown": false
+            };
 
-            this.dom.fixedHeader = new this.$.fn.dataTable.FixedHeader(this.dt.api, fhSettings);
-            var origUpdateClones = this.dom.fixedHeader._fnUpdateClones;
-            var that = this;
 
-            //FixeHeader doesn't have any callback after updating the clones so we have to wrap the orig function
-            this.dom.fixedHeader._fnUpdateClones = function () {
-                origUpdateClones.apply(this, arguments);
-                that.memorizeFixedHeaderNodes();
+            /**
+             * @namespace Common and useful DOM elements for the class instance
+             */
+            this.dom = {
+                /**
+                 * Resizing element (the one the mouse is resizing)
+                 *  @property resize
+                 *  @type     element
+                 *  @default  null
+                 */
+                "resizeCol": null,
+
+                /**
+                 * Resizing element neighbour (the column next to the one the mouse is resizing)
+                 * This is for fixed table resizing.
+                 *  @property resize
+                 *  @type     element
+                 *  @default  null
+                 */
+                "resizeColNeighbour": null,
+
+                /**
+                 *  Array of events to be restored, used for overriding existing events from other plugins for a time.
+                 *  @property restoreEvents
+                 *  @type     array
+                 *  @default  []
+                 */
+                "restoreEvents": []
             };
 
-            //As we missed the first call of _fnUpdateClones we have to call memorizeFixedHeaderNodes function manually
-            this.memorizeFixedHeaderNodes();
-        };
 
-        ColResize.prototype.memorizeFixedHeaderNodes = function () {
-            var _this = this;
-            var fhSettings = this.dom.fixedHeader.fnGetSettings();
-            var fhCache = fhSettings.aoCache;
-            var i, col;
-            for (i = 0; i < fhCache.length; i++) {
-                var type = fhCache[i].sType;
-                var propName;
-                var selector;
-                switch (type) {
-                    case 'fixedHeader':
-                        propName = 'fhTh';
-                        selector = 'thead>tr>th';
-                        this.dt.settings.fhTHead = fhCache[i].nNode;
-                        break;
-                    case 'fixedFooter':
-                        propName = 'fhTf';
-                        selector = 'thead>tr>th';
-
-                        //prepend a cloned thead to the floating footer table so that resizing will work correctly
-                        var tfoot = this.$(fhCache[i].nNode);
-                        var thead = this.$(this.dt.settings.nTHead).clone().css({ height: 0, visibility: 'hidden' });
-                        this.$('tr', thead).css('height', 0);
-                        this.$('tr>th', thead).css({
-                            'height': 0,
-                            'padding-bottom': 0,
-                            'padding-top': 0,
-                            'border-bottom-width': 0,
-                            'border-top-width': 0,
-                            'line-height': 0
-                        });
-                        tfoot.prepend(thead);
-                        this.$('tfoot>tr>th', tfoot).css('width', '');
-                        this.dt.settings.fhTFoot = fhCache[i].nNode;
-                        break;
-                    default:
-                        continue;
+            /* Constructor logic */
+            this.s.dt = oDTSettings.oInstance.fnSettings();
+            this.s.dt._colResize = this;
+            this._fnConstruct();
+
+            /* Add destroy callback */
+            oDTSettings.oApi._fnCallbackReg(oDTSettings, 'aoDestroyCallback', $.proxy(this._fnDestroy, this), 'ColResize');
+
+            return this;
+        };
+
+
+        ColResize.prototype = {
+            /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+             * Public methods
+             * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+            /**
+             * Reset the column widths to the original widths that was detected on
+             * start up.
+             *  @return {this} Returns `this` for chaining.
+             *
+             *  @example
+             *    // DataTables initialisation with ColResize
+             *    var table = $('#example').dataTable( {
+             *        "sDom": 'Zlfrtip'
+             *    } );
+             *
+             *    // Add click event to a button to reset the ordering
+             *    $('#resetOrdering').click( function (e) {
+             *        e.preventDefault();
+             *        $.fn.dataTable.ColResize( table ).fnReset();
+             *    } );
+             */
+            "fnReset": function () {
+                var a = [];
+                for (var i = 0, iLen = this.s.dt.aoColumns.length; i < iLen; i++) {
+                    this.s.dt.aoColumns[i].width = this.s.dt.aoColumns[i]._ColResize_iOrigWidth;
                 }
 
-                this.$(selector, fhCache[i].nNode).each(function (j, th) {
-                    col = _this.getVisibleColumn(j);
-                    col[propName] = th;
-                });
-            }
-        };
+                this.s.dt.adjust().draw();
 
-        //zero based index
-        ColResize.prototype.getVisibleColumn = function (idx) {
-            var columns = this.dt.settings.aoColumns;
-            var currVisColIdx = -1;
-            for (var i = 0; i < columns.length; i++) {
-                if (!columns[i].bVisible)
-                    continue;
-                currVisColIdx++;
-                if (currVisColIdx == idx)
-                    return columns[i];
-            }
-            return null;
-        };
-
-        ColResize.prototype.updateTableSize = function () {
-            if (this.dom.scrollX && this.dom.scrollHeadTable.length)
-                this.tableSize = this.dom.scrollHeadTable.width();
-            else
-                this.tableSize = -1;
-        };
+                return this;
+            },
 
-        ColResize.prototype.proportionallyColumnSizing = function () {
-            var _this = this;
-            var prevWidths = [], newWidths = [], prevWidth, newWidth, newTableWidth, prevTableWidth, moveLength, multiplier, cWidth, i, j, delay = 500, prevTotalColWidths = 0, currTotalColWidths, columnRestWidths = [], columns = this.dt.settings.aoColumns, bodyTableColumns = this.$('thead th', this.dom.scrollBodyTable), headTableColumns = this.$('thead th', this.dom.scrollHeadTable), footTableColumns = this.dom.scrollFootTable.length ? this.$('thead th', this.dom.scrollFootTable) : [], visColumns = [];
 
-            for (i = 0; i < columns.length; i++) {
-                if (!columns[i].bVisible)
-                    continue;
-                visColumns.push(columns[i]);
-                columnRestWidths.push(0); //set default value
-            }
+            /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+             * Private methods (they are of course public in JS, but recommended as private)
+             * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-            for (i = 0; i < bodyTableColumns.length; i++) {
-                cWidth = parseFloat(bodyTableColumns[i].style.width);
-                prevTotalColWidths += cWidth;
-                prevWidths.push(cWidth);
-            }
-
-            for (i = 0; i < bodyTableColumns.length; i++) {
-                bodyTableColumns[i].style.width = '';
-            }
+            /**
+             * Constructor logic
+             *  @method  _fnConstruct
+             *  @returns void
+             *  @private
+             */
+            "_fnConstruct": function () {
+                var that = this;
+                var iLen = that.s.dt.aoColumns.length;
+                var i;
 
-            //Get the new table width calculated by the browser
-            newTableWidth = parseFloat(this.dom.scrollBodyTable.css('width'));
+                that._fnSetupMouseListeners();
 
-            //Get the old table width
-            prevTableWidth = this.dom.table.preWidth;
-            moveLength = newTableWidth - prevTableWidth;
-            if (moveLength == 0) {
-                for (i = 0; i < bodyTableColumns.length; i++) {
-                    bodyTableColumns[i].style.width = prevWidths[i] + 'px';
+                /* Add event handlers for the resize handles */
+                for (i = 0; i < iLen; i++) {
+                    /* Mark the original column width for later reference */
+                    this.s.dt.aoColumns[i]._ColResize_iOrigWidth = this.s.dt.aoColumns[i].width;
                 }
-                return;
-            }
 
-            //var tot = 0;
-            currTotalColWidths = prevTotalColWidths;
-            for (i = 0; i < visColumns.length; i++) {
-                //For each column calculate the new width
-                prevWidth = prevWidths[i];
-                multiplier = (+(prevWidth / prevTotalColWidths).toFixed(2));
-
-                //tot += multiplier;
-                newWidth = prevWidth + (moveLength * multiplier) + columnRestWidths[i];
-                currTotalColWidths -= prevWidth;
-
-                //Check whether the column can be resized to the new calculated value
-                //if not, set it to the min or max width depends on the moveLength value
-                if (!this.canResizeColumn(visColumns[i], newWidth)) {
-                    cWidth = moveLength > 0 ? this.getColumnMaxWidth(visColumns[i]) : this.getColumnMinWidth(visColumns[i]);
-                    var rest = newWidth - cWidth;
-                    newWidth = cWidth;
-
-                    for (j = (i + 1); j < visColumns.length; j++) {
-                        columnRestWidths[j] += rest * (+(visColumns[j] / currTotalColWidths).toFixed(2));
+                this._fnSetColumnIndexes();
+
+                /* State saving */
+                this.s.dt.oApi._fnCallbackReg( this.s.dt, 'aoStateSaveParams', function (oS, oData) {
+                    that._fnStateSave.call(that, oData);
+                }, "ColResize_State" );
+
+                // State loading
+                this._fnStateLoad();
+            },
+
+            /**
+             * @method  _fnStateSave
+             * @param   object oState DataTables state
+             * @private
+             */
+            "_fnStateSave": function (oState) {
+                this.s.dt.aoColumns.forEach(function(col, index) {
+                    oState.columns[index].width = col.sWidthOrig;
+                });
+            },
+
+            /**
+             * If state has been loaded, apply the saved widths to the columns
+             * @method  _fnStateLoad
+             * @private
+             */
+            "_fnStateLoad": function() {
+                var that = this,
+                    loadedState = this.s.dt.oLoadedState;
+                if (loadedState && loadedState.columns) {
+                    var colStates = loadedState.columns,
+                        currCols = this.s.dt.aoColumns;
+                    // Only apply the saved widths if the number of columns is the same.
+                    // Otherwise, we don't know if we're applying the width to the correct column.
+                    if (colStates.length > 0 && colStates.length === currCols.length) {
+                        colStates.forEach(function(state, index) {
+                            var col = that.s.dt.aoColumns[index];
+                            if (state.width) {
+                                col.sWidthOrig = col.sWidth = state.width;
+                            }
+                        });
                     }
                 }
-                newWidths.push(newWidth);
-            }
-
-            //Apply the calculated column widths to the headers cells
-            var tablesWidth = this.dom.scrollBodyTable.outerWidth() + 'px';
-            for (i = 0; i < headTableColumns.length; i++) {
-                headTableColumns[i].style.width = newWidths[i] + 'px';
-            }
-            this.dom.scrollHeadTable.css('width', tablesWidth);
-            this.dom.scrollHeadInner.css('width', tablesWidth);
-
-            for (i = 0; i < bodyTableColumns.length; i++) {
-                bodyTableColumns[i].style.width = newWidths[i] + 'px';
-            }
-
-            if (this.dom.scrollFootTable.length) {
-                for (i = 0; i < footTableColumns.length; i++) {
-                    footTableColumns[i].style.width = newWidths[i] + 'px';
+            },
+
+            /**
+             * Remove events of type from obj add it to restoreEvents array to be restored at a later time
+             * @param until string flag when to restore the event
+             * @param obj Object to remove events from
+             * @param type type of event to remove
+             * @param namespace namespace of the event being removed
+             */
+            "_fnDelayEvents": function (until, obj, type, namespace) {
+                var that = this;
+                //Get the events for the object
+                var events = $._data($(obj).get(0), 'events');
+                $.each(events, function (i, o) {
+                    //If the event type matches
+                    if (i == type) {
+                        //Loop through the possible many events with that type
+                        $.each(o, function (k, v) {
+                            //Somehow it is possible for the event to be undefined make sure it is defined first
+                            if (v) {
+                                if (namespace) {
+                                    //Add the event to the array of events to be restored later
+                                    that.dom.restoreEvents.push({"until": until, "obj": obj, "type": v.type, "namespace": v.namespace, "handler": v.handler});
+                                    //If the namespace matches
+                                    if (v.namespace == namespace) {
+                                        //Turn off/unbind the event
+                                        $(obj).off(type + "." + namespace);
+                                    }
+                                } else {
+                                    //Add the event to the array of events to be restored later
+                                    that.dom.restoreEvents.push({"until": until, "obj": obj, "type": v.type, "namespace": null, "handler": v.handler});
+                                    //Turn off/unbind the event
+                                    $(obj).off(type);
+                                }
+                            }
+                        });
+                    }
+                });
+            },
+
+            /**
+             * Loop through restoreEvents array and restore the events on the elements provided
+             */
+            "_fnRestoreEvents": function (until) {
+                var that = this;
+                //Loop through the events to be restored
+                var i;
+                for (i = that.dom.restoreEvents.length; i--;) {
+                    if (that.dom.restoreEvents[i].until == undefined || that.dom.restoreEvents[i].until == null || that.dom.restoreEvents[i].until == until) {
+                        if (that.dom.restoreEvents[i].namespace) {
+                            //Turn on the event for the object provided
+                            $(that.dom.restoreEvents[i].obj).off(that.dom.restoreEvents[i].type + "." + that.dom.restoreEvents[i].namespace).on(that.dom.restoreEvents[i].type + "." + that.dom.restoreEvents[i].namespace, that.dom.restoreEvents[i].handler);
+                            that.dom.restoreEvents.splice(i, 1);
+                        } else {
+                            //Turn on the event for the object provided
+                            $(that.dom.restoreEvents[i].obj).off(that.dom.restoreEvents[i].type).on(that.dom.restoreEvents[i].type, that.dom.restoreEvents[i].handler);
+                            that.dom.restoreEvents.splice(i, 1);
+                        }
+                    }
                 }
-                this.dom.scrollFootTable[0].style.width = tablesWidth;
-                this.dom.scrollFootInner[0].style.width = tablesWidth;
-            }
+            },
 
-            //console.log('moveLength: ' + moveLength + ' multiplier: ' + tot);
-            //console.log(newWidths);
-            this.dom.table.preWidth = newTableWidth;
-
-            //Call afterResizing function after the window stops resizing
-            if (this.dom.winResizeTimer)
-                clearTimeout(this.dom.winResizeTimer);
-            this.dom.winResizeTimer = setTimeout(function () {
-                _this.afterResizing();
-                _this.dom.winResizeTimer = null;
-            }, delay);
-        };
+            /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+             * Mouse drop and drag
+             */
 
-        ColResize.prototype.getColumnIndex = function (col) {
-            //Get the current column position
-            var colIdx = -1;
-            for (var i = 0; i < this.dt.settings.aoColumns.length; i++) {
-                if (this.dt.settings.aoColumns[i] === col) {
-                    colIdx = i;
-                    break;
+            "_fnSetupMouseListeners":function() {
+                var that = this;
+                $(that.s.dt.nTableWrapper).off("mouseenter.ColResize").on("mouseenter.ColResize","th",function(e) {
+                    e.preventDefault();
+                    that._fnMouseEnter.call(that, e, this);
+                });
+                $(that.s.dt.nTableWrapper).off("mouseleave.ColResize").on("mouseleave.ColResize","th",function(e) {
+                    e.preventDefault();
+                    that._fnMouseLeave.call(that, e, this);
+                });
+            },
+
+            /**
+             * Add mouse listeners to the resize handle on TH element
+             *  @method  _fnMouseListener
+             *  @param   i Column index
+             *  @param   nTh TH resize handle element clicked on
+             *  @returns void
+             *  @private
+             */
+            "_fnMouseListener": function (i, nTh) {
+                var that = this;
+                $(nTh).off('mouseenter.ColResize').on('mouseenter.ColResize', function (e) {
+                    e.preventDefault();
+                    that._fnMouseEnter.call(that, e, nTh);
+                });
+                $(nTh).off('mouseleave.ColResize').on('mouseleave.ColResize', function (e) {
+                    e.preventDefault();
+                    that._fnMouseLeave.call(that, e, nTh);
+                });
+            },
+
+            /**
+             *
+             * @param e Mouse event
+             * @param nTh TH element that the mouse is over
+             */
+            "_fnMouseEnter": function (e, nTh) {
+                var that = this;
+                if(!that.s.isMousedown) {
+                    //Once the mouse has entered the cell add mouse move event to see if the mouse is over resize handle
+                    $(nTh).off('mousemove.ColResizeHandle').on('mousemove.ColResizeHandle', function (e) {
+                        e.preventDefault();
+                        that._fnResizeHandleCheck.call(that, e, nTh);
+                    });
                 }
-            }
-            return colIdx;
-        };
+            },
+
+            /**
+             * Clear mouse events when the mouse has left the th
+             * @param e Mouse event
+             * @param nTh TH element that the mouse has just left
+             */
+            "_fnMouseLeave": function (e, nTh) {
+                //Once the mouse has left the TH make suure to remove the mouse move listener
+                $(nTh).off('mousemove.ColResizeHandle');
+            },
+
+            /**
+             * Mouse down on a TH element in the table header
+             *  @method  _fnMouseDown
+             *  @param   event e Mouse event
+             *  @param   element nTh TH element to be resized
+             *  @returns void
+             *  @private
+             */
+            "_fnMouseDown": function (e, nTh) {
+                var that = this;
+
+                that.s.isMousedown = true;
 
-        ColResize.prototype.getColumnEvent = function (th, type, ns) {
-            var event;
-            var thEvents = this.$._data(th, "events");
-            this.$.each(thEvents[type] || [], function (idx, handler) {
-                if (handler.namespace === ns)
-                    event = handler;
-            });
-            return event;
-        };
-
-        ColResize.prototype.loadState = function (data) {
-            var _this = this;
-            var i, col;
-
-            var onInit = function () {
-                if (_this.settings.fixedLayout) {
-                    _this.setTablesLayout('fixed');
+                /* Store information about the mouse position */
+                var target = $(e.target).closest('th, td');
+                var offset = target.offset();
+
+                /* Store information about the mouse position for resize calculations in mouse move function */
+                this.s.mouse.startX = e.pageX;
+                this.s.mouse.startY = e.pageY;
+
+                //Store the indexes of the columns the mouse is down on
+                var idx = that.dom.resizeCol[0].cellIndex;
+                
+                // the last column has no 'right-side' neighbour
+                // with fixed this can make the table smaller
+               if (that.dom.resizeColNeighbour[0] === undefined){
+                    var idxNeighbour = 0;
                 } else {
-                    _this.setTablesLayout('auto');
+                    var idxNeighbour = that.dom.resizeColNeighbour[0].cellIndex;
                 }
-                if (!data.colResize) {
-                    if (_this.dt.settings.oFeatures.bAutoWidthOrig)
-                        _this.dt.settings.oFeatures.bAutoWidth = true;
-                    else if (_this.dt.settings.sTableWidthOrig)
-                        _this.$(_this.dt.settings.nTable).width(_this.dt.settings.sTableWidthOrig);
-
-                    for (i = 0; i < _this.dt.settings.aoColumns.length; i++) {
-                        col = _this.dt.settings.aoColumns[i];
-                        if (col._ColResize_sWidthOrig) {
-                            col.sWidthOrig = col._ColResize_sWidthOrig;
-                        }
-                    }
-                    _this.dom.origState = true;
-                } else {
-                    var columns = data.colResize.columns || [];
-                    var wMap = {};
+                
+               
 
-                    if (_this.dt.settings.oFeatures.bAutoWidth) {
-                        _this.dt.settings.oFeatures.bAutoWidth = false;
-                    }
+                if (idx === undefined) {
+                    return;
+                }
 
-                    if (_this.dom.scrollX && data.colResize.tableSize > 0) {
-                        _this.dom.scrollHeadTable.width(data.colResize.tableSize);
-                        _this.dom.scrollHeadInner.width(data.colResize.tableSize);
-                        _this.dom.scrollBodyTable.width(data.colResize.tableSize);
-                        _this.dom.scrollFootTable.width(data.colResize.tableSize);
+                this.s.mouse.targetIndex = idx;
+                this.s.mouse.targetColumn = this.s.dt.aoColumns[ idx ];
+
+                this.s.mouse.neighbourIndex = idxNeighbour;
+                this.s.mouse.neighbourColumn = this.s.dt.aoColumns[ idxNeighbour ];
+
+                /* Add event handlers to the document */
+                $(document)
+                    .off('mousemove.ColResize').on('mousemove.ColResize', function (e) {
+                        that._fnMouseMove.call(that, e);
+                    })
+                    .off('mouseup.ColResize').on('mouseup.ColResize', function (e) {
+                        that._fnMouseUp.call(that, e);
+                    });
+            },
+
+            /**
+             * Deal with a mouse move event while dragging to resize a column
+             *  @method  _fnMouseMove
+             *  @param   e Mouse event
+             *  @returns void
+             *  @private
+             */
+            "_fnMouseMove": function (e) {
+                var that = this;
+
+                var offset = $(that.s.mouse.targetColumn.nTh).offset();
+                var relativeX = (e.pageX - offset.left);
+                var distFromLeft = relativeX;
+                var distFromRight = $(that.s.mouse.targetColumn.nTh).outerWidth() - relativeX - 1;
+
+                //Change in mouse x position
+                var dx = e.pageX - that.s.mouse.startX;
+                //Get the minimum width of the column (default minimum 10px)
+                var minColumnWidth = Math.max(parseInt($(that.s.mouse.targetColumn.nTh).css('min-width')), 10);
+                //Store the previous width of the column
+                var prevWidth = $(that.s.mouse.targetColumn.nTh).width();
+                //As long as the cursor is past the handle, resize the columns
+                if ((dx > 0 && distFromRight <= 0) || (dx < 0 && distFromRight >= 0)) {
+                    if (!that.s.init.tableWidthFixed) {
+                        //As long as the width is larger than the minimum
+                        var newColWidth = Math.max(minColumnWidth, prevWidth + dx);
+                        //Get the width difference (take into account the columns minimum width)
+                        var widthDiff = newColWidth - prevWidth;
+                        var colResizeIdx = parseInt(that.dom.resizeCol.attr("data-column-index"));
+                        //Set datatable column widths
+                        that.s.mouse.targetColumn.sWidthOrig = that.s.mouse.targetColumn.sWidth = that.s.mouse.targetColumn.width = newColWidth + "px";
+                        var domCols = $(that.s.dt.nTableWrapper).find("th[data-column-index='"+colResizeIdx+"']");
+                        //For each table expand the width by the same amount as the column
+                        //This accounts for other datatable plugins like FixedColumns
+                        domCols.parents("table").each(function() {
+                            if(!$(this).parent().hasClass("DTFC_LeftBodyLiner")) {
+                                var newWidth = $(this).width() + widthDiff;
+                                $(this).width(newWidth);
+                            } else {
+                                var newWidth =$(that.s.dt.nTableWrapper).find(".DTFC_LeftHeadWrapper").children("table").width();
+                                $(this).parents(".DTFC_LeftWrapper").width(newWidth);
+                                $(this).parent().width(newWidth+15);
+                                $(this).width(newWidth);
+                            }
+                        });
+                        //Apply the new width to the columns after the table has been resized
+                        domCols.width(that.s.mouse.targetColumn.width);
+                    } else {
+                        //A neighbour column must exist in order to resize a column in a table with a fixed width
+                        if (that.s.mouse.neighbourColumn) {
+                            //Get the minimum width of the neighbor column (default minimum 10px)
+                            var minColumnNeighbourWidth = Math.max(parseInt($(that.s.mouse.neighbourColumn.nTh).css('min-width')), 10);
+                            //Store the previous width of the neighbour column
+                            var prevNeighbourWidth = $(that.s.mouse.neighbourColumn.nTh).width();
+                            //As long as the width is larger than the minimum
+                            var newColWidth = Math.max(minColumnWidth, prevWidth + dx);
+                            var newColNeighbourWidth = Math.max(minColumnNeighbourWidth, prevNeighbourWidth - dx);
+                            //Get the width difference (take into account the columns minimum width)
+                            var widthDiff = newColWidth - prevWidth;
+                            var widthDiffNeighbour = newColNeighbourWidth - prevNeighbourWidth;
+                            //Get the column index for the column being changed
+                            var colResizeIdx = parseInt(that.dom.resizeCol.attr("data-column-index"));
+                            var neighbourColResizeIdx = parseInt(that.dom.resizeColNeighbour.attr("data-column-index"));
+                            //Set datatable column widths
+                            that.s.mouse.neighbourColumn.sWidthOrig = that.s.mouse.neighbourColumn.sWidth = that.s.mouse.neighbourColumn.width = newColNeighbourWidth + "px";
+                            that.s.mouse.targetColumn.sWidthOrig = that.s.mouse.targetColumn.sWidth = that.s.mouse.targetColumn.width = newColWidth + "px";
+                            //Get list of columns based on column index in all affected tables tables. This accounts for other plugins like FixedColumns
+                            var domNeighbourCols = $(that.s.dt.nTableWrapper).find("th[data-column-index='" + neighbourColResizeIdx + "']");
+                            var domCols = $(that.s.dt.nTableWrapper).find("th[data-column-index='" + colResizeIdx + "']");
+                            //If dx if positive (the width is getting larger) shrink the neighbour columns first
+                            if(dx>0) {
+                                domNeighbourCols.width(that.s.mouse.neighbourColumn.width);
+                                domCols.width(that.s.mouse.targetColumn.width);
+                            } else {
+                                //Apply the new width to the columns then to the neighbour columns
+                                domCols.width(that.s.mouse.targetColumn.width);
+                                domNeighbourCols.width(that.s.mouse.neighbourColumn.width);
+                            }
+                        }
                     }
+                }
+                that.s.mouse.startX = e.pageX;
+            },
+
+            /**
+             * Check to see if the mouse is over the resize handle area
+             * @param e
+             * @param nTh
+             */
+            "_fnResizeHandleCheck": function (e, nTh) {
+                var that = this;
+
+                var offset = $(nTh).offset();
+                var relativeX = (e.pageX - offset.left);
+                var relativeY = (e.pageY - offset.top);
+                var distFromLeft = relativeX;
+                var distFromRight = $(nTh).outerWidth() - relativeX - 1;
+
+                var handleBuffer = this.s.init.handleWidth / 2;
+                var leftHandleOn = distFromLeft < handleBuffer;
+                var rightHandleOn = distFromRight < handleBuffer;
+
+                //If this is the first table cell
+                if ($(nTh).prev("th").length == 0) {
+                    if(this.s.init.rtl)
+                        rightHandleOn = false;
+                    else
+                        leftHandleOn = false;
+                }
+                //If this is the last cell and the table is fixed width don't let them expand the last cell directly
+                if ($(nTh).next("th").length == 0 && this.s.init.tableWidthFixed) {
+                    if(this.s.init.rtl)
+                        leftHandleOn = false;
+                    else
+                        rightHandleOn = false;
+                }
 
-                    for (i = 0; i < columns.length; i++) {
-                        wMap[i] = columns[i];
+                var resizeAvailable = leftHandleOn||rightHandleOn;
+
+                //If table is in right to left mode flip which TH is being resized
+                if (that.s.init.rtl) {
+                    //Handle is to the left
+                    if (leftHandleOn) {
+                        that.dom.resizeCol = $(nTh);
+                        that.dom.resizeColNeighbour = $(nTh).next();
+                    } else if (rightHandleOn) {
+                        that.dom.resizeCol = $(nTh).prev();
+                        that.dom.resizeColNeighbour = $(nTh);
                     }
-                    for (i = 0; i < _this.dt.settings.aoColumns.length; i++) {
-                        col = _this.dt.settings.aoColumns[i];
-                        var idx = col._ColReorder_iOrigCol != null ? col._ColReorder_iOrigCol : i;
-                        col.sWidth = wMap[idx];
-                        col.sWidthOrig = wMap[idx];
-                        col.nTh.style.width = columns[i];
-
-                        //Check for FixedHeader
-                        if (col.fhTh)
-                            col.fhTh.style.width = columns[i];
-                        if (col.fhTf)
-                            col.fhTf.style.width = columns[i];
+                } else {
+                    //Handle is to the right
+                    if (rightHandleOn) {
+                        that.dom.resizeCol = $(nTh);
+                        that.dom.resizeColNeighbour = $(nTh).next();
+                    } else if (leftHandleOn) {
+                        that.dom.resizeCol = $(nTh).prev();
+                        that.dom.resizeColNeighbour = $(nTh);
                     }
-                    _this.dom.origState = false;
                 }
 
-                _this.dt.api.columns.adjust();
-                if (_this.dom.scrollX || _this.dom.scrollY)
-                    _this.dt.api.draw(false);
-            };
-
-            if (this.initialized) {
-                onInit();
-                return;
-            }
-            this.dt.settings.oApi._fnCallbackReg(this.dt.settings, 'colResizeInitCompleted', function () {
-                onInit();
-            }, "ColResize_Init");
-        };
-
-        ColResize.prototype.saveState = function (data) {
-            if (!this.dt.settings._bInitComplete) {
-                var oData = this.dt.settings.fnStateLoadCallback.call(this.dt.settings.oInstance, this.dt.settings);
-                if (oData && oData.colResize)
-                    data.colResize = oData.colResize;
-                return;
-            }
-            this.updateTableSize();
-            data.colResize = {
-                columns: [],
-                tableSize: this.tableSize
-            };
-
-            data.colResize.columns.length = this.dt.settings.aoColumns.length;
-            for (var i = 0; i < this.dt.settings.aoColumns.length; i++) {
-                var col = this.dt.settings.aoColumns[i];
-                var idx = col._ColReorder_iOrigCol != null ? col._ColReorder_iOrigCol : i;
-                data.colResize.columns[idx] = col.sWidth;
-            }
-        };
-
-        ColResize.prototype.registerCallbacks = function () {
-            var _this = this;
-            /* State saving */
-            this.dt.settings.oApi._fnCallbackReg(this.dt.settings, 'aoStateSaveParams', function (oS, oData) {
-                _this.saveState(oData);
-            }, "ColResize_StateSave");
-
-            /* State loading */
-            this.dt.settings.oApi._fnCallbackReg(this.dt.settings, 'aoStateLoaded', function (oS, oData) {
-                _this.loadState(oData);
-            }, "ColResize_StateLoad");
-
-            if (this.$.fn.DataTable.models.oSettings.remoteStateInitCompleted !== undefined) {
-                //Integrate with remote state
-                this.dt.settings.oApi._fnCallbackReg(this.dt.settings, 'remoteStateLoadedParams', function (s, data) {
-                    _this.loadState(data);
-                }, "ColResize_StateLoad");
-                this.dt.settings.oApi._fnCallbackReg(this.dt.settings, 'remoteStateSaveParams', function (s, data) {
-                    _this.saveState(data);
-                }, "ColResize_StateSave");
-            }
-        };
-
-        ColResize.prototype.setTablesLayout = function (value) {
-            if (this.dom.scrollX || this.dom.scrollY) {
-                this.dom.scrollHeadTable.css('table-layout', value);
-                this.dom.scrollBodyTable.css('table-layout', value);
-                this.dom.scrollFootTable.css('table-layout', value);
-            } else {
-                this.$(this.dt.settings.nTable).css('table-layout', value);
-            }
-            this.dom.fixedLayout = value == 'fixed';
-        };
-
-        //only when scrollX or scrollY are enabled
-        ColResize.prototype.fixFootAndHeadTables = function (e) {
-            var _this = this;
-            if (e != null && e.target !== this.dt.settings.nTable)
-                return;
-
-            if (this.dom.scrollFootTable.length) {
-                this.$('thead', this.dom.scrollFootTable).remove();
-                this.dom.scrollFootTable.prepend(this.$('thead', this.dom.scrollBodyTable).clone());
-            }
-            this.$('tfoot', this.dom.scrollHeadTable).remove();
-            this.dom.scrollHeadTable.append(this.$('tfoot', this.dom.scrollBodyTable).clone());
-            var removeFooterWidth = function (table) {
-                _this.$('tfoot>tr>th', table).each(function (i, th) {
-                    _this.$(th).css('width', '');
-                });
-            };
-
-            //Remove all tfoot headers widths
-            removeFooterWidth(this.dom.scrollFootTable);
-            removeFooterWidth(this.dom.scrollBodyTable);
-            removeFooterWidth(this.dom.scrollHeadTable);
-        };
-
-        ColResize.prototype.onDraw = function (e) {
-            if (e != null && e.target !== this.dt.settings.nTable)
-                return;
-            if (this.dom.scrollX || this.dom.scrollY) {
-                this.fixFootAndHeadTables();
-
-                //Fix the header table padding
-                if (this.dt.settings._bInitComplete) {
-                    var borderWidth = this.dom.scrollHeadTable.outerWidth() - this.dom.scrollHeadTable.innerWidth();
-                    var paddingType = this.dt.settings.oBrowser.bScrollbarLeft ? 'padding-left' : 'padding-right';
-                    var paddingVal = parseFloat(this.dom.scrollHeadInner.css(paddingType));
-                    this.dom.scrollHeadInner.css(paddingType, (paddingVal + borderWidth) + 'px');
-                }
-            }
-
-            var autoWidthTypes = [];
-            if (this.settings.dblClick == 'autoMinFit' || !this.settings.fixedLayout)
-                autoWidthTypes.push('autoMinWidth');
-            if (this.settings.dblClick == 'autoFit')
-                autoWidthTypes.push('autoWidth');
-
-            //Call this only once so that the table will be cloned only one time
-            if (autoWidthTypes.length)
-                this.updateColumnsAutoWidth(autoWidthTypes);
-
-            if (!this.settings.fixedLayout) {
-                var columns = this.dt.settings.aoColumns;
-                var i;
-                for (i = 0; i < columns.length; i++) {
-                    if (!columns[i].bVisible)
-                        continue;
-                    columns[i].minWidth = Math.max((columns[i].minWidthOrig || 0), columns[i].autoMinWidth);
-
-                    //We have to resize if the current column width if is less that the column minWidth
-                    if (this.$(columns[i].nTh).width() < columns[i].minWidth)
-                        this.resize(columns[i], columns[i].minWidth);
+                //If table width is fixed make sure both columns are resizable else just check the one.
+                if(this.s.init.tableWidthFixed)
+                    resizeAvailable &= this.s.init.exclude.indexOf(parseInt($(that.dom.resizeCol).attr("data-column-index"))) == -1 && this.s.init.exclude.indexOf(parseInt($(that.dom.resizeColNeighbour).attr("data-column-index"))) == -1;
+                else
+                    resizeAvailable &= this.s.init.exclude.indexOf(parseInt($(that.dom.resizeCol).attr("data-column-index"))) == -1;
+
+                $(nTh).off('mousedown.ColResize');
+                if (resizeAvailable) {
+                    $(nTh).css("cursor", "ew-resize");
+
+                    //Delay other mousedown events from the Reorder plugin
+                    that._fnDelayEvents(null, nTh, "mousedown", "ColReorder");
+                    that._fnDelayEvents("click", nTh, "click", "DT");
+
+                    $(nTh).off('mousedown.ColResize').on('mousedown.ColResize', function (e) {
+                        e.preventDefault();
+                        that._fnMouseDown.call(that, e, nTh);
+                    })
+                        .off('click.ColResize').on('click.ColResize', function (e) {
+                            that._fnClick.call(that, e);
+                        });
+                } else {
+                    $(nTh).css("cursor", "pointer");
+                    $(nTh).off('mousedown.ColResize click.ColResize');
+                    //Restore any events that were removed
+                    that._fnRestoreEvents();
+                    //This is to restore column sorting on click functionality
+                    if (!that.s.isMousedown)
+                    //Restore click event if mouse is not down
+                        this._fnRestoreEvents("click");
                 }
-            } else {
-                if (!this.dom.fixedLayout) {
-                    this.setTablesLayout('fixed');
-                    this.afterResizing();
+            },
+
+            "_fnClick": function (e) {
+                var that = this;
+                that.s.isMousedown = false;
+                e.stopImmediatePropagation();
+            },
+
+            /**
+             * Finish off the mouse drag
+             *  @method  _fnMouseUp
+             *  @param   e Mouse event
+             *  @returns void
+             *  @private
+             */
+            "_fnMouseUp": function (e) {
+                var that = this;
+                that.s.isMousedown = false;
+
+                //Fix width of column to be the size the dom is limited to (for when user sets min-width on a column)
+                that.s.mouse.targetColumn.width = that.dom.resizeCol.width();
+
+                $(document).off('mousemove.ColResize mouseup.ColResize');
+                this.s.dt.oInstance.fnAdjustColumnSizing();
+                //Table width fix, prevents extra gaps between tables
+                var LeftWrapper = $(that.s.dt.nTableWrapper).find(".DTFC_LeftWrapper");
+                var DTFC_LeftWidth = LeftWrapper.width();
+                LeftWrapper.children(".DTFC_LeftHeadWrapper").children("table").width(DTFC_LeftWidth);
+
+                if (that.s.init.resizeCallback) {
+                    that.s.init.resizeCallback.call(that, that.s.mouse.targetColumn);
                 }
-            }
-        };
-
-        ColResize.prototype.getTableAutoColWidths = function (table, types) {
-            var widths = {}, i, colIdx;
-            var $table = this.$(table);
-            for (i = 0; i < types.length; i++) {
-                widths[types[i]] = [];
-            }
-            if (!types.length || !$table.length)
-                return widths;
-
-            var clnTable = $table.clone().removeAttr('id').css('table-layout', 'auto');
-
-            // Remove any assigned widths from the footer (from scrolling)
-            clnTable.find('thead th, tfoot th, tfoot td').css('width', '');
-            var container = this.$('<div />').css({
-                'position': 'absolute',
-                'width': '9999px',
-                'height': '9999px'
-            });
-            container.append(clnTable);
-            this.$(this.dt.settings.nTableWrapper).append(container);
-
-            var headerCols = this.$('thead>tr>th', clnTable);
-
-            for (i = 0; i < types.length; i++) {
-                var type = types[i];
-                var fn = '';
-                switch (type) {
-                    case 'autoMinWidth':
-                        clnTable.css('width', '1px');
-                        fn = 'width';
+            },
+
+            /**
+             * Clean up ColResize memory references and event handlers
+             *  @method  _fnDestroy
+             *  @returns void
+             *  @private
+             */
+            "_fnDestroy": function () {
+                var i, iLen;
+
+                for (i = 0, iLen = this.s.dt.aoDrawCallback.length; i < iLen; i++) {
+                    if (this.s.dt.aoDrawCallback[i].sName === 'ColResize_Pre') {
+                        this.s.dt.aoDrawCallback.splice(i, 1);
                         break;
-                    case 'autoWidth':
-                        clnTable.css('width', 'auto');
-                        fn = 'outerWidth';
-                        break;
-                    default:
-                        throw 'Invalid widthType ' + type;
-                }
-                for (colIdx = 0; colIdx < headerCols.length; colIdx++) {
-                    widths[type].push(this.$(headerCols[colIdx])[fn]());
-                }
-            }
-
-            container.remove();
-            return widths;
-        };
-
-        ColResize.prototype.updateColumnsAutoWidth = function (types) {
-            var columns = this.dt.settings.aoColumns;
-            var i, j, colLen, type, visColIdx = 0;
-            var widths = {};
-            if (this.dom.scrollX || this.dom.scrollY) {
-                var headWidths = this.getTableAutoColWidths(this.dom.scrollHeadTable, types);
-                var bodyWidths = this.getTableAutoColWidths(this.dom.scrollBodyTable, types);
-                var footWidths = this.getTableAutoColWidths(this.dom.scrollFootTable, types);
-
-                for (i = 0; i < types.length; i++) {
-                    type = types[i];
-                    widths[type] = [];
-                    footWidths[type].length = headWidths[type].length;
-                    colLen = headWidths[type].length;
-                    for (j = 0; j < colLen; j++) {
-                        widths[type].push(Math.max(headWidths[type][j], bodyWidths[type][j], (footWidths[type][j] || 0)));
                     }
                 }
-            } else {
-                widths = this.getTableAutoColWidths(this.dt.settings.nTable, types);
-            }
-
-            for (i = 0; i < columns.length; i++) {
-                if (!columns[i].bVisible)
-                    continue;
-                for (j = 0; j < types.length; j++) {
-                    type = types[j];
-                    columns[i][type] = widths[type][visColIdx];
-                }
-                visColIdx++;
-            }
-        };
 
-        ColResize.prototype.overrideClickHander = function (col, $th) {
-            var dtClickEvent = this.getColumnEvent($th.get(0), 'click', 'DT');
+                $(this.s.dt.nTHead).find('*').off('.ColResize');
 
-            //Remove the DataTables event so that ordering will not occur
-            if (dtClickEvent) {
-                $th.off('click.DT');
-                this.$(document).one('click.ColResize', function (e) {
-                    $th.on('click.DT', dtClickEvent.handler);
+                $.each(this.s.dt.aoColumns, function (i, column) {
+                    $(column.nTh).removeAttr('data-column-index');
                 });
-            }
-        };
-
-        ColResize.prototype.onDblClick = function (e, $th, col) {
-            if (e.target !== $th.get(0))
-                return;
-            if ($th.css('cursor') != 'col-resize')
-                return;
-
-            var width;
-            switch (this.settings.dblClick) {
-                case 'autoMinFit':
-                    width = col.autoMinWidth;
-                    break;
-                case 'autoFit':
-                    width = col.autoWidth;
-                    break;
-                default:
-                    width = col.initWidth;
-            }
-            this.resize(col, width);
-        };
-
-        ColResize.prototype.onMouseDown = function (e, col) {
-            var _this = this;
-            if (e.target !== col.nTh && e.target !== col.fhTh)
-                return true;
-
-            var $th = e.target === col.nTh ? this.$(col.nTh) : this.$(col.fhTh);
-
-            if ($th.css('cursor') != 'col-resize' || col.resizable === false) {
-                var colReorder = this.dt.settings._colReorder;
-                if (colReorder) {
-                    colReorder._fnMouseDown.call(colReorder, e, e.target); //Here we fix the e.preventDefault() in ColReorder so that we can have working inputs in header
-                }
-                return true;
-            }
-            this.dom.mouse.startX = e.pageX;
-            this.dom.mouse.prevX = e.pageX;
-            this.dom.mouse.startWidth = $th.width();
-            this.dom.resize = true;
 
-            this.beforeResizing(col);
+                this.s.dt._colResize = null;
+                this.s = null;
+            },
 
-            /* Add event handlers to the document */
-            this.$(document).on('mousemove.ColResize', function (event) {
-                _this.onMouseMove(event, col);
-            });
-            this.overrideClickHander(col, $th);
-            this.$(document).one('mouseup.ColResize', function (event) {
-                _this.onMouseUp(event, col);
-            });
-
-            return false;
-        };
-
-        ColResize.prototype.resize = function (col, width) {
-            var colWidth = this.$(col.nTh).width();
-            var moveLength = width - this.$(col.nTh).width();
-            this.beforeResizing(col);
-            var resized = this.resizeColumn(col, colWidth, moveLength, moveLength);
-            this.afterResizing();
-            return resized;
-        };
-
-        ColResize.prototype.beforeResizing = function (col) {
-            //if (this.settings.fixedLayout && !this.dom.fixedLayout)
-            //    this.setTablesLayout('fixed');
-        };
-
-        ColResize.prototype.afterResizing = function () {
-            var i;
-            var columns = this.dt.settings.aoColumns;
-            for (i = 0; i < columns.length; i++) {
-                if (!columns[i].bVisible)
-                    continue;
-                columns[i].sWidth = this.$(columns[i].nTh).css('width');
-            }
-
-            //Update the internal storage of the table's width (in case we changed it because the user resized some column and scrollX was enabled
-            this.updateTableSize();
-
-            //Save the state
-            this.dt.settings.oInstance.oApi._fnSaveState(this.dt.settings);
-            this.dom.origState = false;
-        };
 
-        ColResize.prototype.onMouseUp = function (e, col) {
-            this.$(document).off('mousemove.ColResize');
-            if (!this.dom.resize)
-                return;
-            this.dom.resize = false;
-            this.afterResizing();
-        };
-
-        ColResize.prototype.canResizeColumn = function (col, newWidth) {
-            return (col.resizable === undefined || col.resizable) && this.settings.minWidth <= newWidth && (!col.minWidth || col.minWidth <= newWidth) && (!this.settings.maxWidth || this.settings.maxWidth >= newWidth) && (!col.maxWidth || col.maxWidth >= newWidth);
-        };
-
-        ColResize.prototype.getColumnMaxWidth = function (col) {
-            return col.maxWidth ? col.maxWidth : this.settings.maxWidth;
-        };
-
-        ColResize.prototype.getColumnMinWidth = function (col) {
-            return col.minWidth ? col.minWidth : this.settings.minWidth;
-        };
-
-        ColResize.prototype.getPrevResizableColumnIdx = function (col, moveLength) {
-            var columns = this.dt.settings.aoColumns;
-            var colIdx = ColResizeHelper.indexOf(columns, col);
-            for (var i = colIdx; i >= 0; i--) {
-                if (!columns[i].bVisible)
-                    continue;
-                var newWidth = this.$(columns[i].nTh).width() + moveLength;
-                if (this.canResizeColumn(columns[i], newWidth))
-                    return i;
-            }
-            return -1;
-        };
-
-        ColResize.prototype.getNextResizableColumnIdx = function (col, moveLength) {
-            var columns = this.dt.settings.aoColumns;
-            var colIdx = ColResizeHelper.indexOf(columns, col);
-            for (var i = (colIdx + 1); i < columns.length; i++) {
-                if (!columns[i].bVisible)
-                    continue;
-                var newWidth = this.$(columns[i].nTh).width() - moveLength;
-                if (this.canResizeColumn(columns[i], newWidth))
-                    return i;
+            /**
+             * Add a data attribute to the column headers, so we know the index of
+             * the row to be reordered. This allows fast detection of the index, and
+             * for this plug-in to work with FixedHeader which clones the nodes.
+             *  @private
+             */
+            "_fnSetColumnIndexes": function () {
+                $.each(this.s.dt.aoColumns, function (i, column) {
+                    $(column.nTh).attr('data-column-index', i);
+                });
             }
-            return -1;
         };
 
-        ColResize.prototype.resizeColumn = function (col, startWidth, moveLength, lastMoveLength) {
-            if (moveLength == 0 || lastMoveLength == 0 || col.resizable === false)
-                return false;
-            var i;
-            var columns = this.dt.settings.aoColumns;
-            var headCol = this.$(col.nTh);
-            var headColNext = headCol.next();
-            var colIdx = this.getColumnIndex(col);
-            var thWidth = startWidth + moveLength;
-            var thNextWidth;
-            var nextColIdx;
-
-            if (!this.dom.scrollX) {
-                if (lastMoveLength < 0) {
-                    thWidth = headColNext.width() - lastMoveLength;
-                    nextColIdx = this.getPrevResizableColumnIdx(col, lastMoveLength);
-                    if (nextColIdx < 0)
-                        return false;
-                    headCol = headColNext;
-                    colIdx = colIdx + 1;
-                    headColNext = this.$(columns[nextColIdx].nTh);
-                    thNextWidth = headColNext.width() + lastMoveLength;
-                } else {
-                    thWidth = headCol.width() + lastMoveLength;
-                    nextColIdx = this.getNextResizableColumnIdx(col, lastMoveLength);
-
-                    //If there is no columns that can be shrinked dont resize anymore
-                    if (nextColIdx < 0)
-                        return false;
-                    headColNext = this.$(columns[nextColIdx].nTh);
-                    thNextWidth = headColNext.width() - lastMoveLength;
 
-                    if ((this.settings.maxWidth && this.settings.maxWidth < thWidth) || col.maxWidth && col.maxWidth < thWidth)
-                        return false;
-                }
-                if (!this.canResizeColumn(columns[nextColIdx], thNextWidth) || !this.canResizeColumn(columns[colIdx], thWidth))
-                    return false;
-                headColNext.width(thNextWidth);
-
-                //If fixed header is present we have to resize the cloned column too
-                if (this.dom.fixedHeader) {
-                    this.$(columns[nextColIdx].fhTh).width(thNextWidth);
-                    this.$(columns[colIdx].fhTh).width(thWidth);
-
-                    //If fixedfooter was enabled resize that too
-                    if (columns[nextColIdx].fhTf) {
-                        this.$(columns[nextColIdx].fhTf).width(thNextWidth);
-                        this.$(columns[colIdx].fhTf).width(thWidth);
+        /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+         * Static parameters
+         * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+        /**
+         * ColResize default settings for initialisation
+         *  @namespace
+         *  @static
+         */
+        ColResize.defaults = {
+            /**
+             * Callback function that is fired when columns are resized
+             *  @type function():void
+             *  @default null
+             *  @static
+             */
+            "resizeCallback": null,
+
+            /**
+             * Exclude array for columns that are not resizable
+             *  @property exclude
+             *  @type     array of indexes that are excluded from resizing
+             *  @default  []
+             */
+            "exclude": [],
+
+            /**
+             * Check to see if user is using a fixed table width or dynamic
+             * if true:
+             *      -Columns will resize themselves and their neighbour
+             *      -If neighbour is excluded resize will not occur
+             * if false:
+             *      -Columns will resize themselves and increase or decrease the width of the table accordingly
+             */
+            "tableWidthFixed": true,
+
+            /**
+             * Width of the resize handle in pixels
+             *  @property handleWidth
+             *  @type     int (pixels)
+             *  @default  10
+             */
+            "handleWidth": 10,
+
+            /**
+             * Right to left support, when true flips which column they are resizing on mouse down
+             *  @property rtl
+             *  @type     bool
+             *  @default  false
+             */
+            "rtl": false
+        };
+
+
+        /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+         * Constants
+         * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+        /**
+         * ColResize version
+         *  @constant  version
+         *  @type      String
+         *  @default   As code
+         */
+        ColResize.version = "0.0.10";
+
+
+        /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+         * DataTables interfaces
+         * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+        // Expose
+        $.fn.dataTable.ColResize = ColResize;
+        $.fn.DataTable.ColResize = ColResize;
+
+
+        // Register a new feature with DataTables
+        if (typeof $.fn.dataTable == "function" &&
+            typeof $.fn.dataTableExt.fnVersionCheck == "function" &&
+            $.fn.dataTableExt.fnVersionCheck('1.9.3')) {
+            $.fn.dataTableExt.aoFeatures.push({
+                "fnInit": function (settings) {
+                    var table = settings.oInstance;
+
+                    if (!settings._colResize) {
+                        var dtInit = settings.oInit;
+                        var opts = dtInit.colResize || dtInit.oColResize || {};
+
+                        new ColResize(settings, opts);
+                    }
+                    else {
+                        table.oApi._fnLog(settings, 1, "ColResize attempted to initialise twice. Ignoring second");
                     }
-                }
-            } else {
-                if (!this.canResizeColumn(col, thWidth))
-                    return false;
-                var tSize = this.tableSize + moveLength + 'px';
-                this.dom.scrollHeadInner.css('width', tSize);
-                this.dom.scrollHeadTable.css('width', tSize);
-                this.dom.scrollBodyTable.css('width', tSize);
-                this.dom.scrollFootTable.css('width', tSize);
-            }
-            headCol.width(thWidth);
-
-            //scrollX or scrollY enabled
-            if (this.dom.scrollBody.length) {
-                var colDomIdx = 0;
-                for (i = 0; i < this.dt.settings.aoColumns.length && i != colIdx; i++) {
-                    if (this.dt.settings.aoColumns[i].bVisible)
-                        colDomIdx++;
-                }
 
-                //Get the table
-                var bodyCol = this.$('thead>tr>th:nth(' + colDomIdx + ')', this.dom.scrollBodyTable);
-                var footCol = this.$('thead>tr>th:nth(' + colDomIdx + ')', this.dom.scrollFootTable);
+                    return null;
+                    /* No node for DataTables to insert */
+                },
+                "cFeature": "Z",
+                "sFeature": "ColResize"
+            });
+        } else {
+            alert("Warning: ColResize requires DataTables 1.9.3 or greater - www.datatables.net/download");
+        }
 
-                //This will happen only when scrollY is used without scrollX
-                if (!this.dom.scrollX) {
-                    var nextColDomIdx = 0;
-                    for (i = 0; i < this.dt.settings.aoColumns.length && i != nextColIdx; i++) {
-                        if (this.dt.settings.aoColumns[i].bVisible)
-                            nextColDomIdx++;
-                    }
-                    var bodyColNext = this.$('thead>tr>th:nth(' + nextColDomIdx + ')', this.dom.scrollBodyTable);
-                    var footColNext = this.$('thead>tr>th:nth(' + nextColDomIdx + ')', this.dom.scrollFootTable);
 
-                    bodyColNext.width(thNextWidth);
-                    if (thWidth > 0)
-                        bodyCol.width(thWidth);
+// API augmentation
+        if ($.fn.dataTable.Api) {
+            $.fn.dataTable.Api.register('colResize.reset()', function () {
+                return this.iterator('table', function (ctx) {
+                    ctx._colResize.fnReset();
+                });
+            });
+        }
 
-                    footColNext.width(thNextWidth);
-                    if (thWidth > 0)
-                        footCol.width(thWidth);
-                }
+        return ColResize;
+    }; // /factory
 
-                //Resize the table and the column
-                if (this.dom.scrollX && thWidth > 0) {
-                    bodyCol.width(thWidth);
-                    footCol.width(thWidth);
-                }
-            }
-            return true;
-        };
 
-        ColResize.prototype.onMouseMove = function (e, col) {
-            var moveLength = e.pageX - this.dom.mouse.startX;
-            var lastMoveLength = e.pageX - this.dom.mouse.prevX;
-            this.resizeColumn(col, this.dom.mouse.startWidth, moveLength, lastMoveLength);
-            this.dom.mouse.prevX = e.pageX;
-        };
+// Define as an AMD module if possible
+if ( typeof define === 'function' && define.amd ) {
+    define( ['jquery', 'datatables'], factory );
+}
+else if ( typeof exports === 'object' ) {
+    // Node/CommonJS
+    factory( require('jquery'), require('datatables') );
+}
+else if (jQuery && !jQuery.fn.dataTable.ColResize) {
+    // Otherwise simply initialise as normal, stopping multiple evaluation
+    factory(jQuery, jQuery.fn.dataTable);
+}
 
-        ColResize.prototype.destroy = function () {
-        };
-        ColResize.defaultSettings = {
-            minWidth: 1,
-            maxWidth: null,
-            fixedLayout: true,
-            fixedHeader: null,
-            dblClick: 'initWidth'
-        };
-        return ColResize;
-    })();
-    dt.ColResize = ColResize;
 
-    var ColResizeHelper = (function () {
-        function ColResizeHelper() {
-        }
-        ColResizeHelper.indexOf = function (arr, item, equalFun) {
-            if (typeof equalFun === "undefined") { equalFun = null; }
-            for (var i = 0; i < arr.length; i++) {
-                if (equalFun) {
-                    if (equalFun(arr[i], item))
-                        return i;
-                } else if (arr[i] === item)
-                    return i;
-            }
-            return -1;
-        };
-        return ColResizeHelper;
-    })();
-    dt.ColResizeHelper = ColResizeHelper;
-})(dt || (dt = {}));
-
-(function ($, window, document, undefined) {
-    //Register events
-    $.fn.DataTable.models.oSettings.colResizeInitCompleted = [];
-
-    //Register api function
-    $.fn.DataTable.Api.register('colResize.init()', function (settings) {
-        var colResize = new dt.ColResize($, this, settings);
-        if (this.settings()[0]._bInitComplete)
-            colResize.initialize();
-        else
-            this.one('init.dt', function () {
-                colResize.initialize();
-            });
-        return null;
-    });
-
-    $.fn.DataTable.Api.register('column().resize()', function (width) {
-        var oSettings = this.settings()[0];
-        var colResize = oSettings.colResize;
-        return colResize.resize(oSettings.aoColumns[this[0][0]], width);
-    });
-
-    //Add as feature
-    $.fn.dataTable.ext.feature.push({
-        "fnInit": function (oSettings) {
-            return oSettings.oInstance.api().colResize.init(oSettings.oInit.colResize);
-        },
-        "cFeature": "J",
-        "sFeature": "ColResize"
-    });
-}(jQuery, window, document, undefined));
\ No newline at end of file
+})(window, document);
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index a00878a0..c05b694b 100755
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -4,8 +4,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedheader/2.1.2/css/dataTables.fixedHeader.css" >
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -59,30 +57,20 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
-    <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedheader/2.1.2/js/dataTables.fixedHeader.min.js"></script>
-    <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.js"></script>
     <script>
             $('#trait_table').dataTable( {
-                "sDom": "Ztir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
-                "bLengthChange": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "600px",
-                "scrollX": true,
                 "scrollCollapse": true,
-                "colResize": {
-                    "tableWidthFixed": false
-                },
                 "paging": false
             } );
 
-            var table = $('#trait_table').DataTable();
-            //new $.fn.dataTable.FixedHeader( table );
-            new $.fn.dataTable.FixedColumns( table );
-
     </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 49df6af5..29c65058 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -4,8 +4,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedheader/2.1.2/css/dataTables.fixedHeader.css" >
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -121,10 +119,9 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
-    <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedheader/2.1.2/js/dataTables.fixedHeader.min.js"></script>
-    <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.js"></script>
 
 
     <script language="javascript" type="text/javascript">
@@ -152,25 +149,17 @@
                       "width": "15%"  },
                     { "type": "natural" }
                 ],
-                "sDom": "Ztir",
+                "sDom": "ZRtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
-                "bLengthChange": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "600px",
-                "scrollX": true,
                 "scrollCollapse": true,
-                "colResize": {
-                    "tableWidthFixed": false
-                },
                 "paging": false
             } );
             console.timeEnd("Creating table");
 
-            var table = $('#trait_table').DataTable();
-            new $.fn.dataTable.FixedColumns( table );
-
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index d53f930d..62407555 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -229,22 +229,26 @@
                     { "type": "natural" },
                     { "type": "natural" }
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bLengthChange": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
-                "scrollY": "700px",
-                "scrollCollapse": false,
+                //"scrollY": "700px",
+                //"scrollCollapse": false,
                 "colResize": {
                     "tableWidthFixed": false
                 },
                 "paging": false
             } );
+
+            var table = $('#corr_results').DataTable();
+            new $.fn.dataTable.FixedHeader( table );
+
             {% elif target_dataset.type == "Publish" %}
             $('#corr_results').dataTable( {
-                "aoColumns": [
+                "columns": [
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
@@ -257,7 +261,7 @@
                     { "type": "natural" },
                     { "type": "natural" }
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bLengthChange": true,
@@ -280,7 +284,7 @@
                     { "type": "natural" },
                     { "type": "natural" }
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bLengthChange": true,
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 49067e37..2bbfcd91 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -79,7 +79,7 @@
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
                                     <div class="col-xs-10 controls">
                                         <div class="col-xs-8">
-                                          <textarea name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -100,7 +100,7 @@
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
                                     <div class="col-xs-10 controls">
                                         <div class="col-xs-8">
-                                          <textarea name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -265,4 +265,15 @@
 
 {% block js %}
     <script src="/static/new/javascript/dataset_select_menu.js"></script>
+
+    <script>
+        function pressed(e) {
+            // Has the enter key been pressed?
+            if ( (window.event ? event.keyCode : e.which) == 13) { 
+                // If it has been so, manually submit the <form>
+                document.forms[0].submit();
+            }
+        }
+    </script>
+
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index d8f64c20..91808fcf 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -26,26 +26,36 @@
                 
             </div>
         </div>
-        <div>
+        <div style="width:60%;">
             <h2>
                 Results
             </h2>
-            <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+            <table id="qtl_results" class="table table-hover table-striped">
                 <thead>
                     <tr>
-                        <td>Index</td>
-                        <td>LOD Score</td>
-                        <td>Chr</td>
-                        <td>Mb</td>
-                        <td>Locus</td>
+                        <th>Index</th>
+                        <th>LOD Score</th>
+                        <th>Chr</th>
+                        <th>Mb</th>
+                        <th>Locus</th>
                    </tr>
                 </thead>
                 <tbody>
-                    {% for marker in filtered_markers %}
-                        {% if marker.lod_score > lod_cutoff %}
+                    {% for marker in qtl_results %}
+                        {% if (score_type == "LOD" and marker.lod_score > cutoff) or
+                              (score_type == "LRS" and marker.lrs_value > cutoff) %}
                         <tr>
-                            <td>{{loop.index}}</td>
+                            <td>
+                                {{loop.index}}
+                                <input type="checkbox" name="selectCheck"
+                                       class="checkbox edit_sample_checkbox"
+                                       value="{{ marker.name }}" checked="checked">
+                            </td>
+                            {% if score_type == "LOD" %}
                             <td>{{marker.lod_score}}</td>
+                            {% else %}
+                            <td>{{marker.lrs_value}}</td>
+                            {% endif %}
                             <td>{{marker.chr}}</td>
                             <td>{{marker.Mb}}</td>
                             <td>{{marker.name}}</td>
@@ -70,26 +80,24 @@
         $(document).ready( function () {
             console.time("Creating table");
             $('#qtl_results').dataTable( {
-                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
-                "sDom": "lTftipr",
-                "oTableTools": {
-                    "aButtons": [
-                        "copy",
-                        "print",
-                        {
-                            "sExtends":    "collection",
-                            "sButtonText": 'Save <span class="caret" />',
-                            "aButtons":    [ "csv", "xls", "pdf" ]
-                        }
+                "columns": [
+                    { "type": "natural" },
+                    { "type": "natural" },
+                    { "type": "natural" },
+                    { "type": "natural" },
+                    { "type": "natural" }
                     ],
-                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
-                },
-                "iDisplayLength": 50,
-                "bLengthChange": true,
+                "sDom": "ZRtir",
+                "iDisplayLength": -1,
+                "autoWidth": true,
                 "bDeferRender": true,
-                "bSortClasses": false
+                "bSortClasses": false,
+                "scrollY": "700px",
+                "scrollCollapse": true,
+                "paging": false
             } );
             console.timeEnd("Creating table");
+
         });
     </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index b9bb65fd..335ab213 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -188,19 +188,16 @@
                     { "type": "natural", "width": "15%" },
                     { "type": "natural" }
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": false,
-                "bLengthChange": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "700px",
                 "scrollCollapse": false,
-                "colResize": {
-                    "tableWidthFixed": false,
-                },
                 "paging": false
             } );
+
             {% elif dataset.type == 'Publish' %}
             $('#trait_table').DataTable( {
                 "columns": [
@@ -213,17 +210,13 @@
                     { "type": "natural", "width": "15%"},
                     { "type": "natural" }
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
                 "autoWidth": false,
-                "bLengthChange": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "700px",
                 "scrollCollapse": false,
-                "colResize": {
-                    "tableWidthFixed": false,
-                },
                 "paging": false
             } );
             {% elif dataset.type == 'Geno' %}
@@ -233,17 +226,13 @@
                     { "type": "natural" },
                     { "type": "natural", "width": "40%"}
                 ],
-                "sDom": "RJtir",
+                "sDom": "RZtir",
                 "iDisplayLength": -1,
-                "autoWidth": false,
-                "bLengthChange": true,
+                "autoWidth": true,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "700px",
                 "scrollCollapse": false,
-                "colResize": {
-                    "tableWidthFixed": false,
-                },
                 "paging": false
             } );
             {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 40f6eafd..6199f931 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -13,8 +13,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" >
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
 
 {% endblock %}
 {% block content %} <!-- Start of body -->
@@ -82,6 +80,7 @@
                         <div class="panel-body">
                             {% include 'show_trait_mapping_tools.html' %}
                         </div>
+                        <div id="alert_placeholder"></div>
                     </div>
                 </div>                
                 <div class="panel panel-default">
@@ -150,8 +149,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.js"></script>
-    <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script type="text/javascript" charset="utf-8">
@@ -212,7 +209,7 @@
                         { "bSortable": false },
                         { "type": "cust-txt" }
                         ],
-                    "sDom": "RJtir",
+                    "sDom": "RZtir",
                     "oTableTools": {
                         "aButtons": [
                             "copy",
@@ -248,7 +245,7 @@
                         null,
                         { "type": "cust-txt" }
                     ],
-                    "sDom": "RJtir",
+                    "sDom": "RZtir",
                     "oTableTools": {
                         "aButtons": [
                             "copy",
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 5c7b0417..ca8e02de 100755
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -81,12 +81,12 @@
             <table class="table-hover table-striped" id="samples_{{ sample_type.sample_group_type }}" style="float: left;">
                 <thead>
                     <tr>
-                        <th>Index</td>
-                        <th>Sample</td>
-                        <th>Value</td>
+                        <th>Index</th>
+                        <th>Sample</th>
+                        <th>Value</th>
                         {% if sample_type.se_exists() %}
-                        <th>&nbsp;</td>
-                        <th>SE</td>
+                        <th>&nbsp;</th>
+                        <th>SE</th>
                         {% endif %}
                         {% for attribute in sample_type.attributes|sort() %}
                         <th>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 6f69bcfa..eea9b295 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="num_pylmm" value="2000" type="text" class="form-control">
+                                <input name="num_pylmm" value="" type="text" class="form-control">
                             </div>
                         </div>
                         <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
@@ -211,6 +211,7 @@
                                 </button>
                             </div>
                         </div>
+                        <!--<div id="alert_placeholder"></div>-->
                     </div>
                 </div>
                 {% endif %}
@@ -268,7 +269,6 @@
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
         </dl>
     </div>
-    <div id="alert_placeholder"></div>
     <div id="mapping_result_holder_wrapper" style="display:none;">
         <div id="mapping_result_holder"></div>
     </div>