Added option to display selected covariates for GEMMA mapping

Changed layout/appearance of mapping options

Partially fixed issue with deleting collections

Changes to correlation table still in progress; having trouble getting tabulator to load JSON

7 files changed, 146 insertions, 136 deletions

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 2f6c3a96..0f72b29d 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -349,8 +349,11 @@ def delete_collection():
             db_session.delete(uc)
             db_session.commit()
     else:
-        collection_name = params['collection_name']
-        user_manager.AnonUser().delete_collection(collection_name)
+        if "collection_name" in params:
+            collection_name = params['collection_name']
+        else:
+            for this_collection in params['uc_id'].split(":"):
+                user_manager.AnonUser().delete_collection(this_collection)
 
     flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
 
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 233a5c76..7563eb2c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -235,7 +235,7 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     else:
                         marker['chr'] = line.split("\t")[0]
                     marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                    marker['p_value'] = float(line.split("\t")[10])
+                    marker['p_value'] = float(line.split("\t")[11])
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                         #marker['lrs_value'] = 0
@@ -245,6 +245,6 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     marker_obs.append(marker)
 
                     included_markers.append(line.split("\t")[1])
-                    p_values.append(float(line.split("\t")[10]))
+                    p_values.append(float(line.split("\t")[11]))
 
     return marker_obs
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 92e2b13b..f2e694d8 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -24,6 +24,7 @@ collection_click = function() {
 
 submit_click = function() {
   var covariates_string = "";
+  var covariates_display_string = "";
   $('#collections_holder').find('input[type=checkbox]:checked').each(function() {
     var this_dataset, this_trait;
     this_trait = $(this).parents('tr').find('.trait').text();
@@ -31,12 +32,15 @@ submit_click = function() {
     this_dataset = $(this).parents('tr').find('.dataset').text();
     console.log("this_dataset is:", this_dataset);
     covariates_string += this_trait + ":" + this_dataset + ","
+    covariates_display_string += this_trait + "\n"
   });
   // Trim the last comma
   covariates_string = covariates_string.substring(0, covariates_string.length - 1)
+  //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
   console.log("COVARIATES:", covariates_string)
 
   $("input[name=covariates]").val(covariates_string)
+  $(".selected_covariates").val(covariates_display_string)
 
   return $.colorbox.close();
 };
@@ -46,6 +50,7 @@ trait_click = function() {
   trait = $(this).parent().find('.trait').text();
   dataset = $(this).parent().find('.dataset').text();
   $("input[name=covariates]").val(trait + ":" + dataset)
+  $(".selected_covariates").text(trait)
   return $.colorbox.close();
 };
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 099d8010..df10c060 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -88,7 +88,8 @@
       };
     })(this));
     $("#remove_covariates").click(function () {
-        $("input[name=covariates]").val("") 
+        $("input[name=covariates]").val("")
+        $(".selected_covariates").val("")
     });
     d3.select("#clear_compare_trait").on("click", (function(_this) {
       return function() {
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index ad72052e..e7f3229b 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -26,13 +26,13 @@
             {% endif %}
         </div>
         <div>
-          <form id="collections_form" action="/delete" method="post">
-            <input type="hidden" name="uc_id" id="uc_id" value="" />
-          </form>
+            <form id="collections_form" action="/delete" method="post">
+              <input type="hidden" name="uc_id" id="uc_id" value="" />
+            </form>
             <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-            <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button> 
+            <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button>
         </div>
         <br>
         <div id="collections_list" style="width:50%;">
@@ -51,7 +51,11 @@
             <tbody>
             {% for uc in collections %}
                 <tr class="collection_line">
+                    {% if g.user_session.user_ob %}
                     <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
+                    {% else %}
+                    <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td>
+                    {% endif %}
                     <td align="right">{{ loop.index }}
                     {% if g.user_session.user_ob %}
                     <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 1254ea6a..0d305559 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -275,29 +275,32 @@
 
 
             {% if target_dataset.type == "ProbeSet" %}
-            var json_array = new Array();
+            var json_array = [];
 
             for (i=0; i < table_json.length; i++){
-                json_array.push({
-                      checkbox: table_json[i]["checkbox"],
-                      index: table_json[i]["index"],
-                      trait_id: table_json[i]["trait_id"],
-                      symbol: table_json[i]["symbol"],
-                      description: table_json[i]["description"],
-                      location: table_json[i]["location"],
-                      mean: table_json[i]["mean"],
-                      lrs_score: table_json[i]["lrs_score"],
-                      lrs_location: table_json[i]["lrs_location"],
-                      additive: table_json[i]["additive"],
-                      sample_r: table_json[i]["sample_r"],
-                      num_overlap: table_json[i]["num_overlap"],
-                      sample_p: table_json[i]["sample_p"],
-                      lit_corr: table_json[i]["lit_corr"],
-                      tissue_corr: table_json[i]["tissue_corr"]
-                });
-                console.log("JSON_DATA:", json_array);
+                this_array = json_array
+
+                var row_dict = {};
+                row_dict.checkbox = table_json[i]["checkbox"]
+                row_dict.index = table_json[i]["index"]
+                row_dict.trait_id = table_json[i]["trait_id"]
+                row_dict.symbol = table_json[i]["symbol"]
+                row_dict.description = table_json[i]["description"]
+                row_dict.location = table_json[i]["location"]
+                row_dict.mean = table_json[i]["mean"]
+                row_dict.lrs_score = table_json[i]["lrs_score"]
+                row_dict.lrs_location = table_json[i]["lrs_location"]
+                row_dict.additive = table_json[i]["additive"]
+                row_dict.sample_r = table_json[i]["sample_r"]
+                row_dict.num_overlap = table_json[i]["num_overlap"]
+                row_dict.sample_p = table_json[i]["sample_p"]
+                row_dict.lit_corr = table_json[i]["lit_corr"]
+                row_dict.tissue_corr = table_json[i]["tissue_corr"]
+                this_array.push(row_dict);
+                json_array.concat(this_array);
+                //console.log("JSON_ARRAY:", json_array);
             }
-            //console.log("JSON_DATA:", json_array)
+            console.log("JSON_DATA:", json_array)
 
             $("#trait_table").tabulator({
                 data: json_array,
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index dcec2b9e..ab2e2aae 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,6 +1,6 @@
 <div>
     {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
-    <div class="col-xs-4">
+    <div class="col-xs-5">
         <div class="tabbable"> <!-- Only required for left/right tabs -->
 
             <ul class="nav nav-pills">
@@ -38,11 +38,11 @@
                 {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
                 {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane active" id="gemma">
-                    <div style="padding-top: 10px;" class="form-horizontal">
+                    <div style="padding-top: 20px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                            <label for="genofiles" style="text-align: left;" class="col-xs-2 control-label">Genotypes</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_gemma" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -52,14 +52,14 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-3 controls">
+                            <label for="maf_gemma" style="text-align: left;" class="col-xs-2 control-label">MAF</label>
+                            <div style="margin-left:20px;" class="col-xs-3 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-4 control-label">Use LOCO</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align: left;" class="col-xs-2 control-label">Use LOCO</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="use_loco" value="True">
                                     Yes
@@ -70,32 +70,54 @@
                                </label>
                             </div>
                         </div>
+                    <!--
                     </div>
                     <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+                    -->
                         <div class="mapping_method_fields form-group">
-                            <button type="button" id="select_covariates" class="btn btn-default">
-                                Select Covariates
-                            </button>
-                            <button type="button" id="remove_covariates" class="btn btn-default">
-                                Remove Covariates
+                            <label style="text-align: left;" class="col-xs-2 control-label">Covariates</label>
+                            <div style="margin-left:20px;" class="col-xs-7">
+                              {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+                              No collections available. Please add traits to a collection to use them as covariates.
+                              {% elif g.cookie_session.display_num_collections() == "" %}
+                              No collections available. Please add traits to a collection to use them as covariates.
+                              {% else %}
+                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
+                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+                              </div>
+                              <textarea rows="2" cols="40" readonly placeholder="No covariates selected" class="selected_covariates"></textarea>
+                              {% endif %}
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                          <label class="col-xs-2 control-label"></label>
+                          <div style="margin-left:20px;" class="col-xs-4">
+                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+                                Compute
                             </button>
+                          </div>
                         </div>
                     </div>
-
+<!--
                     <div class="form-group">
                         <div class="col-xs-4 controls">
+                            <label class="col-xs-2 control-label"></label>
+                            <div class="col-xs-4">
                             <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
+                            </div>
                         </div>
                     </div>
+-->
                 </div>
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                            <label style="text-align: left;" for="genofiles" class="col-xs-2 control-label">Genotypes</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_reaper" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -105,20 +127,20 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align: left;" for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="num_perm_reaper" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align: left;" for="mapping_bootstraps" class="col-xs-2 control-label">Bootstraps</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="num_bootstrap" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align: left;" for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                                 <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
                                 {% else %}
@@ -162,8 +184,8 @@
 
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align:left;" class="col-xs-2 control-label">Marker<br>Regression</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_reaper" value="True">
                                     Yes
@@ -174,11 +196,12 @@
                                </label>
                             </div>
                         </div>
-                        <div class="form-group">
-                            <div style="padding-left:15px;" class="controls">
-                                <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
-                                    <i class="icon-ok-circle icon-white"></i> Compute
-                                </button>
+                        <div class="mapping_method_fields form-group">
+                            <label class="col-xs-2 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-4">
+                              <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+                                  Compute
+                              </button>
                             </div>
                         </div>
                         <!--<div id="alert_placeholder"></div>-->
@@ -189,8 +212,8 @@
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                            <label style="text-align: left;" for="genofiles" class="col-xs-2 control-label">Genotypes</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_rqtl_geno" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -200,17 +223,14 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="num_perm_rqtl_geno" value="" type="text" class="form-control">
+                            <label style="text-align: left;" for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                                <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
                             </div>
                         </div>
-                        <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
-                            Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
-                        </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align: left;" for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                                 <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
                                 {% else %}
@@ -228,8 +248,8 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label>
-                            <div class="col-xs-4 controls">
+                            <label style="text-align: left;" for="mapmethod_rqtl_geno" class="col-xs-2 control-label">Method</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                               <select name="mapmethod_rqtl_geno" class="form-control">
                                 <option value="em">em</option>
                                 <option value="imp">imp</option>
@@ -243,8 +263,8 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label>
-                            <div class="col-xs-4 controls">
+                            <label style="text-align:left;" for="mapmodel_rqtl_geno" class="col-xs-2 control-label">Model</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                               <select name="mapmodel_rqtl_geno" class="form-control">
                                 <option value="normal">normal</option>
                                 <!--<option value="binary">binary</option>
@@ -269,8 +289,8 @@
                         </div>
                         -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
-                            <div class="col-xs-12 controls">
+                            <label style="text-align:left;" class="col-xs-2 control-label">Marker<br>Regression</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_rqtl" value="True">
                                     Yes
@@ -282,11 +302,12 @@
                             </div>
                         </div>
 
-                        <div class="form-group">
-                            <div style="padding-left:15px;" class="controls">
-                                <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                    <i class="icon-ok-circle icon-white"></i> Compute
-                                </button>
+                        <div class="mapping_method_fields form-group">
+                            <label class="col-xs-2 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-4">
+                              <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+                                  Compute
+                              </button>
                             </div>
                         </div>
                     </div>
@@ -295,8 +316,8 @@
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                            <label style="text-align:left;" class="col-xs-2 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <select id="genofile_pylmm" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -305,44 +326,12 @@
                             </div>
                         </div>
                         {% endif %}
-<!--
                         <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-                                <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
-                                {% else %}
-                                <input name="control_pylmm" value="" type="text" />
-                                {% endif %}
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_pylmm" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_pylmm" value="false" checked="">
-                                    No
-                                </label>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
-                            <div class="col-xs-12 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="True">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
-                                    No
-                               </label>
-                            </div>
-                        </div>
--->
-                        <div class="form-group">
-                            <div style="padding-left:15px;" class="controls">
-                                <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
-                                    <i class="icon-ok-circle icon-white"></i> Compute
-                                </button>
+                            <label class="col-xs-2 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-4">
+                              <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+                                  Compute
+                              </button>
                             </div>
                         </div>
                     </div>
@@ -354,8 +343,8 @@
                     <div style="padding-top: 10px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                            <label style="text-align:left;" class="col-xs-4 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-2 controls">
                                 <select id="genofile_gemma" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -365,29 +354,34 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-3 controls">
+                            <label style="text-align:left;" class="col-xs-2 control-label">MAF</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
-                    </div>
-
-                    <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <button type="button" id="select_covariates" class="btn btn-default">
-                                Select Covariates
-                            </button>
-                            <button type="button" id="remove_covariates" class="btn btn-default">
-                                Remove Covariates
-                            </button>
+                            <label style="text-align: left;" class="col-xs-2 control-label">Covariates</label>
+                            <div style="margin-left:20px;" class="col-xs-7">
+                              {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+                              No collections available. Please add traits to a collection to use them as covariates.
+                              {% elif g.cookie_session.display_num_collections() == "" %}
+                              No collections available. Please add traits to a collection to use them as covariates.
+                              {% else %}
+                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
+                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+                              </div>
+                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+                              {% endif %}
+                            </div>
                         </div>
-                    </div>
-
-                    <div class="form-group">
-                        <div class="col-xs-4 controls">
+                        <div class="mapping_method_fields form-group">
+                          <label class="col-xs-2 control-label"></label>
+                          <div style="margin-left:20px;" class="col-xs-4">
                             <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
+                          </div>
                         </div>
                     </div>
                 </div>
@@ -416,7 +410,7 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-6">
+    <div class="col-xs-5">
         {% if dataset.group.mapping_id == "1" %}
         <dl>
              <dt>Interval Mapping</dt>