Created a class in coffeescript for stats and got several to display dynamically

6 files changed, 215 insertions, 102 deletions

diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 8ee1d9c8..32ecc732 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -1814,7 +1814,7 @@ class DataEditingPage(templatePage):
                 print("No strain %s, let's create it now" % strainName)
                 strain = webqtlCaseData.webqtlCaseData(strainName)
             print("zyt - strainNameOrig:", strainNameOrig)
-          
+
 
             if strains == 'primary':
                 strain.this_id = "Primary_" + str(counter)
diff --git a/wqflask/wqflask/static/new/javascript/stats.coffee b/wqflask/wqflask/static/new/javascript/stats.coffee
new file mode 100644
index 00000000..677dc258
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/stats.coffee
@@ -0,0 +1,46 @@
+class Stats
+    constructor: (@the_values) ->
+        
+    add_value: (value) ->
+        @the_values.push(value)
+    
+    n_of_samples: ->
+        return @the_values.length
+        
+    sum: ->
+        total = 0
+        total += value for value in @the_values
+        return total
+    
+    mean: ->
+        return @sum() / @n_of_samples()
+    
+    median: ->
+        is_odd = @the_values.length % 2
+        median_position = Math.floor(@the_values.length / 2)
+        the_values_sorted = @the_values.sort((a,b) -> return a - b)
+        if is_odd
+            return the_values_sorted[median_position]
+        else
+            return (the_values_sorted[median_position] +
+                    the_values_sorted[median_position - 1]) / 2
+        
+    std_dev: ->
+        sum = 0
+        for value in @the_values
+            step_a = Math.pow(value - @mean(), 2)
+            sum += step_a
+        step_b = sum / @the_values.length
+        return Math.sqrt(step_b)
+    
+    std_error: ->
+        return @std_dev() / Math.sqrt(@n_of_samples())
+
+
+bxd_only = new Stats([3, 5, 7, 8])
+console.log("[red] bxd_only mean:", bxd_only.mean())
+console.log("[green] bxd_only median:", bxd_only.median())
+console.log("[purple] bxd_only std_dev:", bxd_only.std_dev())
+console.log("[magenta] bxd_only std_error:", bxd_only.std_error())
+
+window.Stats = Stats
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
new file mode 100644
index 00000000..f95d03d4
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -0,0 +1,81 @@
+// Generated by CoffeeScript 1.3.3
+(function() {
+  var Stats, bxd_only;
+
+  Stats = (function() {
+
+    function Stats(the_values) {
+      this.the_values = the_values;
+    }
+
+    Stats.prototype.add_value = function(value) {
+      return this.the_values.push(value);
+    };
+
+    Stats.prototype.n_of_samples = function() {
+      return this.the_values.length;
+    };
+
+    Stats.prototype.sum = function() {
+      var total, value, _i, _len, _ref;
+      total = 0;
+      _ref = this.the_values;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        value = _ref[_i];
+        total += value;
+      }
+      return total;
+    };
+
+    Stats.prototype.mean = function() {
+      return this.sum() / this.n_of_samples();
+    };
+
+    Stats.prototype.median = function() {
+      var is_odd, median_position, the_values_sorted;
+      is_odd = this.the_values.length % 2;
+      median_position = Math.floor(this.the_values.length / 2);
+      the_values_sorted = this.the_values.sort(function(a, b) {
+        return a - b;
+      });
+      if (is_odd) {
+        return the_values_sorted[median_position];
+      } else {
+        return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2;
+      }
+    };
+
+    Stats.prototype.std_dev = function() {
+      var step_a, step_b, sum, value, _i, _len, _ref;
+      sum = 0;
+      _ref = this.the_values;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        value = _ref[_i];
+        step_a = Math.pow(value - this.mean(), 2);
+        sum += step_a;
+      }
+      step_b = sum / this.the_values.length;
+      return Math.sqrt(step_b);
+    };
+
+    Stats.prototype.std_error = function() {
+      return this.std_dev() / Math.sqrt(this.n_of_samples());
+    };
+
+    return Stats;
+
+  })();
+
+  bxd_only = new Stats([3, 5, 7, 8]);
+
+  console.log("[red] bxd_only mean:", bxd_only.mean());
+
+  console.log("[green] bxd_only median:", bxd_only.median());
+
+  console.log("[purple] bxd_only std_dev:", bxd_only.std_dev());
+
+  console.log("[magenta] bxd_only std_error:", bxd_only.std_error());
+
+  window.Stats = Stats;
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
index 2952bef5..c44582db 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -19,54 +19,56 @@ $ ->
 
     $(".stats_mdp").change(stats_mdp_change)
 
-    update_stat_values = (the_values)->
+    change_stats_value = (category, value_type, the_value)->
+        id = "#" + process_id(category, value_type)
+        in_box = $(id).html
+        
+        current_value = parseFloat($(in_box)).toFixed(2)
+        
+        if the_value != current_value
+            $(id).html(the_value).effect("highlight")
+
+    update_stat_values = (sample_sets)->
         for category in ['primary_only', 'other_only', 'all_cases']
-            # Mean
-            id = "#" + process_id(category, "mean")
-            total = 0
-            total += value for value in the_values[category]
-            the_mean = total / the_values[category].length
-            the_mean = the_mean.toFixed(2)
-            in_box = $(id).html
-            
-            current_mean = parseFloat($(in_box)).toFixed(2)
-
-            if the_mean != current_mean
-                $(id).html(the_mean).effect("highlight")
-
 
             # Number of samples
-            n_of_samples = the_values[category].length
+            n_of_samples = sample_sets[category].n_of_samples()
             id = "#" + process_id(category, "n_of_samples")
             current_n_of_samples = $(id).html()
             if n_of_samples != current_n_of_samples
                 $(id).html(n_of_samples).effect("highlight")
+
+            # Mean
+            #id = "#" + process_id(category, "mean")
+
+            the_mean = sample_sets[category].mean()
+            the_mean = the_mean.toFixed(2)
+            change_stats_value(category, "mean", the_mean)
+            #in_box = $(id).html
             
+            #current_mean = parseFloat($(in_box)).toFixed(2)
+
+            #if the_mean != current_mean
+            #    $(id).html(the_mean).effect("highlight")            
             
             # Median
             id = "#" + process_id(category, "median")
+            the_median = sample_sets[category].median()
+            the_median = the_median.toFixed(2)
+            in_box = $(id).html
+
+            current_median = parseFloat($(in_box)).toFixed(2)
 
-            is_odd = the_values[category].length % 2
-            median_position = Math.floor(the_values[category].length / 2)
-            
-            # sort numerically
-            the_values_sorted = the_values[category].sort((a, b) -> return a - b)
-            if is_odd
-                the_median = the_values_sorted[median_position]
-            else
-                the_median = (the_values_sorted[median_position] +
-                              the_values_sorted[median_position + 1]) / 2
-            current_median = $(id).html()
             if the_median != current_median
                 $(id).html(the_median).effect("highlight")
 
             # Todo: Compare stat values to genenetwork.org current code / sample vs. population
             # Standard deviation
             sum = 0
-            for value in the_values[category]
+            for value in sample_sets[category]
                 step_a = Math.pow(value - the_mean, 2)
                 sum += step_a
-            step_b = sum / the_values[category].length
+            step_b = sum / sample_sets[category].length
             sd = Math.sqrt(step_b)
             sd = sd.toFixed(2)
             
@@ -76,35 +78,32 @@ $ ->
                 $(id).html(sd).effect("highlight")
             
 
-    edit_data_change = ->
-        the_values =
-            primary_only: []
-            other_only: []
-            all_cases: []
-        console.log("at beginning:", the_values)
+    edit_data_change = ->                
+        sample_sets =
+            primary_only: new Stats([])
+            other_only: new Stats([])
+            all_cases: new Stats([])
+                
+        console.log("at beginning:", sample_sets)
         values = $('#value_table').find(".edit_strain_value")
-        #console.log("values are:", values)
+
         for value in values
             real_value = $(value).val()
-            #console.log("parent is:", $(value).closest("tr"))
             row = $(value).closest("tr")
-            console.log("row is:", row)
-            console.log("row[0].id is:", row[0].id)
             category = row[0].id
             checkbox = $(row).find(".edit_strain_checkbox")
             checked = $(checkbox).attr('checked')
-            if not checked
-                console.log("Not checked")
-                continue
-            if is_number(real_value) and real_value != ""
+
+            if checked and is_number(real_value) and real_value != ""
                 real_value = parseFloat(real_value)
                 if _(category).startsWith("Primary")
-                    the_values.primary_only.push(real_value)
+                    sample_sets.primary_only.add_value(real_value)
                 else if _(category).startsWith("Other")
-                    the_values.other_only.push(real_value)
-                the_values.all_cases.push(real_value)
-        console.log("towards end:", the_values)
-        update_stat_values(the_values)
+                    sample_sets.other_only.add_value(real_value)
+                sample_sets.all_cases.add_value(real_value)
+        console.log("towards end:", sample_sets)
+        update_stat_values(sample_sets)
+        
 
     make_table = ->
         header = "<thead><tr><th>&nbsp;</th>"
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
index 04f43822..b4eed350 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -10,7 +10,7 @@
   };
 
   $(function() {
-    var edit_data_change, hide_tabs, make_table, on_corr_method_change, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
+    var change_stats_value, edit_data_change, hide_tabs, make_table, on_corr_method_change, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
     hide_tabs = function(start) {
       var x, _i, _results;
       _results = [];
@@ -27,55 +27,46 @@
       return $("#stats_tabs" + selected).show();
     };
     $(".stats_mdp").change(stats_mdp_change);
-    update_stat_values = function(the_values) {
-      var category, current_mean, current_median, current_n_of_samples, current_sd, id, in_box, is_odd, median_position, n_of_samples, sd, step_a, step_b, sum, the_mean, the_median, the_values_sorted, total, value, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2, _results;
+    change_stats_value = function(category, value_type, the_value) {
+      var current_value, id, in_box;
+      id = "#" + process_id(category, value_type);
+      in_box = $(id).html;
+      current_value = parseFloat($(in_box)).toFixed(2);
+      if (the_value !== current_value) {
+        return $(id).html(the_value).effect("highlight");
+      }
+    };
+    update_stat_values = function(sample_sets) {
+      var category, current_median, current_n_of_samples, current_sd, id, in_box, n_of_samples, sd, step_a, step_b, sum, the_mean, the_median, value, _i, _j, _len, _len1, _ref, _ref1, _results;
       _ref = ['primary_only', 'other_only', 'all_cases'];
       _results = [];
       for (_i = 0, _len = _ref.length; _i < _len; _i++) {
         category = _ref[_i];
-        id = "#" + process_id(category, "mean");
-        total = 0;
-        _ref1 = the_values[category];
-        for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
-          value = _ref1[_j];
-          total += value;
-        }
-        the_mean = total / the_values[category].length;
-        the_mean = the_mean.toFixed(2);
-        in_box = $(id).html;
-        current_mean = parseFloat($(in_box)).toFixed(2);
-        if (the_mean !== current_mean) {
-          $(id).html(the_mean).effect("highlight");
-        }
-        n_of_samples = the_values[category].length;
+        n_of_samples = sample_sets[category].n_of_samples();
         id = "#" + process_id(category, "n_of_samples");
         current_n_of_samples = $(id).html();
         if (n_of_samples !== current_n_of_samples) {
           $(id).html(n_of_samples).effect("highlight");
         }
+        the_mean = sample_sets[category].mean();
+        the_mean = the_mean.toFixed(2);
+        change_stats_value(category, "mean", the_mean);
         id = "#" + process_id(category, "median");
-        is_odd = the_values[category].length % 2;
-        median_position = Math.floor(the_values[category].length / 2);
-        the_values_sorted = the_values[category].sort(function(a, b) {
-          return a - b;
-        });
-        if (is_odd) {
-          the_median = the_values_sorted[median_position];
-        } else {
-          the_median = (the_values_sorted[median_position] + the_values_sorted[median_position + 1]) / 2;
-        }
-        current_median = $(id).html();
+        the_median = sample_sets[category].median();
+        the_median = the_median.toFixed(2);
+        in_box = $(id).html;
+        current_median = parseFloat($(in_box)).toFixed(2);
         if (the_median !== current_median) {
           $(id).html(the_median).effect("highlight");
         }
         sum = 0;
-        _ref2 = the_values[category];
-        for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
-          value = _ref2[_k];
+        _ref1 = sample_sets[category];
+        for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
+          value = _ref1[_j];
           step_a = Math.pow(value - the_mean, 2);
           sum += step_a;
         }
-        step_b = sum / the_values[category].length;
+        step_b = sum / sample_sets[category].length;
         sd = Math.sqrt(step_b);
         sd = sd.toFixed(2);
         id = "#" + process_id(category, "sd");
@@ -89,39 +80,33 @@
       return _results;
     };
     edit_data_change = function() {
-      var category, checkbox, checked, real_value, row, the_values, value, values, _i, _len;
-      the_values = {
-        primary_only: [],
-        other_only: [],
-        all_cases: []
+      var category, checkbox, checked, real_value, row, sample_sets, value, values, _i, _len;
+      sample_sets = {
+        primary_only: new Stats([]),
+        other_only: new Stats([]),
+        all_cases: new Stats([])
       };
-      console.log("at beginning:", the_values);
+      console.log("at beginning:", sample_sets);
       values = $('#value_table').find(".edit_strain_value");
       for (_i = 0, _len = values.length; _i < _len; _i++) {
         value = values[_i];
         real_value = $(value).val();
         row = $(value).closest("tr");
-        console.log("row is:", row);
-        console.log("row[0].id is:", row[0].id);
         category = row[0].id;
         checkbox = $(row).find(".edit_strain_checkbox");
         checked = $(checkbox).attr('checked');
-        if (!checked) {
-          console.log("Not checked");
-          continue;
-        }
-        if (is_number(real_value) && real_value !== "") {
+        if (checked && is_number(real_value) && real_value !== "") {
           real_value = parseFloat(real_value);
           if (_(category).startsWith("Primary")) {
-            the_values.primary_only.push(real_value);
+            sample_sets.primary_only.add_value(real_value);
           } else if (_(category).startsWith("Other")) {
-            the_values.other_only.push(real_value);
+            sample_sets.other_only.add_value(real_value);
           }
-          the_values.all_cases.push(real_value);
+          sample_sets.all_cases.add_value(real_value);
         }
       }
-      console.log("towards end:", the_values);
-      return update_stat_values(the_values);
+      console.log("towards end:", sample_sets);
+      return update_stat_values(sample_sets);
     };
     make_table = function() {
       var header, key, row, row_line, rows, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 16f2e2be..1f33dee5 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -1310,13 +1310,15 @@
     </tr>
 
     <script>
-		js_data = {{ js_data | safe }}
-	</script>-->
+        js_data = {{ js_data | safe }}
+    </script>
 
 	<script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>-->
 	<script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    
+    <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
 	<script type="text/javascript" src="/static/new/javascript/trait_data_and_analysis.js"></script>
-
+    
 
 	<!-- End of body -->