several major changes in code, several minor changes in style; prepared for OT meeting

1 files changed, 88 insertions, 41 deletions

diff --git a/views/prediction.haml b/views/prediction.haml
index f902504..4002cbd 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -4,7 +4,7 @@
       %img{:src=>"/images/arrow_left_float.png", :alt=>"<"}
         %a{:href => to('/predict')} New Prediction
 
-  / displays all prediction results
+  / displays all prediction result in first table
   .overview
     %table{:width=>"100%", :cellspacing=>"1", :id=>"overview"}
       %thead
@@ -17,9 +17,9 @@
           %td{:id=>"compound"}
             %a{:href => to("/prediction/#{CGI.escape(@compound.uri)}/details"), :id=>"linkCompound", :target=>"details_overview"}
               %img{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"150", :height=>"150"}
-            %br
-            %br
-            %img{:src=>"/images/arrow_up_float.png", :alt=>"^"}
+            %p
+            %a{:href => to("/prediction/#{CGI.escape(@compound.uri)}/details"), :id=>"linkCompound", :target=>"details_overview"} Names and synonyms
+            %p
             :javascript
               $(function() {
                 $("a#linkCompound").on('click', function(e) {
@@ -27,18 +27,18 @@
                 });
               });
           - count=0
-          / var for rule to load neighbors page.
-          - @@neighbors_available = 1
-          - @@predictions.each do |pa|
-            / prediction of one model
+          - @predictions.each do |pa|
+            / unpack to single array/prediction
+            / if p.data_entries array[0].size == 3 -> database hit
+            / change 'result' if database hit
+            / change 'confidence' if database hit
             - pa.each do |p|
-              - $logger.debug "inspect p: #{p.inspect}\n"
-              - $logger.debug "inspect data_entries: #{p.data_entries}\n"
-              / p.data_entries > 1 = neighbors available
-              - p.data_entries.length > 1 ? @@neighbors_available = p.data_entries.length : @@neighbors_available
               / prevent conversion of nil
+              /- $logger.debug "data entries in prediction array:\t#{p.data_entries}\n"
+              - database_hit = 0
+              - if p.data_entries[0].size == 3
+                - database_hit = 1
               - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : ''
-              - $logger.debug "inspect c: #{c.inspect}\n"
               - case c
               - when /(0|false)/
                 - c = "non-carcinogen"
@@ -46,15 +46,17 @@
                 - c = "carcinogen"
               - else
                 - c = Array.new
-                - c[0] = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no value")
+                - c[0] = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no prediction")
               %td
                 %b{:class => "title"}
-                  = @@prediction_models[count].title.split(" ").first
-                %br
-                %br
-                  / classification, regression
-                  %b Type:
-                %br
+                  = @prediction_models[count].title.split(" ").first
+                - @model_uri = @prediction_models[count].uri
+                %p
+                / model type (classification|regression)
+                %b Type:
+                = @model_type[count]
+                %p
+                - unless database_hit > 0
                   %b Result:
                   %b{:class => c[0]}
                     - if c.class == String
@@ -76,18 +78,18 @@
                         %li a majority vote (weighted by compound similarity) for 
                         %em classification 
                         (
-                        %a{:href=>"http://www.in-silico.de/articles/modi020905.pdf"} original publication
+                        %a{:href=>"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract", :target=>"_blank"} original publication
                         )
                         %li a local QSAR model based on neighbors for
                         %em regression
                         (
-                        %a{:href=>"http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+                        %a{:href=>"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract", :target=>"_blank"} original publication
                         )
                       Please keep in mind that predictions are based on the measured activities of neighbors.
-                %br
+                  %p
                   .confidence
                     %b Confidence:
-                    = p.data_entries[0][1] != nil ? p.data_entries[0][1].round(3) : ""
+                    = p.data_entries[0][1] != nil ? p.data_entries[0][1].round(3) : "-"
                     / title must be empty for tooltip
                     %a{:href=>"#confidence", :title=>"", :id=>"confidence"}
                       %img{:src=>"/images/info_white.png"}
@@ -101,20 +103,65 @@
                         Confidence values may take any value between 0 and 1.
                         For most models confidence > 0.025 is a sensible (hard) cutoff to distiguish between 
                         reliable and unreliable predictions.
-                  %br
-                %a{:href=> "#tabs", :id=>"link#{count}"}
-                  %img{:src=>"/images/arrow_down_float.png", :alt=>"v"}
-                  :javascript
-                    $("a#link#{count}").click(function () {
-                      $(".results").show();
-                      document.getElementById('tabs').focus();
-                      $("#tabs").tabs({ active: "#{count}" });
-                    });
-              - count+=1
-  
-  - if @@neighbors_available > 1
-    = haml :neighbors, :layout => false
-  - else
-    %h2
-      no neighbors available
-%iframe{:id=>"iframe_overview", :name=>"details_overview", :height=>"90%", :width=>"90%", :style=>"display:none;border:0px"}
+                  %p
+                  /TODO add tooltip for significant ftagments and descriptors
+                  - if @model_type[count] =~ /classification/i
+                    / Significant fragments:
+                    %a{:href => to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints"), :id=>"linkPredictionSf", :target=>"details_overview"}Significant fragments
+                    :javascript
+                      $(function() {
+                        $("a#linkPredictionSf").on('click', function(e) {
+                          $('#iframe_overview').bPopup();
+                        });
+                      });
+                  - if @model_type[count] =~ /regression/i
+                    / Descriptors
+                    %a{:href => to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints"), :id=>"linkPredictionSf", :target=>"details_overview"} Descriptors
+                    :javascript
+                      $(function() {
+                        $("a#linkPredictionSf").on('click', function(e) {
+                          $('#iframe_overview').bPopup();
+                        });
+                      });
+                  / title must be empty for tooltip
+                  -#%a{:href =>"#sfragments", :title=>"", :id=>"sfragments"}
+                    %img{:src=>"/images/info_white.png"}
+                  -#.tooltip{:style=>"font-weight: normal; font-size: 1em; width: 50%; text-align: left;"}
+                    %dt
+                      Significant fragments
+                    %dd
+                      Significant fragments are solely used to determine activity specific similarities of neighbors.
+                  %p
+                  %b Neighbors:
+                  %a{:href=> "#tabs", :id=>"link#{count}"}
+                    %img{:src=>"/images/arrow_down_float.png", :alt=>"v"}
+                    :javascript
+                      $("a#link#{count}").click(function () {
+                        $(".results").show();
+                        document.getElementById('tabs').focus();
+                        $("#tabs").tabs({ active: "#{count}" });
+                      });
+                  %p
+                  - count+=1
+                - else # database hit
+                  %b Database hit: 
+                  %br Compound found in training dataset
+                  %p
+                  %b Measured activity:
+                  = p.data_entries[0][2]
+                  %p
+                  %b Neighbors:
+                  %a{:href=> "#tabs", :id=>"link#{count}"}
+                    %img{:src=>"/images/arrow_down_float.png", :alt=>"v"}
+                    :javascript
+                      $("a#link#{count}").click(function () {
+                        $(".results").show();
+                        document.getElementById('tabs').focus();
+                        $("#tabs").tabs({ active: "#{count}" });
+                      });
+                    
+                  - count+=1
+
+  / always show the neighbors table, message is given there  
+  = haml :neighbors, :layout => false, :model_type => @model_type
+%iframe{:id=>"iframe_overview", :name=>"details_overview", :height=>"95%", :width=>"95%", :style=>"display:none;border:0px"}