added info icons; neighbors, color by class for text not background

4 files changed, 82 insertions, 42 deletions

diff --git a/views/layout.haml b/views/layout.haml
index 410d150..b9fd06d 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -49,19 +49,24 @@
             });
           });
           $('a#confidence').tooltip({
-            predelay: 800,
+            predelay: 300,
+            position: 'bottom center',
+            offset: [-100, 0],
+          });
+          $('a#result').tooltip({
+            predelay: 300,
             position: 'bottom center',
             offset: [-100, 0],
           });
           $('a#similarity').tooltip({
-            predelay: 800,
+            predelay: 300,
             position: 'bottom center',
             offset: [-600, 0],
           });
           $('a#measured_activity').tooltip({
-            predelay: 800,
+            predelay: 300,
             position: 'bottom center',
-            offset: [-450, 0],
+            offset: [-500, 0],
           });
         });
       #back-top
diff --git a/views/neighbours.haml b/views/neighbors.haml
index 84d9f72..ddea418 100644
--- a/views/neighbours.haml
+++ b/views/neighbors.haml
@@ -1,6 +1,6 @@
 / @@prediction_models and @@predictions defined in POST request '/predict'
 / unpacks multi prediction array ;
-/ prepare it for neighbours ;
+/ prepare it for neighbors ;
 / align single prediction to endpoint ;
 / display preordered in table view ;
 
@@ -28,9 +28,9 @@
       - count_rs += 1
       #results{:id=>"#{count_rs}"}
         - pa.each do |p|
-          / prepare dataset for neighbours table ;
+          / prepare dataset for neighbors table ;
           / delete first array which contains input compound prediction ;
-          / keep the following arrays they are the neighbour predictions ;
+          / keep the following arrays they are the neighbor predictions ;
           - p.data_entries.shift
           - p.compounds.shift
           / call the tablesorter plugin ;
@@ -45,21 +45,25 @@
               });
             });
           / TODO catch table error if tbody is empty      
-          %h2= "Neighbours: "
+          %h2= "Neighbors: "
           %table{:id=>"#{count_rs}", :class=>"tablesorter", :cellspacing=>"1"}
             %thead
               %tr
                 %th
                   Compound
                 %th
-                  %a{:href=>"#", :title=>"", :id=>"measured_activity"} Measured Activity
+                  %b Measured Activity
+                  %a{:href=>"#", :title=>"", :id=>"measured_activity"}
+                    %img{:src=>"/images/info_white.png"}
                   .tooltip{:style=>"font-weight: normal; font-size: 1em; text-align: left;"}
                     %dt
                       Measured Activity
                     %dd
                       Experimental result(s) from the training dataset.
                 %th
-                  %a{:href=>"#", :title=>"", :id=>"similarity"} Similarity
+                  %b Similarity
+                  %a{:href=>"#", :title=>"", :id=>"similarity"}
+                    %img{:src=>"/images/info_white.png"}
                   .tooltip{:style=>"font-weight: normal; font-size: 1em; text-align: left;"}
                     %dt
                       Similarity
@@ -71,24 +75,26 @@
                       similarities based on the presence of statistically significant fragments.
                       This procedure will
                       %ul
-                        %li consider only those parts of a chemical structure that are relevant for a particular endpoint
+                        %li consider only those parts of a chemical structure that are relevant 
+                        for a particular endpoint
                         %li ignore inert parts of the structure
                         %li lead to different similarities, depending on the toxic endpoint
-                        Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.
+                        Similarities of 1 may be encountered even for structurally dissimilar 
+                        compounds, because inert parts are ignored.
                 %th
                   Details
             -#%tbody
             - count = 0
-            - p.compounds.each do |neighbour_compound|
+            - p.compounds.each do |neighbor_compound|
               %tr
-                %td
-                  %img{:src=>"#{neighbour_compound.uri}/image", :alt=>"", :width=>"100px"}
-                %td{:class => p.data_entries[count][2]}
+                %td.compound
+                  %img{:src=>"#{neighbor_compound.uri}/image", :alt=>"", :width=>"100px"}
+                %td{:class => "c"+p.data_entries[count][2]}
                   = p.data_entries[count][2]
-                %td{:class => p.data_entries[count][2]}
-                  = p.data_entries[count][3].round(3)                  
-                %td{:class => p.data_entries[count][2]}
-                  %a{:href => to("/prediction/#{CGI.escape(neighbour_compound.uri)}/details"), :id=>"link#{count_rs}#{count}", :target=>"details"}
+                %td{:class => "c"+p.data_entries[count][2]}
+                  = p.data_entries[count][3] != nil ? p.data_entries[count][3].round(3) : "No prediction result"            
+                %td{:class => "c"+p.data_entries[count][2]}
+                  %a{:href => to("/prediction/#{CGI.escape(neighbor_compound.uri)}/details"), :id=>"link#{count_rs}#{count}", :target=>"details"}
                     %img{:src=>"/images/arrow_right_float.png", :alt=>"arrow"}
                   :javascript
                     $(function() {
@@ -99,4 +105,4 @@
                     
                 - count += 1
 
-%iframe{:id=>"iframe", :name=>"details", :height=>"80%", :width=>"80%", :style=>"display:none;border:0px"}
+%iframe{:id=>"iframe", :name=>"details", :height=>"90%", :width=>"90%", :style=>"display:none;border:0px"}
diff --git a/views/predict.haml b/views/predict.haml
index 369f3b8..98b9edb 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -78,9 +78,9 @@
         #model
           %input{:type => "checkbox", :name => "selection[#{model.title}]", :id => "selection[#{model.title}]", :value => true, :disabled => false}
           %label{:for => "selection[#{model.title}]"}
-            %b= model.title
+            = "DSSTox Carcinogenic Potency DBS "+model.title.split(" ").first
           %a{:href=>"#", :alt=>"#{model.title} validation"}
-            %i Validation Link
+            %i ( Validation Link )
           %br
           
       .close
diff --git a/views/prediction.haml b/views/prediction.haml
index 20be935..89e66f0 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -27,33 +27,62 @@
                 });
               });
           - count=0
-          / var for rule to load neighbours page.
-          - @@neighbours_available = 1
+          / var for rule to load neighbors page.
+          - @@neighbors_available = 1
           - @@predictions.each do |pa|
             / prediction of one model
             - pa.each do |p|
-              / p.data_entries > 1 = neighbours available
-              - $logger.debug "count data_entries: #{p.data_entries.length}"
-              - p.data_entries.length > 1 ? @@neighbours_available = p.data_entries.length : @@neighbours_available
-              %td{:class => p.data_entries[0][0]}
+              / p.data_entries > 1 = neighbors available
+              - p.data_entries.length > 1 ? @@neighbors_available = p.data_entries.length : @@neighbors_available
+              / prevent conversion of nil
+              - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : ''
+              / define color by class; number first is not allowed for css
+              %td{:class => "c"+c}
                 %b{:class => "title"}
                   = @@prediction_models[count].title
                 %br
                 %br            
-                  = "Result:\n"
+                  = "Result:"
                   %b= p.data_entries[0][0] != nil ? p.data_entries[0][0] : "No prediction result"
-                %br
-                  %a{:href=>"#", :title=>"", :id=>"confidence"} Confidence
+                  %a{:href=>"#result", :title=>"", :id=>"result"}
+                    %img{:src=>"/images/info_white.png"}
                   .tooltip{:style=>"font-weight: normal; font-size: 1em; width: 50%; text-align: left;"}
                     %dt
-                      Confidence
+                      Result
                     %dd
-                      Indicates the applicability domain of a model.
-                      Predictions with a high confidence can be expected to be more reliable than predictions with low confidence.
-                      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.
-                  = p.data_entries[0][1].round(3)
+                      %code lazar 
+                      calculates searches the training dataset for similar compounds (neighbors) 
+                      and calculates the prediction from their measured activities. lazar 
+                      calculates predictions using
+                      %ul
+                        %li a majority vote (weighted by compound similarity) for 
+                        %em classification 
+                        (
+                        %a{:href=>"http://www.in-silico.de/articles/modi020905.pdf"} 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
+                        )
+                      Please keep in mind that predictions are based on the measured activities of neighbors.
                 %br
+                  .confidence
+                    %b Confidence:
+                    = p.data_entries[0][1] != nil ? p.data_entries[0][1].round(3) : "No prediction result"
+                    %a{:href=>"#confidence", :title=>"", :id=>"confidence"}
+                      %img{:src=>"/images/info_white.png"}
+                    .tooltip{:style=>"font-weight: normal; font-size: 1em; width: 50%; text-align: left;"}
+                      %dt
+                        Confidence
+                      %dd
+                        Indicates the applicability domain of a model.
+                        Predictions with a high confidence can be expected to be more reliable than predictions 
+                        with low confidence.
+                        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=>"arrow"}
                   :javascript
@@ -64,9 +93,9 @@
                     });
               - count+=1
   
-  - if @@neighbours_available > 1
-    = haml :neighbours, :layout => false
+  - if @@neighbors_available > 1
+    = haml :neighbors, :layout => false
   - else
     %h2
-      no neighbours available             
-%iframe{:id=>"iframe_overview", :name=>"details_overview", :height=>"80%", :width=>"80%", :style=>"display:none;border:0px"}            
+      no neighbors available             
+%iframe{:id=>"iframe_overview", :name=>"details_overview", :height=>"90%", :width=>"90%", :style=>"display:none;border:0px"}