adjustments for nestec release1

3 files changed, 13 insertions, 25 deletions

diff --git a/views/layout.haml b/views/layout.haml
index d0c77b7..974a8ed 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -39,7 +39,7 @@
       = yield
     
     %footer.footer
-      %div.container
+      %div.container-fluid
         %p.text-muted
           © 
           %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 9f60e7c..cfa7858 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -3,21 +3,21 @@
 / align single prediction to endpoint ;
 / display preordered in table view ;
 
-%div.results{:style=>"display:none"}
+%div.results
   %h3 Neighbors:
   / tabs div
   #tabs
     %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
       / each model a tab head ;
       - @models.each_with_index do |model,i|
-        %li
+        %li{:class => ("active" if i == 0)}
           %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}}
             = "#{model.endpoint} (#{model.species})"
     %div.tab-content
       / unpack to single arrays
       - @predictions.each_with_index do |prediction,j|
         / pass model type for significant fragments view
-        #results.tab-pane.fade{:id=>"#{j+1}"}
+        #results.tab-pane{:id=>"#{j+1}", :class => ("active" if j == 0)}
           / prepare dataset for neighbors table ;
           / delete first array which contains prediction ;
           / following arrays are the neighbor predictions ;
@@ -52,16 +52,17 @@
                   %tr
                     %td
                     %td{:style=>"font-size:x-small;padding:0px;"}
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                      / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %td{:style=>"font-size:x-small;padding:0px;"}
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific 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><li>ignore inert parts of the structure</li><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.</li></ul>"}, :style=>"z-index:auto+10;"}
+                      / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific 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><li>ignore inert parts of the structure</li><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.</li></ul>"}, :style=>"z-index:auto+10;"}
                     / %td
                 %tbody
                 - prediction[:neighbors].each_with_index do |neighbor,count|
                   %tr
                     %td{:style =>"vertical-align:middle;padding-left:1em;"}
-                      %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
-                        = Compound.find(neighbor[0]).svg
+                      /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
+                      %p= Compound.find(neighbor[0]).svg
+                      %p= Compound.find(neighbor[0]).smiles
                     %td{:style =>"vertical-align:middle;padding-left:1em;"}
                       = neighbor[2].collect{|n| '%.2e' % n}.join ", "
                     %td{:style =>"vertical-align:middle;padding-left:1em;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 91f7024..3cdfbd6 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,9 +18,8 @@
       %tbody
         %tr
           %td{:id=>"compound", :style=>"vertical-align:top;"}
-            %a.btn.btn-link{:href => "#detailsTop", :id=>"linkCompound", data: { toggle: "modal", remote: to("/prediction/#{@compound.id.to_s}/details")}}
-              / %img.img-responsive{:src=>"#{@compound.id}/image", :alt=>"no image", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"}
-              = @compound.svg
+            %p= @compound.svg
+            %p= @compound.smiles
           - @predictions.each_with_index do |prediction,i|
             %td{:style=>"vertical-align:top;"}
               %b{:class => "title"}
@@ -42,12 +41,12 @@
                 / TODO scientific notation
                 = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{@models[i].unit}" : prediction[:value]
                 / TODO update description
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"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<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
+                / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"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<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
                 / TODO probability
                 %b Confidence:
                 = prediction[:confidence].round(3)
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
+                / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
                 %p
                 /TODO add tooltip for significant ftagments and descriptors
                 / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
@@ -57,15 +56,6 @@
                 / Descriptors
                 / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
                 / %p
-                %a.btn.btn-default.btn-sm{:href=> "#tabs", :id=>"link#{i+1}"}
-                  Neighbors
-                :javascript
-                  $("a#link#{i}").click(function () {
-                    $(".results").show();
-                    //document.getElementById('tabs').focus();
-                    $('#neighborTabs a[href="#results_#{i+1}"]').tab('show');
-                    //$("#tabs").tabs({ active: "#{i}" });
-                  });
                 %p
               - else
                 %p
@@ -73,7 +63,4 @@
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_type
-  %div.modal.fade{:id=>"detailsTop", :role=>"dialog"}
-    %div.modal-dialog.modal-lg
-      %div.modal-content