diff options
author | gebele <gebele@in-silico.ch> | 2015-09-01 12:43:56 +0000 |
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committer | gebele <gebele@in-silico.ch> | 2015-09-01 12:43:56 +0000 |
commit | dab74297422b9fed72f85073fc76a8cd31a1e3cd (patch) | |
tree | fb5bd061dbe401296a458ae162dc4eda4af4edbc /views | |
parent | 7dcae58f3af869b4c58e6091cee099acff113ad2 (diff) |
adjustments for nestec release1
Diffstat (limited to 'views')
-rw-r--r-- | views/layout.haml | 2 | ||||
-rw-r--r-- | views/neighbors.haml | 15 | ||||
-rw-r--r-- | views/prediction.haml | 21 |
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 |