<commit_before><h1><%= @title %></h1>

<% if @lineages.empty? %>
    <p class="lead">No results were found for <%= @original_sequence %>.</p>
<% else %>
<p class="lead"><%= @original_sequence %> was found in <b><%= @entries.size %></b> <%= 'Uniprot record'.pluralize(@entries.size) %> with a lowest common ancestor of <b><%= @lca_taxon.name %></b>.</p>
<p>Summary of the analysis:</p>
<ul>
  <li>Lowest common ancestor: <%= link_to @lca_taxon.name, "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + @lca_taxon.id.to_s, :target => "_blank", :title => @lca_taxon.rank %> (<%=@lca_taxon.rank%>)</li>
  <li>Common lineage: <%= raw @common_lineage.length==0 ? "nothing" : @common_lineage.map{|t| link_to t.name, "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + t.id.to_s, :target => "_blank", :title => t.rank }.join(" > ") %></li>
  <li><%= link_to "Blast "+@original_sequence , "http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&SET_SAVED_SEARCH=on&USER_FORMAT_DEFAULTS=on&PAGE=Proteins&PROGRAM=blastp&QUERY="+@original_sequence+"&GAPCOSTS=11%201&EQ_MENU=Enter%20organism%20name%20or%20id--completions%20will%20be%20suggested&DATABASE=nr&BLAST_PROGRAMS=blastp&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=10&WORD_SIZE=3&MATRIX_NAME=BLOSUM62&COMPOSITION_BASED_STATISTICS=2&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NEW_VIEW=on&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&OLD_BLAST=false", :target => "_blank", :title => "Open in BLAST"%></li>
</ul>
<div id="single-peptide-tabs">
<ul class="nav nav-tabs">
    <li class="active"><a href="#lineage-tree" id="lineage-tree-tab"data-toggle="tab">Lineage tree <span class="small glyphicon glyphicon-info-sign"></span></a></li>
    <li><a href="#lineage-table" id="lineage-table-tab" data-toggle="tab">Lineage table <span class="small glyphicon glyphicon-info-sign"></span></a></li>
    <li><a href="#proteins" data-toggle="tab">Protein matches</a></li>
</ul><commit_msg>add badge with number of matches to tab<commit_after><h1><%= @title %></h1>

<% if @lineages.empty? %>
    <p class="lead">No results were found for <%= @original_sequence %>.</p>
<% else %>
<p class="lead"><%= @original_sequence %> was found in <b><%= @entries.size %></b> <%= 'Uniprot record'.pluralize(@entries.size) %> with a lowest common ancestor of <b><%= @lca_taxon.name %></b>.</p>
<p>Summary of the analysis:</p>
<ul>
  <li>Lowest common ancestor: <%= link_to @lca_taxon.name, "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + @lca_taxon.id.to_s, :target => "_blank", :title => @lca_taxon.rank %> (<%=@lca_taxon.rank%>)</li>
  <li>Common lineage: <%= raw @common_lineage.length==0 ? "nothing" : @common_lineage.map{|t| link_to t.name, "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + t.id.to_s, :target => "_blank", :title => t.rank }.join(" > ") %></li>
  <li><%= link_to "Blast "+@original_sequence , "http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&SET_SAVED_SEARCH=on&USER_FORMAT_DEFAULTS=on&PAGE=Proteins&PROGRAM=blastp&QUERY="+@original_sequence+"&GAPCOSTS=11%201&EQ_MENU=Enter%20organism%20name%20or%20id--completions%20will%20be%20suggested&DATABASE=nr&BLAST_PROGRAMS=blastp&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=10&WORD_SIZE=3&MATRIX_NAME=BLOSUM62&COMPOSITION_BASED_STATISTICS=2&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NEW_VIEW=on&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&OLD_BLAST=false", :target => "_blank", :title => "Open in BLAST"%></li>
</ul>
<div id="single-peptide-tabs">
<ul class="nav nav-tabs">
    <li class="active"><a href="#lineage-tree" id="lineage-tree-tab"data-toggle="tab">Lineage tree <span class="small glyphicon glyphicon-info-sign"></span></a></li>
    <li><a href="#lineage-table" id="lineage-table-tab" data-toggle="tab">Lineage table <span class="small glyphicon glyphicon-info-sign"></span></a></li>
    <li><a href="#proteins" data-toggle="tab">Protein matches <span class="badge"><%= @entries.size %></span></a></li>
</ul>
{'fraction_non_alphanumeric': 0.21103742302226433, 'fraction_numerical': 0.01989578398863098, 'mean_word_length': 7.653688524590164, 'pattern_counts': {'":': 0, '<': 108, '<?xml version=': 0, '>': 122, 'https://': 0, 'lorem ipsum': 0, 'www.': 8, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5810445', 'n_tokens_mistral': 1784, 'n_tokens_neox': 1627, 'n_words': 224}