proteins

app/controllers/private_api/proteins_controller.rb

@@ -21,14 +21,14 @@ def proteins
 
     # Request the suffix array search service
     search_result = search([ peptide ], equate_il).first
-    if search_result.nil?
-      return
-    end
 
     @lca = search_result["lca"] || -1
     @common_lineage = []
 
-    # Collect all protein information
+    if search_result.nil?
+      return
+    end
+
     @proteins = UniprotEntry
       .includes(:taxon)
       .where(uniprot_accession_number: search_result["uniprot_accessions"])
@@ -44,67 +44,6 @@ def proteins
         }
       end
 
-
-    # if sequence.present? && sequence.peptides(equate_il).empty?
-    #   @entries = []
-    #   return
-    # end
-
-    # @common_lineage = []
-
-    # # get the uniprot entries of every peptide
-    # # only used for the open in uniprot links
-    # # and calculate the LCA
-    # if sequence.nil?
-    #   begin
-    #     # we didn't find the sequence in the database, so let's try to split it
-    #     long_sequences = Sequence.advanced_single_search(seq, equate_il)
-    #   rescue NoMatchesFoundError
-    #     return
-    #   end
-    #   # calculate possible uniprot entries
-    #   temp_entries = long_sequences.map { |s| s.peptides(equate_il).map(&:uniprot_entry).to_set }
-    #   # take the intersection of all sets
-    #   @entries = temp_entries.reduce(:&)
-    #   # check if the protein contains the startsequence
-    #   @entries.select! { |e| e.protein_contains?(seq, equate_il) }
-
-    #   # Calculate fa summary
-    #   @fa_summary = UniprotEntry.summarize_fa(@entries)
-
-    #   return if @entries.empty?
-
-    #   @lineages = @entries.map(&:lineage).compact
-    # else
-    #   @entries = sequence.peptides(equate_il).map(&:uniprot_entry)
-    #   @lineages = sequence.lineages(equate_il, true).to_a
-
-    #   # Get FA summary from cache
-    #   @fa_summary = sequence.calculate_fa(equate_il)
-    # end
-
-    # # sort entries
-    # @entries = @entries.to_a.sort_by { |e| e.taxon.nil? ? '' : e.taxon.name }
-
-    # @lca_taxon = Lineage.calculate_lca_taxon(@lineages)
-    # @root = Node.new(1, 'Organism', nil, 'root') # start constructing the tree
-    # common_hits = @lineages.map(&:hits).reduce(:+)
-    # @root.data['count'] = common_hits
-    # last_node = @root
-
-    # # common lineage
-    # # construct the common lineage in this array
-    # l = @lca_taxon.lineage
-    # found = (@lca_taxon.name == 'root')
-    # while !found && l.has_next?
-    #   t = l.next_t
-    #   next if t.nil?
-
-    #   found = (@lca_taxon.id == t.id)
-    #   @common_lineage << t
-    #   node = Node.new(t.id, t.name, @root, t.rank)
-    #   node.data['count'] = common_hits
-    #   last_node = last_node.add_child(node)
-    # end
+    // TODO: Common lineage calculation
   end
 end