links.rb

require 'json'
module SequenceServer
   module Links
       def jbrowse
           qstart = hsps.map(&:qstart).min
           sstart = hsps.map(&:sstart).min
           qend = hsps.map(&:qend).max
           send = hsps.map(&:send).max
           first_hit_start = hsps.map(&:sstart).at(0)
           first_hit_end = hsps.map(&:send).at(0)
           organism = accession.partition('-').first
           sequence_id = accession.partition('-').last
           my_features = ERB::Util.url_encode(JSON.generate([{
               :seq_id => sequence_id,
               :start => sstart,
               :end => send,
               :type => "match",
               :subfeatures =>  hsps.map {
                 |hsp| {
                   :start => hsp.send < hsp.sstart ? hsp.send : hsp.sstart,
                   :end => hsp.send < hsp.sstart ? hsp.sstart : hsp.send,
                   :type => "match_part"
                 }
               }
           }]))
           my_track = ERB::Util.url_encode(JSON.generate([
                {
                   :label => "BLAST",
                   :key => "BLAST hits",
                   :type => "JBrowse/View/Track/CanvasFeatures",
                   :store => "url",
                   :glyph => "JBrowse/View/FeatureGlyph/Segments"
                }
           ]))
           url = "<http://10.150.2.3/jbrowse1>" \
                        "?data=#{organism}" \
                        "&loc=#{sequence_id}:#{first_hit_start-500}..#{first_hit_start+500}" \
                        "&addFeatures=#{my_features}" \
                        "&addTracks=#{my_track}" \
                        "&tracks=BLAST" \
                        "&highlight=#{accession}:#{first_hit_start}..#{first_hit_end}"
           {
             :order => 2,
             :title => 'JBrowse',
             :url   => url,
             :icon  => 'fa-external-link'
           }
       end
   end
end