module SequenceServer
  module Customisation
    ## When not commented out, this method is used to take a
    ## sequence ID, and return a hyperlink that
    ## replaces the hit in the BLAST output.
    ##
    ## Return the hyperlink to link to, or nil
    ## to not not include a hyperlink.
    ##
    ## When this method
    ## is commented out, the default link is used. The default
    ## is a link to the full sequence of
    ## the hit is displayed (if makeblastdb has been run with
    ## -parse_seqids), or no link at all otherwise.
    # def construct_custom_sequence_hyperlink(options)
    #   ## Example:
    #   ## sequence_id comes in like "psu|MAL13P1.200 | organism=Plasmodium_falciparum_3D7 | product=mitochondrial"
    #   ## output: "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/MAL13P1.200"
    #   matches = options[:sequence_id].match(/^\s*psu\|(\S+) /)
    #   if matches #if the sequence_id conforms to our expectations
    #     # All is good. Return the hyperlink.
    #     return "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/#{matches[1]}"
    #   else
    #     # Parsing the sequence_id didn't work. Don't include a hyperlink for this
    #     # sequence_id, but log that there has been a problem.
    #     settings.log.warn "Unable to parse sequence id `#{options[:sequence_id]}'"
    #     # Return nil so no hyperlink is generated.
    #     return nil
    #   end
    # end

    ## Much like construct_custom_sequence_hyperlink, except
    ## instead of just a hyperlink being defined, the whole
    ## line as it appears in the blast results is generated.
    ##
    ## This is a therefore more flexible setup than is possible
    ## with construct_custom_sequence_hyperlink, because doing
    ## things such as adding two hyperlinks for the one hit
    ## are possible.
    ##
    ## When this method is commented out, the behaviour is that
    ## the construct_custom_sequence_hyperlink method is used,
    ## or failing that the default method of that is used.
    # def construct_custom_sequence_hyperlinking_line(options)
    #   matches = options[:sequence_id].match(/^\s*psu\|(\S+) /)
    #   if matches #if the sequence_id conforms to our expectations
    #     # All is good. Return the hyperlink.
    #     link1 = "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/#{matches[1]}"
    #     link2 = "http://google.com/?q=#{matches[1]}"
    #     return "<a href='#{link1}'>ApiLoc page</a>, <a href='#{link2}'>Google search</a>"
    #   else
    #     # Parsing the sequence_id didn't work. Don't include a hyperlink for this
    #     # sequence_id, but log that there has been a problem.
    #     settings.log.warn "Unable to parse sequence id `#{options[:sequence_id]}'"
    #     # Return nil so no hyperlink is generated.
    #     return nil
    #   end
    # end
  end
end