require 'ruby-prof'

$:.unshift '.'

#require 'sinatra/base'
require 'yaml'
require 'logger'
require 'fileutils'
require 'sequenceserver/helpers'
require 'sequenceserver/blast'
require 'sequenceserver/sequencehelpers'
require 'sequenceserver/sinatralikeloggerformatter'
require 'sequenceserver/customisation'
require 'sequenceserver/version'

require 'sequenceserver'


query = '>1111883
GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTG
GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACG
GCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGC
ACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGA
CGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGAC
TCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACG
CCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGG
CTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCG
CGGTAATACGGAGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTG
GCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGC
GAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATAT
CGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGAC
AGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACT
AGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGG
GGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGA
GCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCA
AGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCACAGGTGCTGCATGGCTGTCGT
CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACTCTCGCTCCCAGT
TGCCAGCGGTTCGGCCGGGGACTCTGGGGGGACTGCCGGCGTTAAGCCGGAGGAAGGTGG
GGACGACGTCAAGTCATCATGGCCCTTACGTCCAGGGCGACACACGTGCTACAATGCCTG
GTACAGCGCGTCGCGAACTCGCAAGAGGGAGCCAATCGCCAAAAGCCGGGCTAAGTTCGG
ATTGTCGTCTGCAACTCGACGGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCAC
GCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGAAGCCGGA
GGGACCCGAAACCGGTGGGCCAACCGCAAGGGGGCAGCCGTCTAAGGT'

#blastn -db '/home/ben/git/sequenceserver/db/97_otus.fasta' -query '/tmp/sequenceserver_query20140119-10926-qt2ecp'  -task blastn  -num_threads 1 -html
method        = 'blastn'#params['method']
databases     = ['/home/ben/git/sequenceserver/db/97_otus.fasta']#params[:databases]
sequence      = query #params[:sequence]
advanced_opts = '-max_target_seqs 1'#params['advanced']

# evaluate empty sequence as nil, otherwise as fasta
#      sequence = sequence.empty? ? nil : to_fasta(sequence)

# blastn implies blastn, not megablast; but let's not interfere if a user
# specifies `task` herself
if method == 'blastn' and not advanced_opts =~ /task/
  #advanced_opts << ' -task blastn '
end


# run blast and log
blast = SequenceServer::Blast.new(method, sequence, databases.join(' '), advanced_opts)
blast.run!
puts('Ran: ' + blast.command)


    def format_blast_results(result, databases)
      formatted_result = ''
      @all_retrievable_ids = []
      string_of_used_databases = databases.join(' ')
      blast_database_number = 0
      line_number = 0
      started_query = false
      finished_database_summary = false
      finished_alignments = false
      reference_string = ''
      database_summary_string = ''
      result.each do |line|
        line_number += 1
        next if line_number <= 5 #skip the first 5 lines

        # Add the reference to the end, not the start, of the blast result
        if line_number >= 7 and line_number <= 15
          reference_string += line
          next
        end

        if !finished_database_summary and line_number > 15
          database_summary_string += line
          finished_database_summary = true if line.match(/total letters/)
          next
        end

        # Remove certain lines from the output
        skipped_lines = [/^<\/BODY>/,/^<\/HTML>/,/^<\/PRE>/]
        skip = false
        skipped_lines.each do |skippy|
        #  $stderr.puts "`#{line}' matches #{skippy}?"
          if skippy.match(line)
            skip = true
         #   $stderr.puts 'yes'
          else
          #  $stderr.puts 'no'
          end
        end
        next if skip

        # Remove the javascript inclusion
        line.gsub!(/^<script src=\"blastResult.js\"><\/script>/, '')

        if line.match(/^>/) # If line to possibly replace
          # Reposition the anchor to the end of the line, so that it both still works and
          # doesn't interfere with the diagnostic space at the beginning of the line.
          #
          # There are two cases:
          #
          # database formatted _with_ -parse_seqids
          line.gsub!(/^>(.+)(<a.*><\/a>)(.*)/, '>\1\3\2')
          #
          # database formatted _without_ -parse_seqids
          line.gsub!(/^>(<a.*><\/a>)(.*)/, '>\2\1')

          # get hit coordinates -- useful for linking to genome browsers
          hit_length      = result[line_number..-1].index{|l| l =~ />lcl|Lambda/}
          hit_coordinates = result[line_number, hit_length].grep(/Sbjct/).
            map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax

          # Create the hyperlink (if required)
          formatted_result += construct_sequence_hyperlink_line(line, databases, hit_coordinates)
        else
          # Surround each query's result in <div> tags so they can be coloured by CSS
          if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
            line = "<div class=\"resultn\" id=\"#{matches[1]}\">\n<h3>Query= #{matches[1]}</h3><pre>"
            unless blast_database_number == 0
              line = "</pre></div>\n#{line}"
            end
            blast_database_number += 1
          elsif line.match(/^  Database: /) and !finished_alignments
            formatted_result += "</div>\n<pre>#{database_summary_string}\n\n"
            finished_alignments = true
          end
          formatted_result += line
        end
      end
      formatted_result << "</pre>"

      link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
      # #dbs must be sep by ' '
      retrieval_text       = @all_retrievable_ids.empty? ? '' : "<a href='#{url(link_to_fasta_of_all)}'>FASTA of #{@all_retrievable_ids.length} retrievable hit(s)</a>"

      "<h2>Results</h2>"+
      retrieval_text +
      "<br/><br/>" +
      formatted_result +
      "<br/>" +
      "<pre>#{reference_string.strip}</pre>"
    end

    def construct_sequence_hyperlink_line(line, databases, hit_coordinates)
      matches = line.match(/^>(.+)/)
      sequence_id = matches[1]

      link = nil

      # If a custom sequence hyperlink method has been defined,
      # use that.
      options = {
        :sequence_id => sequence_id,
        :databases => databases,
        :hit_coordinates => hit_coordinates
      }

      # First precedence: construct the whole line to be customised
      if self.respond_to?(:construct_custom_sequence_hyperlinking_line)
        settings.log.debug("Using custom hyperlinking line creator with sequence #{options.inspect}")
        link_line = construct_custom_sequence_hyperlinking_line(options)
        unless link_line.nil?
          return link_line
        end
      end

      # If we have reached here, custom construction of the
      # whole line either wasn't defined, or returned nil
      # (indicating failure)
      if self.respond_to?(:construct_custom_sequence_hyperlink)
 #       settings.log.debug("Using custom hyperlink creator with sequence #{options.inspect}")
        link = construct_custom_sequence_hyperlink(options)
      else
#        settings.log.debug("Using standard hyperlink creator with sequence `#{options.inspect}'")
        link = construct_standard_sequence_hyperlink(options)
      end

      # Return the BLAST output line with the link in it
      if link.nil?
  #      settings.log.debug('No link added link for: `'+ sequence_id +'\'')
        return line
      else
        settings.log.debug('Added link for: `'+ sequence_id +'\''+ link)
        return "><a href='#{url(link)}' target='_blank'>#{sequence_id}</a> \n"
      end

    end

    # Advanced options are specified by the user. Here they are checked for interference with SequenceServer operations.
    # raise ArgumentError if an error has occurred, otherwise return without value
    def validate_advanced_parameters(advanced_options)
      raise ArgumentError, "Invalid characters detected in the advanced options" unless advanced_options =~ /\A[a-z0-9\-_\. ']*\Z/i
      disallowed_options = %w(-out -html -outfmt -db -query)
      disallowed_options.each do |o|
        raise ArgumentError, "The advanced BLAST option \"#{o}\" is used internally by SequenceServer and so cannot be specified by the you" if advanced_options =~ /#{o}/i
      end
    end

puts format_blast_results(blast.result, databases)