require "plugin"

require "make_blast_db"
########################################################
# Author: Almudena Bocinos Rioboo
#
# Defines the main methods that are necessary to execute Pluginclassify
# Inherit: Plugin
########################################################

class PluginUserContaminants < Plugin


  MAX_TARGETS_SEQS=4 #MAXIMUM NUMBER OF DIFFERENT ALIGNED SEQUENCES TO  KEEP FROM BLAST DATABASE


  def near_to_extrem(c,seq,min_cont_size)
    max_to_extreme=(min_cont_size/2).to_i
    return ((c.q_beg-max_to_extreme<0) || (( c.q_end+max_to_extreme)>=seq.seq_fasta.size-1) ) #return if vector is very near to the extremes of insert)
  end
  
  def sum_hits_by_id(hits)
    res={}
    
    hits.each do |c|
      hit_size=c.q_end - c.q_beg + 1
      
      res[c.definition] = (res[c.definition]||0)+hit_size
      
    end
    
    puts res.to_json
    return res
  end

  #Begins the plugin1's execution to warn that there are classify in the sequence "seq"
  def execute(seqs)
    blasts= do_blasts(seqs)

    seqs.each_with_index do |s,i|
      exec_seq(s,blasts.querys[i])
    end
  end

  def do_blasts(seqs)

    # TODO - Culling limit = 2 porque el blast falla con este comando cuando se le pasa cl=1 y dust=no
    # y una secuencia de baja complejidad como entrada

    blast = BatchBlast.new("-db #{@params.get_param('user_contaminant_db')}",'blastn'," -task blastn -evalue #{@params.get_param('blast_evalue_classify')} -perc_identity #{@params.get_param('blast_percent_classify')} -culling_limit 1")  #get classify -max_target_seqs #{MAX_TARGETS_SEQS}

    $LOG.debug('BLAST:'+blast.get_blast_cmd(:xml))

    fastas=[]

    seqs.each do |seq|
      fastas.push ">"+seq.seq_name
      fastas.push seq.seq_fasta
    end


    blast_table_results = blast.do_blast(fastas,:xml)

    return blast_table_results
  end


  def exec_seq(seq,blast_query)
    if blast_query.query_id != seq.seq_name
      # raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
    end

    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for classify into the sequence"

    type = "ActionClassify"

    classify={}

    # classify_ids=[]

    classify=sum_hits_by_id(blast_query.hits)

    actions=[]
    classify_size=0

    min_cont_size=@params.get_param('min_classify_hit_size').to_i
    
    biggest_classify = classify.sort {|c1,c2| c1[1]<=>c2[1]}
    
    if !biggest_classify.empty?

      definition,classify_size = biggest_classify.last
      
      
      a = seq.new_action(-1,-1,type) # adds the correspondent action to the sequence

      a.message = definition
      
      a.tag_id = definition.gsub(' ','_')

      # a.found_definition = c.definition    # save the classify definitions, each separately
      
      #save to this file
      seq.add_file_tag(1, a.tag_id, :file)
      
      
      actions.push a

      add_stats('classify_size',classify_size)
      add_stats('classify_ids',definition)
  
      seq.add_actions(actions)
    end

  end

  #Returns an array with the errors due to parameters are missing
  def self.check_params(params)
    errors=[]


    comment='Blast E-value used as cut-off when searching for contaminations'
    default_value = 1e-10
    params.check_param(errors,'blast_evalue_classify','Float',default_value,comment)

    comment='Minimum required identity (%) for a reliable classify'
    default_value = 85
    params.check_param(errors,'blast_percent_classify','Integer',default_value,comment)

    comment='Minimum hit size (nt) for considering to classify'
    default_value = 30 # era 40
    params.check_param(errors,'min_classify_hit_size','Integer',default_value,comment)

    comment='Path for classify database'
    default_value = File.join($FORMATTED_DB_PATH,'classify.fasta')
    params.check_param(errors,'user_contaminant_db','DB',default_value,comment)


    return errors
  end


end