class CassiopeeMt::CrawlerMt

Multi threaded search using a Crawler per thread Filtering is used to split the input data according to maxthread Matches of each thread are merge to matches of CrawlerMT

Constants

MINSEQSIZE

Attributes

maxthread[RW]

Max number fo threads to use

Public Class Methods

new() click to toggle source

Calls superclass method

# File lib/cassiopee-mt.rb, line 23
def initialize
    super
    @th = []
    @matches = Array.new
end

Public Instance Methods

searchApproximate(s,edit) click to toggle source

# File lib/cassiopee-mt.rb, line 75
def searchApproximate(s,edit)
     len = @sequence.length
     if(@min_position>0)
       min = @min_position
      else
       min = 0 
     end
      if(@max_position>0)
        max = @max_position
      else
        max = @sequence.length
     end
     len = max - min
     if(len<MINSEQSIZE)
           @maxthread=1
     end
     nb = len.div(maxthread)
     (1..maxthread).each do |i|
       crawler = Crawler.new
       setParams(crawler,i)
       curmax = min + nb
       if(i==maxthread)
          curmax = max
       end
       crawler.filter_position(min,curmax)
       $log.debug("Start new Thread between " << min.to_s << " and " << curmax.to_s)
       @th[i-1] = Thread.new{ Thread.current["matches"] = crawler.searchApproximate(s,edit) }
       min = curmax + 1
     end
     @th.each {|t| t.join; t["matches"].each { |m| @matches << m }}
     return @matches
end

searchExact(pattern) click to toggle source

# File lib/cassiopee-mt.rb, line 42
def searchExact(pattern)
     len = @sequence.length
     if(@min_position>0)
       min = @min_position
      else
       min = 0  
     end
      if(@max_position>0)
        max = @max_position
      else
        max= @sequence.length
     end
     len = max - min 
     if(len<MINSEQSIZE)
           @maxthread=1
     end
     nb = len.div(maxthread)
     (1..maxthread).each do |i|
                     crawler = Crawler.new
                     setParams(crawler,i)
                     curmax = min + nb
                     if(i==maxthread)
                             curmax = max
                     end
                     crawler.filter_position(min,curmax)
                     $log.debug("Start new Thread between " << min.to_s << " and " << curmax.to_s)
                     @th[i-1] = Thread.new{ Thread.current["matches"] = crawler.searchExact(pattern) }
                     min = curmax + 1
     end
     @th.each {|t| t.join; t["matches"].each { |m| @matches << m }}
     return @matches
end

setParams(crawler,threadId) click to toggle source

# File lib/cassiopee-mt.rb, line 30
def setParams(crawler,threadId)
  crawler.setLogLevel($log.level)
  crawler.file_suffix = @file_suffix
  crawler.loadIndex()
      crawler.method = @method
  crawler.comments = @comments
  crawler.useAmbiguity = @useAmbiguity
  crawler.ambiguous = @ambiguous
  crawler.useCache = @useCache
  #crawler.file_suffix = @file_suffix+"."+threadId.to_s
end