alg/tsf/trivial_filter.cpp

   1 #include "trivial_filter.hpp"
   2
   3 #include <boost/assign.hpp>
   4 using namespace boost::assign;
   5
   6 #include <iostream>
   7
   8 TSFLookupTable::TSFLookupTable(int nmer, int length)
   9 {
  10   generate_dna_pattern(nmer, length);
  11 }
  12
  13 int TSFLookupTable::next(int state, enum nucleotide symbol)
  14 {
  15 #if 0
  16   // dump what row we're looking at
  17   std::cout << "[" << state << "]: ";
  18   for(int i=0; i != table[state].size(); ++i) {
  19     std::cout << table[state][i] << " ";
  20   }
  21   std::cout << "lookup(" << symbol << ")" << std::endl;
  22 #endif
  23   return table[state][symbol];
  24 }
  25
  26 void TSFLookupTable::generate_dna_pattern(int nmer, int length)
  27 {
  28   // currently we can only handle single nucleotides
  29   assert (nmer == 1);
  30
  31   symbol_vec symbols;
  32   symbols += A, T, G, C;
  33
  34   // add the start state
  35   std::vector<int> transitions(8, failed_state);
  36   table.push_back(transitions);
  37
  38   for (symbol_vec::iterator pattern_itor = symbols.begin();
  39        pattern_itor != symbols.end();
  40        ++pattern_itor)
  41   {
  42     // update the start state to point at the state we're adding
  43     table[0][*pattern_itor] = table.size();
  44
  45     // add the counting states
  46     for(int i = 0; i != length-nmer; ++ i)
  47     {
  48       std::vector<int> transitions(8, failed_state);
  49       transitions[*pattern_itor] = table.size()+1; //point to next state
  50       table.push_back(transitions);
  51     }
  52
  53     // add the accept state
  54     std::vector<int> transitions(8, accept_state);
  55     transitions[*pattern_itor] = table.size();
  56     table.push_back(transitions);
  57   }
  58 }