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 #include <cassert>
   8
   9 TSFLookupTable::TSFLookupTable(int nmer, int length)
  10 {
  11   generate_dna_pattern(nmer, length);
  12 }
  13
  14 int TSFLookupTable::next(int state, enum nucleotide symbol)
  15 {
  16 #if 0
  17   // dump what row we're looking at
  18   std::cout << "[" << state << "]: ";
  19   for(int i=0; i != table[state].size(); ++i) {
  20     std::cout << table[state][i] << " ";
  21   }
  22   std::cout << "lookup(" << symbol << ")" << std::endl;
  23 #endif
  24   return table[state][symbol];
  25 }
  26
  27 void TSFLookupTable::generate_dna_pattern(int nmer, int length)
  28 {
  29   // currently we can only handle single nucleotides
  30   assert (nmer == 1);
  31
  32   symbol_vec symbols;
  33   symbols += A, T, G, C;
  34
  35   // add the start state
  36   std::vector<int> transitions(8, failed_state);
  37   table.push_back(transitions);
  38
  39   for (symbol_vec::iterator pattern_itor = symbols.begin();
  40        pattern_itor != symbols.end();
  41        ++pattern_itor)
  42   {
  43     // update the start state to point at the state we're adding
  44     table[0][*pattern_itor] = table.size();
  45
  46     // add the counting states
  47     for(int i = 0; i != length-nmer; ++ i)
  48     {
  49       std::vector<int> transitions(8, failed_state);
  50       transitions[*pattern_itor] = table.size()+1; //point to next state
  51       table.push_back(transitions);
  52     }
  53
  54     // add the accept state
  55     std::vector<int> transitions(8, accept_state);
  56     transitions[*pattern_itor] = table.size();
  57     table.push_back(transitions);
  58   }
  59 }