binaries/src/ViennaRNA/RNAforester/src/rna_algebra.cpp

   1 #include "rna_algebra.h"
   2
   3 Score::Score(RNAforesterOptions &options)
   4 {
   5   m_isLocal=options.has(RNAforesterOptions::LocalSimilarity);
   6   m_isRIBOSUM=options.has(RNAforesterOptions::RIBOSUMScore);
   7
   8   // distance or similarity ?
   9   if(options.has(RNAforesterOptions::CalculateDistance))
  10     {
  11       m_isDistance=true;
  12       m_bp_rep_score = 0;
  13       m_bp_del_score = 3;
  14       m_b_match_score = 0;
  15       m_b_rep_score =1;
  16       m_b_del_score =2;
  17     }
  18   else
  19     {
  20       m_isDistance=false;
  21
  22           if(options.has(RNAforesterOptions::RIBOSUMScore))
  23           {
  24                   m_bp_del_score=-100;
  25                   m_b_del_score=-200;
  26           }
  27           else
  28           {
  29                 m_bp_rep_score = 10;
  30                 m_bp_del_score =-5;
  31                 m_b_match_score = 1;
  32                 m_b_rep_score = 0;
  33                 m_b_del_score =-10;
  34           }
  35     }
  36
  37   // read scores
  38   options.get(RNAforesterOptions::BpRepScore,m_bp_rep_score,m_bp_rep_score);
  39   options.get(RNAforesterOptions::BpDelScore,m_bp_del_score,m_bp_del_score);
  40   options.get(RNAforesterOptions::BMatchScore,m_b_match_score,m_b_match_score);
  41   options.get(RNAforesterOptions::BRepScore,m_b_rep_score,m_b_rep_score);
  42   options.get(RNAforesterOptions::BDelScore,m_b_del_score,m_b_del_score);
  43 }
  44
  45 Score::Score(const Score &s)
  46 {
  47   // copy scores
  48   m_isDistance = s.m_isDistance;
  49   m_isLocal = s.m_isLocal;
  50   m_bp_rep_score = s.m_bp_rep_score;
  51   m_bp_del_score = s.m_bp_del_score;
  52   m_b_match_score = s.m_b_match_score;
  53   m_b_rep_score = s.m_b_rep_score;
  54   m_b_del_score = s.m_b_del_score;
  55 }
  56
  57 void Score::print()
  58 {
  59   // show score parameters
  60   cout << "*** Scoring parameters ***" << endl << endl;
  61
  62       cout << "Scoring type: ";
  63       if(m_isDistance)
  64         cout << "distance" << endl;
  65       else
  66         {
  67           if(m_isLocal)
  68             cout << "local ";
  69
  70           cout << "similarity" << endl;
  71         }
  72
  73       cout << "Scoring parameters:" << endl;
  74
  75           if(m_isRIBOSUM)
  76           {
  77                   cout << "RIBOSUM85-60 Scoring matrix" << endl;
  78                   cout << "pd:  " << m_bp_del_score << endl;
  79                   cout << "bd:  " << m_b_del_score << endl << endl;
  80           }
  81           else
  82           {
  83                   cout << "pm:   " << m_bp_rep_score << endl;
  84                   cout << "pd:   " << m_bp_del_score << endl;
  85                   cout << "bm:   " << m_b_match_score << endl;
  86                   cout << "br:   " << m_b_rep_score << endl;
  87                   cout << "bd:   " << m_b_del_score << endl << endl;
  88           }
  89 }