X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2FViennaRNA%2FRNAforester%2Fsrc%2Frna_algebra.cpp;fp=binaries%2Fsrc%2FViennaRNA%2FRNAforester%2Fsrc%2Frna_algebra.cpp;h=8fd7dc0a416359b906620b7277cc1230fb2edbf5;hb=7522ace91fc0804a9719dbac9f68bc8154da3132;hp=0000000000000000000000000000000000000000;hpb=8116c0444fe98e8eb21bcdd8ded06e1429085823;p=jabaws.git

diff --git a/binaries/src/ViennaRNA/RNAforester/src/rna_algebra.cpp b/binaries/src/ViennaRNA/RNAforester/src/rna_algebra.cpp
new file mode 100644
index 0000000..8fd7dc0
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/rna_algebra.cpp
@@ -0,0 +1,89 @@
+#include "rna_algebra.h"
+
+Score::Score(RNAforesterOptions &options)
+{
+  m_isLocal=options.has(RNAforesterOptions::LocalSimilarity);
+  m_isRIBOSUM=options.has(RNAforesterOptions::RIBOSUMScore);
+
+  // distance or similarity ?
+  if(options.has(RNAforesterOptions::CalculateDistance))
+    {
+      m_isDistance=true;
+      m_bp_rep_score = 0;
+      m_bp_del_score = 3;
+      m_b_match_score = 0;
+      m_b_rep_score =1;
+      m_b_del_score =2;      
+    }
+  else
+    {
+      m_isDistance=false;
+
+	  if(options.has(RNAforesterOptions::RIBOSUMScore))
+	  {
+		  m_bp_del_score=-100;
+		  m_b_del_score=-200;
+	  }
+	  else
+	  {
+		m_bp_rep_score = 10;
+		m_bp_del_score =-5;
+		m_b_match_score = 1;
+		m_b_rep_score = 0;
+                m_b_del_score =-10;
+	  }
+    }
+  
+  // read scores
+  options.get(RNAforesterOptions::BpRepScore,m_bp_rep_score,m_bp_rep_score);
+  options.get(RNAforesterOptions::BpDelScore,m_bp_del_score,m_bp_del_score);
+  options.get(RNAforesterOptions::BMatchScore,m_b_match_score,m_b_match_score);
+  options.get(RNAforesterOptions::BRepScore,m_b_rep_score,m_b_rep_score);
+  options.get(RNAforesterOptions::BDelScore,m_b_del_score,m_b_del_score);
+}
+
+Score::Score(const Score &s)
+{
+  // copy scores
+  m_isDistance = s.m_isDistance;
+  m_isLocal = s.m_isLocal;
+  m_bp_rep_score = s.m_bp_rep_score;
+  m_bp_del_score = s.m_bp_del_score;
+  m_b_match_score = s.m_b_match_score;
+  m_b_rep_score = s.m_b_rep_score;
+  m_b_del_score = s.m_b_del_score;   
+}
+
+void Score::print()
+{
+  // show score parameters
+  cout << "*** Scoring parameters ***" << endl << endl; 
+
+      cout << "Scoring type: ";
+      if(m_isDistance)
+	cout << "distance" << endl;
+      else
+	{
+	  if(m_isLocal)
+	    cout << "local ";
+	  
+	  cout << "similarity" << endl;	 
+	}
+           
+      cout << "Scoring parameters:" << endl;
+
+	  if(m_isRIBOSUM)
+	  {
+		  cout << "RIBOSUM85-60 Scoring matrix" << endl;
+		  cout << "pd:  " << m_bp_del_score << endl;
+		  cout << "bd:  " << m_b_del_score << endl << endl;
+	  }
+	  else
+	  {
+		  cout << "pm:   " << m_bp_rep_score << endl;
+		  cout << "pd:   " << m_bp_del_score << endl;
+		  cout << "bm:   " << m_b_match_score << endl;
+		  cout << "br:   " << m_b_rep_score << endl;
+		  cout << "bd:   " << m_b_del_score << endl << endl;
+	  }
+}