Basepair probs

src/IntaRNA/HelixHandlerNoBulgeMax.h

@@ -27,7 +27,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler {
 	//! container type for sparse helix information for a given left-most
 	//! base pair (i1,i2)
 	//! it holds both the energy (first) as well as the length of the helix
-	typedef boost::unordered_map< Interaction::BasePair, HelixData > HelixHash;
+	typedef boost::unordered_map< Interaction::BasePair, HelixData, Interaction::BasePair::Hash, Interaction::BasePair::Equal > HelixHash;
 
 protected:
 

src/IntaRNA/Interaction.cpp

@@ -27,6 +27,16 @@ operator<<(std::ostream& out, const Interaction::BasePair& bp)
 
 ////////////////////////////////////////////////////////////////////////////
 
+std::ostream&
+operator<<(std::ostream& out, const Interaction::Boundary& b)
+{
+	out <<"("<<b.i1<<":"<<b.i2<<")-("<<b.j1<<","<<b.j2<<")";
+//	out <<"("<<b.i1<<","<<b.j1<<","<<b.i2<<","<<b.j2<<")";
+	return out;
+}
+
+////////////////////////////////////////////////////////////////////////////
+
 std::ostream&
 operator<<(std::ostream& out, const Interaction& i)
 {

src/IntaRNA/Interaction.h

@@ -28,7 +28,88 @@ class Interaction {
 public:
 
 	//! type of a base pair index encoding
-	typedef std::pair<size_t,size_t> BasePair;
+	struct BasePair {
+		size_t first;  //!< index in first sequence
+		size_t second;  //!< index in second sequence
+
+		/**
+		 * Construction
+		 * @param first index in first sequence
+		 * @param second index in second sequence
+		 */
+		BasePair( const size_t first=RnaSequence::lastPos, const size_t second=RnaSequence::lastPos )
+			: first(first), second(second)
+		{}
+
+		//! hash value computation
+		struct Hash {
+			/**
+			 * Hash value computation for an instance
+			 * @param i instance to hash
+			 * @return the respective hash value
+			 */
+			size_t operator()(const BasePair &i ) const
+		  {
+			  size_t key = 0;
+			  boost::hash_combine(key, i.first);
+			  boost::hash_combine(key, i.second);
+			  return key;
+		  }
+		};
+
+		//! equality check
+		struct Equal {
+			/**
+			 * check equality of two instances
+			 * @param lhs instance 1
+			 * @param rhs instance 2
+			 * @param true if all indices are equal; false otherwise
+			 */
+			bool operator()( const BasePair & lhs, const BasePair & rhs ) const
+			{
+				return lhs.first == rhs.first
+					&& lhs.second == rhs.second ;
+			}
+		};
+
+		/**
+		 * @param bp the basepair to compare to
+		 * @return true if this basepair is considered smaller than bp
+		 */
+		const bool
+		operator <  ( const BasePair &bp ) const {
+			if (first < bp.first)
+			  return true;
+			else if (bp.first < first)
+			  return false;
+			else if (second < bp.second)
+			  return true;
+			return false;
+		}
+
+		/**
+		 * equality check
+		 * @param bp the basepair to compare to
+		 * @return true if this basepair equals bp
+		 */
+		const bool
+		operator ==  ( const BasePair &bp ) const {
+			return first == bp.first
+				&& second == bp.second;
+		}
+
+		/**
+		 * inequality check
+		 * @param bp the basepair to compare to
+		 * @return false if this basepair equals bp
+		 */
+		const bool
+		operator !=  ( const BasePair &bp ) const {
+			return first != bp.first
+				|| second != bp.second;
+		}
+
+	};
 
 	//! type of a vector encoding base pair indices that are interacting
 	typedef std::vector<BasePair> PairingVec;
@@ -88,6 +169,7 @@ class Interaction {
 					&& lhs.j2 == rhs.j2 ;
 			}
 		};
+
 	};
 
 
@@ -311,7 +393,15 @@ class Interaction {
 	 * @param bp the Interaction base pair object to add
 	 * @return the altered stream out
 	 */
-	friend std::ostream& operator<<(std::ostream& out, const Interaction::BasePair& bp);
+	friend std::ostream& operator<<(std::ostream& out, const BasePair& bp);
+
+	/**
+	 * Prints the interaction boundary to stream
+	 * @param out the ostream to write to
+	 * @param b the Boundary object to add
+	 * @return the altered stream out
+	 */
+	friend std::ostream& operator<<(std::ostream& out, const Boundary& b);
 
 	/**
 	 * Prints the interacting base pairs to stream

src/IntaRNA/Makefile.am

@@ -58,6 +58,7 @@ libIntaRNA_a_HEADERS =    \
 					PredictionTrackerSpotProb.h \
 					PredictionTrackerSpotProbAll.h \
 					PredictionTrackerProfileSpotProb.h \
+					PredictionTrackerBasePairProb.h \
 					Predictor.h \
 					PredictorMfe.h \
 					PredictorMfeSeedOnly.h \
@@ -120,6 +121,7 @@ libIntaRNA_a_SOURCES =    \
 					PredictionTrackerSpotProb.cpp \
 					PredictionTrackerSpotProbAll.cpp \
 					PredictionTrackerProfileSpotProb.cpp \
+					PredictionTrackerBasePairProb.cpp \
 					PredictorMfe.cpp \
 					PredictorMfeSeedOnly.cpp \
 					PredictorMfe2d.cpp \

src/IntaRNA/NussinovHandler.cpp

@@ -24,7 +24,7 @@ NussinovHandler::getBasePairs(
       getBasePairs(k + 1, to - 1, traceback, pairs);
     }
 
-    pairs.push_back(std::pair<size_t, size_t>(k, to));
+    pairs.push_back(Interaction::BasePair(k, to));
   }
 }
 

src/IntaRNA/PredictionTracker.h

@@ -4,13 +4,15 @@
 
 
 #include "IntaRNA/general.h"
+#include "IntaRNA/SeedHandlerIdxOffset.h"
 
 namespace IntaRNA {
 
 /**
  * Generic interface to track prediction progress of Predictor instances.
  *
  */
+class PredictorMfeEns;
 class PredictionTracker
 {
 
@@ -43,9 +45,16 @@ class PredictionTracker
 						, const E_type energy
 						) = 0;
 
-};
-
+	/**
+	 * Updates the probability information.
+	 *
+	 * @param predictor the predictor providing the probability information
+	 */
+	virtual
+	void
+	updateZ( PredictorMfeEns *predictor, SeedHandler* seedHandler );
 
+};
 
 ///////////////////////////////////////////////////////////////////////////
 
@@ -63,6 +72,15 @@ PredictionTracker::~PredictionTracker()
 
 ///////////////////////////////////////////////////////////////////////////
 
+inline
+void
+PredictionTracker::updateZ( PredictorMfeEns *predictor, SeedHandler* seedHandler )
+{
+	// override in PredictionTrackers
+}
+
+///////////////////////////////////////////////////////////////////////////
+
 
 } // namespace