Merge pull request #86 from BackofenLab/intarna-2

version 2.0.5

ChangeLog

@@ -1,4 +1,22 @@
 
+version 2.0.5
+
+170926 Martin Mann :
+ * IntaRNA/PredictorMfe4d :
+   * getNextBest() : BUGFIX : matrix access was not using interaction end 
+     distance and interaction data was wrongly storing distance as right index;
+     this was causing segfaults when requesting more than one prediction output
+     (thanks to Rick Gelhausen)
+
+170926 Martin Mann :
+ * IntaRNA/PredictorMfe4dSeed :
+ * IntaRNA/PredictorMfe2dHeuristicSeed :
+   + updateOptima() to disable predTracker updates when fillHybridE() of super
+     class is called; 
+     --> BUGFIX : so far resulting tracker profiles were a mix of non-seeded and
+         seeded interactions and thus not complementary with the predicted
+         interactions
+
 version 2.0.4
 
 170706 Martin Mann :
@@ -9,7 +27,7 @@ version 2.0.4
 
 170705 Martin Mann :
  * perl/Intarna*.pl :
-   * shebang corrected
+   * shebang corrected (thanks to Patrick Wright)
 
 170503 Martin Mann :
  * README.md :

configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT( [IntaRNA], [2.0.4], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT( [IntaRNA], [2.0.5], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 
 # minimal required version of the boost library 

src/IntaRNA/AccessibilityBasePair.h

@@ -11,7 +11,17 @@
 
 namespace IntaRNA {
 
-
+/**
+ * Provides accessibility penalties for a Nussinov-like energy scoring where
+ * each base pair is scored by #basePairEnergy independently from its structural
+ * context.
+ *
+ * This implementation is mainly for teaching and testing purpose.
+ *
+ * @author Mostafa Mahmoud
+ * @author Martin Mann
+ *
+ */
 class AccessibilityBasePair: public Accessibility {
 
 public:

src/IntaRNA/PredictorMfe.cpp

@@ -73,7 +73,7 @@ updateOptima( const size_t i1, const size_t j1
 		, const E_type interE
 		, const bool isHybridE )
 {
-//	LOG(DEBUG) <<"energy( "<<i1<<"-"<<j1<<", "<<i2<<"-"<<j2<<" ) = "
+//	LOG(DEBUG) <<"PredictorMfe::updateOptima( "<<i1<<"-"<<j1<<", "<<i2<<"-"<<j2<<" , E = "
 //			<<interE;
 
 	// check if nothing to be done
@@ -100,8 +100,8 @@ updateOptima( const size_t i1, const size_t j1
 
 	if (mfeInteractions.size() == 1) {
 		if (curE < mfeInteractions.begin()->energy) {
-	//		LOG(DEBUG) <<"PredictorMfe::updateOptima() : new mfe ( "
-	//			<<i1<<"-"<<j1<<", "<<i2<<"-"<<j2<<" ) = " <<interE <<" : "<<curE;
+//			LOG(DEBUG) <<"PredictorMfe::updateOptima() : new mfe ( "
+//				<<i1<<"-"<<j1<<", "<<i2<<"-"<<j2<<" ) = " <<interE <<" : "<<curE;
 			// store new global min
 			mfeInteractions.begin()->energy = (curE);
 			// store interaction boundaries

src/IntaRNA/PredictorMfe2dHeuristicSeed.cpp

@@ -107,7 +107,7 @@ predict( const IndexRange & r1
 
 	// compute hybridization energies WITHOUT seed condition
 	// sets also -energy -hybridE
-	// -> no hybrid update since updateOptima overwritten
+	// -> no tracker update since updateOptima overwritten
 	PredictorMfe2dHeuristic::fillHybridE();
 
 	// check if any interaction possible
@@ -118,7 +118,7 @@ predict( const IndexRange & r1
 		return;
 	}
 
-	// init mfe for later updates
+	// reinit mfe for later updates with final information
 	initOptima( outConstraint );
 
 	// compute entries

src/IntaRNA/PredictorMfe2dHeuristicSeed.h

@@ -88,6 +88,23 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic {
 
 protected:
 
+	/**
+	 * optima update without tracker notification
+	 *
+	 * @param i1 the index of the first sequence interacting with i2
+	 * @param j1 the index of the first sequence interacting with j2
+	 * @param i2 the index of the second sequence interacting with i1
+	 * @param j2 the index of the second sequence interacting with j1
+	 * @param energy ignored
+	 * @param isHybridE ignored
+	 */
+	virtual
+	void
+	updateOptima( const size_t i1, const size_t j1
+			, const size_t i2, const size_t j2
+			, const E_type energy
+			, const bool isHybridE );
+
 	/**
 	 * Fills a given interaction (boundaries given) with the according
 	 * hybridizing base pairs.
@@ -116,6 +133,29 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic {
 
 };
 
+//////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////
+
+inline
+void
+PredictorMfe2dHeuristicSeed::
+updateOptima( const size_t i1, const size_t j1
+		, const size_t i2, const size_t j2
+		, const E_type energy
+		, const bool isHybridE )
+{
+	// temporarily disable tracker
+	PredictionTracker * curPredTracker = this->predTracker;
+	this->predTracker = NULL;
+	// update optimum information
+	PredictorMfe2dHeuristic::updateOptima(i1,j1,i2,j2,energy,isHybridE);
+	// reenable tracker
+	this->predTracker = curPredTracker;
+}
+
+//////////////////////////////////////////////////////////////////////////
+
 } // namespace
 
 #endif /* INTARNA_PREDICTORMFE2DHEURISTICSEED_H_ */

src/IntaRNA/PredictorMfe4d.cpp

@@ -402,6 +402,7 @@ getNextBest( Interaction & curBest )
 	// iterate (decreasingly) over all left interaction starts
 	E2dMatrix * curTable = NULL;
 	IndexRange r1,r2;
+	size_t d1 = 0, d2 = 0;  // temp vars to deals with possible interaction lengths
 	E_type curE = E_INF;
 	for (r1.from=hybridE.size1(); r1.from-- > 0;) {
 
@@ -422,26 +423,33 @@ getNextBest( Interaction & curBest )
 				continue;
 			}
 
+			// access energy table for left-most interaction base pair
 			curTable = hybridE(r1.from,r2.from);
 
-			for (r1.to=r1.from; r1.to<curTable->size1(); r1.to++) {
+			// iterate over all available interaction site lengths in seq1
+			for (d1 = 0; d1<curTable->size1(); d1++) {
 
+				// set according right interaction boundary in seq1
+				r1.to = r1.from + d1;
 				// check of overlapping
 				if (reportedInteractions.first.overlaps(r1)) {
 					// stop since all larger sites will overlap as well
 					break;;
 				}
 
-				for (r2.to=r2.from; r2.to<curTable->size2(); r2.to++) {
+				// iterate over all available interaction site lengths in seq2
+				for (d2=0; d2<curTable->size2(); d2++) {
 
+					// set according right interaction boundary in seq2
+					r2.to = r2.from + d2;
 					// check of overlapping
 					if (reportedInteractions.second.overlaps(r2)) {
 						// stop since all larger sites will overlap as well
 						break;;
 					}
 
 					// get overall energy of entry
-					curE = energy.getE( r1.from, r1.to, r2.from, r2.to, (*curTable)(r1.to,r2.to));
+					curE = energy.getE( r1.from, r1.to, r2.from, r2.to, (*curTable)(d1,d2));
 
 					// skip sites with energy too low
 					// or higher than current best found so far

src/IntaRNA/PredictorMfe4dSeed.cpp

@@ -190,6 +190,9 @@ predict( const IndexRange & r1
 	initOptima( tmpOutConstraint );
 
 	// fill matrix
+	// compute hybridization energies WITHOUT seed condition
+	// sets also -energy -hybridE
+	// -> no tracker update since updateOptima overwritten
 	fillHybridE( );
 
 	// check if any interaction possible
@@ -324,7 +327,7 @@ fillHybridE_seed( )
 
 			// update mfe if needed (call super class)
 			if (E_isNotINF(curMinE)) {
-				updateOptima( i1,j1,i2,j2, curMinE, true );
+				PredictorMfe4d::updateOptima( i1,j1,i2,j2, curMinE, true );
 			}
 
 		}

src/IntaRNA/PredictorMfe4dSeed.h

@@ -89,6 +89,23 @@ class PredictorMfe4dSeed: public PredictorMfe4d {
 
 protected:
 
+	/**
+	 * optima update without tracker notification
+	 *
+	 * @param i1 the index of the first sequence interacting with i2
+	 * @param j1 the index of the first sequence interacting with j2
+	 * @param i2 the index of the second sequence interacting with i1
+	 * @param j2 the index of the second sequence interacting with j1
+	 * @param energy ignored
+	 * @param isHybridE ignored
+	 */
+	virtual
+	void
+	updateOptima( const size_t i1, const size_t j1
+			, const size_t i2, const size_t j2
+			, const E_type energy
+			, const bool isHybridE );
+
 	/**
 	 * Removes all temporary data structures and resets the predictor
 	 */
@@ -126,6 +143,29 @@ class PredictorMfe4dSeed: public PredictorMfe4d {
 
 };
 
+//////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////
+
+inline
+void
+PredictorMfe4dSeed::
+updateOptima( const size_t i1, const size_t j1
+		, const size_t i2, const size_t j2
+		, const E_type energy
+		, const bool isHybridE )
+{
+	// temporarily disable tracker
+	PredictionTracker * curPredTracker = this->predTracker;
+	this->predTracker = NULL;
+	// update optimum information
+	PredictorMfe4d::updateOptima(i1,j1,i2,j2,energy,isHybridE);
+	// reenable tracker
+	this->predTracker = curPredTracker;
+}
+
+//////////////////////////////////////////////////////////////////////////
+
 } // namespace
 
 #endif /* INTARNA_PREDICTORMFE4DSEED_H_ */