Merge pull request #169 from BackofenLab/dev

version 3.1.0.2

ChangeLog

@@ -14,7 +14,17 @@
 ################################################################################  
 
 ################################################################################
-### version 3.1.0  
+### version 3.1.0.2  
+################################################################################  
+
+190920 Martin Raden :
+ * IntaRNA/PredictorMfe :
+   * getNextBest() :
+     * ensure deterministic output for degenerate bestE interactions (left most)
+ * tests updated
+
+################################################################################
+### version 3.1.0.1
 ################################################################################  
 
 # IntaRNA

configure.ac

@@ -1,7 +1,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT([IntaRNA], [3.1.0], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT([IntaRNA], [3.1.0.2], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0

src/IntaRNA/PredictorMfe.cpp

@@ -327,12 +327,32 @@ getNextBest( Interaction & curBest )
 		curCellE = energy.getE(curLeftBound->first.first, curLeftBound->second.j1
 							, curLeftBound->first.second, curLeftBound->second.j2
 							, curLeftBound->second.val );
+		// deal with degeneracy of energy model, ie. multiple sites with bestE
+		if (E_equal(curCellE,curBestCellE)) {
+			// select left most to be deterministic in output
+			if (curLeftBound->first.first > curBestCellStart.first
+					|| (curLeftBound->first.first == curBestCellStart.first
+							&& curLeftBound->first.second > curBestCellStart.second)
+					|| (curLeftBound->first.first == curBestCellStart.first
+							&& curLeftBound->first.second == curBestCellStart.second
+							&& curLeftBound->second.j1 > curBestCell->j1)
+					|| (curLeftBound->first.first == curBestCellStart.first
+							&& curLeftBound->first.second == curBestCellStart.second
+							&& curLeftBound->second.j1 == curBestCell->j1
+							&& curLeftBound->second.j2 > (curBestCell->j2))
+				)
+			{
+				// right of curBest
+				continue;
+			}
+		} else
 		// or energy is too low to be considered
 		// or energy is higher than current best found so far
-		if (curCellE < curBestE || curCellE >= curBestCellE )
+		if (curCellE < curBestE || curCellE > curBestCellE)
 		{
 			continue;
 		}
+
 		//// FOUND THE NEXT BETTER SOLUTION
 		// overwrite current best found so far
 		curBestCell = curCell;

tests/data/energyB-accN-overlapN-heuristic-seed-modelX.testresult

@@ -1,3 +1,3 @@
 id1;start1;end1;id2;start2;end2;subseqDP;hybridDP;E
 target;1;2;query;1;2;CC≫((&));-2
-target;6;7;query;3;4;CC≫((&));-2
+target;5;6;query;3;4;CC≫((&));-2

tests/data/energyB-accN-overlapQ-heuristic-seed-modelX.testresult

@@ -1,4 +1,4 @@
 id1;start1;end1;id2;start2;end2;subseqDP;hybridDP;E
 target;1;2;query;1;2;CC≫((&));-2
-target;6;7;query;3;4;CC≫((&));-2
-target;9;10;query;1;2;CC≫((&));-2
+target;5;6;query;3;4;CC≫((&));-2
+target;9;10;query;3;4;CC≫((&));-2