Merge pull request biojava#744 from lafita/mcbug

josemduarte · web-flow · commit fe8671bd37d4 · 2018-03-09T10:10:33.000-08:00
Fix biojava#741
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -493,7 +493,7 @@ private boolean shiftRow() {
 			} else if (block.getAlignRes().get(str).get(rightRes) == null) {
 				// Choose the sequentially next residue of the known one
 				Integer residue = block.getAlignRes().get(str).get(leftRes) + 1;
-				if (freePool.contains(residue)) {
+				if (freePool.get(str).contains(residue)) {
 					block.getAlignRes().get(str).set(res, residue);
 					freePool.get(str).remove(residue);
 				} else
@@ -626,7 +626,7 @@ else if (block.getAlignRes().get(str).get(rightPrevRes1) + 1 < block
 			if (resR1 != null)
 				resR1 += 1;
 
-			if (freePool.contains(resR1)) {
+			if (freePool.get(str).contains(resR1)) {
 				if (rightBoundary1 == block.length() - 1) {
 					block.getAlignRes().get(str).add(resR1);
 				} else
