line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / nastreport.cpp

diff --git a/nastreport.cpp b/nastreport.cpp
index 67ec702fdd122b732b0f7e0598fe54f791a121c8..0f361f1dc1401848e4a39fc15cd3def8a3f37a2d 100644 (file)
--- a/nastreport.cpp
+++ b/nastreport.cpp
@@ -7,8 +7,6 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 #include "nast.hpp"
 #include "alignment.hpp"
@@ -48,14 +46,14 @@ void NastReport::print(){
 
 void NastReport::setCandidate(Sequence* candSeq){ 
        queryName = candSeq->getName();
-       queryLength = candSeq->getUnalignLength();
+       queryLength = candSeq->getNumBases();
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setTemplate(Sequence* tempSeq){ 
        templateName = tempSeq->getName();
-       templateLength = tempSeq->getUnalignLength();
+       templateLength = tempSeq->getNumBases();
 }
 
 /******************************************************************************************************************/