added remove.seqs command

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
index ce7485469fadce116664f4f26d5556192fe5866c..90b7724ed709ac27f510cad9c928a8b48fca9675 100644 (file)
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -8,9 +8,6 @@
  */
 
 
-using namespace std;
-
-
 #include "database.hpp"
 #include "sequence.hpp"
 #include "distancedb.hpp"
@@ -36,14 +33,14 @@ DistanceDB::DistanceDB(string fastaFileName, string distanceFileName) : Database
 //             getline(inputData, junk);       
                mostSimSequenceVector[i] = closestMatch;
        }
-       cout << numCandSeqs << endl;
+       mothurOut(toString(numCandSeqs)); mothurOutEndLine();
        searchIndex = 0;
        inputData.close();
 }
 
 /**************************************************************************************************/
 
-Sequence* DistanceDB::findClosestSequence(Sequence* candidateSeq){
+Sequence DistanceDB::findClosestSequence(Sequence* candidateSeq){
        
        hit simAccession = mostSimSequenceVector[searchIndex];
 //     string candidateSeqName, closestMatchSeqName, junk;