removed make count from make.contigs

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 93ecb70f066fd8a1da6415453347aac66c57d0dd..4c631a23451d4d9723aec3a29bed423737b243ba 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -575,6 +575,15 @@ string Sequence::getUnaligned(){
 int Sequence::getNumBases(){
        return numBases;
 }
+//********************************************************************************************************************
+
+int Sequence::getNumNs(){
+    int numNs = 0;
+       for (int i = 0; i < unaligned.length(); i++) {
+        if(toupper(unaligned[i]) == 'N') { numNs++; }
+    }
+    return numNs;
+}
 
 //********************************************************************************************************************
 
@@ -763,6 +772,8 @@ void Sequence::trim(int length){
        if(numBases > length){
                unaligned = unaligned.substr(0,length);
                numBases = length;
+        aligned = "";
+        isAligned = 0;
        }
        
 }