pat's updates on 7/19/10

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index b9e1c4b3ffbc4951d23204b3b761a74708003edc..38e9b6230838424dd136562111f25967f6822099 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -480,6 +480,18 @@ int Sequence::getAmbigBases(){
 
 //********************************************************************************************************************
 
+void Sequence::removeAmbigBases(){
+       
+       for(int j=0;j<alignmentLength;j++){
+               if(aligned[j] != 'A' && aligned[j] != 'T' && aligned[j] != 'G' && aligned[j] != 'C'){
+                       aligned[j] = '-';
+               }
+       }
+       setUnaligned(aligned);
+}
+       
+//********************************************************************************************************************
+
 int Sequence::getLongHomoPolymer(){
        if(longHomoPolymer == -1){
                longHomoPolymer = 1;