minor changes to pcr.seqs. Added filterToPos and filterFromPos to sequence class...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 090ee14c1c838098aaaeb1a831ec01e3272ed512..cfd8ec21498120614b94d3adbdade7275eb6a8b7 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -571,7 +571,35 @@ void Sequence::padToPos(int start){
        startPos = start;
 
 }
+//********************************************************************************************************************
+
+int Sequence::filterToPos(int start){
+    
+    if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
+    
+       for(int j = 0; j < start-1; j++) {
+               aligned[j] = '.';
+       }
+       
+    setUnaligned(aligned);
+    
+    return 0;
+    
+}
+//********************************************************************************************************************
 
+int Sequence::filterFromPos(int end){
+    
+    if (end > aligned.length()) { end = aligned.length(); m->mothurOut("[ERROR]: end to large.\n"); }
+    
+       for(int j = end; j < aligned.length(); j++) {
+               aligned[j] = '.';
+       }
+       
+    setUnaligned(aligned);
+    
+    return 0;
+}
 //********************************************************************************************************************
 
 int Sequence::getEndPos(){
@@ -591,7 +619,7 @@ int Sequence::getEndPos(){
 //********************************************************************************************************************
 
 void Sequence::padFromPos(int end){
-       
+       cout << end << '\t' << endPos << endl;
        for(int j = end; j < endPos; j++) {
                aligned[j] = '.';
        }