This contains Pat's bug fixes and updates. It represents mothur v.1.3.0

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index f136426b327fdbd13d4143645b80cb060059325e..2f167c52bb225edce6a31cbc623b8bcfd3d4c61c 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -64,7 +64,7 @@ string Sequence::convert2ints() {
        string processed;
        
        for(int i=0;i<unaligned.length();i++) {
-               if(toupper(unaligned[i]) == 'A')                        {       processed += '0';       }
+               if(toupper(unaligned[i]) == 'A')                {       processed += '0';       }
                else if(toupper(unaligned[i]) == 'C')   {       processed += '1';       }
                else if(toupper(unaligned[i]) == 'G')   {       processed += '2';       }
                else if(toupper(unaligned[i]) == 'T')   {       processed += '3';       }
@@ -101,6 +101,27 @@ void Sequence::setUnaligned(string sequence){
 //********************************************************************************************************************
 
 void Sequence::setAligned(string sequence){
+       
+       //if the alignment starts or ends with a gap, replace it with a period to indicate missing data
+       
+       if(sequence[0] == '-'){
+               for(int i=0;i<sequence.length();i++){
+                       if(sequence[i] == '-'){
+                               sequence[i] = '.';
+                       }
+                       else{
+                               break;
+                       }
+               }
+               for(int i=sequence.length()-1;i>=0;i--){
+                       if(sequence[i] == '-'){
+                               sequence[i] = '.';
+                       }
+                       else{
+                               break;
+                       }
+               }
+       }
        aligned = sequence;
 }