added pairwise.seqs

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index b9e1c4b3ffbc4951d23204b3b761a74708003edc..78fa266105c6be21ce5442250ef8c00f389ab078 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -74,14 +74,14 @@ Sequence::Sequence(istringstream& fastaString){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaString);              
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence);         
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -116,13 +116,14 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaString);              
                        
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence);         
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -160,15 +161,15 @@ Sequence::Sequence(ifstream& fastaFile){
                        }
                        
                        //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
+                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){  break;      }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaFile);                
-               
+       
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-               
+
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -202,14 +203,14 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                        }
                        
                        //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
+                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){       break; }       } // get rest of line if there's any crap there
                        
                        sequence = getSequenceString(fastaFile);                
                        
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "Sequence");
@@ -253,7 +254,7 @@ string Sequence::getCommentString(ifstream& fastaFile) {
                while(fastaFile){
                        letter=fastaFile.get();
                        if((letter == '\r') || (letter == '\n')){  
-                               gobble(fastaFile);  //in case its a \r\n situation
+                               m->gobble(fastaFile);  //in case its a \r\n situation
                                break;
                        }
                }
@@ -302,7 +303,7 @@ string Sequence::getCommentString(istringstream& fastaFile) {
                while(fastaFile){
                        letter=fastaFile.get();
                        if((letter == '\r') || (letter == '\n')){  
-                               gobble(fastaFile);  //in case its a \r\n situation
+                               m->gobble(fastaFile);  //in case its a \r\n situation
                                break;
                        }
                }
@@ -480,6 +481,18 @@ 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;