small change to shhh.seqs

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 42c26d59ab4df8cd9e0d75937a476617135adbd7..69e905e6bc93e401a242f695577b95019be191c3 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -139,7 +139,7 @@ Sequence::Sequence(ifstream& fastaFile){
                m = MothurOut::getInstance();
                initialize();
                fastaFile >> name;
-
+               
                if (name.length() != 0) { 
                
                        name = name.substr(1); 
@@ -233,6 +233,9 @@ string Sequence::getSequenceString(ifstream& fastaFile) {
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
+                               if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G'  && letter != 'C'){
+                                       letter = 'N';
+                               }
                                sequence += letter;
                        }
                }
@@ -427,6 +430,13 @@ string Sequence::getAligned(){
        else                            {  return aligned;  }
 }
 
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+       return name + '\t' + aligned;   
+}
+
+
 //********************************************************************************************************************
 
 string Sequence::getPairwise(){
@@ -514,7 +524,7 @@ int Sequence::getLongHomoPolymer(){
 //********************************************************************************************************************
 
 int Sequence::getStartPos(){
-       if(endPos == -1){
+       if(startPos == -1){
                for(int j = 0; j < alignmentLength; j++) {
                        if(aligned[j] != '.'){
                                startPos = j + 1;
@@ -529,6 +539,17 @@ int Sequence::getStartPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padToPos(int start){
+
+       for(int j = startPos-1; j < start-1; j++) {
+               aligned[j] = '.';
+       }
+       startPos = start;
+
+}
+
+//********************************************************************************************************************
+
 int Sequence::getEndPos(){
        if(endPos == -1){
                for(int j=alignmentLength-1;j>=0;j--){
@@ -545,6 +566,17 @@ int Sequence::getEndPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padFromPos(int end){
+       
+       for(int j = end; j < endPos; j++) {
+               aligned[j] = '.';
+       }
+       endPos = end;
+       
+}
+
+//********************************************************************************************************************
+
 bool Sequence::getIsAligned(){
        return isAligned;
 }