X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;h=87699739d34ad012b121a295be53f976b122a5b7;hb=e946299389ed49b4afc4262a4e8070ee3d804769;hp=8183d51cc2e68466f186a354e315578d4175ad49;hpb=96f25c3c0f3ba2a1634094de146630dbc9ee0d03;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
index 8183d51..8769973 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -24,7 +24,7 @@ public:
 	QualityScores();
 	QualityScores(ifstream&);
 	string getName();
-	
+	int getLength(){    return (int)qScores.size();  }
 	vector<int> getQualityScores() { return qScores; }
 	void printQScores(ofstream&);
 	void trimQScores(int, int);
@@ -36,6 +36,9 @@ public:
 	void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
 	void updateForwardMap(vector<vector<int> >&, int, int, int);
 	void updateReverseMap(vector<vector<int> >&, int, int, int);
+    void setName(string n); 
+    void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+    
 	
 private:
 	
@@ -45,6 +48,8 @@ private:
 	
 	string seqName;
 	int seqLength;
+    
+    string getSequenceName(ifstream&);
 };
 	
 /**************************************************************************************************/