X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;h=87699739d34ad012b121a295be53f976b122a5b7;hb=4e3080b15a3d0c02f7ef2fd779ead433ffdece31;hp=e522938ec91895aceb4cf11a4b7acd9ec2239822;hpb=6da6af5c7f43f9f4f602d224af447805fb01c46c;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
index e522938..8769973 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -10,6 +10,8 @@
  *
  */
 
+//DataStructure for a quality file.
+
 
 #include "mothur.h"
 #include "mothurout.h"
@@ -22,7 +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);
@@ -34,6 +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:
 	
@@ -43,6 +48,8 @@ private:
 	
 	string seqName;
 	int seqLength;
+    
+    string getSequenceName(ifstream&);
 };
 	
 /**************************************************************************************************/