added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / readblast.h

diff --git a/readblast.h b/readblast.h
index 128c144fc3d29109453331c059b478c18f7a6bfe..fd32380c20c1a7145a8c65d07700b54d2d5bc63b 100644 (file)
--- a/readblast.h
+++ b/readblast.h
@@ -25,7 +25,7 @@ public:
        ReadBlast(string, float, float, int, bool, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr, hclusterWanted
        ~ReadBlast() {}
        
-       void read(NameAssignment*);
+       int read(NameAssignment*);
        SparseMatrix* getDistMatrix()           {       return matrix;          }
        vector<seqDist> getOverlapMatrix()      {       return overlap;         }
        string getOverlapFile()                         {       return overlapFile;     }
@@ -40,8 +40,9 @@ private:
        
        SparseMatrix* matrix;
        vector<seqDist> overlap;
+       MothurOut* m;
        
-       void readNames(NameAssignment*);
+       int readNames(NameAssignment*);
 };
 
 /*******************************************************************************************/