added diffs and percent parameters to cluster.fragments command

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 842485e15c1c9679cf6cd8b1cb16f987454a27c5..01f38e45ff55518238894a79503928759124679c 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -43,6 +43,7 @@ public:
 private:
        bool abort;
        string fastafile, namefile, outputDir;
+       int diffs, percent;
        vector<seqRNode> alignSeqs; 
        map<string, string> names; //represents the names file first column maps to second column
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
@@ -53,6 +54,7 @@ private:
        int readFASTA();
        void readNameFile();
        void printData(string, string); //fasta filename, names file name
+       bool isFragment(string, string);
        
 };