fixed bugs for 1.8

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 5113fa44e0e5b848a22d52c6c8c03f29a646ffd0..643a36783594cf6d0716e2e4b79fedf3413a6861 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -38,14 +38,16 @@ public:
 private:
        int diffs, length;
        bool abort;
-       string fastafile, namefile;
+       string fastafile, namefile, outputDir;
        vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
-//     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
+       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
+       map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
        
        int readFASTA();
-       int readNamesFASTA();
+       void readNameFile();
+       //int readNamesFASTA();
        int calcMisMatches(string, string);
        void printData(string, string); //fasta filename, names file name
 };