pat's mods to morisitahorn and pre.cluster

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index bb666cdd1bd93fd9b17740e69d68d7a5ec2ff1ff..5113fa44e0e5b848a22d52c6c8c03f29a646ffd0 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -19,8 +19,10 @@
 struct seqPNode {
        int numIdentical;
        Sequence seq;
+       string names;
+       bool active;
        seqPNode() {}
-       seqPNode(int s, Sequence q) : numIdentical(s), seq(q) {}
+       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
        ~seqPNode() {}
 };
 /************************************************************/
@@ -38,13 +40,13 @@ private:
        bool abort;
        string fastafile, namefile;
        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, bool> active; //maps sequence name to whether it has already been merged or not.
+//     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, bool> active; //maps sequence name to whether it has already been merged or not.
        
-       int readSeqs();
+       int readFASTA();
+       int readNamesFASTA();
        int calcMisMatches(string, string);
-       void readNameFile();
        void printData(string, string); //fasta filename, names file name
 };