modified precluster to use less memory.

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index de6a5727575a7f35d2605239968a37435faa388f..a26fda41cba8e316fd8649604e6934a5960f22f4 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -20,9 +20,8 @@ struct seqPNode {
        int numIdentical;
        Sequence seq;
        string names;
-       bool active;
        seqPNode() {}
-       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
+       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm) {}
        ~seqPNode() {}
 };
 /************************************************************/
@@ -39,7 +38,7 @@ private:
        int diffs, length;
        bool abort;
        string fastafile, namefile, outputDir;
-       vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
+       list<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, int>::iterator itSize; 
@@ -49,7 +48,7 @@ private:
        void readNameFile();
        //int readNamesFASTA();
        int calcMisMatches(string, string);
-       void printData(string, string); //fasta filename, names file name
+       void printData(ofstream&, ofstream&, seqPNode); //fasta filename, names file name
 };
 
 /************************************************************/