working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 3a12413d6f055d0c4f12e0291a442ed4dcc8fb63..38bcd37cf1ffc33a8ee3572c6f24053e1372c1fc 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -47,8 +47,8 @@ public:
        
 private:
        int diffs, length;
-       bool abort;
-       string fastafile, namefile, outputDir;
+       bool abort, bygroup;
+       string fastafile, namefile, outputDir, groupfile;
        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
@@ -62,6 +62,8 @@ private:
        //int readNamesFASTA();
        int calcMisMatches(string, string);
        void printData(string, string); //fasta filename, names file name
+       int process();
+       int loadSeqs(map<string, string>&, vector<Sequence>&);
 };
 
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