major change to the tree class to use the count table class instead of tree map....

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 4965642e7f77f0d8638bceb177bd79788c8e39ad..6d43dcb9dd2067bab91f46d42ff8afa238a4a191 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -62,6 +62,7 @@ private:
        vector<linePair*> lines;
        vector<string> fastaFileNames;
        vector<string> namefileNames;
+    vector<string> countfileNames;
        vector<string> groupfileNames;
        vector<string> outputNames;
        map<string, vector<string> > nameMap;
@@ -70,10 +71,10 @@ private:
        Classify* classify;
        ReferenceDB* rdb;
        
-       string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
+       string fastaFileName, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
-       bool abort, probs, save, flip;
+       bool abort, probs, save, flip, hasName, hasCount;
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);