]> git.donarmstrong.com Git - mothur.git/blobdiff - consensusseqscommand.h
major change to the tree class to use the count table class instead of tree map....
[mothur.git] / consensusseqscommand.h
index 1459b43d25bd54b525459721b5de55a5a1d6d9f6..e0c97150bfb0bc3e5baafcea911c4ba1c6c60dcb 100644 (file)
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 class ConsensusSeqsCommand : public Command {
 public:
@@ -34,19 +35,20 @@ public:
        
 private:
        
+    CountTable ct;
        bool abort, allLines;
-       string fastafile, listfile, namefile, label, outputDir;
+       string fastafile, listfile, namefile, countfile, label, outputDir;
        set<string> labels;
        vector<string> outputNames;
        map<string, string> fastaMap;
        map<string, string> nameMap;
-       map<string, string> nameFileMap;
-       int cutoff;
+       map<string, int> nameFileMap;
+       int cutoff, seqLength;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
-       string getConsSeq(string, ofstream&, string&, int);
+       string getConsSeq(string, ofstream&, int);
        char getBase(vector<int>, int);
 };