added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d19a396410f2e2c9850f9b20a93d65c03000bac2..390632975afc85aac5b714c7194c81e74d58e16e 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,6 +18,7 @@
 #include "groupmap.h"
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
+#include "counttable.h"
 
 typedef map<int, float> SeqMap;
 
@@ -60,10 +61,11 @@ private:
        ReadMatrix* readMatrix;
        FormatMatrix* formatMatrix;
        NameAssignment* nameMap;
-       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
+    CountTable ct;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups;
        ofstream out;
        ifstream in, inNames, inRow;
-       bool abort, allLines, groupError, large, weighted;
+       bool abort, allLines, groupError, large, weighted, hasGroups;
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
        map<string, string> nameFileMap;
@@ -79,9 +81,10 @@ private:
        void readNamesFile(bool);
        int process(ListVector*);
        SeqMap getMap(int);
-       string findRep(vector<string>);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+       string findRep(vector<string>, string);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
        int processNames(string, string);
        int processFastaNames(string, string);
+    int readDist();
 };
 
 #endif