changes while testing

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 6f4453316a33d41cb18774d6c9b435bc563980e2..3865bb20811a0ac29e29e0fec02392268ea0a657 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
@@ -32,8 +31,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "mgcluster";   }
        string getCommandCategory()             { return "Clustering";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
        string getDescription()         { return "cluster your sequences into OTUs using a blast file"; }
 
@@ -47,6 +47,7 @@ private:
        Cluster* cluster;
        HCluster* hcluster;
        ListVector* list;
+    CountTable* ct;
        ListVector oldList;
     RAbundVector rav;
        vector<seqDist> overlapMatrix;
@@ -55,15 +56,15 @@ private:
        string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
        double cutoff;
-       float penalty;
+       float penalty, adjust;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard, large;
+       bool abort, minWanted, hclusterWanted, merge, hard, cutoffSet;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-    void createRabund(CountTable);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };