fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 268ec315a81e1bbbcbd80051986703f3e02f03d4..f70bb322c76cd3bf897fd5498333e5da379557fd 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -14,7 +14,8 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
 
 /* The cluster() command:
        The cluster command outputs a .list , .rabund and .sabund files.  
@@ -34,6 +35,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "cluster";             }
        string getCommandCategory()             { return "Clustering";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; }
        string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
@@ -43,7 +45,7 @@ public:
        
 private:
        Cluster* cluster;
-       SparseMatrix* matrix;
+       SparseDistanceMatrix* matrix;
        ListVector* list;
        RAbundVector* rabund;
        RAbundVector oldRAbund;
@@ -51,7 +53,7 @@ private:
 
        bool abort, hard, sim;
 
-       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
+       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
        double cutoff;
        string showabund, timing;
        int precision, length;
@@ -63,6 +65,8 @@ private:
        
        void printData(string label);
        vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif