changes while testing

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 7349961e252104c93cf26942d79b44f11ba7c0f5..96b7c08861f216862de0c1e600d07fed463eb56a 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.  
@@ -34,9 +35,10 @@ 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 getOutputPattern(string);   
+       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 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster"; }
        string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
        
        int execute(); 
@@ -44,7 +46,7 @@ public:
        
 private:
        Cluster* cluster;
-       SparseMatrix* matrix;
+       SparseDistanceMatrix* matrix;
        ListVector* list;
        RAbundVector* rabund;
        RAbundVector oldRAbund;
@@ -52,7 +54,7 @@ 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;
@@ -64,6 +66,8 @@ private:
        
        void printData(string label);
        vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif