added modify names parameter to set.dir

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index d5c784e27a28bb27e6b7cbdadbb8b94e25b199b5..008bd222a0a91869e14895738ea852b383c0395f 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,12 +12,12 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -31,9 +31,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "mgcluster";   }
        string getCommandCategory()             { return "Clustering";  }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
        
+       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"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -44,11 +47,13 @@ private:
        Cluster* cluster;
        HCluster* hcluster;
        ListVector* list;
+    CountTable* ct;
        ListVector oldList;
+    RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
-       string blastfile, method, namefile, overlapFile, distFile, outputDir;
+       string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
        double cutoff;
        float penalty;
@@ -59,6 +64,7 @@ private:
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };