changes while testing

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index c7ea7e0d078f0abfe404afd41cab0b4500bc5c48..ee25fb30da91c4ab338b0b173bcf05a6f1689c81 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -37,7 +38,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "cluster.fragments";           }
        string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
        string getDescription()         { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
        
@@ -45,8 +48,9 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
+    CountTable ct;
        bool abort;
-       string fastafile, namefile, outputDir;
+       string fastafile, namefile, countfile, outputDir;
        int diffs, percent;
        vector<seqRNode> alignSeqs; 
        map<string, string> names; //represents the names file first column maps to second column