added pairwise.seqs

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 5c57b69d1bd5dc0495925cb452df908ff5cb5b81..787f835a0f33d1d157aeab41568286c28a752520 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -30,7 +30,12 @@ class ClusterCommand : public Command {
        
 public:
        ClusterCommand(string);
+       ClusterCommand();
        ~ClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -43,7 +48,7 @@ private:
        RAbundVector oldRAbund;
        ListVector oldList;
 
-       bool abort;
+       bool abort, hard;
 
        string method, fileroot, tag, outputDir;
        double cutoff;
@@ -57,6 +62,7 @@ private:
        
        void printData(string label);
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 };
 
 #endif