changes while testing

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
index e45e21b74a9ae58a6beef19a9a484344364c31de..ef8b8f17e37051be4951d6dd662d0db1beb1dbaa 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -21,22 +21,27 @@ class PhylotypeCommand : public Command {
 public:
        PhylotypeCommand(string);       
        PhylotypeCommand();
-       ~PhylotypeCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute(); 
-       void help();    
+       ~PhylotypeCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "phylotype";           }
+       string getCommandCategory()             { return "Clustering";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+       string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
        bool abort, allLines;
-       string taxonomyFileName, label, outputDir, namefile;
+       string taxonomyFileName, label, outputDir, namefile, countfile;
        set<string> labels; //holds labels to be used
        int cutoff;
        map<string, string> namemap;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        map<int, int> currentNodes;
        map<int, int> parentNodes;