changes while testing

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
index b61c03939492fe4147225fadb159e00b9a0ef71e..ef8b8f17e37051be4951d6dd662d0db1beb1dbaa 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -20,19 +20,34 @@ class PhylotypeCommand : public Command {
        
 public:
        PhylotypeCommand(string);       
-       ~PhylotypeCommand();
-       int execute(); 
-       void help();    
+       PhylotypeCommand();
+       ~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;
+       string taxonomyFileName, label, outputDir, namefile, countfile;
        set<string> labels; //holds labels to be used
        int cutoff;
+       map<string, string> namemap;
+       vector<string> outputNames;
        
        map<int, int> currentNodes;
        map<int, int> parentNodes;
        map<int, int>::iterator itCurrent;
+       
+       int readNamesFile();
 
 };