bug fixes

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 0322daf423ab716022e2146b6d4f352911fed693..e45e21b74a9ae58a6beef19a9a484344364c31de 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -20,19 +20,29 @@ 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();    
        
 private:
        bool abort, allLines;
-       string taxonomyFileName, label;
+       string taxonomyFileName, label, outputDir, namefile;
        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;
        map<int, int>::iterator itCurrent;
+       
+       int readNamesFile();
 
 };