added pipeline commands which involved change to command factory and command class...

[mothur.git] / pcacommand.h

diff --git a/pcacommand.h b/pcacommand.h
index 089d1c102f38d66bfa0d83c2120dd3d3f1cd883e..22f288a7e768a74c939781df1302e42b92124600 100644 (file)
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -18,7 +18,12 @@ class PCACommand : public Command {
        
 public:
        PCACommand(string);     
+       PCACommand();
        ~PCACommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -28,6 +33,7 @@ private:
        string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
        float cutoff, precision;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        void get_comment(istream&, char, char);
        int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);