added pairwise.seqs

[mothur.git] / chimerabellerophoncommand.h

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index e450b52bbe3326f5677cd914f0fa19c9c7970962..6e1ae50794f23d92c75d0224011251e385ae8f43 100644 (file)
--- a/chimerabellerophoncommand.h
+++ b/chimerabellerophoncommand.h
@@ -20,7 +20,12 @@
 class ChimeraBellerophonCommand : public Command {
 public:
        ChimeraBellerophonCommand(string);
+       ChimeraBellerophonCommand();
        ~ChimeraBellerophonCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map< string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
                
@@ -30,6 +35,9 @@ private:
        string fastafile, outputDir;
        int processors, window, increment, numSeqs;
        Chimera* chimera;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       vector<string> fastaFileNames;
 };
 
 /***********************************************************/