working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
index d6c0a57d9628a124c3bc900d6865f0ed4e7cc606..ea6e279b88ca0f6d59312936b2c1652ff5b1a9b6 100644 (file)
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -25,14 +25,21 @@ class ClearcutCommand : public Command {
 
 public:
        ClearcutCommand(string);
+       ClearcutCommand();
        ~ClearcutCommand() {};
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
 private:
        string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
-       bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted;
+       bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
        bool abort;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 };
 
 /****************************************************************************/