pat's changes to seq.error command

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b6bda8faa00a274369e7a23803440025c241e612..88b7a382d4c175a14c243d21e97a7580cba9c32d 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -19,16 +19,20 @@
 class DeconvoluteCommand : public Command {
 
 public:
-       DeconvoluteCommand(string);     
-       ~DeconvoluteCommand() { delete fastamap; };
+       DeconvoluteCommand(string);
+       DeconvoluteCommand();
+       ~DeconvoluteCommand() {}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
 private:
-       FastaMap* fastamap;
-       ifstream in;
-       ofstream out, outFasta;
-       string filename, outputFileName, outFastafile;
+       string inFastaName, oldNameMapFName, outputDir;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort;
 };