added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / shhhercommand.h

diff --git a/shhhercommand.h b/shhhercommand.h
index acceb7fdba0aa19c3e5f8b032d11d5ad872dca5c..bdc850362b4b08e6c2e14655360e455353e74793 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -12,31 +12,34 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
+
 
 class ShhherCommand : public Command {
        
 public:
        ShhherCommand(string);
        ShhherCommand();
-       ~ShhherCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ShhherCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "shhh.seqs";   }
+       string getCommandCategory()             { return "Hidden";              }
+       string getHelpString(); 
+       string getCitation() { return "no citation"; }
+       string getDescription()         { return "shhh.seqs"; }
+
        
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
-       GlobalData* globaldata;
        
        int abort;
-       map<string, vector<string> > outputTypes;
        
-       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
 
        int processors, maxIters;
        float cutoff, sigma, minDelta;
+       string flowOrder;
        
        vector<int> nSeqsBreaks;
        vector<int> nOTUsBreaks;
@@ -65,7 +68,9 @@ private:
        vector<int> mapSeqToUnique;
        vector<int> mapUniqueToSeq;
        vector<int> uniqueLengths;
-       
+
+       vector<string> outputNames;
+
        int numSeqs, numUniques, numOTUs, numFlowCells;
        
        void getSingleLookUp();