added cluster.classic command

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
new file mode 100644 (file)
index 0000000..98085ee
--- /dev/null
+++ b/subsamplecommand.h
@@ -0,0 +1,53 @@
+#ifndef SUBSAMPLECOMMAND_H
+#define SUBSAMPLECOMMAND_H
+
+/*
+ *  subsamplecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/27/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "sharedrabundvector.h"
+
+class GlobalData;
+
+class SubSampleCommand : public Command {
+
+public:
+       SubSampleCommand(string);
+       SubSampleCommand();
+       ~SubSampleCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       GlobalData* globaldata;
+       ReadOTUFile* read;
+       InputData* input;
+       vector<SharedRAbundVector*> lookup;
+       ListVector* list;
+       RAbundVector* rabund;
+       SAbundVector* sabund;
+       
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int getSubSampleShared(vector<SharedRAbundVector*>&, ofstream&);
+};
+
+#endif
+