chimera.slayer fix

[mothur.git] / corraxescommand.h

diff --git a/corraxescommand.h b/corraxescommand.h
new file mode 100644 (file)
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+++ b/corraxescommand.h
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+#ifndef CORRAXESCOMMAND_H
+#define CORRAXESCOMMAND_H
+
+/*
+ *  corraxescommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 12/22/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "sharedrabundfloatvector.h"
+#include "inputdata.h"
+
+class CorrAxesCommand : public Command {
+public:
+       CorrAxesCommand(string);
+       CorrAxesCommand();
+       ~CorrAxesCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       GlobalData* globaldata;
+       string axesfile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+       bool abort, pickedGroups;
+       int numaxes;
+       set<string> names;
+       
+       vector<string> outputNames, Groups;
+       map<string, vector<string> > outputTypes;
+       vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
+       
+       int getShared();
+       int getSharedFloat();
+       int convertToRelabund();
+       int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
+       map<string, vector<float> > readAxes();
+       int calcPearson(map<string, vector<float> >&, ofstream&);
+       
+};
+
+
+#endif
+
+