X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;fp=corraxescommand.h;h=507399c9ca4b3b686439bf7e37e7da019244724c;hb=8af930b692ff87d1b7031fdd5c9a0b88cdd61245;hp=0000000000000000000000000000000000000000;hpb=15cde0905641f8adddc1cc704f8c064f760e7461;p=mothur.git

diff --git a/corraxescommand.h b/corraxescommand.h
new file mode 100644
index 0000000..507399c
--- /dev/null
+++ b/corraxescommand.h
@@ -0,0 +1,54 @@
+#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
+
+