added amova command

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
new file mode 100644 (file)
index 0000000..3b90b96
--- /dev/null
+++ b/amovacommand.h
@@ -0,0 +1,64 @@
+#ifndef AMOVACOMMAND_H
+#define AMOVACOMMAND_H
+
+/*
+ *  amovacommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/7/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+#include "validcalculator.h"
+#include "readphylipvector.h"
+
+class GlobalData;
+
+class AmovaCommand : public Command {
+       
+public:
+       AmovaCommand(string);
+       AmovaCommand();
+       ~AmovaCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       struct linePair {
+               int start;
+               int num;
+               linePair(int i, int j) : start(i), num(j) {}
+       };
+       vector<linePair> lines;
+       
+       GlobalData* globaldata;
+       GroupMap* designMap;
+       map<string, vector<string> > outputTypes;
+       
+       vector< vector<double> > matrix;
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
+       vector<string> Groups, outputNames, Sets;
+       vector< vector<string> > namesOfGroupCombos;
+       int iters, processors;
+       vector<Calculator*> calculators;
+       
+       int driver(int, int, vector<SharedRAbundVector*>, string);
+       int driver(int, int, vector<string>, string, vector< vector<double> >&);
+       int process(vector<SharedRAbundVector*>);
+       int calcAmova(ofstream&, int, vector<string>);
+       double calcWithin(vector< vector<double> >&, int, vector<string>);
+       double calcTotal(int);
+};
+
+#endif
+