X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=homovacommand.h;fp=homovacommand.h;h=1ac2aa0471d445b14fa460319cde361841cfa505;hb=17d3033f832c6b8fff5875eb4de29f44a926d4dd;hp=0000000000000000000000000000000000000000;hpb=1e0359c041eedc99670c93d824a2cf7fa72577cc;p=mothur.git

diff --git a/homovacommand.h b/homovacommand.h
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+#ifndef HOMOVACOMMAND_H
+#define HOMOVACOMMAND_H
+
+/*
+ *  homovacommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/8/11.
+ *  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 HomovaCommand : public Command {
+	
+public:
+	HomovaCommand(string);
+	HomovaCommand();
+	~HomovaCommand();
+	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 calcHomova(ofstream&, int, vector<string>);
+	map<string, double> calcWithin(vector< vector<double> >&, int, vector<string>, map<string, int>&);
+	double calcTotal(int);
+};
+
+#endif
+
+