X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=anosimcommand.h;fp=anosimcommand.h;h=5b62df52451251a99cc895cc24fcf488bd4f9349;hb=e74ac2023625728a7e1e57fa15004101a6270cd9;hp=0000000000000000000000000000000000000000;hpb=83bf613d5a7ffb4dcc75b3cad106d1eed1f9e498;p=mothur.git

diff --git a/anosimcommand.h b/anosimcommand.h
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+#ifndef ANOSIMCOMMAND_H
+#define ANOSIMCOMMAND_H
+
+/*
+ *  anosimcommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/14/11.
+ *  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 AnosimCommand : public Command {
+	
+public:
+	AnosimCommand(string);
+	AnosimCommand();
+	~AnosimCommand();
+	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 calcAnosim(ofstream&, int, vector<string>);
+	double calcWithin(vector<seqDist>&, vector<string>);
+	double calcBetween(vector<seqDist>&);
+	vector<seqDist> convertToRanks();
+};
+
+#endif
+
+
+