X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=anosimcommand.h;h=6e5aba0e65980914e6c25e6e0e55fadc4b0136b9;hp=0b145639d8b0f8551988e67d29ee4a2612efa809;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ef05a77005bf7af1eb40192a7c2816da01c9499c

diff --git a/anosimcommand.h b/anosimcommand.h
index 0b14563..6e5aba0 100644
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -12,53 +12,45 @@
 
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+class GroupMap;
 
 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; }
+	~AnosimCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "anosim";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+	string getDescription()		{ return "analysis of similarity"; }
+	
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
-	struct linePair {
-		int start;
-		int num;
-		linePair(int i, int j) : start(i), num(j) {}
-	};
-	vector<linePair> lines;
-	
-	GlobalData* globaldata;
+	bool abort;
 	GroupMap* designMap;
-	map<string, vector<string> > outputTypes;
+	string outputDir, inputDir, designFileName, phylipFileName;
 	
-	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<double> > convertToRanks(vector<vector<double> >);
+	double calcR(vector<vector<double> >, map<string, vector<int> >);
+	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+	double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
+	
+	vector< vector<double> > distanceMatrix;
+	vector<string> outputNames;
+	int iters;
+	double experimentwiseAlpha;
 	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 calcWithinBetween(vector<seqDist>&, vector<string>, double&);
-	vector<seqDist> convertToRanks();
+	
 };
 
 #endif