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[mothur.git] / libshuffcommand.h

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+#ifndef LIBSHUFFCOMMAND_H
+#define LIBSHUFFCOMMAND_H
+
+/*
+ *  libshuffcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/9/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "fullmatrix.h"
+#include "libshuff.h"
+#include "groupmap.h"
+
+
+class LibShuffCommand : public Command {
+       
+public:
+       LibShuffCommand(string);
+       LibShuffCommand();      
+       ~LibShuffCommand(){};
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "libshuff";                            }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
+       string getDescription()         { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       vector<string> groupNames;
+       
+       void setGroups();
+       int printCoverageFile();
+       int printSummaryFile();
+       
+       GroupMap* groupMap;
+       FullMatrix* matrix;
+       Libshuff* form;
+       float cutOff, step;
+       int numGroups, numComp, iters;
+       string coverageFile, summaryFile, phylipfile, groupfile;
+       vector<vector<int> > pValueCounts;
+       vector<vector<double> > savedDXYValues;
+       vector<vector<vector<double> > > savedMinValues;
+
+       bool abort, sim;
+       string outputFile, groups, userform, savegroups, outputDir;
+       vector<string> Groups, outputNames; //holds groups to be used
+};
+
+#endif