moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
deleted file mode 100644 (file)
index 465a67f..0000000
--- a/libshuffcommand.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#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