#include "command.hpp"
#include "fullmatrix.h"
#include "libshuff.h"
+#include "groupmap.h"
-class GlobalData;
-
class LibShuffCommand : public Command {
public:
LibShuffCommand(string);
LibShuffCommand();
~LibShuffCommand(){};
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "libshuff"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ 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();
-
- GlobalData* globaldata;
+
+ GroupMap* groupMap;
FullMatrix* matrix;
Libshuff* form;
float cutOff, step;
int numGroups, numComp, iters;
- string coverageFile, summaryFile;
+ string coverageFile, summaryFile, phylipfile, groupfile;
vector<vector<int> > pValueCounts;
vector<vector<double> > savedDXYValues;
vector<vector<vector<double> > > savedMinValues;
- bool abort;
+ bool abort, sim;
string outputFile, groups, userform, savegroups, outputDir;
vector<string> Groups, outputNames; //holds groups to be used
- map<string, vector<string> > outputTypes;
};
#endif