#include "treemap.h"
#include "sharedutilities.h"
#include "fileoutput.h"
-
-
-class GlobalData;
+#include "readtree.h"
class UnifracUnweightedCommand : public Command {
public:
UnifracUnweightedCommand(string);
- ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
+ UnifracUnweightedCommand();
+ ~UnifracUnweightedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "unifrac.unweighted"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
+ ReadTree* read;
SharedUtil* util;
FileOutput* output;
vector<Tree*> T; //user trees
Unweighted* unweighted;
string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
- int iters, numGroups, numComp, counter;
+ int iters, numGroups, numComp, counter, processors, numUniquesInName;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
vector< vector<float> > utreeScores; //scores for users trees for each comb.
vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
- bool abort, phylip, random;
- string groups, itersString, outputDir;
+ bool abort, phylip, random, includeRoot;
+ string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
vector<string> Groups, outputNames; //holds groups to be used
ofstream outSum, out;
ifstream inFile;
+ map<string, string> nameMap;
void printUWSummaryFile(int);
void printUnweightedFile();
void createPhylipFile(int);
+ int readNamesFile();
};