#include "command.hpp"
#include "unweighted.h"
#include "treemap.h"
-
-using namespace std;
-
-class GlobalData;
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
class UnifracUnweightedCommand : public Command {
public:
- UnifracUnweightedCommand();
- ~UnifracUnweightedCommand() { delete unweighted; }
- int execute();
+ UnifracUnweightedCommand(string);
+ UnifracUnweightedCommand();
+ ~UnifracUnweightedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "unifrac.unweighted"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
+ string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
+ FileOutput* output;
vector<Tree*> T; //user trees
TreeMap* tmap;
- Unweighted* unweighted;
- string sumFile, unweightedFile, unweightedFileout;
+ string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
- int iters, numGroups, numComp, counter;
- EstOutput userData; //unweighted score info for user tree
- EstOutput randomData; //unweighted score info for random trees
+ int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
vector< vector<float> > utreeScores; //scores for users trees for each comb.
vector< vector<float> > UWScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
map<float, float> validScores; //map contains scores from random
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.
- map<float, float>::iterator it2;
- map<float, float>::iterator it;
+ bool abort, phylip, random, includeRoot, consensus, subsample;
+ string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
+ vector<string> Groups, outputNames; //holds groups to be used
+
ofstream outSum, out;
ifstream inFile;
- void printUWSummaryFile();
+ int runRandomCalcs(Tree*, vector<double>);
+ void printUWSummaryFile(int);
void printUnweightedFile();
- void setGroups();
- void initFile(string);
- void output(vector<double>);
- void resetFile();
-
+ void createPhylipFile(int);
+ vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+ int getConsensusTrees(vector< vector<double> >&, int);
+ int getAverageSTDMatrices(vector< vector<double> >&, int);
};
-
-
-#endif
\ No newline at end of file
+#endif