#include "command.hpp"
#include "unweighted.h"
-#include "treemap.h"
+#include "counttable.h"
#include "sharedutilities.h"
#include "fileoutput.h"
#include "readtree.h"
vector<string> setParameters();
string getCommandName() { return "unifrac.unweighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getHelpString();
+ string getOutputFileNameTag(string, string);
+ 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"; }
private:
FileOutput* output;
vector<Tree*> T; //user trees
- TreeMap* tmap;
+ CountTable* ct;
string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
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, includeRoot, consensus, subsample;
- string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
+ string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
vector<string> Groups, outputNames; //holds groups to be used
ofstream outSum, out;
void printUWSummaryFile(int);
void printUnweightedFile();
void createPhylipFile(int);
- vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+ vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
int getConsensusTrees(vector< vector<double> >&, int);
int getAverageSTDMatrices(vector< vector<double> >&, int);