#include "command.hpp"
#include "weighted.h"
-#include "treemap.h"
+#include "counttable.h"
#include "progress.hpp"
#include "sharedutilities.h"
#include "fileoutput.h"
vector<string> setParameters();
string getCommandName() { return "unifrac.weighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getHelpString();
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
linePair(int i, int j) : start(i), num(j) {}
};
vector<linePair> lines;
- TreeMap* tmap;
+ CountTable* ct;
FileOutput* output;
vector<Tree*> T; //user trees
vector<double> utreeScores; //user tree unweighted scores
map<float, float> validScores; //map contains scores from random
bool abort, phylip, random, includeRoot, subsample, consensus;
- string groups, itersString, outputForm, treefile, groupfile, namefile;
+ string groups, itersString, outputForm, treefile, groupfile, namefile, countfile;
vector<string> Groups, outputNames; //holds groups to be used
int processors, subsampleSize, subsampleIters;
ofstream outSum;
int createProcesses(Tree*, vector< vector<string> >, vector< vector<double> >&);
int driver(Tree*, vector< vector<string> >, int, int, vector< vector<double> >&);
int runRandomCalcs(Tree*, vector<double>);
- 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);