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#ifndef UNIFRACWEIGHTEDCOMMAND_H
#define UNIFRACWEIGHTEDCOMMAND_H
/*
* unifracweightedcommand.h
* Mothur
*
* Created by Sarah Westcott on 2/9/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "weighted.h"
#include "treemap.h"
#include "progress.hpp"
#include "sharedutilities.h"
#include "fileoutput.h"
#include "readtree.h"
class UnifracWeightedCommand : public Command {
public:
UnifracWeightedCommand(string);
UnifracWeightedCommand();
~UnifracWeightedCommand() {}
vector<string> setParameters();
string getCommandName() { return "unifrac.weighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
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"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
int start;
int num;
linePair(int i, int j) : start(i), num(j) {}
};
vector<linePair> lines;
ReadTree* read;
SharedUtil* util;
FileOutput* output;
vector<Tree*> T; //user trees
vector<double> utreeScores; //user tree unweighted scores
vector<double> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
vector<string> groupComb; // AB. AC, BC...
TreeMap* tmap;
Weighted* weighted;
string sumFile, outputDir;
int iters, numGroups, numComp, counter;
EstOutput userData; //weighted score info for user tree
EstOutput randomData; //weighted score info for random trees
vector< vector<double> > rScores; //vector<weighted scores for random trees.> each group comb has an entry
vector< vector<double> > uScores; //vector<weighted scores for user trees.> each group comb has an entry
vector< map<float, float> > rScoreFreq; //map <weighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
map<float, float> validScores; //map contains scores from random
bool abort, phylip, random, includeRoot;
string groups, itersString, outputForm, treefile, groupfile, namefile;
vector<string> Groups, outputNames; //holds groups to be used
int processors, numUniquesInName;
ofstream outSum;
map<string, string> nameMap;
void printWSummaryFile();
void printWeightedFile();
void createPhylipFile();
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
int createProcesses(Tree*, vector< vector<string> >, vector< vector<double> >&);
int driver(Tree*, vector< vector<string> >, int, int, vector< vector<double> >&);
int readNamesFile();
};
#endif
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