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#ifndef PARSIMONYCOMMAND_H
#define PARSIMONYCOMMAND_H
/*
* parsimonycommand.h
* Mothur
*
* Created by Sarah Westcott on 1/26/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "treereader.h"
#include "parsimony.h"
#include "counttable.h"
#include "fileoutput.h"
#include "readtree.h"
class ParsimonyCommand : public Command {
public:
ParsimonyCommand(string);
~ParsimonyCommand(){}
vector<string> setParameters();
string getCommandName() { return "parsimony"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
FileOutput* output;
vector<Tree*> T; //user trees
Tree* randT; //random tree
Tree* copyUserTree;
CountTable* ct;
CountTable* savect;
vector<string> groupComb; // AB. AC, BC...
string sumFile, randomtree, allGroups, treefile, groupfile, namefile, countfile;
int iters, numGroups, numComp, counter, processors, numUniquesInName;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector< vector<float> > userTreeScores; //scores for users trees for each comb.
vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
EstOutput userData; //pscore info for user tree
EstOutput randomData; //pscore info for random trees
map<int, double> validScores; //map contains scores from both user and random
vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
ofstream outSum;
bool abort;
string groups, itersString;
vector<string> Groups, outputNames; //holds groups to be used
map<string, string> nameMap;
vector<string> Treenames;
void printParsimonyFile();
int printUSummaryFile();
void getUserInput();
int readNamesFile();
};
#endif
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