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[mothur.git] / parsimonycommand.h

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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 "parsimony.h"
+#include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
+
+
+class ParsimonyCommand : public Command {
+
+public:
+       ParsimonyCommand(string);       
+       ParsimonyCommand();
+       ~ParsimonyCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "parsimony";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       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; 
+       TreeMap* tmap; 
+       TreeMap* savetmap;
+       vector<string> groupComb; // AB. AC, BC...
+       string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+       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;
+       
+       void printParsimonyFile();  
+       int printUSummaryFile();
+       void getUserInput();
+       int readNamesFile();
+       
+};
+
+
+#endif