X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;fp=parsimonycommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=917255696166a505ae5734e20f0aaab47573876c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/parsimonycommand.h b/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