moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
deleted file mode 100644 (file)
index 9172556..0000000
--- a/parsimonycommand.h
+++ /dev/null
@@ -1,73 +0,0 @@
-#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