1 #ifndef PARSIMONYCOMMAND_H
2 #define PARSIMONYCOMMAND_H
7 * Created by Sarah Westcott on 1/26/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "parsimony.h"
14 #include "counttable.h"
15 #include "progress.hpp"
16 #include "sharedutilities.h"
17 #include "fileoutput.h"
21 class ParsimonyCommand : public Command {
24 ParsimonyCommand(string);
28 vector<string> setParameters();
29 string getCommandName() { return "parsimony"; }
30 string getCommandCategory() { return "Hypothesis Testing"; }
32 string getHelpString();
33 string getOutputPattern(string);
34 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"; }
35 string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }
38 void help() { m->mothurOut(getHelpString()); }
42 vector<Tree*> T; //user trees
43 Tree* randT; //random tree
47 vector<string> groupComb; // AB. AC, BC...
48 string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile, countfile;
49 int iters, numGroups, numComp, counter, processors, numUniquesInName;
50 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
51 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
52 vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
53 EstOutput userData; //pscore info for user tree
54 EstOutput randomData; //pscore info for random trees
55 map<int, double> validScores; //map contains scores from both user and random
56 vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
57 vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
58 vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
59 vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
63 string groups, itersString;
64 vector<string> Groups, outputNames; //holds groups to be used
65 map<string, string> nameMap;
67 void printParsimonyFile();
68 int printUSummaryFile();