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"
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"; }
31 string getHelpString();
34 void help() { m->mothurOut(getHelpString()); }
40 vector<Tree*> T; //user trees
41 Tree* randT; //random tree
46 vector<string> groupComb; // AB. AC, BC...
47 string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
48 int iters, numGroups, numComp, counter, processors, numUniquesInName;
49 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
50 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
51 vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
52 EstOutput userData; //pscore info for user tree
53 EstOutput randomData; //pscore info for random trees
54 map<int, double> validScores; //map contains scores from both user and random
55 vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
56 vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
57 vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
58 vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
62 string groups, itersString;
63 vector<string> Groups, outputNames; //holds groups to be used
64 map<string, string> nameMap;
66 void printParsimonyFile();
67 int printUSummaryFile();