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"
20 class ParsimonyCommand : public Command {
24 ~ParsimonyCommand() { delete pars; }
28 GlobalData* globaldata;
29 vector<Tree*> T; //user trees
30 Tree* randT; //random tree
35 string parsFile, sumFile, randomtree;
37 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
38 vector<float> userTreeScores; //scores for users trees
39 vector<float> UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
40 EstOutput userData; //pscore info for user tree
41 EstOutput randomData; //pscore info for random trees
42 map<int, float> validScores; //contains scores from both user and random
43 map<int, float> rscoreFreq; //pscore, number of random trees with that score.
44 map<int, float> uscoreFreq; //pscore, number of user trees with that score.
45 map<int, float> rCumul; //pscore, cumulative percentage of number of random trees with that score or lower.
46 map<int, float> uCumul; //pscore, cumulative percentage of number of user trees with that score or lower .
47 map<int, float>::iterator it;
48 map<int, float>::iterator it2;
52 void printParsimonyFile();
53 void printUSummaryFile();