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"
21 class ParsimonyCommand : public Command {
25 ~ParsimonyCommand() { delete pars; }
29 GlobalData* globaldata;
30 vector<Tree*> T; //user trees
31 Tree* randT; //random tree
36 vector<string> groupComb; // AB. AC, BC...
37 string parsFile, parsFileout, sumFile, randomtree;
38 int iters, numGroups, numComp, counter;
39 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
40 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
41 vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
42 EstOutput userData; //pscore info for user tree
43 EstOutput randomData; //pscore info for random trees
44 map<int, double> validScores; //map contains scores from both user and random
45 vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
46 vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
47 vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
48 vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
49 map<int, double>::iterator it;
50 map<int, double>::iterator it2;
55 void printParsimonyFile();
56 void printUSummaryFile();
59 void initFile(string);
60 void output(vector<double>);