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 vector<string> groupComb; // AB. AC, BC...
36 string parsFile, parsFileout, sumFile, randomtree;
37 int iters, numGroups, numComp, counter;
38 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
39 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
40 vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
41 EstOutput userData; //pscore info for user tree
42 EstOutput randomData; //pscore info for random trees
43 map<int, double> validScores; //map contains scores from both user and random
44 vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
45 vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
46 vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
47 vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
48 map<int, double>::iterator it;
49 map<int, double>::iterator it2;
54 void printParsimonyFile();
55 void printUSummaryFile();
58 void initFile(string);
59 void output(vector<double>);