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