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 {
25 ParsimonyCommand(string);
27 ~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; } }
28 vector<string> getRequiredParameters();
29 vector<string> getValidParameters();
30 vector<string> getRequiredFiles();
31 map<string, vector<string> > getOutputFiles() { return outputTypes; }
36 GlobalData* globaldata;
39 vector<Tree*> T; //user trees
40 Tree* randT; //random tree
45 vector<string> groupComb; // AB. AC, BC...
46 string sumFile, randomtree, allGroups, outputDir;
47 int iters, numGroups, numComp, counter, processors;
48 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
49 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
50 vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
51 EstOutput userData; //pscore info for user tree
52 EstOutput randomData; //pscore info for random trees
53 map<int, double> validScores; //map contains scores from both user and random
54 vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
55 vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
56 vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
57 vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
63 string groups, itersString;
64 vector<string> Groups, outputNames; //holds groups to be used
65 map<string, vector<string> > outputTypes;
67 void printParsimonyFile();
68 int printUSummaryFile();