1 #ifndef UNIFRACUNWEIGHTEDCOMMAND_H
2 #define UNIFRACUNWEIGHTEDCOMMAND_H
5 * unifracunweightedcommand.h
8 * Created by Sarah Westcott on 2/9/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "unweighted.h"
16 #include "sharedutilities.h"
17 #include "fileoutput.h"
22 class UnifracUnweightedCommand : public Command {
25 UnifracUnweightedCommand(string);
26 ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
31 GlobalData* globaldata;
34 vector<Tree*> T; //user trees
36 Unweighted* unweighted;
37 string sumFile, allGroups;
38 vector<string> groupComb; // AB. AC, BC...
39 int iters, numGroups, numComp, counter;
40 EstOutput userData; //unweighted score info for user tree
41 EstOutput randomData; //unweighted score info for random trees
42 vector< vector<float> > utreeScores; //scores for users trees for each comb.
43 vector< vector<float> > UWScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
44 map<float, float> validScores; //map contains scores from random
45 vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
46 vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
48 bool abort, phylip, random;
49 string groups, itersString, outputDir;
50 vector<string> Groups, outputNames; //holds groups to be used
55 void printUWSummaryFile(int);
56 void printUnweightedFile();
57 void createPhylipFile(int);