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();
27 ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
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
41 Unweighted* unweighted;
42 string sumFile, allGroups;
43 vector<string> groupComb; // AB. AC, BC...
44 int iters, numGroups, numComp, counter, processors;
45 EstOutput userData; //unweighted score info for user tree
46 EstOutput randomData; //unweighted score info for random trees
47 vector< vector<float> > utreeScores; //scores for users trees for each comb.
48 vector< vector<float> > UWScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
49 map<float, float> validScores; //map contains scores from random
50 vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
51 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.
53 bool abort, phylip, random;
54 string groups, itersString, outputDir, outputForm;
55 vector<string> Groups, outputNames; //holds groups to be used
56 map<string, vector<string> > outputTypes;
61 void printUWSummaryFile(int);
62 void printUnweightedFile();
63 void createPhylipFile(int);