1 #ifndef CONCENSUSCOMMAND_H
2 #define CONCENSUSCOMMAND_H
7 * Created by Sarah Westcott on 4/29/09.
8 * Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
12 #include "command.hpp"
15 #include "sharedutilities.h"
19 class ConcensusCommand : public Command {
22 ConcensusCommand(string);
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 GlobalData* globaldata;
38 vector<string> treeSet; //set containing all members of the tree to start recursion. filled in getSets().
39 map< vector<string>, int > nodePairs; //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
40 // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
41 // if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
42 // requires vectors to be sorted to find key.
43 map< vector<string>, vector< vector<string> > > bestSplit; //maps a group to its best split
44 map< vector<string>, int > nodePairsInitialRate;
45 map< vector<string>, int > nodePairsInTree;
46 map<string, int>::iterator it;
47 map< vector<string>, int>::iterator it2;
48 string outputFile, notIncluded, filename;
50 int numNodes, numLeaves, count; //count is the next available spot in the tree vector
51 vector<string> outputNames;
52 map<string, vector<string> > outputTypes;
55 int getSubgroupRating(vector<string>);
56 vector<string> getSmallest(map< vector<string>, int>);
57 vector<string> getNextAvailableSet(vector<string>, vector<string>&);
58 vector<string> getRestSet(vector<string>, vector<string>);
59 bool isSubset(vector<string>, vector<string>);
61 int buildConcensusTree(vector<string>);