#include "sharedutilities.h"
#include "fileoutput.h"
-using namespace std;
class GlobalData;
class UnifracWeightedCommand : public Command {
public:
- UnifracWeightedCommand();
- ~UnifracWeightedCommand() { delete weighted; delete util; }
+ UnifracWeightedCommand(string);
+ UnifracWeightedCommand();
+ ~UnifracWeightedCommand() { if (abort == false) { delete weighted; delete util; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair> lines;
+
GlobalData* globaldata;
SharedUtil* util;
FileOutput* output;
vector<double> utreeScores; //user tree unweighted scores
vector<double> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
vector<string> groupComb; // AB. AC, BC...
- Tree* randT; //random tree
TreeMap* tmap;
Weighted* weighted;
- string sumFile;
+ string sumFile, outputDir;
int iters, numGroups, numComp, counter;
EstOutput userData; //weighted score info for user tree
EstOutput randomData; //weighted score info for random trees
vector< map<float, float> > rScoreFreq; //map <weighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
map<float, float> validScores; //map contains scores from random
- map<float, float>::iterator it2;
- map<float, float>::iterator it;
- ofstream outSum, out;
- ifstream inFile;
+ bool abort, phylip, random;
+ string groups, itersString, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
+ int processors;
+
+
+ ofstream outSum;
void printWSummaryFile();
void printWeightedFile();
+ void createPhylipFile();
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
+ int createProcesses(Tree*, vector< vector<string> >, vector< vector<double> >&);
+ int driver(Tree*, vector< vector<string> >, int, int, vector< vector<double> >&);
};