*
*/
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
#include "command.hpp"
#include "weighted.h"
#include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
-using namespace std;
class GlobalData;
class UnifracWeightedCommand : public Command {
public:
- UnifracWeightedCommand();
- ~UnifracWeightedCommand() { delete weighted; }
+ 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<Tree*> T; //user trees
- vector<float> utreeScores; //user tree unweighted scores
- vector<float> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ 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 weightedFile, sumFile, distFile;
- int iters, numGroups, numComp;
+ 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> > validScores; //vector<contains scores from both user and random> each group comb has an entry
- vector< map<float, float> > rscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
- vector< map<float, float> > uscoreFreq; //vector<weighted, number of user trees with that score.> each group comb has an entry
- vector< map<float, float> > totalrscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
- vector< map<float, float> > rCumul; //vector<weighted score, number of random trees with that score or higher.> each group comb has an entry
- vector< map<float, float> > uCumul; //vector<weighted, cumulative percentage of number of user trees with that score or higher.> each group comb has an entry
- map<float, float>::iterator it;
- map<float, float>::iterator it2;
+ vector< vector<double> > rScores; //vector<weighted scores for random trees.> each group comb has an entry
+ vector< vector<double> > uScores; //vector<weighted scores for user trees.> each group comb has an entry
+ 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
+
+ bool abort, phylip, random, includeRoot;
+ string groups, itersString, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
+ int processors;
+
- ofstream outSum, outDist, out;
+ ofstream outSum;
void printWSummaryFile();
void printWeightedFile();
- void saveRandomScores();
+ 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> >&);
+
};