#include "command.hpp"
#include "unweighted.h"
#include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
-using namespace std;
class GlobalData;
class UnifracUnweightedCommand : public Command {
public:
- UnifracUnweightedCommand();
- ~UnifracUnweightedCommand() { delete unweighted; }
- int execute();
+ UnifracUnweightedCommand(string);
+ UnifracUnweightedCommand();
+ ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
private:
GlobalData* globaldata;
+ SharedUtil* util;
+ FileOutput* output;
vector<Tree*> T; //user trees
- vector<float> utreeScores; //user tree unweighted scores
- vector<float> UWScoreSig; //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
- Tree* randT; //random tree
TreeMap* tmap;
Unweighted* unweighted;
- string sumFile, distFile, unweightedFile;
- int iters;
+ string sumFile, allGroups;
+ vector<string> groupComb; // AB. AC, BC...
+ int iters, numGroups, numComp, counter, processors;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
- map<float, float> validScores; //contains scores from both user and random
- map<float, float> rscoreFreq; //unweighted score, number of random trees with that score.
- map<float, float> uscoreFreq; //unweighted, number of user trees with that score.
- map<float, float> totalrscoreFreq; //unweighted score, number of random trees with that score.
- map<float, float> rCumul; //unweighted score, cumulative percentage of number of random trees with that score or higher.
- map<float, float> uCumul; //unweighted, cumulative percentage of number of user trees with that score or higher .
- map<float, float>::iterator it;
- map<float, float>::iterator it2;
+ vector< vector<float> > utreeScores; //scores for users trees for each comb.
+ vector< vector<float> > UWScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
+ map<float, float> validScores; //map contains scores from random
+ vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
+ 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.
- ofstream outSum, outDist, out;
+ bool abort, phylip, random;
+ string groups, itersString, outputDir, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
+
+ ofstream outSum, out;
+ ifstream inFile;
- void printUWSummaryFile();
+ void printUWSummaryFile(int);
void printUnweightedFile();
- void saveRandomScores();
- void setGroups();
+ void createPhylipFile(int);
+
};
-
-
-#endif
\ No newline at end of file
+#endif