#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; delete util; }
- int execute();
+ UnifracUnweightedCommand(string);
+ ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
+ int execute();
+ void help();
private:
GlobalData* globaldata;
SharedUtil* util;
+ FileOutput* output;
vector<Tree*> T; //user trees
TreeMap* tmap;
Unweighted* unweighted;
- string sumFile, unweightedFile, unweightedFileout, allGroups;
+ string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
int iters, numGroups, numComp, counter;
EstOutput userData; //unweighted score info for user tree
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.
- map<float, float>::iterator it2;
- map<float, float>::iterator it;
+ bool abort, phylip, random;
+ string groups, itersString, outputDir;
+ vector<string> Groups, outputNames; //holds groups to be used
+
ofstream outSum, out;
ifstream inFile;
- void printUWSummaryFile();
+ void printUWSummaryFile(int);
void printUnweightedFile();
- void initFile(string);
- void output(vector<double>);
- void resetFile();
-
+ void createPhylipFile(int);
+
};
-
-
-#endif
\ No newline at end of file
+#endif