@@ -36,10+43,9 @@ class UnifracWeightedCommand : public Command {
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...
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;
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
int iters, numGroups, numComp, counter;
EstOutput userData; //weighted score info for user tree
EstOutput randomData; //weighted score info for random trees
@@ -49,18+55,22 @@ class UnifracWeightedCommand : public Command {
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
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;
+ bool abort, phylip, random;
string groups, itersString;
string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ vector<string> Groups, outputNames; //holds groups to be used
+ int processors;
ofstream outSum;
void printWSummaryFile();
void printWeightedFile();
ofstream outSum;
void printWSummaryFile();
void printWeightedFile();
+ void createPhylipFile();
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
+ int createProcesses(Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);