linePair(int i, int j) : start(i), num(j) {}
};
vector<linePair> lines;
-
- ReadTree* read;
- SharedUtil* util;
+ TreeMap* tmap;
FileOutput* output;
vector<Tree*> T; //user trees
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...
- TreeMap* tmap;
string sumFile, outputDir;
int iters, numGroups, numComp, counter;
vector< vector<double> > rScores; //vector<weighted scores for random trees.> each group comb has an entry
bool abort, phylip, random, includeRoot, subsample, consensus;
string groups, itersString, outputForm, treefile, groupfile, namefile;
vector<string> Groups, outputNames; //holds groups to be used
- int processors, numUniquesInName, subsampleSize, subsampleIters;
+ int processors, subsampleSize, subsampleIters;
ofstream outSum;
map<string, string> nameMap;
void calculateFreqsCumuls();
int createProcesses(Tree*, vector< vector<string> >, vector< vector<double> >&);
int driver(Tree*, vector< vector<string> >, int, int, vector< vector<double> >&);
- int readNamesFile();
int runRandomCalcs(Tree*, vector<double>);
- int readTrees();
- vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap*);
+ vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
int getConsensusTrees(vector< vector<double> >&, int);
int getAverageSTDMatrices(vector< vector<double> >&, int);