public:
ParsimonyCommand(string);
+ ParsimonyCommand();
~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
Parsimony* pars;
vector<string> groupComb; // AB. AC, BC...
string sumFile, randomtree, allGroups, outputDir;
- int iters, numGroups, numComp, counter;
+ int iters, numGroups, numComp, counter, processors;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector< vector<float> > userTreeScores; //scores for users trees for each comb.
vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
bool abort;
string groups, itersString;
vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
void printParsimonyFile();
int printUSummaryFile();