- public:
- ParsimonyCommand(string);
- ~ParsimonyCommand() { delete pars; delete util; delete output; }
- int execute();
- void help();
-
- private:
- GlobalData* globaldata;
- SharedUtil* util;
- FileOutput* output;
- vector<Tree*> T; //user trees
- Tree* randT; //random tree
- Tree* copyUserTree;
- TreeMap* tmap;
- TreeMap* savetmap;
- Parsimony* pars;
- vector<string> groupComb; // AB. AC, BC...
- string sumFile, randomtree, allGroups;
- int iters, numGroups, numComp, counter;
- 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.
- EstOutput userData; //pscore info for user tree
- EstOutput randomData; //pscore info for random trees
- map<int, double> validScores; //map contains scores from both user and random
- vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
- vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
- vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
- vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
- map<int, double>::iterator it;
- map<int, double>::iterator it2;
-
- ofstream out, outSum;
- ifstream inFile;
-
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it4;
- bool abort;
- string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ vector<string> setParameters();
+ string getCommandName() { return "parsimony"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
+ string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }