#include "progress.hpp"
#include "sharedutilities.h"
#include "fileoutput.h"
+#include "readtree.h"
-class GlobalData;
-
class ParsimonyCommand : public Command {
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();
+ ~ParsimonyCommand(){}
+
+ 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"; }
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
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, outputDir;
- int iters, numGroups, numComp, counter;
+ string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+ int iters, numGroups, numComp, counter, processors, numUniquesInName;
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.
vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
ofstream outSum;
-
-
bool abort;
string groups, itersString;
vector<string> Groups, outputNames; //holds groups to be used
- map<string, vector<string> > outputTypes;
-
+ map<string, string> nameMap;
+
void printParsimonyFile();
int printUSummaryFile();
void getUserInput();
+ int readNamesFile();
};