#include "command.hpp"
#include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
#include "progress.hpp"
#include "sharedutilities.h"
#include "fileoutput.h"
vector<string> setParameters();
string getCommandName() { return "parsimony"; }
string getCommandCategory() { return "Hypothesis Testing"; }
+
string getHelpString();
+ string getOutputPattern(string);
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:
- ReadTree* read;
- SharedUtil* util;
FileOutput* output;
vector<Tree*> T; //user trees
Tree* randT; //random tree
Tree* copyUserTree;
- TreeMap* tmap;
- TreeMap* savetmap;
- Parsimony* pars;
+ CountTable* ct;
+ CountTable* savect;
vector<string> groupComb; // AB. AC, BC...
- string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+ string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile, countfile;
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.