#include "command.hpp"
#include "readtree.h"
#include "treemap.h"
+#include "counttable.h"
class ClassifyTreeCommand : public Command {
public:
vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
string getDescription() { return "Find the consensus taxonomy for the descendant of each tree node"; }
void help() { m->mothurOut(getHelpString()); }
private:
- string treefile, taxonomyfile, groupfile, namefile, outputDir;
+ string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
+ CountTable* ct;
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
string getTaxonomy(set<string>, int&);
- int readNamesFile();
- int readTaxonomyFile();
};