#include "groupmap.h"
#include "validcalculator.h"
#include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
#include "readmatrix.hpp"
#include "readcolumn.h"
#include "readphylip.h"
-#include "sparsematrix.hpp"
#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
They can also use as many or as few calculators as they wish. */
-typedef list<PCell>::iterator MatData;
-
class TreeGroupCommand : public Command {
public:
vector<string> setParameters();
string getCommandName() { return "tree.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
NameAssignment* nameMap;
ListVector* list;
- TreeMap* tmap;
+ CountTable* ct;
Tree* t;
InputData* input;
vector<Calculator*> treeCalculators;
vector<SharedRAbundVector*> lookup;
string lastLabel;
- string format, groupNames, filename, sharedfile, inputfile;
+ string format, groupNames, filename, sharedfile, countfile, inputfile;
int numGroups, subsampleSize, iters, processors;
ofstream out;
float precision, cutoff;
unsigned long long start;
unsigned long long end;
MothurOut* m;
+ int count;
treeSharedData(){}
treeSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
end = en;
Estimators = est;
thisLookup = lu;
+ count=0;
}
};
/**************************************************************************************************/
vector<SharedRAbundVector*> subset;
for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
+ pDataArray->count++;
+
for (int l = 0; l < k; l++) {
if (k != l) { //we dont need to similiarity of a groups to itself