#include "mothur.h"
#include "mothurout.h"
#include "groupmap.h"
+#include "counttable.h"
/**************************************************************************************************/
class PhyloSummary {
public:
- PhyloSummary(string);
- PhyloSummary(string, string);
- ~PhyloSummary() { if (groupmap != NULL) { delete groupmap; } }
+ PhyloSummary(GroupMap*, bool);
+ PhyloSummary(string, GroupMap*, bool);
+ PhyloSummary(CountTable*, bool);
+ PhyloSummary(string, CountTable*, bool);
+ ~PhyloSummary() {}
int summarize(string); //pass it a taxonomy file and a group file and it makes the tree
int addSeqToTree(string, string);
- int addSeqToTree(string, vector<string>);
+ int addSeqToTree(string, map<string, bool>);
void print(ofstream&);
+ void print(ofstream&, bool);
int getMaxLevel() { return maxLevel; }
private:
string getNextTaxon(string&);
vector<rawTaxNode> tree;
void print(int, ofstream&);
+ void print(int, ofstream&, bool);
void assignRank(int);
void readTreeStruct(ifstream&);
GroupMap* groupmap;
- bool ignore;
+ CountTable* ct;
+ bool ignore, relabund;
int numNodes;
int numSeqs;