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#ifndef RAWTRAININGDATAMAKER_H
#define RAWTRAININGDATAMAKER_H
/*
* rawTrainingDataMaker.h
* Mothur
*
* Created by westcott on 4/21/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "mothurout.h"
#include "groupmap.h"
#include "counttable.h"
/**************************************************************************************************/
struct rawTaxNode {
map<string, int> children; //childs name to index in tree
int parent, level;
string name, rank;
map<string, int> groupCount;
int total;
rawTaxNode(string n) : name(n), level(0), parent(-1), total(0) {}
rawTaxNode(){}
};
/**************************************************************************************************/
//doesn't use MPI ifdefs since only pid 0 uses this class
class PhyloSummary {
public:
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, 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;
CountTable* ct;
bool ignore, relabund;
int numNodes;
int numSeqs;
int maxLevel;
MothurOut* m;
};
/**************************************************************************************************/
#endif
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