X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.h;fp=phylosummary.h;h=cdec0d0a4ac7ca83cb0845988adb90152bcae07b;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/phylosummary.h b/phylosummary.h
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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"
+
+/**************************************************************************************************/
+
+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(string);
+	PhyloSummary(string, string);
+	~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+	
+	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>);
+	void print(ofstream&);
+	int getMaxLevel() { return maxLevel; }
+	
+private:
+	string getNextTaxon(string&);
+	vector<rawTaxNode> tree;
+	void print(int, ofstream&);
+	void assignRank(int);
+	void readTreeStruct(ifstream&);
+	GroupMap* groupmap;
+	bool ignore;
+	
+	int numNodes;
+	int numSeqs;
+	int maxLevel;
+	MothurOut* m;
+};
+
+/**************************************************************************************************/
+
+#endif
+
+