X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=taxonomyequalizer.h;fp=taxonomyequalizer.h;h=191267c1a44833c69437b2f8dbbb616e7566cf60;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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+#ifndef TAXONOMYEQUALIZER_H
+#define TAXONOMYEQUALIZER_H
+
+
+/*
+ *  taxonomyequalizer.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/20/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "mothurout.h"
+
+//reads in taxonomy file and makes all the taxonomies the same length 
+//by appending the last taxon to a given taxonomy as many times as needed to 
+//make it as long as the longest taxonomy in the file 
+
+/**************************************************************************************************/
+
+class TaxEqualizer  {
+	
+public:
+	TaxEqualizer(string, int, string);
+	~TaxEqualizer() {};
+	
+	string getEqualizedTaxFile()	{	return equalizedFile;	}
+	int getHighestLevel()			{	return highestLevel;	}
+	
+	
+private:
+	string equalizedFile, testTax, outputDir;
+	bool containsConfidence;
+	int cutoff, highestLevel;
+	map<string, int> seqLevels;  //maps name to level of taxonomy
+	
+	int getHighestLevel(ifstream&);  //scans taxonomy file to find taxonomy with highest level
+	void extendTaxonomy(string, string&, int);  //name, taxonomy, desired level
+	void truncateTaxonomy(string, string&, int);  //name, taxonomy, desired level
+	MothurOut* m;
+	
+};
+
+/**************************************************************************************************/
+
+
+#endif
+
+