X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=taxonomyequalizer.h;h=191267c1a44833c69437b2f8dbbb616e7566cf60;hp=6308d7168e72651f349ab3bf0a28942949063f62;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=7a2154809d332281cf4006943a9bd94b8208c837

diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
index 6308d71..191267c 100644
--- a/taxonomyequalizer.h
+++ b/taxonomyequalizer.h
@@ -12,6 +12,7 @@
  */
 
 #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 
@@ -22,23 +23,23 @@
 class TaxEqualizer  {
 	
 public:
-	TaxEqualizer(string, int);
+	TaxEqualizer(string, int, string);
 	~TaxEqualizer() {};
 	
-	string getEqualizedTaxFile()	{  return equalizedFile;	}
+	string getEqualizedTaxFile()	{	return equalizedFile;	}
+	int getHighestLevel()			{	return highestLevel;	}
 	
 	
 private:
-	string equalizedFile, testTax;
+	string equalizedFile, testTax, outputDir;
 	bool containsConfidence;
-	int cutoff;
+	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
-	void removeConfidences(string&);  //removes the confidence limits on the taxon 
-
+	MothurOut* m;
 	
 };