X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=taxonomyequalizer.h;h=191267c1a44833c69437b2f8dbbb616e7566cf60;hp=e060c9e8e1f58e28b1eb083287e697a364c05268;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
index e060c9e..191267c 100644
--- a/taxonomyequalizer.h
+++ b/taxonomyequalizer.h
@@ -23,7 +23,7 @@
 class TaxEqualizer  {
 	
 public:
-	TaxEqualizer(string, int);
+	TaxEqualizer(string, int, string);
 	~TaxEqualizer() {};
 	
 	string getEqualizedTaxFile()	{	return equalizedFile;	}
@@ -31,7 +31,7 @@ public:
 	
 	
 private:
-	string equalizedFile, testTax;
+	string equalizedFile, testTax, outputDir;
 	bool containsConfidence;
 	int cutoff, highestLevel;
 	map<string, int> seqLevels;  //maps name to level of taxonomy
@@ -39,7 +39,6 @@ private:
 	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;
 	
 };