X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=taxonomyequalizer.h;fp=taxonomyequalizer.h;h=6308d7168e72651f349ab3bf0a28942949063f62;hb=7a2154809d332281cf4006943a9bd94b8208c837;hp=0000000000000000000000000000000000000000;hpb=9354b70bb84f6dd52ff4a1955754bcbf7edeedbf;p=mothur.git

diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
new file mode 100644
index 0000000..6308d71
--- /dev/null
+++ b/taxonomyequalizer.h
@@ -0,0 +1,50 @@
+#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"
+
+//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);
+	~TaxEqualizer() {};
+	
+	string getEqualizedTaxFile()	{  return equalizedFile;	}
+	
+	
+private:
+	string equalizedFile, testTax;
+	bool containsConfidence;
+	int cutoff;
+	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 
+
+	
+};
+
+/**************************************************************************************************/
+
+
+#endif
+
+