added phylotype command which reads a taxonomy file and creates a .list, .rabund...

[mothur.git] / taxonomyequalizer.h

diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
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+++ b/taxonomyequalizer.h
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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"
+
+//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
+
+