changed random forest output filename

[mothur.git] / taxonomyequalizer.h

diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
index 6308d7168e72651f349ab3bf0a28942949063f62..191267c1a44833c69437b2f8dbbb616e7566cf60 100644 (file)
--- 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;
        
 };