X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=taxonomyequalizer.cpp;h=c0507261eaf2c96c9381172a646317c7cb6a1db3;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=d3b24d1297f280f0b4f11a30724a3c9d61d8427f;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index d3b24d1..c050726 100644
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -46,7 +46,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
 				
 				in >> name >> tax;   m->gobble(in);
 				
-				if (containsConfidence) {  removeConfidences(tax);	}
+				if (containsConfidence) {  m->removeConfidences(tax);	}
 				
 				//is this a taxonomy that needs to be extended?
 				if (seqLevels[name] < highestLevel) {
@@ -61,7 +61,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
 			in.close();
 			out.close();
 			
-			if (m->control_pressed) { remove(equalizedFile.c_str());  }
+			if (m->control_pressed) { m->mothurRemove(equalizedFile);  }
 		}else { inTax.close(); }
 		
 	}
@@ -152,29 +152,4 @@ void TaxEqualizer::truncateTaxonomy(string name, string& tax, int desiredLevel)
 	}
 }
 /**************************************************************************************************/
-void TaxEqualizer::removeConfidences(string& tax) {
-	try {
-		
-		string taxon;
-		string newTax = "";
-		
-		while (tax.find_first_of(';') != -1) {
-			//get taxon
-			taxon = tax.substr(0,tax.find_first_of(';'));
-			taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
-			taxon += ";";
-			
-			tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-			newTax += taxon;
-		}
-		
-		tax = newTax;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TaxEqualizer", "removeConfidences");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/