X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=taxonomyequalizer.cpp;h=d3b24d1297f280f0b4f11a30724a3c9d61d8427f;hb=9489965363593bb2a3e94f801b4079a32ddf8732;hp=c7e8cb9e4add8388602dc2bfc12cff28673f7db3;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index c7e8cb9..d3b24d1 100644
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -16,7 +16,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
 		containsConfidence = false;
 		
 		ifstream inTax;
-		openInputFile(tfile, inTax);
+		m->openInputFile(tfile, inTax);
 	
 		highestLevel = getHighestLevel(inTax);
 		
@@ -32,11 +32,11 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
 			
 			inTax.close(); 
 			ifstream in; 
-			openInputFile(tfile, in);
+			m->openInputFile(tfile, in);
 			
 			ofstream out;
-			equalizedFile = outputDir + getRootName(getSimpleName(tfile)) + "equalized.taxonomy";
-			openOutputFile(equalizedFile, out);
+			equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+			m->openOutputFile(equalizedFile, out);
 			
 	
 			string name, tax;
@@ -44,7 +44,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
 			
 				if (m->control_pressed) {  break; }
 				
-				in >> name >> tax;   gobble(in);
+				in >> name >> tax;   m->gobble(in);
 				
 				if (containsConfidence) {  removeConfidences(tax);	}
 				
@@ -78,7 +78,7 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
 		string name, tax;
 		
 		while (in) {
-			in >> name >> tax;   gobble(in);
+			in >> name >> tax;   m->gobble(in);
 		
 			//count levels in this taxonomy
 			int thisLevel = 0;
@@ -88,19 +88,19 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
 		
 			//save sequences level
 			seqLevels[name] = thisLevel;
-		
+	
 			//is this the longest taxonomy?
 			if (thisLevel > level) {  
 				level = thisLevel;  
 				testTax = tax; //testTax is used to figure out if this file has confidences we need to strip out
-			}  
+			} 
 		}
 		
 		int pos = testTax.find_first_of('(');
 
 		//if there are '(' then there are confidences we need to take out
 		if (pos != -1) {  containsConfidence = true;  }
-		
+	
 		return level;
 					
 	}