X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=taxonomyequalizer.cpp;h=c0507261eaf2c96c9381172a646317c7cb6a1db3;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=fc36eb643c30c549810ff462671c38ba36e118b8;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index fc36eb6..c050726 100644
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -10,13 +10,13 @@
 #include "taxonomyequalizer.h"
 
 /**************************************************************************************************/
-TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
+TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir(o) {
 	try {
 		m = MothurOut::getInstance();
 		containsConfidence = false;
 		
 		ifstream inTax;
-		openInputFile(tfile, inTax);
+		m->openInputFile(tfile, inTax);
 	
 		highestLevel = getHighestLevel(inTax);
 		
@@ -32,11 +32,11 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
 			
 			inTax.close(); 
 			ifstream in; 
-			openInputFile(tfile, in);
+			m->openInputFile(tfile, in);
 			
 			ofstream out;
-			equalizedFile = getRootName(tfile) + "equalized.taxonomy";
-			openOutputFile(equalizedFile, out);
+			equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+			m->openOutputFile(equalizedFile, out);
 			
 	
 			string name, tax;
@@ -44,9 +44,9 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
 			
 				if (m->control_pressed) {  break; }
 				
-				in >> name >> tax;   gobble(in);
+				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) : cutoff(c) {
 			in.close();
 			out.close();
 			
-			if (m->control_pressed) { remove(equalizedFile.c_str());  }
+			if (m->control_pressed) { m->mothurRemove(equalizedFile);  }
 		}else { inTax.close(); }
 		
 	}
@@ -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;
 					
 	}
@@ -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);
-	}
-}
-
-/**************************************************************************************************/