X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=taxonomyequalizer.cpp;h=c0507261eaf2c96c9381172a646317c7cb6a1db3;hp=e7fa07af76ea792137475c6dff67b2ec0c9bcf7c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=bee7952bbdc4ed46c7a12bef11769345fa3224d7

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index e7fa07a..c050726 100644
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -10,52 +10,63 @@
 #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);
-	
-		//if the user has specified a cutoff and it's smaller than the highest level
-		if ((cutoff != -1) && (cutoff < highestLevel)) { 
-			highestLevel = cutoff;
-		}else if (cutoff > highestLevel) {
-			mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
-			mothurOutEndLine();
-		}
-		
-		inTax.close();  
-		openInputFile(tfile, inTax);
-		
-		ofstream out;
-		equalizedFile = getRootName(tfile) + "equalized.taxonomy";
-		openOutputFile(equalizedFile, out);
 		
-		string name, tax;
-		while (inTax) {
-			inTax >> name >> tax;   gobble(inTax);
+		if (!m->control_pressed) { 
+			
+			//if the user has specified a cutoff and it's smaller than the highest level
+			if ((cutoff != -1) && (cutoff < highestLevel)) { 
+				highestLevel = cutoff;
+			}else if (cutoff > highestLevel) {
+				m->mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
+				m->mothurOutEndLine();
+			}
+			
+			inTax.close(); 
+			ifstream in; 
+			m->openInputFile(tfile, in);
 			
-			if (containsConfidence) {  removeConfidences(tax);	}
+			ofstream out;
+			equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+			m->openOutputFile(equalizedFile, out);
 			
-			//is this a taxonomy that needs to be extended?
-			if (seqLevels[name] < highestLevel) {
-				extendTaxonomy(name, tax, highestLevel);
-			}else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
-				truncateTaxonomy(name, tax, highestLevel);
+	
+			string name, tax;
+			while (in) {
+			
+				if (m->control_pressed) {  break; }
+				
+				in >> name >> tax;   m->gobble(in);
+				
+				if (containsConfidence) {  m->removeConfidences(tax);	}
+				
+				//is this a taxonomy that needs to be extended?
+				if (seqLevels[name] < highestLevel) {
+					extendTaxonomy(name, tax, highestLevel);
+				}else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
+					truncateTaxonomy(name, tax, highestLevel);
+				}
+				
+				out << name << '\t' << tax << endl;
 			}
 			
-			out << name << '\t' << tax << endl;
-		}
+			in.close();
+			out.close();
+			
+			if (m->control_pressed) { m->mothurRemove(equalizedFile);  }
+		}else { inTax.close(); }
 		
-		inTax.close();
-		out.close();
-					
 	}
 	catch(exception& e) {
-		errorOut(e, "TaxEqualizer", "TaxEqualizer");
+		m->errorOut(e, "TaxEqualizer", "TaxEqualizer");
 		exit(1);
 	}
 }
@@ -67,7 +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;
@@ -77,24 +88,24 @@ 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;
 					
 	}
 	catch(exception& e) {
-		errorOut(e, "TaxEqualizer", "getHighestLevel");
+		m->errorOut(e, "TaxEqualizer", "getHighestLevel");
 		exit(1);
 	}
 }
@@ -117,7 +128,7 @@ void TaxEqualizer::extendTaxonomy(string name, string& tax, int desiredLevel) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "TaxEqualizer", "extendTaxonomy");
+		m->errorOut(e, "TaxEqualizer", "extendTaxonomy");
 		exit(1);
 	}
 }
@@ -136,34 +147,9 @@ void TaxEqualizer::truncateTaxonomy(string name, string& tax, int desiredLevel)
 		tax += ";";
 	}
 	catch(exception& e) {
-		errorOut(e, "TaxEqualizer", "truncateTaxonomy");
+		m->errorOut(e, "TaxEqualizer", "truncateTaxonomy");
 		exit(1);
 	}
 }
 /**************************************************************************************************/
-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) {
-		errorOut(e, "TaxEqualizer", "removeConfidences");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/