X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=knn.cpp;h=c11626a082ac9003785fd937e87b922e3bf8025a;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=6d57fb135f14398fb6b7ab776eb81e84e4728406;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/knn.cpp b/knn.cpp
index 6d57fb1..c11626a 100644
--- a/knn.cpp
+++ b/knn.cpp
@@ -10,7 +10,7 @@
 #include "knn.h"
 
 /**************************************************************************************************/
-Knn::Knn(string tfile, string tempFile, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch, int n) 
+Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int n) 
 : Classify(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch), num(n)  {}
 /**************************************************************************************************/
 string Knn::getTaxonomy(Sequence* seq) {
@@ -18,8 +18,9 @@ string Knn::getTaxonomy(Sequence* seq) {
 		string tax;
 		
 		//use database to find closest seq
+
 		vector<int> closest = database->findClosestSequences(seq, num);
-		
+
 		vector<string> closestNames;
 		for (int i = 0; i < closest.size(); i++) {
 			//find that sequences taxonomy in map
@@ -27,22 +28,23 @@ string Knn::getTaxonomy(Sequence* seq) {
 		
 			//is this sequence in the taxonomy file
 			if (it == taxonomy.end()) { //error not in file
-				mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file.  It will be eliminated as a match to sequence " + seq->getName() + "."); mothurOutEndLine();
+				m->mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file.  It will be eliminated as a match to sequence " + seq->getName() + "."); m->mothurOutEndLine();
 			}else{   closestNames.push_back(it->first);	}
 		}
 		
 		if (closestNames.size() == 0) {
-			mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); mothurOutEndLine();
+			m->mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); m->mothurOutEndLine();
 			tax = "bad seq";
 		}else{
 			tax = findCommonTaxonomy(closestNames);
-			if (tax == "") { mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); mothurOutEndLine(); tax = "bad seq"; }
+			if (tax == "") { m->mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); m->mothurOutEndLine(); tax = "bad seq"; }
 		}
 		
+		simpleTax = tax;
 		return tax;	
 	}
 	catch(exception& e) {
-		errorOut(e, "Knn", "getTaxonomy");
+		m->errorOut(e, "Knn", "getTaxonomy");
 		exit(1);
 	}
 }
@@ -60,18 +62,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
 		
 			string tax = taxonomy[closest[i]];  //we know its there since we checked in getTaxonomy
 		
-			tax = tax.substr(0, tax.length()-1);  //get rid of last ';'
-	
-			//parse taxonomy
-			string individual;
-			while (tax.find_first_of(';') != -1) {
-				individual = tax.substr(0,tax.find_first_of(';'));
-				tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-				taxons[i].push_back(individual);
-			
-			}
-			//get last one
-			taxons[i].push_back(tax);
+			taxons[i] = parseTax(tax);
 		
 			//figure out who has the shortest taxonomy info. so you can start comparing there
 			if (taxons[i].size() < smallest) {
@@ -101,7 +92,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
 		return common;
 	}
 	catch(exception& e) {
-		errorOut(e, "Knn", "findCommonTaxonomy");
+		m->errorOut(e, "Knn", "findCommonTaxonomy");
 		exit(1);
 	}
 }