X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=knn.cpp;h=1835c48f802b861f29a6a6c2360a47788d13bc46;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=0a62e743b0dd8d4f5435d504127a70724f9f27a8;hpb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63;p=mothur.git

diff --git a/knn.cpp b/knn.cpp
index 0a62e74..1835c48 100644
--- a/knn.cpp
+++ b/knn.cpp
@@ -10,8 +10,42 @@
 #include "knn.h"
 
 /**************************************************************************************************/
-Knn::Knn(string tfile, string tempFile, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch, int n) 
-: Classify(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch), num(n)  {}
+Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int n) 
+: Classify(), num(n), search(method) {
+	try {
+		//create search database and names vector
+		generateDatabaseAndNames(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Knn", "Knn");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+void Knn::setDistName(string s) {
+	try {
+		outDistName = s;
+		ofstream outDistance;
+		m->openOutputFile(outDistName, outDistance);
+		outDistance << "Name\tBestMatch\tDistance" << endl;
+		outDistance.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Knn", "setDistName");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+Knn::~Knn() {
+	try {
+		 delete phyloTree; 
+		 if (database != NULL) {  delete database; }
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Knn", "~Knn");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 string Knn::getTaxonomy(Sequence* seq) {
 	try {
@@ -19,7 +53,11 @@ string Knn::getTaxonomy(Sequence* seq) {
 		
 		//use database to find closest seq
 		vector<int> closest = database->findClosestSequences(seq, num);
-		
+	
+		if (search == "distance") { ofstream outDistance; m->openOutputFileAppend(outDistName, outDistance); outDistance << seq->getName() << '\t' << database->getName(closest[0]) << '\t' << database->getSearchScore() << endl; outDistance.close();  }
+	
+		if (m->control_pressed) { return tax; }
+
 		vector<string> closestNames;
 		for (int i = 0; i < closest.size(); i++) {
 			//find that sequences taxonomy in map
@@ -27,22 +65,23 @@ 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);
 	}
 }
@@ -57,6 +96,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
 		int smallest = 100;
 		
 		for (int i = 0; i < closest.size(); i++) {
+			if (m->control_pressed) { return "control"; }
 		
 			string tax = taxonomy[closest[i]];  //we know its there since we checked in getTaxonomy
 		
@@ -71,6 +111,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
 		//start at the highest level all the closest seqs have
 		string common = "";
 		for (int i = (smallest-1); i >= 0; i--) {
+			if (m->control_pressed) { return "control"; }
 
 			string thistax = taxons[0][i];
 			int num = 0;
@@ -90,7 +131,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
 		return common;
 	}
 	catch(exception& e) {
-		errorOut(e, "Knn", "findCommonTaxonomy");
+		m->errorOut(e, "Knn", "findCommonTaxonomy");
 		exit(1);
 	}
 }