X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=knn.cpp;h=1835c48f802b861f29a6a6c2360a47788d13bc46;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=93a7aa33faa6e2e1d9cb43c0505464056cbb1f08;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/knn.cpp b/knn.cpp
index 93a7aa3..1835c48 100644
--- a/knn.cpp
+++ b/knn.cpp
@@ -11,16 +11,51 @@
 
 /**************************************************************************************************/
 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)  {}
+: 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 {
 		string tax;
 		
 		//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;