/**************************************************************************************************/
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;