#include "knn.h"
/**************************************************************************************************/
-Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int n)
+Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int n, int tid)
: Classify(), num(n), search(method) {
try {
+ threadID = tid;
+ shortcuts = true;
+
//create search database and names vector
generateDatabaseAndNames(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch);
}
}
if (closestNames.size() == 0) {
- m->mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); m->mothurOutEndLine();
- tax = "bad seq";
+ m->mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. "); m->mothurOutEndLine();
+ tax = "unknown;";
}else{
tax = findCommonTaxonomy(closestNames);
- if (tax == "") { m->mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); m->mothurOutEndLine(); tax = "bad seq"; }
+ if (tax == "") { m->mothurOut("There are no common levels for sequence " + seq->getName() + ". "); m->mothurOutEndLine(); tax = "unknown;"; }
}
simpleTax = tax;
/**************************************************************************************************/
string Knn::findCommonTaxonomy(vector<string> closest) {
try {
- vector< vector<string> > taxons; //taxon[0] = vector of taxonomy info for closest[0].
+ /*vector< vector<string> > taxons; //taxon[0] = vector of taxonomy info for closest[0].
//so if closest[0] taxonomy is Bacteria;Alphaproteobacteria;Rhizobiales;Azorhizobium_et_rel.;Methylobacterium_et_rel.;Bosea;
//taxon[0][0] = Bacteria, taxon[0][1] = Alphaproteobacteria....
if (m->control_pressed) { return "control"; }
string tax = taxonomy[closest[i]]; //we know its there since we checked in getTaxonomy
+ cout << tax << endl;
taxons[i] = parseTax(tax);
}
break;
}
+ }*/
+
+ string conTax;
+
+ //create a tree containing sequences from this bin
+ PhyloTree* p = new PhyloTree();
+
+ for (int i = 0; i < closest.size(); i++) {
+ p->addSeqToTree(closest[i], taxonomy[closest[i]]);
}
-
- return common;
+
+ //build tree
+ p->assignHeirarchyIDs(0);
+
+ TaxNode currentNode = p->get(0);
+
+ //at each level
+ while (currentNode.children.size() != 0) { //you still have more to explore
+
+ TaxNode bestChild;
+ int bestChildSize = 0;
+
+ //go through children
+ for (map<string, int>::iterator itChild = currentNode.children.begin(); itChild != currentNode.children.end(); itChild++) {
+
+ TaxNode temp = p->get(itChild->second);
+
+ //select child with largest accessions - most seqs assigned to it
+ if (temp.accessions.size() > bestChildSize) {
+ bestChild = p->get(itChild->second);
+ bestChildSize = temp.accessions.size();
+ }
+
+ }
+
+ if (bestChildSize == closest.size()) { //if yes, add it
+ conTax += bestChild.name + ";";
+ }else{ //if no, quit
+ break;
+ }
+
+ //move down a level
+ currentNode = bestChild;
+ }
+
+ delete p;
+
+ return conTax;
}
catch(exception& e) {
m->errorOut(e, "Knn", "findCommonTaxonomy");