changes while testing

[mothur.git] / knn.cpp

diff --git a/knn.cpp b/knn.cpp
index 6053b6e47a1f16c1398c2c183cd40eef0aefeda0..81b21b265785c2f8a83392ee52e7aeffbc9d4370 100644 (file)
--- a/knn.cpp
+++ b/knn.cpp
@@ -14,6 +14,7 @@ Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOp
 : 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);
@@ -72,11 +73,11 @@ string Knn::getTaxonomy(Sequence* seq) {
                }
                
                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;
@@ -90,7 +91,7 @@ string Knn::getTaxonomy(Sequence* seq) {
 /**************************************************************************************************/
 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....
                                                                                
@@ -101,6 +102,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
                        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);
                
@@ -128,9 +130,54 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
                                }
                                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");