knn.cpp

   1 /*
   2  *  knn.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/4/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "knn.h"
  11
  12 /**************************************************************************************************/
  13 Knn::Knn(string tfile, string tempFile, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch, int n)
  14 : Classify(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch), num(n)  {}
  15 /**************************************************************************************************/
  16 string Knn::getTaxonomy(Sequence* seq) {
  17         try {
  18                 string tax;
  19
  20                 //use database to find closest seq
  21                 vector<int> closest = database->findClosestSequences(seq, num);
  22
  23                 vector<string> closestNames;
  24                 for (int i = 0; i < closest.size(); i++) {
  25                         //find that sequences taxonomy in map
  26                         it = taxonomy.find(names[closest[i]]);
  27
  28                         //is this sequence in the taxonomy file
  29                         if (it == taxonomy.end()) { //error not in file
  30                                 mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file.  It will be eliminated as a match to sequence " + seq->getName() + "."); mothurOutEndLine();
  31                         }else{   closestNames.push_back(it->first);     }
  32                 }
  33
  34                 if (closestNames.size() == 0) {
  35                         mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); mothurOutEndLine();
  36                         tax = "bad seq";
  37                 }else{
  38                         tax = findCommonTaxonomy(closestNames);
  39                         if (tax == "") { mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); mothurOutEndLine(); tax = "bad seq"; }
  40                 }
  41
  42                 return tax;
  43         }
  44         catch(exception& e) {
  45                 errorOut(e, "Knn", "getTaxonomy");
  46                 exit(1);
  47         }
  48 }
  49 /**************************************************************************************************/
  50 string Knn::findCommonTaxonomy(vector<string> closest)  {
  51         try {
  52                 vector< vector<string> > taxons;  //taxon[0] = vector of taxonomy info for closest[0].
  53                                                                                 //so if closest[0] taxonomy is Bacteria;Alphaproteobacteria;Rhizobiales;Azorhizobium_et_rel.;Methylobacterium_et_rel.;Bosea;
  54                                                                                 //taxon[0][0] = Bacteria, taxon[0][1] = Alphaproteobacteria....
  55
  56                 taxons.resize(closest.size());
  57                 int smallest = 100;
  58
  59                 for (int i = 0; i < closest.size(); i++) {
  60
  61                         string tax = taxonomy[closest[i]];  //we know its there since we checked in getTaxonomy
  62
  63                         taxons[i] = parseTax(tax);
  64
  65                         //figure out who has the shortest taxonomy info. so you can start comparing there
  66                         if (taxons[i].size() < smallest) {
  67                                 smallest = taxons[i].size();
  68                         }
  69                 }
  70
  71                 //start at the highest level all the closest seqs have
  72                 string common = "";
  73                 for (int i = (smallest-1); i >= 0; i--) {
  74
  75                         string thistax = taxons[0][i];
  76                         int num = 0;
  77                         for (int j = 1; j < taxons.size(); j++) {
  78                                 if (taxons[j][i] != thistax) { break; }
  79                                 num = j;
  80                         }
  81
  82                         if (num == (taxons.size()-1)) { //they all match at this level
  83                                 for (int k = 0; k <= i; k++) {
  84                                         common += taxons[0][k] + ';';
  85                                 }
  86                                 break;
  87                         }
  88                 }
  89
  90                 return common;
  91         }
  92         catch(exception& e) {
  93                 errorOut(e, "Knn", "findCommonTaxonomy");
  94                 exit(1);
  95         }
  96 }
  97 /**************************************************************************************************/
  98