working on pam

[mothur.git] / kmer.cpp

diff --git a/kmer.cpp b/kmer.cpp
index dcb6475161ce6f29f89d746fa1581ca7cab380c4..50574f4a5ee0709daf2ebb67b8f0e49971e20ef0 100644 (file)
--- a/kmer.cpp
+++ b/kmer.cpp
@@ -7,9 +7,6 @@
  *
  */
 
-using namespace std;
-
-
 #include "kmer.hpp"
 
 /**************************************************************************************************/
@@ -41,6 +38,32 @@ string Kmer::getKmerString(string sequence){ //      Calculate kmer for each position
        
        return kmerString;      
 }
+/**************************************************************************************************/
+
+vector< map<int, int> > Kmer::getKmerCounts(string sequence){  //      Calculate kmer for each position in the sequence, save info in a map
+       int length = sequence.length();                         //      so you know at each spot in the sequence what kmers were found
+       int nKmers = length - kmerSize + 1;                     //      
+       vector< map<int, int> > counts; counts.resize(nKmers);  // a map kmer counts for each spot
+        map<int, int>::iterator it;
+       
+       for(int i=0;i<nKmers;i++){                                      //      Go though sequence and get the number between 0 and maxKmer for that
+               if (i == 0) {
+                       int kmerNumber = getKmerNumber(sequence, i);//  kmer. 
+                       counts[i][kmerNumber] = 1;                      // add this kmer if not already there
+               }else { 
+                       //your count is everything that came before and whatever you find now
+                       counts[i] = counts[i-1];
+                       int kmerNumber = getKmerNumber(sequence, i);//  kmer.  
+                       
+                       it = counts[i].find(kmerNumber);
+                       if (it!= counts[i].end()) {   counts[i][kmerNumber]++;  }  //increment number of times you have seen this kmer
+                       else {   counts[i][kmerNumber] = 1;   }  // add this kmer since not already there
+               }
+       }
+       
+       return counts;  
+}
+       
        
 /**************************************************************************************************/
 
@@ -108,6 +131,27 @@ string Kmer::getKmerBases(int kmerNumber){
        }
        return kmer;
 }
+/**************************************************************************************************/
+
+int Kmer::getReverseKmerNumber(int kmerNumber){
+               
+       string kmerString = getKmerBases(kmerNumber);
+       
+       //get Reverse
+       string reverse = "";
+       for(int i=kmerString.length()-1;i>=0;i--){
+               if(kmerString[i] == 'A')                {       reverse += 'T'; }
+               else if(kmerString[i] == 'T'){  reverse += 'A'; }
+               else if(kmerString[i] == 'G'){  reverse += 'C'; }
+               else if(kmerString[i] == 'C'){  reverse += 'G'; }
+               else                                            {       reverse += 'N'; }
+       }
+       
+       int reverseNumber = getKmerNumber(reverse, 0);
+       
+       return reverseNumber;
+       
+}
 
 /**************************************************************************************************/