X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmer.cpp;h=50574f4a5ee0709daf2ebb67b8f0e49971e20ef0;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=dcb6475161ce6f29f89d746fa1581ca7cab380c4;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/kmer.cpp b/kmer.cpp
index dcb6475..50574f4 100644
--- 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;
+	
+}
 
 /**************************************************************************************************/