X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=kmer.cpp;fp=kmer.cpp;h=2c2783384c3849c2941509547d2a67b83dee6f9f;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/kmer.cpp b/kmer.cpp
new file mode 100644
index 0000000..2c27833
--- /dev/null
+++ b/kmer.cpp
@@ -0,0 +1,94 @@
+/*
+ *  kmer.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/15/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include <string>
+#include <vector>
+
+#include "kmer.hpp"
+
+/**************************************************************************************************/
+
+Kmer::Kmer(int size) : kmerSize(size) {
+	
+	int power4s[9] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536 };
+	maxKmer = power4s[kmerSize]+1;// (int)pow(4.,k)+1;
+	
+}
+
+/**************************************************************************************************/
+
+string Kmer::getKmerString(string sequence){
+	int length = sequence.length();
+	int nKmers = length - kmerSize + 1;
+	vector<int> counts(maxKmer, 0);
+	
+	for(int i=0;i<nKmers;i++){
+		int kmerNumber = getKmerNumber(sequence, i);
+		counts[kmerNumber]++;
+	}
+	
+	string kmerString = "";
+	for(int i=0;i<maxKmer;i++){
+		kmerString += getASCII(counts[i]);
+	}		
+	
+	return kmerString;	
+}
+	
+/**************************************************************************************************/
+
+int Kmer::getKmerNumber(string sequence, int index){
+	int power4s[9] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536 };
+	int kmer = 0;
+	for(int i=0;i<kmerSize;i++){
+		if(toupper(sequence[i+index]) == 'A')		{	kmer += (0 * power4s[kmerSize-i-1]);	}
+		else if(toupper(sequence[i+index]) == 'C')	{	kmer += (1 * power4s[kmerSize-i-1]);	}
+		else if(toupper(sequence[i+index]) == 'G')	{	kmer += (2 * power4s[kmerSize-i-1]);	}
+		else if(toupper(sequence[i+index]) == 'U')	{	kmer += (3 * power4s[kmerSize-i-1]);	}
+		else if(toupper(sequence[i+index]) == 'T')	{	kmer += (3 * power4s[kmerSize-i-1]);	}
+		else if(toupper(sequence[i+index]) == 'N')	{	return (int)power4s[kmerSize];			}
+	}
+	return kmer;	
+}
+	
+/**************************************************************************************************/
+	
+string Kmer::getKmerBases(int kmerNumber){
+	int power4s[9] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536 };
+	
+	string kmer = "";
+	
+	if(kmerNumber == power4s[kmerSize]){//pow(4.,7)){	
+		for(int i=0;i<kmerSize;i++){
+			kmer += 'N';
+		}
+	}
+	else{
+		for(int i=0;i<kmerSize;i++){
+			int nt = (int)(kmerNumber / (float)power4s[i]) % 4;
+			if(nt == 0)		{	kmer = 'A' + kmer;	}
+			else if(nt == 1){	kmer = 'C' + kmer;	}
+			else if(nt == 2){	kmer = 'G' + kmer;	}
+			else if(nt == 3){	kmer = 'T' + kmer;	}
+		}
+	}
+	return kmer;
+}
+
+/**************************************************************************************************/
+
+char Kmer::getASCII(int number)		{	return (char)(33+number);			}
+
+/**************************************************************************************************/
+
+int Kmer::getNumber(char character)	{	return ((int)(character-'!'));		}
+
+/**************************************************************************************************/