Created
November 28, 2010 16:57
-
-
Save Schabernack/719089 to your computer and use it in GitHub Desktop.
alignment
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import java.util.Arrays; | |
public class alignment { | |
public static int D= 1; | |
public static int MATCH = 2; | |
public static int MISMATCH = -1; | |
public static void main(String[] args){ | |
//int[][] foo = computeMatrix(Sequenzen.NP_000913, Sequenzen.NP_246273); | |
int[][] bar = computeMatrix("IVVGSAAHCYGEDN", "IVLTAAHCVSASGEHN"); | |
//System.out.println(foo[1][1]); | |
System.out.println(bar[1][1]); | |
} | |
public static int[][] computeMatrix(String seq1, String seq2){ | |
int[][] matrix = new int[seq1.length()+1][seq2.length()+1]; | |
for(int i = seq1.length()-1; i>0; i--){ | |
for(int j=seq2.length()-1; j>0; j--){ | |
matrix[i][j] = max(matrix, i, j, seq1, seq2); | |
} | |
} | |
return matrix; | |
} | |
public static int max(int[][] matrix, int i, int j, String seq1, String seq2){ | |
char[] a = StringToArray(seq1); | |
char[] b = StringToArray(seq2); | |
int [] foo = {matrix[i+1][j+1]+s(matrix, a, b, i, j), matrix[i+1][j] -D , matrix[i][j+1] -D}; | |
Arrays.sort(foo); | |
return foo[foo.length-1]; | |
} | |
public static char[] StringToArray(String s){ | |
char[] foo = new char[s.length()+1]; | |
for(int i=0; i<s.length();i++){ | |
foo[i+1] = s.charAt(i); | |
} | |
return foo; | |
} | |
private static int s(int[][] matrix, char[] t1Array, char[] t2Array, int i, int j) { | |
int hier; | |
if(t1Array[i] == t2Array[j]) | |
hier = matrix[i+1][j+1] + MATCH; | |
else | |
hier = matrix[i+1][j+1] + MISMATCH; | |
return hier; | |
} | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment