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/*
kalign2_string_matching.c
Released under GPL - see the 'COPYING' file
Copyright (C) 2006 Timo Lassmann <timolassmann@gmail.com>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Please send bug reports, comments etc. to:
timolassmann@gmail.com
*/
#include <string.h>
int byg_detect(int* text,int n)
{
int Tc;
int i = 0;
int s = 0;
int T[256];
for (i = 0;i < 256;i++){
T[i] = 0;
}
int mb = 1;
//char *unique_aa = "EFILPQXZ";//permissiv
//ABCDEFGHIJKLMNOPQRSTUVWXYZ
char *unique_aa = "BDEFHIJKLMNOPQRSVWYZ";//restrictive
int aacode[26] = {0,1,2,3,4,5,6,7,8,-1,9,10,11,12,23,13,14,15,16,17,17,18,19,20,21,22};
for (i= 0;i < 20;i++){
T[(int)aacode[unique_aa[i]-65]] |= 1;
}
for (i = 0;i < n;i++){
// fprintf(stderr,"%d\n",text[i]);
if(text[i] != -1){
s <<= 1;
s |= 1;
Tc = T[text[i]];
s &= Tc;
if(s & mb){
return 0;
}
}
}
return 1;
}
int check_identity(char* n,char*m)
{
int len_n;
int len_m;
int i;
len_n = strlen(n);
len_m = strlen(m);
if(len_m != len_n){
return -1;
}
for (i = 0; i < len_n;i++){
if(n[i] != m[i]){
return -1;
}
}
return 1;
}
int byg_count(char* pattern,char*text)
{
int Tc;
int count = 0;
int i = 0;
int s = 0;
int T[256];
for (i = 0;i < 256;i++){
T[i] = 0;
}
int m = strlen(pattern);
int n = strlen (text);
int mb = (1 << (m-1));
for (i= 0;i < m;i++){
T[(int)pattern[i]] |= (1 << i);
}
for (i = 0;i < n;i++){
s <<= 1;
s |= 1;
Tc = T[(int)text[i]];
s &= Tc;
if(s & mb){
count++;
}
}
return count;
}
int byg_end(char* pattern,char*text)
{
int Tc;
int i = 0;
int s = 0;
int T[256];
for (i = 0;i < 256;i++){
T[i] = 0;
}
int m = strlen(pattern);
int n = strlen (text);
int mb = (1 << (m-1));
for (i= 0;i < m;i++){
T[(int)pattern[i]] |= (1 << i);
}
for (i = 0;i < n;i++){
s <<= 1;
s |= 1;
if(!text[i]){
return -1;
}
Tc = T[(int)text[i]];
s &= Tc;
if(s & mb){
return i+1;
}
}
return -1;
}
int byg_start(char* pattern,char*text)
{
int Tc;
int i = 0;
int s = 0;
int T[256];
for (i = 0;i < 256;i++){
T[i] = 0;
}
int m = strlen(pattern);
int n = strlen(text);
int mb = (1 << (m-1));
for (i= 0;i < m;i++){
T[(int)pattern[i]] |= (1 << i);
}
for (i = 0;i < n;i++){
s <<= 1;
s |= 1;
Tc = T[(int)text[i]];
s &= Tc;
if(s & mb){
return i-m+1;
}
}
return -1;
}
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