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1 #include <stdio.h>
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2 #include <stdlib.h>
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3 #include <string.h>
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4 #include <ctype.h>
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5 #include <inttypes.h>
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6 #include "structs.h"
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7 #include "commonFunctions.h"
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8
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9 int seq2word(char* buf, int wsize, word* w) {
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10 int i;
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11 int b = 6;
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12 memset(w, 0, sizeof(word));
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13
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14 for (i = 0; i < wsize; i++) {
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15 if (buf[i] >= 4)
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16 return -1;
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17 w->b[i / 4] |= buf[i] << b;
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18 b -= 2;
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19 if (b < 0)
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20 b = 6;
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21 }
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22 return 0;
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23 }
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24
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25 void skipIDLine(FILE *fIn) {
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26 char c;
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27 // first line (skip ID fasta Line)
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28 c = fgetc(fIn);
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29 while (c != '\n')
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30 c = fgetc(fIn);
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31 }
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32
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33 int letterToIndex(char c) {
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34 // coding (a=0,c=1,g=2,t=3,'>'=4 others=9 )
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35 switch (c) {
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36 case 'A':
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37 return 0;
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38 case 'C':
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39 return 1;
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40 case 'G':
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41 return 2;
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42 case 'T':
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43 return 3;
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44 case '>':
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45 return 4;
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46 default:
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47 return 9;
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48 }
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49 }
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50
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51 int wordcmp(unsigned char *w1, unsigned char *w2, int n) {
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52
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53 int i = 0, limit;
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54
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55 if(n%4 != 0){
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56 w1[n/4] = w1[n/4] >> (2*(3-((n-1)%4)));
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57 w1[n/4] = w1[n/4] << (2*(3-((n-1)%4)));
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58 w2[n/4] = w2[n/4] >> (2*(3-((n-1)%4)));
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59 w2[n/4] = w2[n/4] << (2*(3-((n-1)%4)));
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60 limit=(n/4)+1;
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61 } else {
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62 limit = n/4;
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63 }
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64
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65 for (i=0;i<limit;i++) {
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66 if (w1[i]<w2[i]) return -1;
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67 if (w1[i]>w2[i]) return +1;
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68 }
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69 return 0;
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70 }
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71
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72 void showWord(word* w, char *ws) {
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73 char Alf[] = { 'A', 'C', 'G', 'T' };
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74 int i;
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75 int wsize = 8;
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76 unsigned char c;
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77 for (i = 0; i < wsize; i++) {
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78 c = w->b[i];
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79 c = c >> 6;
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80 ws[4*i] = Alf[(int) c];
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81 c = w->b[i];
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82 c = c << 2;
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83 c = c >> 6;
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84 ws[4*i+1] = Alf[(int) c];
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85 c = w->b[i];
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86 c = c << 4;
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87 c = c >> 6;
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88 ws[4*i+2] = Alf[(int) c];
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89 c = w->b[i];
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90 c = c << 6;
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91 c = c >> 6;
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92 ws[4*i+3] = Alf[(int) c];
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93 }
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94 }
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