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comparison gecko/src/dictionaryFunctions.c @ 1:35af401890c0 draft

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author bitlab
date Thu, 13 Dec 2018 07:59:25 -0500
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0:ee6b15b409e5 1:35af401890c0
1 #include <stdio.h>
2 #include <stdlib.h>
3 #include <string.h>
4 #include <ctype.h>
5 #include <inttypes.h>
6 #include "structs.h"
7 #include "commonFunctions.h"
8
9 int seq2word(char* buf, int wsize, word* w) {
10 int i;
11 int b = 6;
12 memset(w, 0, sizeof(word));
13
14 for (i = 0; i < wsize; i++) {
15 if (buf[i] >= 4)
16 return -1;
17 w->b[i / 4] |= buf[i] << b;
18 b -= 2;
19 if (b < 0)
20 b = 6;
21 }
22 return 0;
23 }
24
25 void skipIDLine(FILE *fIn) {
26 char c;
27 // first line (skip ID fasta Line)
28 c = fgetc(fIn);
29 while (c != '\n')
30 c = fgetc(fIn);
31 }
32
33 int letterToIndex(char c) {
34 // coding (a=0,c=1,g=2,t=3,'>'=4 others=9 )
35 switch (c) {
36 case 'A':
37 return 0;
38 case 'C':
39 return 1;
40 case 'G':
41 return 2;
42 case 'T':
43 return 3;
44 case '>':
45 return 4;
46 default:
47 return 9;
48 }
49 }
50
51 int wordcmp(unsigned char *w1, unsigned char *w2, int n) {
52
53 int i = 0, limit;
54
55 if(n%4 != 0){
56 w1[n/4] = w1[n/4] >> (2*(3-((n-1)%4)));
57 w1[n/4] = w1[n/4] << (2*(3-((n-1)%4)));
58 w2[n/4] = w2[n/4] >> (2*(3-((n-1)%4)));
59 w2[n/4] = w2[n/4] << (2*(3-((n-1)%4)));
60 limit=(n/4)+1;
61 } else {
62 limit = n/4;
63 }
64
65 for (i=0;i<limit;i++) {
66 if (w1[i]<w2[i]) return -1;
67 if (w1[i]>w2[i]) return +1;
68 }
69 return 0;
70 }
71
72 void showWord(word* w, char *ws) {
73 char Alf[] = { 'A', 'C', 'G', 'T' };
74 int i;
75 int wsize = 8;
76 unsigned char c;
77 for (i = 0; i < wsize; i++) {
78 c = w->b[i];
79 c = c >> 6;
80 ws[4*i] = Alf[(int) c];
81 c = w->b[i];
82 c = c << 2;
83 c = c >> 6;
84 ws[4*i+1] = Alf[(int) c];
85 c = w->b[i];
86 c = c << 4;
87 c = c >> 6;
88 ws[4*i+2] = Alf[(int) c];
89 c = w->b[i];
90 c = c << 6;
91 c = c >> 6;
92 ws[4*i+3] = Alf[(int) c];
93 }
94 }