1 #include "myutils.h"
2 #include "alpha.h"
3 #include "timing.h"
4
isgap(byte c)5 bool isgap(byte c)
6 {
7 return c == '-' || c == '.';
8 }
9
WordToStrAmino(unsigned Word,unsigned WordLength)10 const char *WordToStrAmino(unsigned Word, unsigned WordLength)
11 {
12 static char Str[32];
13 for (unsigned i = 0; i < WordLength; ++i)
14 {
15 unsigned Letter = Word%20;
16 Str[WordLength-i-1] = g_LetterToCharAmino[Letter];
17 Word /= 20;
18 }
19 Str[WordLength] = 0;
20 return Str;
21 }
22
WordToStrAmino2(unsigned Word,unsigned WordLength,char * Str)23 const char *WordToStrAmino2(unsigned Word, unsigned WordLength, char *Str)
24 {
25 for (unsigned i = 0; i < WordLength; ++i)
26 {
27 unsigned Letter = Word%20;
28 Str[WordLength-i-1] = g_LetterToCharAmino[Letter];
29 Word /= 20;
30 }
31 Str[WordLength] = 0;
32 return Str;
33 }
34
WordToStrNucleo(unsigned Word,unsigned WordLength)35 const char *WordToStrNucleo(unsigned Word, unsigned WordLength)
36 {
37 static char Str[32];
38 for (unsigned i = 0; i < WordLength; ++i)
39 {
40 unsigned Letter = Word%4;
41 Str[WordLength-i-1] = g_LetterToCharNucleo[Letter];
42 Word /= 4;
43 }
44 Str[WordLength] = 0;
45 return Str;
46 }
47
WordToStr(unsigned Word,unsigned WordLength,bool Nucleo)48 const char *WordToStr(unsigned Word, unsigned WordLength, bool Nucleo)
49 {
50 return (Nucleo ? WordToStrNucleo : WordToStrAmino)(Word, WordLength);
51 }
52
RevCompAlloc(const byte * Seq,unsigned L)53 byte *RevCompAlloc(const byte *Seq, unsigned L)
54 {
55 byte *RCSeq = MYALLOC(byte, L, Alpha);
56
57 for (unsigned i = 0; i < L; ++i)
58 RCSeq[L-i-1] = g_CharToCompChar[Seq[i]];
59
60 return RCSeq;
61 }
62
RevCompInPlace(byte * Seq,unsigned L)63 void RevCompInPlace(byte *Seq, unsigned L)
64 {
65 unsigned L1 = L - 1;
66 unsigned L2 = L/2;
67 for (unsigned i = 0; i < L2; ++i)
68 {
69 unsigned j = L1 - i;
70 unsigned ci = Seq[i];
71 unsigned cj = Seq[j];
72
73 unsigned ri = g_CharToCompChar[ci];
74 unsigned rj = g_CharToCompChar[cj];
75
76 Seq[i] = rj;
77 Seq[j] = ri;
78 }
79
80 if (L%2 == 1)
81 Seq[L2] = g_CharToCompChar[Seq[L2]];
82 }
83
RevComp(const byte * Seq,unsigned L,byte * RCSeq)84 void RevComp(const byte *Seq, unsigned L, byte *RCSeq)
85 {
86 for (unsigned i = 0; i < L; ++i)
87 RCSeq[L-i-1] = g_CharToCompChar[Seq[i]];
88 }
89
GetAminoCharFrom3NucChars(unsigned char c1,unsigned char c2,unsigned char c3)90 unsigned char GetAminoCharFrom3NucChars(unsigned char c1, unsigned char c2,
91 unsigned char c3)
92 {
93 unsigned Letter1 = g_CharToLetterNucleo[c1];
94 unsigned Letter2 = g_CharToLetterNucleo[c2];
95 unsigned Letter3 = g_CharToLetterNucleo[c3];
96 unsigned Word = Letter1*(4*4) + Letter2*4 + Letter3;
97
98 unsigned Letter = g_CodonWordToAminoLetter[Word];
99 return g_LetterToCharAmino[Letter];
100 }
101