1 /*
2 * hhbiterbimatrix-inl.h
3 *
4 * Created on: Jun 16, 2014
5 * Author: meiermark
6 */
7
8 #ifndef HHBITERBIMATRIX_INL_H_
9 #define HHBITERBIMATRIX_INL_H_
10
11
hasCellOff()12 inline bool ViterbiMatrix::ViterbiMatrix::hasCellOff(){
13 return this->cellOff;
14 }
15
16
getRow(int row)17 inline unsigned char * ViterbiMatrix::ViterbiMatrix::getRow(int row){
18 return this->bCO_MI_DG_IM_GD_MM_vec[row];
19 }
20
21
setCellOff(bool value)22 inline void ViterbiMatrix::setCellOff(bool value){
23 this->cellOff = value;
24 }
25
26
setCellOff(int row,int col,int elem,bool value)27 inline void ViterbiMatrix::setCellOff(int row,int col,int elem,bool value){
28 if(value){
29 BIT_SET(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem],7);
30 this->setCellOff(true);
31 }else{
32 BIT_CLEAR(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem], 7);
33 }
34 }
35
setMatIns(int row,int col,int elem,bool value)36 inline void ViterbiMatrix::setMatIns(int row,int col,int elem,bool value){
37 if(value){
38 BIT_SET(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem],6);
39 }else{
40 BIT_CLEAR(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem], 6);
41 }
42 }
43
setDelGap(int row,int col,int elem,bool value)44 inline void ViterbiMatrix::setDelGap(int row,int col,int elem,bool value){
45 if(value){
46 BIT_SET(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem],5);
47 }else{
48 BIT_CLEAR(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem], 5);
49 }
50 }
51
setInsMat(int row,int col,int elem,bool value)52 inline void ViterbiMatrix::setInsMat(int row,int col,int elem,bool value){
53 if(value){
54 BIT_SET(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem],4);
55 }else{
56 BIT_CLEAR(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem], 4);
57 }
58 }
59
setGapDel(int row,int col,int elem,bool value)60 inline void ViterbiMatrix::setGapDel(int row,int col,int elem,bool value){
61 if(value){
62 BIT_SET(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem],3);
63 }else{
64 BIT_CLEAR(this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem], 3);
65 }
66 }
67
68
setMatMat(int row,int col,int elem,unsigned char value)69 inline void ViterbiMatrix::setMatMat(int row,int col,int elem,unsigned char value){
70 //0xF8 11111000
71 // this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem]&=(0xF8 ^ value);
72 unsigned char c = 0xF8;
73 this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem] =
74 (this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem] & c) | value;
75 }
76
getCellOff(int row,int col,int elem)77 inline bool ViterbiMatrix::getCellOff(int row,int col,int elem){
78 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
79 return (bool) (vCO_MI_DG_GD_MM & 128);
80 }
81
82
getMatIns(int row,int col,int elem)83 inline bool ViterbiMatrix::getMatIns(int row,int col,int elem){
84 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
85 return (bool) (vCO_MI_DG_GD_MM & 64);
86 }
87
88
getDelGap(int row,int col,int elem)89 inline bool ViterbiMatrix::getDelGap(int row,int col,int elem){
90 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
91 return (bool) (vCO_MI_DG_GD_MM & 32);
92 }
93
94
getInsMat(int row,int col,int elem)95 inline bool ViterbiMatrix::getInsMat(int row,int col,int elem){
96 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
97 return (bool) (vCO_MI_DG_GD_MM & 16);
98 }
99
100
getGapDel(int row,int col,int elem)101 inline bool ViterbiMatrix::getGapDel(int row,int col,int elem){
102 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
103 return (bool) (vCO_MI_DG_GD_MM & 8);
104 }
105
106
getMatMat(int row,int col,int elem)107 inline int ViterbiMatrix::getMatMat(int row,int col,int elem){
108 unsigned char vCO_MI_DG_GD_MM=this->bCO_MI_DG_IM_GD_MM_vec[row][(col*VECSIZE_FLOAT)+elem];
109 return (int) (vCO_MI_DG_GD_MM & 7);
110 }
111
printCellOff(int row_size,int col_size,int elem)112 inline void ViterbiMatrix::printCellOff(int row_size,int col_size,int elem){
113 for(int row = 0; row < row_size; row++){
114 for(int col = 0; col < col_size;col++){
115 std::cout << getCellOff(row,col,elem) << " ";
116 }
117 std::cout << std::endl;
118 }
119 }
120
121 #endif /* HHBITERBIMATRIX_INL_H_ */
122