1 #include <stdio.h>
2 #include "dp.h"
3 #include "mltaln.h"
4
5 int TLS commonAlloc1 = 0;
6 int TLS commonAlloc2 = 0;
7 int TLS **commonIP = NULL;
8 int TLS **commonJP = NULL;
9 int nthread = 1;
10 int randomseed = 0;
11 int parallelizationstrategy = BAATARI1;
12
13
14 char modelname[500];
15 int njob, nlenmax;
16 int amino_n[0x80];
17 char amino_grp[0x80];
18 int amino_dis[0x80][0x80];
19 double **n_disLN;
20 double amino_dis_consweight_multi[0x80][0x80];
21 int **n_dis;
22 int **n_disFFT;
23 double **n_dis_consweight_multi;
24 char amino[0x80];
25 double polarity[0x80];
26 double volume[0x80];
27 int ribosumdis[37][37];
28
29 int ppid;
30 double thrinter;
31 double fastathreshold;
32 int pslocal, ppslocal;
33 int constraint;
34 int divpairscore;
35 int fmodel; // 1-> fmodel 0->default -1->raw
36 int nblosum; // 45, 50, 62, 80
37 int kobetsubunkatsu;
38 int bunkatsu;
39 int dorp;
40 int niter;
41 int contin;
42 int calledByXced;
43 int devide;
44 int scmtd;
45 int weight;
46 int utree;
47 int tbutree;
48 int refine;
49 int check;
50 double cut;
51 int cooling;
52 int trywarp = 0;
53 int penalty, ppenalty, penaltyLN;
54 int penalty_dist, ppenalty_dist;
55 int RNApenalty, RNAppenalty;
56 int RNApenalty_ex, RNAppenalty_ex;
57 int penalty_ex, ppenalty_ex, penalty_exLN;
58 int penalty_EX, ppenalty_EX;
59 int penalty_OP, ppenalty_OP;
60 int penalty_shift, ppenalty_shift;
61 double penalty_shift_factor = 100.0;
62 int RNAthr, RNApthr;
63 int offset, poffset, offsetLN, offsetFFT;
64 int scoremtx;
65 int TMorJTT;
66 char use_fft;
67 char force_fft;
68 int nevermemsave;
69 int fftscore;
70 int fftWinSize;
71 int fftThreshold;
72 int fftRepeatStop;
73 int fftNoAnchStop;
74 int divWinSize;
75 int divThreshold;
76 int disp;
77 int outgap = 1;
78 char alg;
79 int cnst;
80 int mix;
81 int tbitr;
82 int tbweight;
83 int tbrweight;
84 int disopt;
85 int pamN;
86 int checkC;
87 double geta2;
88 int treemethod;
89 int kimuraR;
90 char *swopt;
91 int fftkeika;
92 int score_check;
93 int makedistmtx;
94 char *inputfile;
95 char *addfile;
96 int addprofile = 1;
97 int rnakozo;
98 char rnaprediction;
99 int scoreout = 0;
100 int spscoreout = 0;
101 int outnumber = 0;
102 int legacygapcost = 0;
103 double minimumweight = 0.0005;
104
105 char *signalSM;
106 FILE *prep_g;
107 FILE *trap_g;
108 char **seq_g;
109 char **res_g;
110
111 double consweight_multi = 1.0;
112 double consweight_rna = 0.0;
113 char RNAscoremtx = 'n';
114
115 char TLS *newgapstr = "-";
116
117 int nalphabets = 26;
118 int nscoredalphabets = 20;
119
120 double specificityconsideration = 0.0;
121 int ndistclass = 10;
122 int maxdistclass = -1;
123
124 int gmsg = 0;
125
126 double sueff_global = SUEFF;
127
initglobalvariables()128 void initglobalvariables()
129 {
130 commonAlloc1 = 0;
131 commonAlloc2 = 0;
132 commonIP = NULL;
133 commonJP = NULL;
134 nthread = 1;
135 randomseed = 0;
136 parallelizationstrategy = BAATARI1;
137
138 trywarp = 0;
139 penalty_shift_factor = 100.0;
140 outgap = 1;
141 addprofile = 1;
142 scoreout = 0;
143 outnumber = 0;
144 legacygapcost = 0;
145 consweight_multi = 1.0;
146 consweight_rna = 0.0;
147 RNAscoremtx = 'n';
148
149 newgapstr = "-";
150
151 nalphabets = 26;
152 nscoredalphabets = 20;
153
154 specificityconsideration = 0.0;
155 ndistclass = 10;
156 maxdistclass = -1;
157
158 gmsg = 0;
159 }
160