5 int TLS commonAlloc1 = 0;
6 int TLS commonAlloc2 = 0;
7 int TLS **commonIP = NULL;
8 int TLS **commonJP = NULL;
11 int parallelizationstrategy = BAATARI1;
18 int amino_dis[0x80][0x80];
19 int amino_disLN[0x80][0x80];
20 double amino_dis_consweight_multi[0x80][0x80];
23 float n_dis_consweight_multi[26][26];
27 int ribosumdis[37][37];
31 double fastathreshold;
32 int pslocal, ppslocal;
35 int fmodel; // 1-> fmodel 0->default -1->raw
36 int nblosum; // 45, 50, 62, 80
52 int penalty, ppenalty, penaltyLN;
53 int RNApenalty, RNAppenalty;
54 int RNApenalty_ex, RNAppenalty_ex;
55 int penalty_ex, ppenalty_ex, penalty_exLN;
56 int penalty_EX, ppenalty_EX;
57 int penalty_OP, ppenalty_OP;
59 int offset, poffset, offsetLN, offsetFFT;
104 float consweight_multi = 1.0;
105 float consweight_rna = 0.0;
106 char RNAscoremtx = 'n';
108 char *newgapstr = "-";