| #include <stdio.h> |
| #include "dp.h" |
| #include "mltaln.h" |
| |
| int commonAlloc1 = 0; |
| int commonAlloc2 = 0; |
| int **commonIP = NULL; |
| int **commonJP = NULL; |
| |
| char modelname[100]; |
| int njob, nlenmax; |
| int amino_n[0x80]; |
| char amino_grp[0x80]; |
| int amino_dis[0x80][0x80]; |
| int amino_disLN[0x80][0x80]; |
| double amino_dis_consweight_multi[0x80][0x80]; |
| int n_dis[26][26]; |
| int n_disFFT[26][26]; |
| float n_dis_consweight_multi[26][26]; |
| char amino[26]; |
| double polarity[20]; |
| double volume[20]; |
| int ribosumdis[37][37]; |
| |
| int ppid; |
| double thrinter; |
| double fastathreshold; |
| int pslocal, ppslocal; |
| int constraint; |
| int divpairscore; |
| int fmodel; // 1-> fmodel 0->default -1->raw |
| int nblosum; // 45, 50, 62, 80 |
| int kobetsubunkatsu; |
| int bunkatsu; |
| int dorp; |
| int niter; |
| int contin; |
| int calledByXced; |
| int devide; |
| int scmtd; |
| int weight; |
| int utree; |
| int tbutree; |
| int refine; |
| int check; |
| double cut; |
| int cooling; |
| int penalty, ppenalty, penaltyLN; |
| int RNApenalty, RNAppenalty; |
| int RNApenalty_ex, RNAppenalty_ex; |
| int penalty_ex, ppenalty_ex, penalty_exLN; |
| int penalty_EX, ppenalty_EX; |
| int penalty_OP, ppenalty_OP; |
| int RNAthr, RNApthr; |
| int offset, poffset, offsetLN, offsetFFT; |
| int scoremtx; |
| int TMorJTT; |
| char use_fft; |
| char force_fft; |
| int nevermemsave; |
| int fftscore; |
| int fftWinSize; |
| int fftThreshold; |
| int fftRepeatStop; |
| int fftNoAnchStop; |
| int divWinSize; |
| int divThreshold; |
| int disp; |
| int outgap; |
| char alg; |
| int cnst; |
| int mix; |
| int tbitr; |
| int tbweight; |
| int tbrweight; |
| int disopt; |
| int pamN; |
| int checkC; |
| float geta2; |
| int treemethod; |
| int kimuraR; |
| char *swopt; |
| int fftkeika; |
| int score_check; |
| int makedistmtx; |
| char *inputfile; |
| int rnakozo; |
| char rnaprediction; |
| |
| char *signalSM; |
| FILE *prep_g; |
| FILE *trap_g; |
| char **seq_g; |
| char **res_g; |
| |
| float consweight_multi = 1.0; |
| float consweight_rna = 0.0; |
| char RNAscoremtx = 'n'; |