| 1 | #include <stdio.h> |
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| 2 | #include "dp.h" |
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| 3 | #include "mltaln.h" |
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| 4 | |
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| 5 | int TLS commonAlloc1 = 0; |
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| 6 | int TLS commonAlloc2 = 0; |
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| 7 | int TLS **commonIP = NULL; |
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| 8 | int TLS **commonJP = NULL; |
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| 9 | int nthread = 1; |
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| 10 | int randomseed = 0; |
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| 11 | int parallelizationstrategy = BAATARI1; |
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| 12 | |
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| 13 | |
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| 14 | char modelname[100]; |
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| 15 | int njob, nlenmax; |
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| 16 | int amino_n[0x80]; |
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| 17 | char amino_grp[0x80]; |
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| 18 | int amino_dis[0x80][0x80]; |
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| 19 | int amino_disLN[0x80][0x80]; |
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| 20 | double amino_dis_consweight_multi[0x80][0x80]; |
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| 21 | int n_dis[26][26]; |
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| 22 | int n_disFFT[26][26]; |
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| 23 | float n_dis_consweight_multi[26][26]; |
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| 24 | char amino[26]; |
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| 25 | double polarity[20]; |
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| 26 | double volume[20]; |
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| 27 | int ribosumdis[37][37]; |
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| 28 | |
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| 29 | int ppid; |
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| 30 | double thrinter; |
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| 31 | double fastathreshold; |
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| 32 | int pslocal, ppslocal; |
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| 33 | int constraint; |
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| 34 | int divpairscore; |
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| 35 | int fmodel; // 1-> fmodel 0->default -1->raw |
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| 36 | int nblosum; // 45, 50, 62, 80 |
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| 37 | int kobetsubunkatsu; |
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| 38 | int bunkatsu; |
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| 39 | int dorp; |
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| 40 | int niter; |
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| 41 | int contin; |
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| 42 | int calledByXced; |
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| 43 | int devide; |
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| 44 | int scmtd; |
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| 45 | int weight; |
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| 46 | int utree; |
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| 47 | int tbutree; |
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| 48 | int refine; |
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| 49 | int check; |
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| 50 | double cut; |
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| 51 | int cooling; |
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| 52 | int penalty, ppenalty, penaltyLN; |
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| 53 | int RNApenalty, RNAppenalty; |
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| 54 | int RNApenalty_ex, RNAppenalty_ex; |
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| 55 | int penalty_ex, ppenalty_ex, penalty_exLN; |
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| 56 | int penalty_EX, ppenalty_EX; |
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| 57 | int penalty_OP, ppenalty_OP; |
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| 58 | int RNAthr, RNApthr; |
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| 59 | int offset, poffset, offsetLN, offsetFFT; |
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| 60 | int scoremtx; |
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| 61 | int TMorJTT; |
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| 62 | char use_fft; |
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| 63 | char force_fft; |
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| 64 | int nevermemsave; |
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| 65 | int fftscore; |
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| 66 | int fftWinSize; |
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| 67 | int fftThreshold; |
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| 68 | int fftRepeatStop; |
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| 69 | int fftNoAnchStop; |
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| 70 | int divWinSize; |
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| 71 | int divThreshold; |
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| 72 | int disp; |
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| 73 | int outgap = 1; |
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| 74 | char alg; |
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| 75 | int cnst; |
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| 76 | int mix; |
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| 77 | int tbitr; |
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| 78 | int tbweight; |
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| 79 | int tbrweight; |
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| 80 | int disopt; |
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| 81 | int pamN; |
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| 82 | int checkC; |
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| 83 | float geta2; |
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| 84 | int treemethod; |
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| 85 | int kimuraR; |
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| 86 | char *swopt; |
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| 87 | int fftkeika; |
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| 88 | int score_check; |
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| 89 | int makedistmtx; |
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| 90 | char *inputfile; |
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| 91 | char *addfile; |
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| 92 | int addprofile = 1; |
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| 93 | int rnakozo; |
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| 94 | char rnaprediction; |
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| 95 | int scoreout = 0; |
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| 96 | int outnumber = 0; |
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| 97 | |
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| 98 | char *signalSM; |
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| 99 | FILE *prep_g; |
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| 100 | FILE *trap_g; |
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| 101 | char **seq_g; |
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| 102 | char **res_g; |
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| 103 | |
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| 104 | float consweight_multi = 1.0; |
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| 105 | float consweight_rna = 0.0; |
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| 106 | char RNAscoremtx = 'n'; |
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| 107 | |
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| 108 | char TLS *newgapstr = "-"; |
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