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annotate mafft/core/mltaln.h @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #define USE_XCED 0
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2
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3 #if USE_XCED
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4 #include "config.h"
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5 #include "share.h"
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6 #else
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7 #endif
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8
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9 #include "mafft.h"
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10 #include <stdio.h>
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11 #include <stdlib.h>
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12 #include <stddef.h>
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13 #include <sys/types.h>
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14 #include <string.h>
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15 #include <unistd.h>
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16 #include <math.h>
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17 #include <ctype.h>
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18 #include "mtxutl.h"
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19 #include <float.h>
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20 #include <stdarg.h>
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21 #ifdef enablemultithread
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22 #include <pthread.h>
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23 #endif
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24
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25 #define VERSION "7.221"
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26 #define SHOWVERSION reporterr( "%s (%s) Version " VERSION " alg=%c, model=%s, amax=%3.1f\n%d thread(s)\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )
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27
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28 #define FFT_THRESHOLD 80
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29 #define FFT_WINSIZE_P 20
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30 #define FFT_WINSIZE_D 100
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31 #define DISPSEQF 60
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32 #define DISPSITEI 0
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33 #define MAXITERATION 500
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34 #define M 500000 /* njob no saidaiti */
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35 #define N 5000000 /* nlen no saidaiti */
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36 #define MAXSEG 100000
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37 #define B 256
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38 #define C 60 /* 1 gyou no mojisuu */
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39 #define D 6
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40 #define rnd() ( ( 1.0 / ( RAND_MAX + 1.0 ) ) * rand() )
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41 #define MAX(X,Y) ( ((X)>(Y))?(X):(Y) )
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42 #define MIN(X,Y) ( ((X)<(Y))?(X):(Y) )
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43 #define G(X) ( ((X)>(0))?(X):(0) )
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44 #define BEFF 1.0 /* 0.6 ni suruto zureru */
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45 #define WIN 3
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46 #define SGAPP -1000
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47 #define GETA2 0.001
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48 #define GETA3 0.001
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49 #define NOTSPECIFIED 100009
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50 #define SUEFF 0.1 /* upg/(spg+upg) -> sueff.sed */
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51 #define DIVLOCAL 0
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52 #define INTMTXSCALE 1000000.0
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53 #define JTT 201
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54 #define TM 202
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55
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56 extern char modelname[500];
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57 extern int njob, nlenmax;
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58 extern int amino_n[0x80];
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59 extern char amino_grp[0x80];
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60 extern int amino_dis[0x80][0x80];
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61 extern double **n_disLN;
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62 extern double amino_dis_consweight_multi[0x80][0x80];
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63 extern int **n_dis;
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64 extern int **n_disFFT;
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65 extern double **n_dis_consweight_multi;
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66 extern char amino[0x80];
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67 extern double polarity[0x80];
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68 extern double volume[0x80];
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69 extern int ribosumdis[37][37];
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70
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71 extern int ppid;
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72 extern double thrinter;
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73 extern double fastathreshold;
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74 extern int pslocal, ppslocal;
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75 extern int constraint;
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76 extern int divpairscore;
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77 extern int fmodel; // 1-> fmodel 0->default -1->raw
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78 extern int nblosum; // 45, 50, 62, 80
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79 extern int kobetsubunkatsu;
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80 extern int bunkatsu;
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81 extern int dorp;
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82 extern int niter;
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83 extern int contin;
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84 extern int calledByXced;
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85 extern int devide;
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86 extern int scmtd;
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87 extern int weight;
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88 extern int utree;
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89 extern int tbutree;
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90 extern int refine;
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91 extern int check;
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92 extern double cut;
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93 extern int cooling;
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94 extern int trywarp;
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95 extern int penalty, ppenalty, penaltyLN;
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96 extern int penalty_dist, ppenalty_dist;
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97 extern int RNApenalty, RNAppenalty;
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98 extern int RNApenalty_ex, RNAppenalty_ex;
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99 extern int penalty_ex, ppenalty_ex, penalty_exLN;
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100 extern int penalty_EX, ppenalty_EX;
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101 extern int penalty_OP, ppenalty_OP;
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102 extern int penalty_shift;
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103 extern double penalty_shift_factor;
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104 extern int offset, poffset, offsetLN, offsetFFT;
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105 extern int RNAthr, RNApthr;
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106 extern int scoremtx;
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107 extern int TMorJTT;
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108 extern char use_fft;
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109 extern char force_fft;
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110 extern int nevermemsave;
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111 extern int fftscore;
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112 extern int fftWinSize;
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113 extern int fftThreshold;
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114 extern int fftRepeatStop;
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115 extern int fftNoAnchStop;
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116 extern int divWinSize;
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117 extern int divThreshold;
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118 extern int disp;
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119 extern int outgap;
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120 extern char alg;
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121 extern int cnst;
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122 extern int mix;
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123 extern int tbitr;
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124 extern int tbweight;
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125 extern int tbrweight;
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126 extern int disopt;
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127 extern int pamN;
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128 extern int checkC;
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129 extern float geta2;
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130 extern int treemethod;
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131 extern int kimuraR;
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132 extern char *swopt;
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133 extern int fftkeika;
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134 extern int score_check;
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135 extern char *inputfile;
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136 extern char *addfile;
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137 extern int addprofile;
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138 extern float consweight_multi;
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139 extern float consweight_rna;
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140 extern char RNAscoremtx;
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141
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142 extern char *signalSM;
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143 extern FILE *prep_g;
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144 extern FILE *trap_g;
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145 extern char **seq_g;
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146 extern char **res_g;
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147 extern int rnakozo;
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148 extern char rnaprediction;
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149
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150 /* sengen no ichi ha koko dake de ha nai */
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151 extern void constants();
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152 extern char **Calignm1();
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153 extern char **Dalignm1();
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154 extern char **align0();
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155 extern double Cscore_m_1( char **, int, int, double ** );
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156 extern double score_m_1( char **, int, int, double ** );
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157 extern double score_calc0( char **, int, double **, int );
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158 extern char seqcheck( char ** );
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159 extern float substitution( char *, char * );
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160 extern float substitution_score( char *, char * );
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161 extern float substitution_nid( char *, char * );
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162 extern float substitution_hosei( char *, char * );
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163 extern double ipower( double, int );
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164 extern float translate_and_Calign();
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165 extern float A__align();
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166 extern float A__align11();
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167 extern float A__align_gapmap();
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168 extern float partA__align();
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169 extern float L__align11( double **scoringmtx, float scoreoffset, char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
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170 extern float G__align11();
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171 extern float Falign();
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172 extern float Falign_localhom();
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173 extern float Conalign();
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174 extern float Aalign();
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175 extern float imp_match_out_sc( int, int );
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176 extern float part_imp_match_out_sc( int, int );
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177 extern void ErrorExit();
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178 extern void cpmx_calc();
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179 extern void intergroup_score( char **, char **, double *, double *, int, int, int, double * );
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180 extern int conjuctionfortbfast();
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181 extern int fastconjuction();
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182 extern char seqcheck( char ** );
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183
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184 typedef struct _LocalHom
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185 {
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186 int nokori;
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187 struct _LocalHom *next;
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188 struct _LocalHom *last;
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189 int start1;
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190 int end1;
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191 int start2;
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192 int end2;
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193 double opt;
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194 int overlapaa;
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195 int extended;
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196 double importance;
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197 float fimportance;
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198 double wimportance;
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199 char korh;
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200 } LocalHom;
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201
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202 typedef struct _NodeInCub
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203 {
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204 int step;
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205 int LorR;
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206 } NodeInCub;
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207
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208 typedef struct _Node
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209 {
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210 struct _Node *children[3];
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211 int tmpChildren[3];
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212 double length[3];
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213 double *weightptr[3];
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214 int top[3];
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215 int *members[3];
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216 } Node;
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217
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218 typedef struct _Segment
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219 {
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220 int start;
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221 int end;
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222 int center;
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223 double score;
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224 int skipForeward;
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225 int skipBackward;
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226 struct _Segment *pair;
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227 int number;
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228 } Segment;
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229
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230 typedef struct _Segments
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231 {
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232 Segment group1;
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233 Segment group2;
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234 int number1;
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235 int number2;
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236 } Segments;
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237
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238 typedef struct _Bchain
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239 {
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240 struct _Bchain *next;
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241 struct _Bchain *prev;
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242 int pos;
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243 } Bchain;
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244
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245 typedef struct _Achain
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246 {
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247 int next;
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248 int prev;
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249 // int curr;
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250 } Achain;
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251
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252
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253 typedef struct _Fukusosuu
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254 {
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255 double R;
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256 double I;
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257 } Fukusosuu;
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258
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259 typedef struct _Gappattern
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260 {
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261 int len;
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262 float freq;
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263 } Gappat;
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264
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265 typedef struct _RNApair
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266 {
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267 int uppos;
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268 float upscore;
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269 int downpos;
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270 float downscore;
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271 int bestpos;
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272 float bestscore;
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273 } RNApair;
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274
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275 typedef struct _Treedep
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276 {
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277 int child0;
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278 int child1;
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279 int done;
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280 float distfromtip;
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281 } Treedep;
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282
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283 typedef struct _Addtree
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284 {
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285 int nearest;
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286 float dist1;
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287 char *neighbors;
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288 float dist2;
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289 } Addtree;
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290
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291 #include "fft.h"
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292 #include "dp.h"
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293 #include "functions.h"
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294
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295 #ifdef enablemultithread
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296 #define TLS __thread
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297 #else
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298 #define TLS
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299 #endif
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300
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301 extern TLS int commonAlloc1;
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302 extern TLS int commonAlloc2;
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303 extern TLS int **commonIP;
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304 extern TLS int **commonJP;
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305 extern int nthread;
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306 extern int randomseed;
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307 extern int parallelizationstrategy;
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308 #define BESTFIRST 0
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309 #define BAATARI0 1
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310 #define BAATARI1 2
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311 #define BAATARI2 3
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312
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313 extern int scoreout;
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314 extern int spscoreout;
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315 extern int outnumber;
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316
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317 extern int legacygapcost;
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318
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319 extern TLS char *newgapstr;
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320
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321 extern int nalphabets;
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322 extern int nscoredalphabets;
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323 extern double specificityconsideration;
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324 extern int ndistclass, maxdistclass;
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325
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326 extern int gmsg;
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327
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328 extern double sueff_global;