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annotate mafft/core/mafft-distance.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2 #include "mtxutl.h"
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3
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4 #define DEBUG 0
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5 #define TEST 0
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6
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7 #define END_OF_VEC -1
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8
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9 static int maxl;
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10 static int tsize;
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11 static char outputformat;
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12 static float lenfaca, lenfacb, lenfacc, lenfacd;
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13 static int nadd;
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14 #define PLENFACA 0.01
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15 #define PLENFACB 10000
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16 #define PLENFACC 10000
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17 #define PLENFACD 0.1
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18 #define DLENFACA 0.01
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19 #define DLENFACB 2500
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20 #define DLENFACC 2500
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21 #define DLENFACD 0.1
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22
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23 void arguments( int argc, char *argv[] )
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24 {
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25 int c;
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26
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27 inputfile = NULL;
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28 outputformat = 's';
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29 scoremtx = 1;
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30 nblosum = 62;
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31 dorp = NOTSPECIFIED;
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32 nadd = 0;
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33 alg = 'X';
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34
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35 while( --argc > 0 && (*++argv)[0] == '-' )
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36 {
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37 while ( (c = *++argv[0]) )
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38 {
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39 switch( c )
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40 {
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41 case 'i':
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42 inputfile = *++argv;
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43 fprintf( stderr, "inputfile = %s\n", inputfile );
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44 --argc;
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45 goto nextoption;
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46 case 'I':
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47 nadd = myatoi(*++argv);
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48 if( nadd == 0 )
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49 {
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50 fprintf( stderr, "nadd = %d?\n", nadd );
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51 exit( 1 );
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52 }
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53 --argc;
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54 goto nextoption;
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55 case 'p':
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56 outputformat = 'p';
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57 break;
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58 case 'D':
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59 dorp = 'd';
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60 break;
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61 case 'P':
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62 dorp = 'p';
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63 break;
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64 default:
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65 fprintf( stderr, "illegal option %c\n", c );
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66 argc = 0;
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67 break;
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68 }
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69 }
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70 nextoption:
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71 ;
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72 }
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73 if( inputfile == NULL )
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74 {
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75 argc--;
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76 inputfile = *argv;
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77 fprintf( stderr, "inputfile = %s\n", inputfile );
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78 }
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79 if( argc != 0 )
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80 {
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81 fprintf( stderr, "Usage: mafft-distance [-PD] [-i inputfile] inputfile > outputfile\n" );
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82 exit( 1 );
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83 }
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84 }
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85
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86 void seq_grp_nuc( int *grp, char *seq )
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87 {
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88 int tmp;
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89 int *grpbk = grp;
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90 while( *seq )
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91 {
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92 tmp = amino_grp[(int)*seq++];
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93 if( tmp < 4 )
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94 *grp++ = tmp;
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95 else
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96 fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
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97 }
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98 *grp = END_OF_VEC;
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99 if( grp - grpbk < 6 )
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100 {
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101 fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
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102 // exit( 1 );
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103 *grpbk = -1;
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104 }
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105 }
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106
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107 void seq_grp( int *grp, char *seq )
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108 {
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109 int tmp;
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110 int *grpbk = grp;
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111 while( *seq )
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112 {
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113 tmp = amino_grp[(int)*seq++];
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114 if( tmp < 6 )
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115 *grp++ = tmp;
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116 else
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117 fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
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118 }
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119 *grp = END_OF_VEC;
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120 if( grp - grpbk < 6 )
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121 {
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122 fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
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123 // exit( 1 );
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124 *grpbk = -1;
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125 }
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126 }
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127
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128 void makecompositiontable_p( short *table, int *pointt )
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129 {
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130 int point;
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131
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132 while( ( point = *pointt++ ) != END_OF_VEC )
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133 table[point]++;
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134 }
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135
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136 int commonsextet_p( short *table, int *pointt )
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137 {
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138 int value = 0;
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139 short tmp;
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140 int point;
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141 static short *memo = NULL;
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142 static int *ct = NULL;
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143 static int *cp;
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144
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145 if( *pointt == -1 )
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146 return( 0 );
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147
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148 if( !memo )
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149 {
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150 memo = (short *)calloc( tsize, sizeof( short ) );
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151 if( !memo ) ErrorExit( "Cannot allocate memo\n" );
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152 ct = (int *)calloc( MIN( maxl, tsize)+1, sizeof( int ) );
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153 if( !ct ) ErrorExit( "Cannot allocate memo\n" );
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154 }
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155
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156 cp = ct;
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157 while( ( point = *pointt++ ) != END_OF_VEC )
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158 {
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159 tmp = memo[point]++;
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160 if( tmp < table[point] )
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161 value++;
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162 if( tmp == 0 ) *cp++ = point;
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163 // fprintf( stderr, "cp - ct = %d (tsize = %d)\n", cp - ct, tsize );
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164 }
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165 *cp = END_OF_VEC;
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166
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167 cp = ct;
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168 while( *cp != END_OF_VEC )
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169 memo[*cp++] = 0;
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170
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171 return( value );
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172 }
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173
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174 void makepointtable_nuc( int *pointt, int *n )
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175 {
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176 int point;
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177 register int *p;
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178
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179 if( *n == -1 )
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180 {
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181 *pointt = -1;
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182 return;
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183 }
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184
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185 p = n;
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186 point = *n++ * 1024;
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187 point += *n++ * 256;
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188 point += *n++ * 64;
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189 point += *n++ * 16;
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190 point += *n++ * 4;
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191 point += *n++;
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192 *pointt++ = point;
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193
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194 while( *n != END_OF_VEC )
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195 {
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196 point -= *p++ * 1024;
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197 point *= 4;
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198 point += *n++;
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199 *pointt++ = point;
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200 }
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201 *pointt = END_OF_VEC;
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202 }
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203
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204 void makepointtable( int *pointt, int *n )
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205 {
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206 int point;
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207 register int *p;
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208
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209 if( *n == -1 )
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210 {
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211 *pointt = -1;
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212 return;
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213 }
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214
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215 p = n;
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216 point = *n++ * 7776;
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217 point += *n++ * 1296;
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218 point += *n++ * 216;
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219 point += *n++ * 36;
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220 point += *n++ * 6;
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221 point += *n++;
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222 *pointt++ = point;
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223
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224 while( *n != END_OF_VEC )
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225 {
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226 point -= *p++ * 7776;
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227 point *= 6;
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228 point += *n++;
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229 *pointt++ = point;
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230 }
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231 *pointt = END_OF_VEC;
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232 }
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233
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234 int main( int argc, char **argv )
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235 {
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236 int i, j, initj;
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237 FILE *infp;
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238 char **seq;
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239 int *grpseq;
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240 char *tmpseq;
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241 int **pointt;
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242 static char **name;
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243 static int *nlen;
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244 double *mtxself;
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245 float score;
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246 static short *table1;
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247 float longer, shorter;
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248 float lenfac;
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249 float bunbo;
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250 int norg;
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251
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252 arguments( argc, argv );
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253
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254
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255 if( inputfile )
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256 {
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257 infp = fopen( inputfile, "r" );
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258 if( !infp )
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259 {
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260 fprintf( stderr, "Cannot open %s\n", inputfile );
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261 exit( 1 );
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262 }
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263 }
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264 else
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265 infp = stdin;
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266
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267 #if 0
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268 PreRead( stdin, &njob, &nlenmax );
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269 #else
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270 getnumlen( infp );
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271 #endif
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272 rewind( infp );
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273 if( njob < 2 )
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274 {
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275 fprintf( stderr, "At least 2 sequences should be input!\n"
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276 "Only %d sequence found.\n", njob );
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277 exit( 1 );
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278 }
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279
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280 tmpseq = AllocateCharVec( nlenmax+1 );
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281 seq = AllocateCharMtx( njob, nlenmax+1 );
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282 grpseq = AllocateIntVec( nlenmax+1 );
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283 pointt = AllocateIntMtx( njob, nlenmax+1 );
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284 mtxself = AllocateDoubleVec( njob );
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285 pamN = NOTSPECIFIED;
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286 name = AllocateCharMtx( njob, B );
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287 nlen = AllocateIntVec( njob );
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288
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289 #if 0
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290 FRead( infp, name, nlen, seq );
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291 #else
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292 readData_pointer( infp, name, nlen, seq );
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293 #endif
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294
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295 fclose( infp );
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296
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297 constants( njob, seq );
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298
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299
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300 if( nadd ) outputformat = 's';
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301 norg = njob - nadd;
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302
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303 if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
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304 else tsize = (int)pow( 6, 6 );
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305
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306 if( dorp == 'd' )
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307 {
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308 lenfaca = DLENFACA;
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309 lenfacb = DLENFACB;
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310 lenfacc = DLENFACC;
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311 lenfacd = DLENFACD;
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312 }
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313 else
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314 {
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315 lenfaca = PLENFACA;
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316 lenfacb = PLENFACB;
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317 lenfacc = PLENFACC;
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318 lenfacd = PLENFACD;
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319 }
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320
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321 maxl = 0;
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322 for( i=0; i<njob; i++ )
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323 {
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324 gappick0( tmpseq, seq[i] );
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325 nlen[i] = strlen( tmpseq );
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326 // if( nlen[i] < 6 )
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327 // {
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328 // fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
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329 // exit( 1 );
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330 // }
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331 if( nlen[i] > maxl ) maxl = nlen[i];
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332 if( dorp == 'd' ) /* nuc */
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333 {
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334 seq_grp_nuc( grpseq, tmpseq );
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335 makepointtable_nuc( pointt[i], grpseq );
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336 }
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337 else /* amino */
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338 {
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339 seq_grp( grpseq, tmpseq );
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340 makepointtable( pointt[i], grpseq );
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341 }
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342 }
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343 fprintf( stderr, "\nCalculating i-i scores ... " );
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344 for( i=0; i<njob; i++ )
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345 {
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346 table1 = (short *)calloc( tsize, sizeof( short ) );
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347 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
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348 makecompositiontable_p( table1, pointt[i] );
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349
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350 score = commonsextet_p( table1, pointt[i] );
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351 mtxself[i] = score;
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352 free( table1 );
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353 }
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354
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355 fprintf( stderr, "done.\n" );
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356 fprintf( stderr, "\nCalculating i-j scores ... \n" );
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357 if( outputformat == 'p' ) fprintf( stdout, "%-5d", njob );
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358 for( i=0; i<norg; i++ )
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359 {
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360 if( outputformat == 'p' ) fprintf( stdout, "\n%-9d ", i+1 );
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361 table1 = (short *)calloc( tsize, sizeof( short ) );
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362 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
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363 if( i % 10 == 0 )
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364 {
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365 fprintf( stderr, "%4d / %4d\r", i+1, njob );
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366 }
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367 makecompositiontable_p( table1, pointt[i] );
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368
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369
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370 if( nadd == 0 )
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371 {
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372 if( outputformat == 'p' ) initj = 0;
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373 else initj = i+1;
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374 }
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375 else
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376 {
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377 initj = norg;
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378 }
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379 for( j=initj; j<njob; j++ )
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380 {
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381 if( nlen[i] > nlen[j] )
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382 {
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383 longer=(float)nlen[i];
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384 shorter=(float)nlen[j];
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385 }
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386 else
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387 {
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388 longer=(float)nlen[j];
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389 shorter=(float)nlen[i];
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390 }
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391 // lenfac = 3.0 / ( LENFACA + LENFACB / ( longer + LENFACC ) + shorter / longer * LENFACD );
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392 lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
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393 // lenfac = 1.0;
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394 // fprintf( stderr, "lenfac = %f (%.0f,%.0f)\n", lenfac, longer, shorter );
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395 score = commonsextet_p( table1, pointt[j] );
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396 bunbo = MIN( mtxself[i], mtxself[j] );
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397 if( outputformat == 'p' )
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398 {
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399 if( bunbo == 0.0 )
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400 fprintf( stdout, " %8.6f", 1.0 );
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401 else
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402 fprintf( stdout, " %8.6f", ( 1.0 - score / bunbo ) * lenfac );
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403 if( j % 7 == 6 ) fprintf( stdout, "\n" );
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404 }
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405 else
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406 {
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407 if( bunbo == 0.0 )
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408 fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, 1.0, nlen[i], nlen[j] );
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409 else
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410 fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, ( 1.0 - score / bunbo ) * lenfac, nlen[i], nlen[j] );
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411 }
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412 // fprintf( stderr, "##### mtx = %f, mtx[i][0]=%f, mtx[j][0]=%f, bunbo=%f\n", mtx[i][j-i], mtx[i][0], mtx[j][0], bunbo );
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413 // score = (double)commonsextet_p( table1, pointt[j] );
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414 // fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, ( 1.0 - score / MIN( mtxself[i], mtxself[j] ) ) * 3, nlen[i], nlen[j] );
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415
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416
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417 }
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418 free( table1 );
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419 }
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420
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421 fprintf( stderr, "\n" );
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422 if( outputformat == 'p' ) fprintf( stdout, "\n" );
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423 SHOWVERSION;
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424 exit( 0 );
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425 }