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annotate mafft/core/dndpre.c @ 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 #include "mltaln.h"
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2
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3 #define TEST 0
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4
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5 static int treeout = 0;
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6 static int maxdist = 1;
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7 static int nadd = 0;
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8
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9 #ifdef enablemultithread
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10 typedef struct _jobtable
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11 {
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12 int i;
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13 int j;
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14 } Jobtable;
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15
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16 typedef struct _thread_arg
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17 {
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18 int njob;
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19 int thread_no;
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20 float *selfscore;
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21 double **mtx;
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22 char **seq;
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23 int **skiptable;
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24 Jobtable *jobpospt;
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25 pthread_mutex_t *mutex;
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26 } thread_arg_t;
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27
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28 void *athread( void *arg )
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29 {
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30 thread_arg_t *targ = (thread_arg_t *)arg;
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31 int njob = targ->njob;
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32 int thread_no = targ->thread_no;
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33 float *selfscore = targ->selfscore;
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34 double **mtx = targ->mtx;
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35 char **seq = targ->seq;
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36 int **skiptable = targ->skiptable;
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37 Jobtable *jobpospt = targ->jobpospt;
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38
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39 int i, j;
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40 float ssi, ssj, bunbo;
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41 double mtxv;
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42
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43 if( njob == 1 ) return( NULL );
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44
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45 while( 1 )
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46 {
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47 pthread_mutex_lock( targ->mutex );
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48 j = jobpospt->j;
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49 i = jobpospt->i;
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50 j++;
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51 // fprintf( stderr, "\n i=%d, j=%d before check\n", i, j );
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52 if( j == njob )
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53 {
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54 // fprintf( stderr, "\n j = %d, i = %d, njob = %d\n", j, i, njob );
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55 fprintf( stderr, "%4d/%4d (thread %4d), dndpre\r", i+1, njob, thread_no );
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56 i++;
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57 j = i + 1;
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58 if( i == njob-1 )
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59 {
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60 // fprintf( stderr, "\n i=%d, njob-1=%d\n", i, njob-1 );
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61 pthread_mutex_unlock( targ->mutex );
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62 return( NULL );
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63 }
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64 }
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65 // fprintf( stderr, "\n i=%d, j=%d after check\n", i, j );
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66 jobpospt->j = j;
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67 jobpospt->i = i;
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68 pthread_mutex_unlock( targ->mutex );
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69
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70 ssi = selfscore[i];
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71 ssj = selfscore[j];
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72
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73 bunbo = MIN( ssi, ssj );
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74 if( bunbo == 0.0 )
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75 mtxv = maxdist;
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76 else
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77 // mtxv = maxdist * ( 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo );
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78 mtxv = maxdist * ( 1.0 - (double)naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty ) / bunbo );
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79 #if 1
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80 if( mtxv > 9.0 || mtxv < 0.0 )
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81 {
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82 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
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83 exit( 1 );
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84 }
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85 #else // CHUUI!!! 2012/05/16
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86 if( mtxv > 2.0 )
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87 {
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88 mtxv = 2.0;
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89 }
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90 if( mtxv < 0.0 )
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91 {
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92 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
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93 exit( 1 );
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94 }
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95 #endif
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96 mtx[i][j] = mtxv;
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97 }
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98 }
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99
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100 #endif
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101
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102 void arguments( int argc, char *argv[] )
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103 {
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104 int c;
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105
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106 nadd = 0;
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107 nthread = 1;
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108 alg = 'X';
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109 fmodel = 0;
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110 treeout = 0;
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111 scoremtx = 1;
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112 nblosum = 62;
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113 dorp = NOTSPECIFIED;
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114 inputfile = NULL;
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115 ppenalty = NOTSPECIFIED; //?
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116 ppenalty_ex = NOTSPECIFIED; //?
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117 poffset = NOTSPECIFIED; //?
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118 kimuraR = NOTSPECIFIED;
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119 pamN = NOTSPECIFIED;
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diff changeset
120
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diff changeset
121 while( --argc > 0 && (*++argv)[0] == '-' )
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122 {
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diff changeset
123 while ( (c = *++argv[0]) )
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124 {
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diff changeset
125 switch( c )
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diff changeset
126 {
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diff changeset
127 case 't':
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128 treeout = '1';
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diff changeset
129 break;
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130 case 'D':
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131 dorp = 'd';
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132 break;
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133 case 'a':
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134 fmodel = 1;
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135 break;
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136 case 'P':
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137 dorp = 'p';
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diff changeset
138 break;
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139 case 'K': // Hontou ha iranai. disttbfast.c, tbfast.c to awaserutame.
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140 break;
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141 case 'I':
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142 nadd = myatoi( *++argv );
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143 fprintf( stderr, "nadd = %d\n", nadd );
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144 --argc;
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145 goto nextoption;
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146 case 'f':
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147 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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148 --argc;
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149 goto nextoption;
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150 case 'g':
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151 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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152 --argc;
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153 goto nextoption;
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154 case 'h':
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155 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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156 --argc;
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157 goto nextoption;
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158 case 'k':
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159 kimuraR = myatoi( *++argv );
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diff changeset
160 // fprintf( stderr, "kimuraR = %d\n", kimuraR );
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161 --argc;
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162 goto nextoption;
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163 case 'b':
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164 nblosum = myatoi( *++argv );
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165 scoremtx = 1;
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166 // fprintf( stderr, "blosum %d\n", nblosum );
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167 --argc;
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168 goto nextoption;
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169 case 'j':
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170 pamN = myatoi( *++argv );
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171 scoremtx = 0;
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172 TMorJTT = JTT;
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173 fprintf( stderr, "jtt %d\n", pamN );
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174 --argc;
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175 goto nextoption;
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176 case 'm':
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177 pamN = myatoi( *++argv );
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178 scoremtx = 0;
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179 TMorJTT = TM;
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180 fprintf( stderr, "TM %d\n", pamN );
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181 --argc;
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182 goto nextoption;
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183 case 'i':
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184 inputfile = *++argv;
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185 fprintf( stderr, "inputfile = %s\n", inputfile );
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186 --argc;
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187 goto nextoption;
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188 case 'M':
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189 maxdist = myatoi( *++argv );
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diff changeset
190 fprintf( stderr, "maxdist = %d\n", maxdist );
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diff changeset
191 --argc;
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192 goto nextoption;
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193 case 'C':
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194 nthread = myatoi( *++argv );
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195 fprintf( stderr, "nthread = %d\n", nthread );
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parents:
diff changeset
196 --argc;
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197 goto nextoption;
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diff changeset
198 }
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diff changeset
199 }
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diff changeset
200 nextoption:
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201 ;
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diff changeset
202 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
203 if( argc != 0 )
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parents:
diff changeset
204 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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205 fprintf( stderr, "options: Check source file !\n" );
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parents:
diff changeset
206 exit( 1 );
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parents:
diff changeset
207 }
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208 }
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diff changeset
209
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diff changeset
210 int main( int argc, char **argv )
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211 {
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212 int i, j, ilim;
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213 char **seq;
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214 static char **name;
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215 int *nlen;
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216 float *selfscore;
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217 double **mtx;
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218 double mtxv;
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diff changeset
219 FILE *fp;
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220 FILE *infp;
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221 float ssi, ssj, bunbo;
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222 int **skiptable = NULL;
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diff changeset
223
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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224
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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225 arguments( argc, argv );
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226 #ifndef enablemultithread
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227 nthread = 0;
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diff changeset
228 #endif
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229
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230 if( inputfile )
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231 {
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232 infp = fopen( inputfile, "r" );
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diff changeset
233 if( !infp )
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234 {
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235 fprintf( stderr, "Cannot open %s\n", inputfile );
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diff changeset
236 exit( 1 );
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diff changeset
237 }
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diff changeset
238 }
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diff changeset
239 else
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240 infp = stdin;
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diff changeset
241
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242 #if 0
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243 PreRead( stdin, &njob, &nlenmax );
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244 #else
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245 getnumlen( infp );
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246 #endif
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247 rewind( infp );
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248
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249 njob -= nadd; // atarashii hairetsu ha mushi
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250
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251 seq = AllocateCharMtx( njob, nlenmax+1 );
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252 name = AllocateCharMtx( njob, B+1 );
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253 mtx = AllocateDoubleMtx( njob, njob );
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254 selfscore = AllocateFloatVec( njob );
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255 nlen = AllocateIntVec( njob );
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256
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257
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258 #if 0
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259 FRead( stdin, name, nlen, seq );
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260 #else
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261 readData_pointer( infp, name, nlen, seq );
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262 #endif
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263 fclose( infp );
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264
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265
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266 for( i=1; i<njob; i++ )
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267 {
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268 if( nlen[i] != nlen[0] )
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269 {
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270 reporterr( "Not aligned!\n" );
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271 exit( 1 );
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272 }
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273 }
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274
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275 constants( njob, seq );
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276
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277 #if 0
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278 for( i=0; i<njob-1; i++ )
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279 {
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280 fprintf( stderr, "%4d/%4d\r", i+1, njob );
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281 for( j=i+1; j<njob; j++ )
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282 mtx[i][j] = (double)substitution_hosei( seq[i], seq[j] );
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283 // fprintf( stderr, "i=%d,j=%d, l=%d &&& %f\n", i, j, nlen[0], mtx[i][j] );
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284 }
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285 #else // 061003
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286 for( i=0; i<njob; i++ )
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287 {
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288 selfscore[i] = (float)naivepairscore11( seq[i], seq[i], penalty );
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289 }
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290
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291 skiptable = AllocateIntMtx( njob, 0 );
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292 makeskiptable( njob, skiptable, seq ); // allocate suru.
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293
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294 #ifdef enablemultithread
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295 if( nthread > 0 )
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296 {
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297 thread_arg_t *targ;
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298 Jobtable jobpos;
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299 pthread_t *handle;
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300 pthread_mutex_t mutex;
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301
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302 jobpos.i = 0;
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303 jobpos.j = 0;
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304
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305 targ = calloc( nthread, sizeof( thread_arg_t ) );
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306 handle = calloc( nthread, sizeof( pthread_t ) );
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307 pthread_mutex_init( &mutex, NULL );
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308
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309 for( i=0; i<nthread; i++ )
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310 {
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311 targ[i].thread_no = i;
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312 targ[i].njob = njob;
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313 targ[i].selfscore = selfscore;
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314 targ[i].mtx = mtx;
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315 targ[i].seq = seq;
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316 targ[i].skiptable = skiptable;
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317 targ[i].jobpospt = &jobpos;
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318 targ[i].mutex = &mutex;
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319
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320 pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
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321 }
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322
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323 for( i=0; i<nthread; i++ )
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324 {
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325 pthread_join( handle[i], NULL );
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326 }
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327 pthread_mutex_destroy( &mutex );
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328 }
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329 else
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330 #endif
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331 {
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332 ilim = njob-1;
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333 for( i=0; i<ilim; i++ )
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334 {
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335 ssi = selfscore[i];
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336 fprintf( stderr, "%4d/%4d\r", i+1, njob );
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337 for( j=i+1; j<njob; j++ )
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338 {
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339 ssj = selfscore[j];
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340 bunbo = MIN( ssi, ssj );
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341 if( bunbo == 0.0 )
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342 mtxv = maxdist;
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343 else
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344 mtxv = maxdist * ( 1.0 - (double)naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty ) / bunbo );
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345 // mtxv = maxdist * ( 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo );
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346 // mtxv = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
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347 // fprintf( stderr, "i=%d,j=%d, l=%d### %f, score = %f, %f, %f\n", i, j, nlen[0], mtxv, naivepairscore11( seq[i], seq[j], penalty ), ssi, ssj );
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348
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349 #if 1
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350 if( mtxv > 9.0 || mtxv < 0.0 )
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351 {
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352 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
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353 exit( 1 );
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354 }
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355 #else // CHUUI!!! 2012/05/16
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356 if( mtxv > 2.0 )
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357 {
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358 mtxv = 2.0;
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359 }
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360 if( mtxv < 0.0 )
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361 {
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362 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
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363 exit( 1 );
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364 }
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365 #endif
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366 mtx[i][j] = mtxv;
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367 }
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368 }
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369 }
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370 #endif
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371
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372 #if TEST
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373 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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374 fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
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375 #endif
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376
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377 fp = fopen( "hat2", "w" );
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378 WriteHat2_pointer( fp, njob, name, mtx );
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379 fclose( fp );
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380 #if 0
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381 if( treeout )
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382 {
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383 int ***topol;
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384 double **len;
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385
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386 topol = AllocateIntCub( njob, 2, njob );
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387 len = AllocateDoubleMtx( njob, njob );
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388 veryfastsupg_double_outtree( njob, mtx, topol, len );
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389 }
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390 #endif
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391 if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
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392 SHOWVERSION;
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393 exit( 0 );
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394 /*
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395 res = system( ALNDIR "/spgsdl < hat2" );
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396 if( res ) exit( 1 );
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397 else exit( 0 );
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398 */
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399 }