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annotate mafft/core/makedirectionlist.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
parents
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4 #define IODEBUG 0
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5 #define SCOREOUT 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 int nadd;
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10 float thresholdtorev;
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11 int dodp;
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12 int addfragment;
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13
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14 typedef struct _thread_arg
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15 {
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16 int iend;
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17 char **seq;
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18 char *tmpseq;
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19 int *res;
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20 int **spointt;
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21 short *table1;
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22 int iq;
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23 #ifdef enablemultithread
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24 int *jshare;
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25 int thread_no;
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26 pthread_mutex_t *mutex_counter;
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27 #endif
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28 } thread_arg_t;
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29
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30
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31
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32 void arguments( int argc, char *argv[] )
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33 {
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34 int c;
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35
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36 nthread = 1;
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37 inputfile = NULL;
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38 nadd = 0;
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39 dodp = 0;
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40 alg = 'a';
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41 alg = 'm';
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42 dorp = NOTSPECIFIED;
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43 fmodel = 0;
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44 // ppenalty = (int)( -2.0 * 1000 - 0.5 );
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45 // ppenalty_ex = (int)( -0.1 * 1000 - 0.5 );
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46 // poffset = (int)( 0.1 * 1000 - 0.5 );
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47 ppenalty = NOTSPECIFIED;
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48 ppenalty_ex = NOTSPECIFIED;
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49 poffset = NOTSPECIFIED;
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50 kimuraR = 2;
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51 pamN = 200;
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52 thresholdtorev = 0.1;
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53 addfragment = 0;
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54
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55
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56 while( --argc > 0 && (*++argv)[0] == '-' )
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57 {
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58 while ( (c = *++argv[0]) )
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59 {
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60 switch( c )
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61 {
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62 case 'i':
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63 inputfile = *++argv;
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64 fprintf( stderr, "inputfile = %s\n", inputfile );
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65 --argc;
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66 goto nextoption;
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67 case 'I':
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68 nadd = myatoi( *++argv );
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69 fprintf( stderr, "nadd = %d\n", nadd );
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70 --argc;
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71 goto nextoption;
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72 case 'C':
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73 nthread = myatoi( *++argv );
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74 fprintf( stderr, "nthread = %d\n", nthread );
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75 --argc;
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76 goto nextoption;
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77 case 'f':
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78 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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79 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
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80 --argc;
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81 goto nextoption;
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82 case 'g':
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83 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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84 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
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85 --argc;
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86 goto nextoption;
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87 case 'h':
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88 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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89 // fprintf( stderr, "poffset = %d\n", poffset );
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90 --argc;
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91 goto nextoption;
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92 case 'k':
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93 kimuraR = myatoi( *++argv );
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94 fprintf( stderr, "kappa = %d\n", kimuraR );
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95 --argc;
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96 goto nextoption;
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97 case 'j':
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98 pamN = myatoi( *++argv );
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99 scoremtx = 0;
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100 TMorJTT = JTT;
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101 fprintf( stderr, "jtt/kimura %d\n", pamN );
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102 --argc;
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103 goto nextoption;
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104 case 't':
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105 thresholdtorev = atof( *++argv );
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106 fprintf( stderr, "thresholdtorev = %f\n", thresholdtorev );
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107 --argc;
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108 goto nextoption;
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109 case 'd':
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110 dodp = 1;
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111 break;
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112 case 'F':
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113 addfragment = 1;
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114 break;
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115 #if 1
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116 case 'a':
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117 fmodel = 1;
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118 break;
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119 #endif
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120 case 'S':
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121 alg = 'S';
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122 break;
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123 case 'M':
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124 alg = 'M';
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125 break;
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126 case 'm':
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127 alg = 'm';
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128 break;
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129 case 'G':
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130 alg = 'G';
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131 break;
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132 case 'D':
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133 dorp = 'd';
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134 break;
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135 case 'P':
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136 dorp = 'p';
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137 break;
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138 default:
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139 fprintf( stderr, "illegal option %c\n", c );
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140 argc = 0;
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141 break;
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142 }
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143 }
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144 nextoption:
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145 ;
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146 }
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147 if( argc == 1 )
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148 {
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149 cut = atof( (*argv) );
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150 argc--;
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151 }
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152 if( argc != 0 )
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153 {
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154 fprintf( stderr, "options: Check source file !\n" );
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155 exit( 1 );
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156 }
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157 if( tbitr == 1 && outgap == 0 )
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158 {
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159 fprintf( stderr, "conflicting options : o, m or u\n" );
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160 exit( 1 );
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161 }
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162 }
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163
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164
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165
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166
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167 static int maxl;
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168 static int tsize;
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169
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170 void seq_grp_nuc( int *grp, char *seq )
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171 {
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172 int tmp;
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173 int *grpbk = grp;
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174 while( *seq )
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175 {
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176 tmp = amino_grp[(int)*seq++];
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177 if( tmp < 4 )
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178 *grp++ = tmp;
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179 else
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180 // fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
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181 ;
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182 }
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183 *grp = END_OF_VEC;
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184 if( grp - grpbk < 6 )
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185 {
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186 // fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
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187 // exit( 1 );
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188 *grpbk = -1;
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189 }
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190 }
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191
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192 void seq_grp( int *grp, char *seq )
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193 {
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194 int tmp;
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195 int *grpbk = grp;
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196 while( *seq )
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197 {
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198 tmp = amino_grp[(int)*seq++];
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199 if( tmp < 6 )
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200 *grp++ = tmp;
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201 else
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202 // fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
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203 ;
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204 }
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205 *grp = END_OF_VEC;
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206 if( grp - grpbk < 6 )
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207 {
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208 // fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
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209 // exit( 1 );
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210 *grpbk = -1;
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211 }
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212 }
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213
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214 void makecompositiontable_p( short *table, int *pointt )
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215 {
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216 int point;
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217
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218 while( ( point = *pointt++ ) != END_OF_VEC )
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219 table[point]++;
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220 }
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221
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222
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223 void makepointtable_nuc( int *pointt, int *n )
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224 {
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225 int point;
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226 register int *p;
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227
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228 if( *n == -1 )
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229 {
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230 *pointt = -1;
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231 return;
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232 }
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233
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234 p = n;
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235 point = *n++ * 1024;
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236 point += *n++ * 256;
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237 point += *n++ * 64;
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238 point += *n++ * 16;
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239 point += *n++ * 4;
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240 point += *n++;
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241 *pointt++ = point;
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242
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243 while( *n != END_OF_VEC )
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244 {
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245 point -= *p++ * 1024;
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246 point *= 4;
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247 point += *n++;
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248 *pointt++ = point;
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249 }
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250 *pointt = END_OF_VEC;
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251 }
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252
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253 void makepointtable( int *pointt, int *n )
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254 {
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255 int point;
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256 register int *p;
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257
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258 if( *n == -1 )
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259 {
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260 *pointt = -1;
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261 return;
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262 }
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263
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264 p = n;
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265 point = *n++ * 7776;
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266 point += *n++ * 1296;
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267 point += *n++ * 216;
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268 point += *n++ * 36;
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269 point += *n++ * 6;
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270 point += *n++;
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271 *pointt++ = point;
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272
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273 while( *n != END_OF_VEC )
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274 {
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275 point -= *p++ * 7776;
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276 point *= 6;
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277 point += *n++;
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278 *pointt++ = point;
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279 }
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280 *pointt = END_OF_VEC;
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281 }
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282
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283 static int commonsextet_p2( short *table, int *pointt )
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284 {
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285 int value = 0;
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286 short tmp;
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287 int point;
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288 short *memo;
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289 int *ct;
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290 int *cp;
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291
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292 if( *pointt == -1 )
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293 return( 0 );
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294
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295 memo = (short *)calloc( tsize, sizeof( short ) );
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296 if( !memo ) ErrorExit( "Cannot allocate memo\n" );
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297 ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) ); // chuui!!
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298 if( !ct ) ErrorExit( "Cannot allocate memo\n" );
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299
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300 cp = ct;
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301 while( ( point = *pointt++ ) != END_OF_VEC )
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302 {
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303 tmp = memo[point]++;
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304 if( tmp < table[point] )
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305 value++;
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306 if( tmp == 0 ) *cp++ = point;
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307 }
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308 *cp = END_OF_VEC;
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309
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310 cp = ct;
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311 while( *cp != END_OF_VEC )
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312 memo[*cp++] = 0;
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313
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314 free( memo );
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315 free( ct );
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316 return( value );
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317 }
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318
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319 static void *directionthread( void *arg )
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320 {
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321 thread_arg_t *targ = (thread_arg_t *)arg;
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322 int iend = targ->iend;
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323 char **seq = targ->seq;
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324 char *tmpseq = targ->tmpseq;
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325 int *res = targ->res;
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326 int **spointt = targ->spointt;
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327 short *table1 = targ->table1;
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328 int iq = targ->iq;
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329 #ifdef enablemultithread
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330 int thread_no = targ->thread_no;
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331 int *jshare = targ->jshare;
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332 #endif
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333 int j;
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334 char **mseq1, **mseq2;
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335
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336
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337 if( dodp ) // nakuserukamo
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338 {
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339 mseq1 = AllocateCharMtx( 1, 0 );
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340 mseq2 = AllocateCharMtx( 1, 0 );
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341 }
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342
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343 j = -1;
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344 while( 1 )
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345 {
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346 #ifdef enablemultithread
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347 if( nthread )
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348 {
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349 pthread_mutex_lock( targ->mutex_counter );
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350 j = *jshare;
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351 if( j == iend )
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352 {
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353 fprintf( stderr, "\r %d / %d (thread %d) \r", iq, njob, thread_no );
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354 pthread_mutex_unlock( targ->mutex_counter );
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355 break;
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356 }
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357 ++(*jshare);
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358 pthread_mutex_unlock( targ->mutex_counter );
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359 }
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360 else
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361 #endif
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362 {
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363 j++;
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364 if( j == iend )
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365 {
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366 fprintf( stderr, "\r %d / %d \r", iq, njob );
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367 break;
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368 }
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369 }
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370
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371
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372 if( dodp )
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373 {
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374 // strcpy( mseq1[0], tmpseq );
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375 // strcpy( mseq2[0], seq[j] );
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376 mseq1[0] = tmpseq;
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377 mseq2[0] = seq[j];
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378 // res[j] = G__align11_noalign( n_dis_consweight_multi, penalty, penalty_ex, mseq1, mseq2, 0 );
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379 res[j] = L__align11_noalign( n_dis_consweight_multi, mseq1, mseq2 );
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380 }
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381 else
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382 res[j] = commonsextet_p2( table1, spointt[j] );
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383 }
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384 if( dodp ) // nakuserukamo
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385 {
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386 free( mseq1 );
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387 free( mseq2 );
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388 // G__align11_noalign( NULL, 0, 0, NULL, NULL, 0 );
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389 L__align11_noalign( NULL, NULL, NULL );
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390 }
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391 // else
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392 // if( nthread ) // inthread == 0 no toki free suru to, error. nazeda
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393 // commonsextet_p( NULL, NULL );
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394 return( NULL );
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395 }
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396
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397 int main( int argc, char *argv[] )
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398 {
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399 static int *nlen;
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400 static int *nogaplen;
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401 static char **name, **seq;
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402 int i, j, istart, iend;
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403 FILE *infp;
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404 // FILE *adfp;
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405 char c;
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406
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407 int *grpseq;
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408 char *tmpseq, *revseq;
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409 int **pointt, **pointt_rev, **spointt;
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410 float res_forward, res_reverse, res_max;
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411 int ires, mres, mres2;
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412 int *res;
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413 static short *table1, *table1_rev;
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414 static char **mseq1f, **mseq1r, **mseq2;
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415
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416 arguments( argc, argv );
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417 #ifndef enablemultithread
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418 nthread = 0;
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419 #endif
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420
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421 if( inputfile )
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422 {
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423 infp = fopen( inputfile, "r" );
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424 if( !infp )
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425 {
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426 fprintf( stderr, "Cannot open %s\n", inputfile );
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427 exit( 1 );
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428 }
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429 }
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430 else
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431 infp = stdin;
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432
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433 getnumlen( infp );
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434 rewind( infp );
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435
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436 if( alg == 'a' )
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437 {
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438 if( nlenmax < 10000 )
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439 alg = 'G';
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440 else
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441 alg = 'S';
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442 }
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443
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444 seq = AllocateCharMtx( njob, nlenmax*1+1 );
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445
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446 #if 0
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447 Read( name, nlen, seq );
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448 readData( infp, name, nlen, seq );
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449 #else
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450 name = AllocateCharMtx( njob, B+1 );
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451 nlen = AllocateIntVec( njob );
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452 nogaplen = AllocateIntVec( njob );
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453 readData_pointer( infp, name, nlen, seq );
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454 fclose( infp );
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455
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456 if( dorp != 'd' )
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457 {
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458 fprintf( stderr, "Not necessary!\n" );
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459 for( i=0; i<njob; i++ )
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460 fprintf( stdout, "_F_%-10.10s\n", name[i]+1 );
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461 exit( 1 );
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462 }
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463 #endif
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464
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465 constants( njob, seq );
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466
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467
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468 #if 0
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469 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
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470 #endif
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471
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472 initSignalSM();
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473
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474 initFiles();
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475
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476 c = seqcheck( seq );
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477 if( c )
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478 {
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479 fprintf( stderr, "Illegal character %c\n", c );
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480 exit( 1 );
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481 }
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482
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483 fprintf( stderr, "\n" );
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484 if( alg == 'G' ) // do to the first sequence
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485 {
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486 mseq1f = AllocateCharMtx( 1, nlenmax+nlenmax );
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487 mseq1r = AllocateCharMtx( 1, nlenmax+nlenmax );
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488 mseq2 = AllocateCharMtx( 1, nlenmax+nlenmax );
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489 tmpseq = AllocateCharVec( MAX( nlenmax, B ) +1 );
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490
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491 gappick0( mseq1f[0], seq[0] );
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492 sreverse( mseq1r[0], mseq1f[0] );
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493 strcpy( seq[0], mseq1f[0] );
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494
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495 if( nadd )
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496 istart = njob - nadd;
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497 else
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498 istart = 1;
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499
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500 fprintf( stderr, "\n" );
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501
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502 for( i=0; i<istart; i++ )
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503 {
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504 gappick0( tmpseq, seq[i] );
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505 strcpy( seq[i], tmpseq );
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506 strcpy( tmpseq, name[i] );
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507 strcpy( name[i], "_F_" );
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508 strncpy( name[i]+3, tmpseq+1, 10 );
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509 name[i][13] = 0;
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510 }
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511 for( i=istart; i<njob; i++ )
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512 {
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513 gappick0( mseq2[0], seq[i] );
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514
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515 // res_forward = G__align11_noalign( n_dis_consweight_multi, penalty, penalty_ex, mseq1f, mseq2, 0 );
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516 // res_reverse = G__align11_noalign( n_dis_consweight_multi, penalty, penalty_ex, mseq1r, mseq2, 0 );
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517
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518 res_forward = L__align11_noalign( n_dis_consweight_multi, mseq1f, mseq2 );
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519 res_reverse = L__align11_noalign( n_dis_consweight_multi, mseq1r, mseq2 );
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520 #if 0
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521
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522 strcpy( mseq2[0], seq[i] );
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523 strcpy( mseq1f[0], seq[0] );
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524 res_forward = G__align11( n_dis_consweight_multi, mseq1f, mseq2, nlenmax*2, 0, 0 );
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525 fprintf( stdout, "%s\n", mseq1f[0] );
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526 fprintf( stdout, "%s\n", mseq2[0] );
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527
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528 strcpy( mseq2[0], seq[i] );
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529 sreverse( mseq1r[0], seq[0] );
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530 res_reverse = G__align11( n_dis_consweight_multi, mseq1r, mseq2, nlenmax*2, 0, 0 );
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531 fprintf( stdout, "%s\n", mseq1r[0] );
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532 fprintf( stdout, "%s\n", mseq2[0] );
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533 #endif
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534
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535 // fprintf( stdout, "\nscore_for(%d,%d) = %f\n", 0, i, res_forward );
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536 // fprintf( stdout, "score_rev(%d,%d) = %f\n", 0, i, res_reverse );
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537 res_max = MAX(res_reverse,res_forward);
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538 if( (res_reverse-res_forward)/res_max > thresholdtorev ) // tekitou
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539 {
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540 // fprintf( stderr, "REVERSE!!!\n" );
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541 sreverse( seq[i], mseq2[0] );
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542
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543 strcpy( tmpseq, name[i] );
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544 strcpy( name[i], "_R_" );
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545 strncpy( name[i]+3, tmpseq+1, 10 );
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546 name[i][13] = 0;
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547 }
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548 else
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549 {
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550 strcpy( seq[i], mseq2[0] );
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551
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552 strcpy( tmpseq, name[i] );
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553 strcpy( name[i], "_F_" );
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554 strncpy( name[i]+3, tmpseq+1, 10 );
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555 name[i][13] = 0;
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556 }
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557 }
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558 FreeCharMtx( mseq1f );
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559 FreeCharMtx( mseq1r );
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560 FreeCharMtx( mseq2 );
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561 free( tmpseq );
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562 }
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563 else if( alg == 'm' )
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564 {
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565 if( dodp ) // nakuserukamo
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566 {
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567 mseq1f = AllocateCharMtx( 1, nlenmax+1);
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568 mseq1r = AllocateCharMtx( 1, nlenmax+1 );
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569 mseq2 = AllocateCharMtx( 1, nlenmax+1 );
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570 }
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571 else
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572 {
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573 spointt = AllocateIntMtx( njob, 0 );
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574 pointt = AllocateIntMtx( njob, nlenmax+1 );
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575 pointt_rev = AllocateIntMtx( njob, nlenmax+1 );
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576 }
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577 tmpseq = AllocateCharVec( MAX( nlenmax, B ) +1 );
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578 revseq = AllocateCharVec( nlenmax+1 );
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579 grpseq = AllocateIntVec( nlenmax+1 );
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580 res = AllocateIntVec( njob );
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581 if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
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582 else tsize = (int)pow( 6, 6 ); // iranai
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583
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584 maxl = 0;
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585 for( i=0; i<njob; i++ )
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586 {
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587 gappick0( tmpseq, seq[i] );
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588 nogaplen[i] = strlen( tmpseq );
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589 if( nogaplen[i] > maxl ) maxl = nogaplen[i];
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590 }
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591
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592 if( nadd )
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593 iend = njob - nadd;
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594 else
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595 iend = 1;
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596
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597 for( i=0; i<iend; i++ )
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598 {
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599 // fprintf( stdout, "%d, SKIP\n", i );
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600 gappick0( tmpseq, seq[i] );
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601 strcpy( seq[i], tmpseq );
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602 // if( !nadd ) strcpy( seq[i], tmpseq ); // seq ha tsukawanaikara ii.
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603
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604 if( !dodp )
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605 {
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606 seq_grp_nuc( grpseq, tmpseq );
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nick
parents:
diff changeset
607 makepointtable_nuc( pointt[i], grpseq );
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nick
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diff changeset
608 spointt[i] = pointt[i];
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609 }
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610
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611 strcpy( tmpseq, name[i] );
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612 strcpy( name[i], "_F_" );
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613 strncpy( name[i]+3, tmpseq+1, 10 );
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nick
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diff changeset
614 name[i][13] = 0;
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nick
parents:
diff changeset
615 }
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616
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617 if( nadd )
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618 istart = njob - nadd;
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619 else
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620 istart = 1;
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621
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622 fprintf( stderr, "\n" );
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623 for( i=istart; i<njob; i++ )
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624 {
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625 // fprintf( stderr, "\r %d / %d ", i, njob );
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626 gappick0( tmpseq, seq[i] );
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627 strcpy( seq[i], tmpseq );
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628 sreverse( revseq, tmpseq );
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629
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630 if( !dodp )
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631 {
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632 table1 = (short *)calloc( tsize, sizeof( short ) );
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633 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
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634 table1_rev = (short *)calloc( tsize, sizeof( short ) );
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635 if( !table1_rev ) ErrorExit( "Cannot allocate table1_rev\n" );
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636 seq_grp_nuc( grpseq, tmpseq );
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637 makepointtable_nuc( pointt[i], grpseq );
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diff changeset
638 makecompositiontable_p( table1, pointt[i] );
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639 seq_grp_nuc( grpseq, revseq );
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nick
parents:
diff changeset
640 makepointtable_nuc( pointt_rev[i], grpseq );
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nick
parents:
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641 makecompositiontable_p( table1_rev, pointt_rev[i] );
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642 }
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643
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644 if( nadd && addfragment )
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645 iend = njob-nadd;
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646 else
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647 iend = i;
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648
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649
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650 #ifdef enablemultithread
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651 if( nthread )
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652 {
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653 pthread_t *handle;
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654 pthread_mutex_t mutex_counter;
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655 thread_arg_t *targ;
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656 int *jsharept;
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657
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658 targ = calloc( nthread, sizeof( thread_arg_t ) );
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659 handle = calloc( nthread, sizeof( pthread_t ) );
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660 pthread_mutex_init( &mutex_counter, NULL );
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661 jsharept = calloc( 1, sizeof(int) );
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662 *jsharept = 0;
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663
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664 for( j=0; j<nthread; j++ )
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665 {
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666 targ[j].iend = iend;
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667 targ[j].seq = seq;
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668 targ[j].tmpseq = tmpseq;
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669 targ[j].res = res;
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670 targ[j].spointt = spointt;
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671 targ[j].table1 = table1;
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672 targ[j].jshare = jsharept;
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673 targ[j].iq = i;
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674 targ[j].mutex_counter = &mutex_counter;
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675 targ[j].thread_no = j;
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676 pthread_create( handle+j, NULL, directionthread, (void *)(targ+j) );
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677 }
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678 for( j=0; j<nthread; j++ ) pthread_join( handle[j], NULL );
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679 pthread_mutex_destroy( &mutex_counter );
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680 free( handle );
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681 free( targ );
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682 free( jsharept );
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683 }
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684 else
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685 #endif
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686 {
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687 thread_arg_t *targ;
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688 targ = calloc( 1, sizeof( thread_arg_t ) );
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689 targ[0].iend = iend;
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690 targ[0].seq = seq;
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691 targ[0].tmpseq = tmpseq;
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692 targ[0].res = res;
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693 targ[0].spointt = spointt;
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694 targ[0].table1 = table1;
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695 targ[0].iq = i;
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696 directionthread( targ );
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697 free( targ );
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698 }
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699
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700
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701 mres = mres2 = 0;
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702 for( j=0; j<iend; j++ )
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703 {
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704 ires = res[j];
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705 // fprintf( stdout, "ires (%d,%d) = %d\n", i, j, ires );
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706 // fflush( stdout );
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707 if( ires>mres2 )
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708 {
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709 if( ires>mres )
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710 {
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711 mres2 = mres;
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712 mres = ires;
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713 }
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714 else
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715 mres2 = ires;
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716 }
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717 }
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718 res_forward = (float)( mres + mres2 ) / 2;
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719
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720 #ifdef enablemultithread
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721 if( nthread )
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722 {
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723 pthread_t *handle;
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parents:
diff changeset
724 pthread_mutex_t mutex_counter;
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nick
parents:
diff changeset
725 thread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
726 int *jsharept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
727
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
728 targ = calloc( nthread, sizeof( thread_arg_t ) );
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nick
parents:
diff changeset
729 handle = calloc( nthread, sizeof( pthread_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
730 pthread_mutex_init( &mutex_counter, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
731 jsharept = calloc( 1, sizeof(int) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
732 *jsharept = 0;
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nick
parents:
diff changeset
733
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nick
parents:
diff changeset
734 for( j=0; j<nthread; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
735 {
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nick
parents:
diff changeset
736 targ[j].iend = iend;
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nick
parents:
diff changeset
737 targ[j].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
738 targ[j].tmpseq = revseq;
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nick
parents:
diff changeset
739 targ[j].res = res;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
740 targ[j].spointt = spointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
741 targ[j].table1 = table1_rev;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
742 targ[j].jshare = jsharept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
743 targ[j].iq = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
744 targ[j].mutex_counter = &mutex_counter;
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nick
parents:
diff changeset
745 targ[j].thread_no = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
746 pthread_create( handle+j, NULL, directionthread, (void *)(targ+j) );
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nick
parents:
diff changeset
747 }
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nick
parents:
diff changeset
748 for( j=0; j<nthread; j++ ) pthread_join( handle[j], NULL );
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nick
parents:
diff changeset
749 pthread_mutex_destroy( &mutex_counter );
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nick
parents:
diff changeset
750 free( handle );
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nick
parents:
diff changeset
751 free( targ );
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nick
parents:
diff changeset
752 free( jsharept );
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nick
parents:
diff changeset
753 }
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nick
parents:
diff changeset
754 else
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nick
parents:
diff changeset
755 #endif
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nick
parents:
diff changeset
756 {
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nick
parents:
diff changeset
757 thread_arg_t *targ;
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nick
parents:
diff changeset
758 targ = calloc( 1, sizeof( thread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
759 targ[0].iend = iend;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
760 targ[0].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
761 targ[0].tmpseq = revseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
762 targ[0].res = res;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
763 targ[0].spointt = spointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
764 targ[0].table1 = table1_rev;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
765 targ[0].iq = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
766 directionthread( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
767 free( targ );
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nick
parents:
diff changeset
768 }
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nick
parents:
diff changeset
769
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nick
parents:
diff changeset
770 mres = mres2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
771 for( j=0; j<iend; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
772 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
773 ires = res[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
774 if( ires>mres2 )
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nick
parents:
diff changeset
775 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
776 if( ires>mres )
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nick
parents:
diff changeset
777 {
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nick
parents:
diff changeset
778 mres2 = mres;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
779 mres = ires;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
780 }
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nick
parents:
diff changeset
781 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
782 mres2 = ires;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
783 }
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nick
parents:
diff changeset
784 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
785 res_reverse = (float)( mres + mres2 ) / 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
786
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
787 // fprintf( stdout, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
788 // fprintf( stdout, "score_for(%d,%d) = %f\n", 0, i, res_forward );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
789 // fprintf( stdout, "score_rev(%d,%d) = %f\n", 0, i, res_reverse );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
790 // fflush( stdout );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
791 res_max = MAX(res_reverse,res_forward);
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
792 if( (res_reverse-res_forward)/res_max > thresholdtorev ) // tekitou
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
793
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
794 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
795 strcpy( seq[i], revseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
796
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
797 strcpy( tmpseq, name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
798 strcpy( name[i], "_R_" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
799 strncpy( name[i]+3, tmpseq+1, 10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
800 name[i][13] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
801 if( !dodp ) spointt[i] = pointt_rev[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
802 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
803 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
804 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
805 strcpy( tmpseq, name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
806 strcpy( name[i], "_F_" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
807 strncpy( name[i]+3, tmpseq+1, 10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
808 name[i][13] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
809 if( !dodp ) spointt[i] = pointt[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
810 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
811
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
812 if( !dodp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
813 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
814 free( table1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
815 free( table1_rev );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
816 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
817 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
818
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
819 free( grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
820 free( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
821 free( revseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
822 free( res );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
823 if( dodp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
824 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
825 FreeCharMtx( mseq1f );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
826 FreeCharMtx( mseq1r );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
827 FreeCharMtx( mseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
828 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
829 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
830 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
831 FreeIntMtx( pointt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
832 FreeIntMtx( pointt_rev );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
833 free( spointt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
834 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
835 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
836 else
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nick
parents:
diff changeset
837 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
838 fprintf( stderr, "Unknown alg %c\n", alg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
839 exit( 1 );
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nick
parents:
diff changeset
840 }
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nick
parents:
diff changeset
841 // writeData_pointer( stdout, njob, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
842 for( i=0; i<njob; i++ )
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nick
parents:
diff changeset
843 {
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nick
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844 // fprintf( stdout, ">%s\n", name[i] );
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845 // fprintf( stdout, "%s\n", seq[i] );
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846 fprintf( stdout, "%s\n", name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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847 }
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848
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849 fprintf( stderr, "\n" );
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850 SHOWVERSION;
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851 return( 0 );
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852 }
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853