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annotate mafft/core/Falign.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 #if 0
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4 static FILE *fftfp;
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5 #endif
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6 static TLS int n20or4or2;
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7
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8 #define KEIKA 0
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9 #define RND 0
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10 #define DEBUG 0
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11
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12 #if RND // by D.Mathog
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13 static void generateRndSeq( char *seq, int len )
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14 {
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15 while( len-- )
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16 #if 1
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17 *seq++ = (int)( rnd() * n20or4or2 );
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18 #else
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19 *seq++ = (int)1;
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20 #endif
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21 }
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22 #endif
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23
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24 static void vec_init( Fukusosuu *result, int nlen )
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25 {
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26 while( nlen-- )
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27 {
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28 result->R = result->I = 0.0;
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29 result++;
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30 }
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31 }
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32
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33 #if 0 // by D.Mathog
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34 static void vec_init2( Fukusosuu **result, char *seq, double eff, int st, int ed )
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35 {
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36 int i;
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37 for( i=st; i<ed; i++ )
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38 result[(int)*seq++][i].R += eff;
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39 }
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40 #endif
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41
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42 static void seq_vec_2( Fukusosuu *result, double *score, double incr, char *seq )
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43 {
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44 static TLS int n;
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45 for( ; *seq; result++ )
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46 {
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47 n = amino_n[(int)*seq++];
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48 if( n < 20 && n >= 0 ) result->R += incr * score[n];
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49 #if 0
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50 fprintf( stderr, "n=%d, score=%f, inc=%f R=%f\n",n, score[n], incr * score[n], result->R );
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51 #endif
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52 }
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53 }
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54
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55 static void seq_vec_3( Fukusosuu **result, double incr, char *seq )
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56 {
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57 int i;
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58 int n;
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59 for( i=0; *seq; i++ )
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60 {
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61 n = amino_n[(int)*seq++];
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62 if( n < n20or4or2 && n >= 0 ) result[n][i].R += incr;
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63 }
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64 }
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65
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66 static void seq_vec_5( Fukusosuu *result, double *score1, double *score2, double incr, char *seq )
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67 {
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68 int n;
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69 for( ; *seq; result++ )
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70 {
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71 n = amino_n[(int)*seq++];
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72 if( n > 20 ) continue;
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73 result->R += incr * score1[n];
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74 result->I += incr * score2[n];
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75 #if 0
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76 fprintf( stderr, "n=%d, score=%f, inc=%f R=%f\n",n, score[n], incr * score[n], result->R );
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77 #endif
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78 }
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79 }
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80
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81
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82 static void seq_vec_4( Fukusosuu *result, double incr, char *seq )
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83 {
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84 char s;
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85 for( ; *seq; result++ )
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86 {
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87 s = *seq++;
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88 if( s == 'a' )
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89 result->R += incr;
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90 else if( s == 't' )
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91 result->R -= incr;
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92 else if( s == 'g' )
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93 result->I += incr;
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94 else if( s == 'c' )
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95 result->I -= incr;
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96 }
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97 }
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98
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99 #if 0 // by D.Mathog
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100 static void seq_vec( Fukusosuu *result, char query, double incr, char *seq )
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101 {
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102 #if 0
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103 int bk = nlen;
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104 #endif
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105 while( *seq )
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106 {
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107 if( *seq++ == query ) result->R += incr;
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108 result++;
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109 #if 0
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110 fprintf( stderr, "i = %d result->R = %f\n", bk-nlen, (result-1)->R );
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111 #endif
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112 }
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113 }
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114
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115 static int checkRepeat( int num, int *cutpos )
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116 {
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117 int tmp, buf;
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118
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119 buf = *cutpos;
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120 while( num-- )
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121 {
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122 if( ( tmp = *cutpos++ ) < buf ) return( 1 );
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123 buf = tmp;
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124 }
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125 return( 0 );
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126 }
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127
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128 static int segcmp( void *ptr1, void *ptr2 )
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129 {
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130 int diff;
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131 Segment **seg1 = (Segment **)ptr1;
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132 Segment **seg2 = (Segment **)ptr2;
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133 #if 0
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134 return( (*seg1)->center - (*seg2)->center );
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135 #else
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136 diff = (*seg1)->center - (*seg2)->center;
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137 if( diff ) return( diff );
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138
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139 diff = (*seg1)->start - (*seg2)->start;
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140 if( diff ) return( diff );
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141
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142 diff = (*seg1)->end - (*seg2)->end;
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143 if( diff ) return( diff );
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144
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145 fprintf( stderr, "USE STABLE SORT !!\n" );
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146 exit( 1 );
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147 return( 0 );
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148 #endif
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149 }
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150 #endif
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151
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152
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153 static void mymergesort( int first, int last, Segment **seg )
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154 {
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155 int middle;
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156 static TLS int i, j, k, p;
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157 static TLS int allo = 0;
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158 static TLS Segment **work = NULL;
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159
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160 if( seg == NULL )
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161 {
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162 if( work ) free( work );
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163 work = NULL;
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164 allo = 0;
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165 return;
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166 }
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167
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168 if( last > allo )
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169 {
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170 allo = last;
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171 if( work ) free( work );
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172 work = (Segment **)calloc( allo / 2 + 1, sizeof( Segment *) );
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173 }
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174
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175 if( first < last )
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176 {
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177 middle = ( first + last ) / 2;
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178 mymergesort( first, middle, seg );
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179 mymergesort( middle+1, last, seg );
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180 p = 0;
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181 for( i=first; i<=middle; i++ ) work[p++] = seg[i];
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182 i = middle + 1; j = 0; k = first;
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183 while( i <= last && j < p )
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184 {
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185 if( work[j]->center <= seg[i]->center )
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186 seg[k++] = work[j++];
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187 else
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188 seg[k++] = seg[i++];
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189 }
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190 while( j < p ) seg[k++] = work[j++];
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191 }
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192 }
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193
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194
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195 double Fgetlag(
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196 double **n_dynamicmtx,
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197 char **seq1, char **seq2,
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198 double *eff1, double *eff2,
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199 int clus1, int clus2,
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200 int alloclen )
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201 {
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202 int i, j, k, l, m;
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203 int nlen, nlen2, nlen4;
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204 static TLS int crossscoresize = 0;
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205 static TLS char **tmpseq1 = NULL;
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206 static TLS char **tmpseq2 = NULL;
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207 static TLS char **tmpptr1 = NULL;
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208 static TLS char **tmpptr2 = NULL;
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209 static TLS char **tmpres1 = NULL;
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210 static TLS char **tmpres2 = NULL;
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211 static TLS char **result1 = NULL;
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212 static TLS char **result2 = NULL;
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213 #if RND
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214 static TLS char **rndseq1 = NULL;
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215 static TLS char **rndseq2 = NULL;
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216 #endif
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217 static TLS Fukusosuu **seqVector1 = NULL;
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218 static TLS Fukusosuu **seqVector2 = NULL;
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219 static TLS Fukusosuu **naiseki = NULL;
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220 static TLS Fukusosuu *naisekiNoWa = NULL;
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221 static TLS double *soukan = NULL;
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222 static TLS double **crossscore = NULL;
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223 int nlentmp;
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224 static TLS int *kouho = NULL;
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225 static TLS Segment *segment = NULL;
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226 static TLS Segment *segment1 = NULL;
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227 static TLS Segment *segment2 = NULL;
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228 static TLS Segment **sortedseg1 = NULL;
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229 static TLS Segment **sortedseg2 = NULL;
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230 static TLS int *cut1 = NULL;
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231 static TLS int *cut2 = NULL;
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232 static TLS int localalloclen = 0;
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233 int lag;
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234 int tmpint;
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235 int count, count0;
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236 int len1, len2;
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237 int totallen;
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238 float dumfl = 0.0;
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239 int headgp, tailgp;
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240
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241 len1 = strlen( seq1[0] );
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242 len2 = strlen( seq2[0] );
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243 nlentmp = MAX( len1, len2 );
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244
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245 nlen = 1;
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246 while( nlentmp >= nlen ) nlen <<= 1;
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247 #if 0
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248 fprintf( stderr, "### nlen = %d\n", nlen );
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249 #endif
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250
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251 nlen2 = nlen/2; nlen4 = nlen2 / 2;
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252
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253 #if DEBUG
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254 fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
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255 fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
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256 #endif
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257
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258 if( !localalloclen )
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259 {
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260 kouho = AllocateIntVec( NKOUHO );
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261 cut1 = AllocateIntVec( MAXSEG );
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262 cut2 = AllocateIntVec( MAXSEG );
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263 tmpptr1 = AllocateCharMtx( njob, 0 );
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264 tmpptr2 = AllocateCharMtx( njob, 0 );
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265 result1 = AllocateCharMtx( njob, alloclen );
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266 result2 = AllocateCharMtx( njob, alloclen );
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267 tmpres1 = AllocateCharMtx( njob, alloclen );
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268 tmpres2 = AllocateCharMtx( njob, alloclen );
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269 // crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
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270 segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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271 segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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272 segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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273 sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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274 sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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275 if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
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276 ErrorExit( "Allocation error\n" );
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277
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278 if ( scoremtx == -1 ) n20or4or2 = 4;
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279 else if( fftscore == 1 ) n20or4or2 = 2;
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280 else n20or4or2 = 20;
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281 }
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282 if( localalloclen < nlen )
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283 {
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284 if( localalloclen )
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285 {
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286 #if 1
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287 FreeFukusosuuMtx ( seqVector1 );
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288 FreeFukusosuuMtx ( seqVector2 );
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289 FreeFukusosuuVec( naisekiNoWa );
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290 FreeFukusosuuMtx( naiseki );
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291 FreeDoubleVec( soukan );
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292 FreeCharMtx( tmpseq1 );
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293 FreeCharMtx( tmpseq2 );
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294 #endif
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295 #if RND
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296 FreeCharMtx( rndseq1 );
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297 FreeCharMtx( rndseq2 );
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298 #endif
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299 }
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300
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301
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302 tmpseq1 = AllocateCharMtx( njob, nlen );
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303 tmpseq2 = AllocateCharMtx( njob, nlen );
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304 naisekiNoWa = AllocateFukusosuuVec( nlen );
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305 naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
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306 seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
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307 seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
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308 soukan = AllocateDoubleVec( nlen+1 );
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309
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310 #if RND
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311 rndseq1 = AllocateCharMtx( njob, nlen );
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312 rndseq2 = AllocateCharMtx( njob, nlen );
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313 for( i=0; i<njob; i++ )
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314 {
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315 generateRndSeq( rndseq1[i], nlen );
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316 generateRndSeq( rndseq2[i], nlen );
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317 }
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318 #endif
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319 localalloclen = nlen;
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320 }
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321
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322 for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
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323 for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
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324
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325 #if 0
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326 fftfp = fopen( "input_of_Falign", "w" );
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327 fprintf( fftfp, "nlen = %d\n", nlen );
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328 fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
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329 for( i=0; i<clus1; i++ )
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330 fprintf( fftfp, "%s\n", seq1[i] );
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331 fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
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332 for( i=0; i<clus2; i++ )
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333 fprintf( fftfp, "%s\n", seq2[i] );
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334 fclose( fftfp );
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335 system( "less input_of_Falign < /dev/tty > /dev/tty" );
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336 #endif
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337
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338 if( fftkeika ) fprintf( stderr, " FFT ... " );
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339
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340 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
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341 if( fftscore && scoremtx != -1 )
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342 {
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343 for( i=0; i<clus1; i++ )
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344 {
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345 seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
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346 seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
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347 }
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348 }
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349 else
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350 {
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351 #if 0
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352 for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
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353 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
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354 #else
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355 for( i=0; i<clus1; i++ )
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356 seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
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357 #endif
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358 }
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359 #if RND
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360 for( i=0; i<clus1; i++ )
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361 {
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362 vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
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363 }
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364 #endif
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365 #if 0
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366 fftfp = fopen( "seqVec", "w" );
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367 fprintf( fftfp, "before transform\n" );
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368 for( k=0; k<n20or4or2; k++ )
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369 {
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370 fprintf( fftfp, "nlen=%d\n", nlen );
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371 fprintf( fftfp, "%c\n", amino[k] );
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372 for( l=0; l<nlen; l++ )
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373 fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
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374 }
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375 fclose( fftfp );
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376 system( "less seqVec < /dev/tty > /dev/tty" );
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377 #endif
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378
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379 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
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380 if( fftscore && scoremtx != -1 )
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381 {
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382 for( i=0; i<clus2; i++ )
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383 {
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384 seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
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385 seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
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386 }
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387 }
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388 else
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389 {
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390 #if 0
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391 for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
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392 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
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393 #else
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394 for( i=0; i<clus2; i++ )
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395 seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
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396 #endif
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397 }
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398 #if RND
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399 for( i=0; i<clus2; i++ )
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400 {
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401 vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
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402 }
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403 #endif
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404
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405 #if 0
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406 fftfp = fopen( "seqVec2", "w" );
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407 fprintf( fftfp, "before fft\n" );
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408 for( k=0; k<n20or4or2; k++ )
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409 {
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410 fprintf( fftfp, "%c\n", amino[k] );
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411 for( l=0; l<nlen; l++ )
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412 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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413 }
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414 fclose( fftfp );
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415 system( "less seqVec2 < /dev/tty > /dev/tty" );
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416 #endif
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417
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418 for( j=0; j<n20or4or2; j++ )
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419 {
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420 fft( nlen, seqVector2[j], 0 );
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421 fft( nlen, seqVector1[j], 0 );
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422 }
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423 #if 0
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424 fftfp = fopen( "seqVec2", "w" );
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425 fprintf( fftfp, "#after fft\n" );
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426 for( k=0; k<n20or4or2; k++ )
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427 {
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428 fprintf( fftfp, "#%c\n", amino[k] );
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429 for( l=0; l<nlen; l++ )
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430 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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431 }
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432 fclose( fftfp );
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433 system( "less seqVec2 < /dev/tty > /dev/tty" );
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434 #endif
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435
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436 for( k=0; k<n20or4or2; k++ )
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437 {
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438 for( l=0; l<nlen; l++ )
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439 calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
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440 }
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441 for( l=0; l<nlen; l++ )
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442 {
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443 naisekiNoWa[l].R = 0.0;
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444 naisekiNoWa[l].I = 0.0;
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445 for( k=0; k<n20or4or2; k++ )
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446 {
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447 naisekiNoWa[l].R += naiseki[k][l].R;
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448 naisekiNoWa[l].I += naiseki[k][l].I;
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449 }
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450 }
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451
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452 #if 0
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453 fftfp = fopen( "naisekiNoWa", "w" );
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454 fprintf( fftfp, "#Before fft\n" );
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455 for( l=0; l<nlen; l++ )
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456 fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
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457 fclose( fftfp );
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458 system( "less naisekiNoWa < /dev/tty > /dev/tty " );
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459 #endif
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460
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461 fft( -nlen, naisekiNoWa, 0 );
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462
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463 for( m=0; m<=nlen2; m++ )
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464 soukan[m] = naisekiNoWa[nlen2-m].R;
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465 for( m=nlen2+1; m<nlen; m++ )
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466 soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
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467
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468 #if 0
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469 fftfp = fopen( "naisekiNoWa", "w" );
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470 fprintf( fftfp, "#After fft\n" );
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471 for( l=0; l<nlen; l++ )
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472 fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
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473 fclose( fftfp );
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474 fftfp = fopen( "list.plot", "w" );
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475 fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
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476 fclose( fftfp );
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477 system( "/usr/bin/gnuplot list.plot &" );
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478 #endif
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479 #if 0
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480 fprintf( stderr, "frt write start\n" );
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481 fftfp = fopen( "frt", "w" );
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482 for( l=0; l<nlen; l++ )
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483 fprintf( fftfp, "%d %f\n", l-nlen2, soukan[l] );
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484 fclose( fftfp );
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485 system( "less frt < /dev/tty > /dev/tty" );
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486 #if 0
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487 fftfp = fopen( "list.plot", "w" );
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488 fprintf( fftfp, "plot 'frt'\n pause +1" );
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489 fclose( fftfp );
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490 system( "/usr/bin/gnuplot list.plot" );
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491 #endif
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492 #endif
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493
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494
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495 getKouho( kouho, NKOUHO, soukan, nlen );
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496
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497 #if 0
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498 for( i=0; i<NKOUHO; i++ )
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499 {
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500 fprintf( stdout, "kouho[%d] = %d\n", i, kouho[i] );
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501 }
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502 #endif
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503
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504 #if KEIKA
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505 fprintf( stderr, "Searching anchors ... " );
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506 #endif
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507 count = 0;
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508
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509
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510
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511 #define CAND 0
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512 #if CAND
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513 fftfp = fopen( "cand", "w" );
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514 fclose( fftfp );
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515 #endif
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516
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517 for( k=0; k<NKOUHO; k++ )
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518 {
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519
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520 lag = kouho[k];
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521 zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
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522 #if CAND
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523 fftfp = fopen( "cand", "a" );
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524 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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525 fprintf( fftfp, "%s\n", tmpptr1[0] );
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526 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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527 fprintf( fftfp, "%s\n", tmpptr2[0] );
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528 fprintf( fftfp, ">\n", k+1, lag );
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529 fclose( fftfp );
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530 #endif
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531 tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
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532
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533 if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
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534
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535
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536 if( tmpint == 0 ) break; // 060430 iinoka ?
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537 while( tmpint-- > 0 )
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538 {
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539 if( lag > 0 )
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540 {
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541 segment1[count].start = segment[count].start ;
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542 segment1[count].end = segment[count].end ;
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543 segment1[count].center = segment[count].center;
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544 segment1[count].score = segment[count].score;
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545
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546 segment2[count].start = segment[count].start + lag;
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547 segment2[count].end = segment[count].end + lag;
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548 segment2[count].center = segment[count].center + lag;
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549 segment2[count].score = segment[count].score ;
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550 }
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551 else
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552 {
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553 segment1[count].start = segment[count].start - lag;
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554 segment1[count].end = segment[count].end - lag;
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555 segment1[count].center = segment[count].center - lag;
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556 segment1[count].score = segment[count].score ;
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557
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558 segment2[count].start = segment[count].start ;
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559 segment2[count].end = segment[count].end ;
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560 segment2[count].center = segment[count].center;
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561 segment2[count].score = segment[count].score ;
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562 }
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563 #if 0
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564 fprintf( stderr, "Goukaku=%dko\n", tmpint );
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565 fprintf( stderr, "in 1 %d\n", segment1[count].center );
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566 fprintf( stderr, "in 2 %d\n", segment2[count].center );
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567 #endif
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568 segment1[count].pair = &segment2[count];
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569 segment2[count].pair = &segment1[count];
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570 count++;
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571 #if 0
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572 fprintf( stderr, "count=%d\n", count );
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573 #endif
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574 }
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575 }
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576
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577 #if 1
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578 fprintf( stderr, "done. (%d anchors)\r", count );
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579 #endif
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580 if( !count && fftNoAnchStop )
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581 ErrorExit( "Cannot detect anchor!" );
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582 #if 0
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583 fprintf( stdout, "RESULT before sort:\n" );
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584 for( l=0; l<count+1; l++ )
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585 {
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586 fprintf( stdout, "cut[%d]=%d, ", l, segment1[l].center );
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587 fprintf( stdout, "%d score = %f\n", segment2[l].center, segment1[l].score );
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588 }
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589 exit( 1 );
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590 #endif
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591
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592 #if KEIKA
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593 fprintf( stderr, "Aligning anchors ... " );
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594 #endif
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595 for( i=0; i<count; i++ )
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596 {
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597 sortedseg1[i] = &segment1[i];
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598 sortedseg2[i] = &segment2[i];
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599 }
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600
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601 {
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602 mymergesort( 0, count-1, sortedseg1 );
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603 mymergesort( 0, count-1, sortedseg2 );
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604 for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
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605 for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
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606
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607 if( crossscoresize < count+2 )
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608 {
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609 crossscoresize = count+2;
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610 fprintf( stderr, "####################################################################################################################################allocating crossscore, size = %d\n", crossscoresize );
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611 if( crossscore ) FreeDoubleMtx( crossscore );
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612 crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
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613 }
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614
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615 for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
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616 crossscore[i][j] = 0.0;
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617 for( i=0; i<count; i++ )
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618 {
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619 crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
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620 cut1[i+1] = sortedseg1[i]->center;
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621 cut2[i+1] = sortedseg2[i]->center;
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622 }
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623
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624 #if DEBUG
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625 fprintf( stderr, "AFTER SORT\n" );
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626 for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start );
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627 #endif
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628
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629 crossscore[0][0] = 10000000.0;
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630 cut1[0] = 0;
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631 cut2[0] = 0;
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632 crossscore[count+1][count+1] = 10000000.0;
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633 cut1[count+1] = len1;
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634 cut2[count+1] = len2;
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635 count += 2;
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636 count0 = count;
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637
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638 blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
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639 }
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640 if( fftkeika )
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641 {
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642 if( count0 > count )
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643 {
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644 fprintf( stderr, "REPEAT!? \n" );
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645 if( fftRepeatStop ) exit( 1 );
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646 }
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647 #if KEIKA
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648 else
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649 fprintf( stderr, "done\n" );
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650 fprintf( stderr, "done. (%d anchors)\n", count );
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651 #endif
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652 }
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653
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654 #if 0
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655 fftfp = fopen( "fft", "a" );
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656 fprintf( fftfp, "RESULT after sort:\n" );
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657 for( l=0; l<count; l++ )
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658 {
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659 fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
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660 fprintf( fftfp, "%d\n", segment2[l].center );
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661 }
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662 fclose( fftfp );
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663 #endif
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664
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665 #if 0
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666 fftfp = fopen( "fft", "a" );
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667 fprintf( fftfp, "RESULT after sort:\n" );
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668 for( l=0; l<count; l++ )
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669 {
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670 fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] );
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671 }
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672 fclose( fftfp );
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673 #endif
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674
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675 #if KEIKA
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676 fprintf( trap_g, "Devided to %d segments\n", count-1 );
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677 fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
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678 #endif
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679
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680 totallen = 0;
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681 for( j=0; j<clus1; j++ ) result1[j][0] = 0;
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682 for( j=0; j<clus2; j++ ) result2[j][0] = 0;
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683 for( i=0; i<count-1; i++ )
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684 {
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685 if( i == 0 ) headgp = outgap; else headgp = 1;
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686 if( i == count-2 ) tailgp = outgap; else tailgp = 1;
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687
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688 #if DEBUG
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689 fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
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690 #else
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691 #if KEIKA
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692 fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
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693 #endif
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694 #endif
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695 for( j=0; j<clus1; j++ )
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696 {
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697 strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
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698 tmpres1[j][cut1[i+1]-cut1[i]] = 0;
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699 }
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700 for( j=0; j<clus2; j++ )
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701 {
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702 strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
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703 tmpres2[j][cut2[i+1]-cut2[i]] = 0;
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704 }
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diff changeset
705 switch( alg )
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706 {
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diff changeset
707 case( 'a' ):
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nick
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diff changeset
708 Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
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diff changeset
709 break;
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nick
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diff changeset
710 case( 'M' ):
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diff changeset
711 MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
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diff changeset
712 break;
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nick
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diff changeset
713 case( 'A' ):
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nick
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diff changeset
714 if( clus1 == 1 && clus2 == 1 )
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nick
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diff changeset
715 G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
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diff changeset
716 else
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diff changeset
717 A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
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diff changeset
718 break;
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diff changeset
719 default:
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diff changeset
720 fprintf( stderr, "alg = %c\n", alg );
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diff changeset
721 ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
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diff changeset
722 break;
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diff changeset
723 }
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diff changeset
724
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725 nlen = strlen( tmpres1[0] );
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diff changeset
726 if( totallen + nlen > alloclen ) ErrorExit( "LENGTH OVER in Falign\n " );
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diff changeset
727 for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
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diff changeset
728 for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
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diff changeset
729 totallen += nlen;
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diff changeset
730 #if 0
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731 fprintf( stderr, "%4d\r", totallen );
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diff changeset
732 fprintf( stderr, "\n\n" );
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nick
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diff changeset
733 for( j=0; j<clus1; j++ )
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diff changeset
734 {
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735 fprintf( stderr, "%s\n", tmpres1[j] );
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736 }
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diff changeset
737 fprintf( stderr, "-------\n" );
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nick
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diff changeset
738 for( j=0; j<clus2; j++ )
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739 {
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740 fprintf( stderr, "%s\n", tmpres2[j] );
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741 }
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742 #endif
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743 }
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diff changeset
744 #if KEIKA
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diff changeset
745 fprintf( stderr, "DP ... done \n" );
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diff changeset
746 #endif
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747
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748 for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
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diff changeset
749 for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
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diff changeset
750 #if 0
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diff changeset
751 for( j=0; j<clus1; j++ )
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752 {
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753 fprintf( stderr, "%s\n", result1[j] );
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754 }
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755 fprintf( stderr, "- - - - - - - - - - -\n" );
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diff changeset
756 for( j=0; j<clus2; j++ )
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diff changeset
757 {
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758 fprintf( stderr, "%s\n", result2[j] );
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759 }
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diff changeset
760 #endif
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diff changeset
761 return( 0.0 );
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diff changeset
762 }
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763
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diff changeset
764
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diff changeset
765
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diff changeset
766 float Falign( double **offsetmtx, double ***scoringmatrices, double **n_dynamicmtx,
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diff changeset
767 char **seq1, char **seq2,
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diff changeset
768 double *eff1, double *eff2,
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diff changeset
769 double **eff1s, double **eff2s,
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diff changeset
770 int clus1, int clus2,
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diff changeset
771 int alloclen, int *fftlog,
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nick
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diff changeset
772 int *chudanpt, int chudanref, int *chudanres )
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773 {
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diff changeset
774 int i, j, k, l, m, maxk;
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diff changeset
775 int nlen, nlen2, nlen4;
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diff changeset
776 static TLS int prevalloclen = 0;
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diff changeset
777 static TLS int crossscoresize = 0;
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diff changeset
778 static TLS char **tmpseq1 = NULL;
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779 static TLS char **tmpseq2 = NULL;
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diff changeset
780 static TLS char **tmpptr1 = NULL;
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diff changeset
781 static TLS char **tmpptr2 = NULL;
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diff changeset
782 static TLS char **tmpres1 = NULL;
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diff changeset
783 static TLS char **tmpres2 = NULL;
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784 static TLS char **result1 = NULL;
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785 static TLS char **result2 = NULL;
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diff changeset
786 #if RND
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diff changeset
787 static TLS char **rndseq1 = NULL;
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788 static TLS char **rndseq2 = NULL;
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diff changeset
789 #endif
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790 static TLS Fukusosuu **seqVector1 = NULL;
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791 static TLS Fukusosuu **seqVector2 = NULL;
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diff changeset
792 static TLS Fukusosuu **naiseki = NULL;
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793 static TLS Fukusosuu *naisekiNoWa = NULL;
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diff changeset
794 static TLS double *soukan = NULL;
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795 static TLS double **crossscore = NULL;
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diff changeset
796 int nlentmp;
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797 static TLS int *kouho = NULL;
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diff changeset
798 static TLS Segment *segment = NULL;
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diff changeset
799 static TLS Segment *segment1 = NULL;
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diff changeset
800 static TLS Segment *segment2 = NULL;
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diff changeset
801 static TLS Segment **sortedseg1 = NULL;
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802 static TLS Segment **sortedseg2 = NULL;
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diff changeset
803 static TLS int *cut1 = NULL;
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diff changeset
804 static TLS int *cut2 = NULL;
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diff changeset
805 static TLS char *sgap1, *egap1, *sgap2, *egap2;
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diff changeset
806 static TLS int localalloclen = 0;
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diff changeset
807 int lag;
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808 int tmpint;
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809 int count, count0;
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diff changeset
810 int len1, len2;
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811 int totallen;
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diff changeset
812 float totalscore;
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diff changeset
813 float dumfl = 0.0;
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diff changeset
814 int headgp, tailgp;
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diff changeset
815
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816
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817 if( seq1 == NULL )
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818 {
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819 if( result1 )
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820 {
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821 // fprintf( stderr, "Freeing localarrays in Falign\n" );
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822 localalloclen = 0;
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823 prevalloclen = 0;
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824 crossscoresize = 0;
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825 mymergesort( 0, 0, NULL );
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826 alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
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827 fft( 0, NULL, 1 );
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828 A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
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829 A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
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830 G__align11( NULL, NULL, NULL, 0, 0, 0 );
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831 blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
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832 if( crossscore ) FreeDoubleMtx( crossscore );
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833 crossscore = NULL;
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834 FreeCharMtx( result1 ); result1 = NULL;
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835 FreeCharMtx( result2 );
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836 FreeCharMtx( tmpres1 );
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837 FreeCharMtx( tmpres2 );
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838 FreeCharMtx( tmpseq1 );
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839 FreeCharMtx( tmpseq2 );
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840 free( sgap1 );
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841 free( egap1 );
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842 free( sgap2 );
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843 free( egap2 );
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844 free( kouho );
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845 free( cut1 );
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846 free( cut2 );
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847 free( tmpptr1 );
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848 free( tmpptr2 );
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849 free( segment );
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850 free( segment1 );
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851 free( segment2 );
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852 free( sortedseg1 );
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853 free( sortedseg2 );
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854 if( !kobetsubunkatsu )
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855 {
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856 FreeFukusosuuMtx ( seqVector1 );
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857 FreeFukusosuuMtx ( seqVector2 );
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858 FreeFukusosuuVec( naisekiNoWa );
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859 FreeFukusosuuMtx( naiseki );
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860 FreeDoubleVec( soukan );
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861 }
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862 }
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863 else
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864 {
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865 // fprintf( stderr, "Did not allocate localarrays in Falign\n" );
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866 }
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867
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868 return( 0.0 );
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869 }
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870
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871 len1 = strlen( seq1[0] );
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872 len2 = strlen( seq2[0] );
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873 nlentmp = MAX( len1, len2 );
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874
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875 nlen = 1;
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876 while( nlentmp >= nlen ) nlen <<= 1;
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877 #if 0
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878 fprintf( stderr, "### nlen = %d\n", nlen );
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879 #endif
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880
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881 nlen2 = nlen/2; nlen4 = nlen2 / 2;
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882
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883 #if DEBUG
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884 fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
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885 fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
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886 #endif
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887
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888 if( prevalloclen != alloclen ) // Falign_noudp mo kaeru
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889 {
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890 if( prevalloclen )
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891 {
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892 FreeCharMtx( result1 );
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893 FreeCharMtx( result2 );
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894 FreeCharMtx( tmpres1 );
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895 FreeCharMtx( tmpres2 );
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896 }
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897 // fprintf( stderr, "\n\n\nreallocating ...\n" );
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898 result1 = AllocateCharMtx( njob, alloclen );
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899 result2 = AllocateCharMtx( njob, alloclen );
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900 tmpres1 = AllocateCharMtx( njob, alloclen );
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901 tmpres2 = AllocateCharMtx( njob, alloclen );
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902 prevalloclen = alloclen;
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903 }
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904 if( !localalloclen )
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905 {
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906 sgap1 = AllocateCharVec( njob );
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907 egap1 = AllocateCharVec( njob );
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908 sgap2 = AllocateCharVec( njob );
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909 egap2 = AllocateCharVec( njob );
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910 kouho = AllocateIntVec( NKOUHO );
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911 cut1 = AllocateIntVec( MAXSEG );
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912 cut2 = AllocateIntVec( MAXSEG );
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913 tmpptr1 = AllocateCharMtx( njob, 0 );
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914 tmpptr2 = AllocateCharMtx( njob, 0 );
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915 // crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
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916 segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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917 segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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918 segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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919 sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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920 sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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921 if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
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922 ErrorExit( "Allocation error\n" );
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923
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924 if ( scoremtx == -1 ) n20or4or2 = 1;
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925 else if( fftscore ) n20or4or2 = 1;
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926 else n20or4or2 = 20;
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927 }
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928 if( localalloclen < nlen )
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929 {
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930 if( localalloclen )
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931 {
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932 #if 1
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933 if( !kobetsubunkatsu )
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934 {
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935 FreeFukusosuuMtx ( seqVector1 );
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936 FreeFukusosuuMtx ( seqVector2 );
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937 FreeFukusosuuVec( naisekiNoWa );
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938 FreeFukusosuuMtx( naiseki );
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939 FreeDoubleVec( soukan );
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940 }
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941 FreeCharMtx( tmpseq1 );
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942 FreeCharMtx( tmpseq2 );
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943 #endif
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944 #if RND
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945 FreeCharMtx( rndseq1 );
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946 FreeCharMtx( rndseq2 );
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947 #endif
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948 }
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949
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950 tmpseq1 = AllocateCharMtx( njob, nlen );
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951 tmpseq2 = AllocateCharMtx( njob, nlen );
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952 if( !kobetsubunkatsu )
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953 {
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954 naisekiNoWa = AllocateFukusosuuVec( nlen );
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955 naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
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956 seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
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957 seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
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958 soukan = AllocateDoubleVec( nlen+1 );
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959 }
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960 #if RND
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961 rndseq1 = AllocateCharMtx( njob, nlen );
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962 rndseq2 = AllocateCharMtx( njob, nlen );
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963 for( i=0; i<njob; i++ )
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964 {
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965 generateRndSeq( rndseq1[i], nlen );
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966 generateRndSeq( rndseq2[i], nlen );
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967 }
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968 #endif
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969 localalloclen = nlen;
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970 }
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971
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972 for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
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973 for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
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974
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975 #if 0
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976 fftfp = fopen( "input_of_Falign", "w" );
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977 fprintf( fftfp, "nlen = %d\n", nlen );
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978 fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
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979 for( i=0; i<clus1; i++ )
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980 fprintf( fftfp, "%s\n", seq1[i] );
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981 fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
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982 for( i=0; i<clus2; i++ )
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983 fprintf( fftfp, "%s\n", seq2[i] );
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984 fclose( fftfp );
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985 system( "less input_of_Falign < /dev/tty > /dev/tty" );
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986 #endif
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987 if( !kobetsubunkatsu )
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988 {
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989 if( fftkeika ) fprintf( stderr, " FFT ... " );
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990
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991 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
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992 if( fftscore && scoremtx != -1 )
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993 {
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994 for( i=0; i<clus1; i++ )
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995 {
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996 #if 1
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997 seq_vec_5( seqVector1[0], polarity, volume, eff1[i], tmpseq1[i] );
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998 #else
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999 seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
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1000 seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
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1001 #endif
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1002 }
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1003 }
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1004 else
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1005 {
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1006 #if 0
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1007 for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
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1008 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
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1009 #else
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1010 for( i=0; i<clus1; i++ )
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1011 seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
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1012 #endif
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1013 }
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1014 #if RND
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1015 for( i=0; i<clus1; i++ )
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1016 {
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1017 vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
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1018 }
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1019 #endif
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1020 #if 0
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1021 fftfp = fopen( "seqVec", "w" );
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1022 fprintf( fftfp, "before transform\n" );
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1023 for( k=0; k<n20or4or2; k++ )
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1024 {
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1025 fprintf( fftfp, "nlen=%d\n", nlen );
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1026 fprintf( fftfp, "%c\n", amino[k] );
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1027 for( l=0; l<nlen; l++ )
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1028 fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
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1029 }
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1030 fclose( fftfp );
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1031 system( "less seqVec < /dev/tty > /dev/tty" );
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1032 #endif
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1033
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1034 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
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1035 if( fftscore && scoremtx != -1 )
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1036 {
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1037 for( i=0; i<clus2; i++ )
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1038 {
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1039 #if 1
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1040 seq_vec_5( seqVector2[0], polarity, volume, eff2[i], tmpseq2[i] );
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1041 #else
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1042 seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
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1043 seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
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1044 #endif
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1045 }
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1046 }
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1047 else
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1048 {
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1049 #if 0
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1050 for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
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1051 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
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1052 #else
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1053 for( i=0; i<clus2; i++ )
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1054 seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
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1055 #endif
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1056 }
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1057 #if RND
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1058 for( i=0; i<clus2; i++ )
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1059 {
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1060 vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
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1061 }
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1062 #endif
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1063
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1064 #if 0
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1065 fftfp = fopen( "seqVec2", "w" );
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1066 fprintf( fftfp, "before fft\n" );
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1067 for( k=0; k<n20or4or2; k++ )
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1068 {
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1069 fprintf( fftfp, "%c\n", amino[k] );
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1070 for( l=0; l<nlen; l++ )
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1071 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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1072 }
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1073 fclose( fftfp );
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1074 system( "less seqVec2 < /dev/tty > /dev/tty" );
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1075 #endif
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1076
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1077 for( j=0; j<n20or4or2; j++ )
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1078 {
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1079 fft( nlen, seqVector2[j], 0 );
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1080 fft( nlen, seqVector1[j], 0 );
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1081 }
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1082 #if 0
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1083 fftfp = fopen( "seqVec2", "w" );
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1084 fprintf( fftfp, "#after fft\n" );
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1085 for( k=0; k<n20or4or2; k++ )
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1086 {
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1087 fprintf( fftfp, "#%c\n", amino[k] );
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1088 for( l=0; l<nlen; l++ )
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1089 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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1090 }
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1091 fclose( fftfp );
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1092 system( "less seqVec2 < /dev/tty > /dev/tty" );
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1093 #endif
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1094
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1095 for( k=0; k<n20or4or2; k++ )
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1096 {
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1097 for( l=0; l<nlen; l++ )
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1098 calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
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1099 }
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1100 for( l=0; l<nlen; l++ )
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1101 {
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1102 naisekiNoWa[l].R = 0.0;
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1103 naisekiNoWa[l].I = 0.0;
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1104 for( k=0; k<n20or4or2; k++ )
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1105 {
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1106 naisekiNoWa[l].R += naiseki[k][l].R;
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1107 naisekiNoWa[l].I += naiseki[k][l].I;
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1108 }
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1109 }
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1110
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1111 #if 0
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1112 fftfp = fopen( "naisekiNoWa", "w" );
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1113 fprintf( fftfp, "#Before fft\n" );
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1114 for( l=0; l<nlen; l++ )
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1115 fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
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1116 fclose( fftfp );
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1117 system( "less naisekiNoWa < /dev/tty > /dev/tty " );
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1118 #endif
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1119
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1120 fft( -nlen, naisekiNoWa, 0 );
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1121
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1122 for( m=0; m<=nlen2; m++ )
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1123 soukan[m] = naisekiNoWa[nlen2-m].R;
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1124 for( m=nlen2+1; m<nlen; m++ )
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1125 soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
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1126
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1127 #if 0
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1128 fftfp = fopen( "naisekiNoWa", "w" );
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1129 fprintf( fftfp, "#After fft\n" );
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1130 for( l=0; l<nlen; l++ )
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1131 fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
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1132 fclose( fftfp );
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1133 fftfp = fopen( "list.plot", "w" );
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1134 fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
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1135 fclose( fftfp );
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1136 system( "/usr/bin/gnuplot list.plot &" );
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1137 #endif
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1138 #if 0
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1139 fprintf( stderr, "soukan\n" );
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1140 for( l=0; l<nlen; l++ )
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1141 fprintf( stderr, "%d %f\n", l-nlen2, soukan[l] );
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1142 #if 0
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1143 fftfp = fopen( "list.plot", "w" );
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1144 fprintf( fftfp, "plot 'frt'\n pause +1" );
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1145 fclose( fftfp );
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1146 system( "/usr/bin/gnuplot list.plot" );
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1147 #endif
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1148 #endif
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1149
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1150
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1151 getKouho( kouho, NKOUHO, soukan, nlen );
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1152
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1153 #if 0
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1154 for( i=0; i<NKOUHO; i++ )
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1155 {
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1156 fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
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1157 }
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1158 #endif
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1159 }
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1160
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1161 #if KEIKA
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1162 fprintf( stderr, "Searching anchors ... " );
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1163 #endif
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1164 count = 0;
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1165
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1166
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1167
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1168 #define CAND 0
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1169 #if CAND
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1170 fftfp = fopen( "cand", "w" );
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1171 fclose( fftfp );
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1172 #endif
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1173 if( kobetsubunkatsu )
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1174 {
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1175 maxk = 1;
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1176 kouho[0] = 0;
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1177 }
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1178 else
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1179 {
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1180 maxk = NKOUHO;
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1181 }
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1182
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1183 for( k=0; k<maxk; k++ )
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1184 {
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1185 lag = kouho[k];
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1186 if( lag <= -len1 || len2 <= lag ) continue;
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1187 zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
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1188 #if CAND
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1189 fftfp = fopen( "cand", "a" );
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1190 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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1191 fprintf( fftfp, "%s\n", tmpptr1[0] );
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1192 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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1193 fprintf( fftfp, "%s\n", tmpptr2[0] );
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1194 fprintf( fftfp, ">\n", k+1, lag );
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1195 fclose( fftfp );
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1196 #endif
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1197
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1198 // fprintf( stderr, "lag = %d\n", lag );
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1199 tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
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1200
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1201 // if( lag == -50 ) exit( 1 );
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1202
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1203 if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
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1204
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1205
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1206 if( tmpint == 0 ) break; // 060430 iinoka ?
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1207 while( tmpint-- > 0 )
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1208 {
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1209 #if 0
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1210 if( segment[count].end - segment[count].start < fftWinSize )
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1211 {
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1212 count++;
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1213 continue;
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1214 }
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1215 #endif
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1216 if( lag > 0 )
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1217 {
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1218 segment1[count].start = segment[count].start ;
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1219 segment1[count].end = segment[count].end ;
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1220 segment1[count].center = segment[count].center;
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1221 segment1[count].score = segment[count].score;
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1222
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1223 segment2[count].start = segment[count].start + lag;
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1224 segment2[count].end = segment[count].end + lag;
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1225 segment2[count].center = segment[count].center + lag;
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1226 segment2[count].score = segment[count].score ;
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1227 }
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1228 else
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1229 {
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1230 segment1[count].start = segment[count].start - lag;
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1231 segment1[count].end = segment[count].end - lag;
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1232 segment1[count].center = segment[count].center - lag;
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1233 segment1[count].score = segment[count].score ;
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1234
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1235 segment2[count].start = segment[count].start ;
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1236 segment2[count].end = segment[count].end ;
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1237 segment2[count].center = segment[count].center;
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1238 segment2[count].score = segment[count].score ;
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1239 }
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1240 #if 0
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1241 fprintf( stderr, "in 1 %d\n", segment1[count].center );
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1242 fprintf( stderr, "in 2 %d\n", segment2[count].center );
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1243 #endif
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1244 segment1[count].pair = &segment2[count];
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1245 segment2[count].pair = &segment1[count];
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1246 count++;
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1247 }
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1248 }
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1249 #if 0
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1250 if( !kobetsubunkatsu && fftkeika )
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1251 fprintf( stderr, "%d anchors found\r", count );
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1252 #endif
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1253 if( !count && fftNoAnchStop )
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1254 ErrorExit( "Cannot detect anchor!" );
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1255 #if 0
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1256 fprintf( stderr, "RESULT before sort:\n" );
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1257 for( l=0; l<count+1; l++ )
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1258 {
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1259 fprintf( stderr, "cut[%d]=%d, ", l, segment1[l].center );
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1260 fprintf( stderr, "%d score = %f\n", segment2[l].center, segment1[l].score );
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1261 }
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1262 #endif
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1263
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1264 #if KEIKA
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1265 fprintf( stderr, "done. (%d anchors)\n", count );
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1266 fprintf( stderr, "Aligning anchors ... " );
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1267 #endif
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1268 for( i=0; i<count; i++ )
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1269 {
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1270 sortedseg1[i] = &segment1[i];
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diff changeset
1271 sortedseg2[i] = &segment2[i];
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1272 }
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1273 #if 0
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1274 tmpsort( count, sortedseg1 );
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1275 tmpsort( count, sortedseg2 );
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1276 qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
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1277 qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
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1278 #else
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1279 mymergesort( 0, count-1, sortedseg1 );
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1280 mymergesort( 0, count-1, sortedseg2 );
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1281 #endif
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diff changeset
1282 for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
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nick
parents:
diff changeset
1283 for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
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nick
parents:
diff changeset
1284
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nick
parents:
diff changeset
1285
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nick
parents:
diff changeset
1286 if( kobetsubunkatsu )
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nick
parents:
diff changeset
1287 {
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nick
parents:
diff changeset
1288 for( i=0; i<count; i++ )
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nick
parents:
diff changeset
1289 {
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nick
parents:
diff changeset
1290 cut1[i+1] = sortedseg1[i]->center;
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nick
parents:
diff changeset
1291 cut2[i+1] = sortedseg2[i]->center;
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nick
parents:
diff changeset
1292 }
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nick
parents:
diff changeset
1293 cut1[0] = 0;
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nick
parents:
diff changeset
1294 cut2[0] = 0;
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nick
parents:
diff changeset
1295 cut1[count+1] = len1;
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nick
parents:
diff changeset
1296 cut2[count+1] = len2;
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nick
parents:
diff changeset
1297 count += 2;
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diff changeset
1298 }
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diff changeset
1299 else
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parents:
diff changeset
1300 {
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nick
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diff changeset
1301 if( crossscoresize < count+2 )
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1302 {
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diff changeset
1303 crossscoresize = count+2;
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nick
parents:
diff changeset
1304 #if 1
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nick
parents:
diff changeset
1305 if( fftkeika ) fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
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parents:
diff changeset
1306 #endif
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nick
parents:
diff changeset
1307 if( crossscore ) FreeDoubleMtx( crossscore );
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nick
parents:
diff changeset
1308 crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
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diff changeset
1309 }
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parents:
diff changeset
1310 for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
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nick
parents:
diff changeset
1311 crossscore[i][j] = 0.0;
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nick
parents:
diff changeset
1312 for( i=0; i<count; i++ )
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diff changeset
1313 {
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diff changeset
1314 crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
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nick
parents:
diff changeset
1315 cut1[i+1] = sortedseg1[i]->center;
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nick
parents:
diff changeset
1316 cut2[i+1] = sortedseg2[i]->center;
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diff changeset
1317 }
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nick
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diff changeset
1318
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nick
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diff changeset
1319 #if 0
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diff changeset
1320 fprintf( stderr, "AFTER SORT\n" );
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nick
parents:
diff changeset
1321 for( i=0; i<count+1; i++ ) fprintf( stderr, "%d, %d\n", cut1[i], cut2[i] );
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nick
parents:
diff changeset
1322 fprintf( stderr, "crossscore = \n" );
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nick
parents:
diff changeset
1323 for( i=0; i<count+1; i++ )
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diff changeset
1324 {
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nick
parents:
diff changeset
1325 for( j=0; j<count+1; j++ )
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nick
parents:
diff changeset
1326 fprintf( stderr, "%.0f ", crossscore[i][j] );
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nick
parents:
diff changeset
1327 fprintf( stderr, "\n" );
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parents:
diff changeset
1328 }
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parents:
diff changeset
1329 #endif
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nick
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diff changeset
1330
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nick
parents:
diff changeset
1331 crossscore[0][0] = 10000000.0;
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nick
parents:
diff changeset
1332 cut1[0] = 0;
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nick
parents:
diff changeset
1333 cut2[0] = 0;
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nick
parents:
diff changeset
1334 crossscore[count+1][count+1] = 10000000.0;
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nick
parents:
diff changeset
1335 cut1[count+1] = len1;
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nick
parents:
diff changeset
1336 cut2[count+1] = len2;
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nick
parents:
diff changeset
1337 count += 2;
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nick
parents:
diff changeset
1338 count0 = count;
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nick
parents:
diff changeset
1339
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parents:
diff changeset
1340 blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
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parents:
diff changeset
1341
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nick
parents:
diff changeset
1342 // if( count-count0 )
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nick
parents:
diff changeset
1343 // fprintf( stderr, "%d unused anchors\n", count0-count );
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diff changeset
1344
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diff changeset
1345 if( !kobetsubunkatsu && fftkeika )
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nick
parents:
diff changeset
1346 fprintf( stderr, "%d anchors found\n", count );
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nick
parents:
diff changeset
1347 if( fftkeika )
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nick
parents:
diff changeset
1348 {
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nick
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diff changeset
1349 if( count0 > count )
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nick
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diff changeset
1350 {
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nick
parents:
diff changeset
1351 #if 0
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diff changeset
1352 fprintf( stderr, "\7 REPEAT!? \n" );
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nick
parents:
diff changeset
1353 #else
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parents:
diff changeset
1354 fprintf( stderr, "REPEAT!? \n" );
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nick
parents:
diff changeset
1355 #endif
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parents:
diff changeset
1356 if( fftRepeatStop ) exit( 1 );
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diff changeset
1357 }
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nick
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diff changeset
1358 #if KEIKA
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diff changeset
1359 else fprintf( stderr, "done\n" );
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parents:
diff changeset
1360 #endif
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diff changeset
1361 }
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diff changeset
1362 }
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nick
parents:
diff changeset
1363
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nick
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diff changeset
1364 #if 0
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nick
parents:
diff changeset
1365 fftfp = fopen( "fft", "a" );
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nick
parents:
diff changeset
1366 fprintf( fftfp, "RESULT after sort:\n" );
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nick
parents:
diff changeset
1367 for( l=0; l<count; l++ )
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parents:
diff changeset
1368 {
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parents:
diff changeset
1369 fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
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parents:
diff changeset
1370 fprintf( fftfp, "%d\n", segment2[l].center );
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diff changeset
1371 }
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diff changeset
1372 fclose( fftfp );
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parents:
diff changeset
1373 #endif
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parents:
diff changeset
1374
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parents:
diff changeset
1375 #if 0
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diff changeset
1376 fprintf( stderr, "RESULT after blckalign:\n" );
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nick
parents:
diff changeset
1377 for( l=0; l<count+1; l++ )
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1378 {
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diff changeset
1379 fprintf( stderr, "cut : %d %d\n", cut1[l], cut2[l] );
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parents:
diff changeset
1380 }
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nick
parents:
diff changeset
1381 #endif
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nick
parents:
diff changeset
1382
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nick
parents:
diff changeset
1383 #if 0
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nick
parents:
diff changeset
1384 fprintf( trap_g, "Devided to %d segments\n", count-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1385 fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1386 #endif
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nick
parents:
diff changeset
1387
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nick
parents:
diff changeset
1388 totallen = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1389 for( j=0; j<clus1; j++ ) result1[j][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1390 for( j=0; j<clus2; j++ ) result2[j][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1391 totalscore = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1392 *fftlog = -1;
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nick
parents:
diff changeset
1393 for( i=0; i<count-1; i++ )
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nick
parents:
diff changeset
1394 {
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nick
parents:
diff changeset
1395 *fftlog += 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1396 if( i == 0 ) headgp = outgap; else headgp = 1;
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nick
parents:
diff changeset
1397 if( i == count-2 ) tailgp = outgap; else tailgp = 1;
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diff changeset
1398
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diff changeset
1399
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1400 if( cut1[i] ) // chuui
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1401 {
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1402 // getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
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diff changeset
1403 // getkyokaigap( sgap2, tmpres2, nlen-1, clus2 );
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diff changeset
1404 getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
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diff changeset
1405 getkyokaigap( sgap2, tmpres2, nlen-1, clus2 );
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1406 }
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1407 else
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diff changeset
1408 {
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1409 for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
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1410 for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
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1411 }
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1412 if( cut1[i+1] != len1 ) // chuui
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1413 {
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1414 getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
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1415 getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
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1416 }
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1417 else
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1418 {
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1419 for( j=0; j<clus1; j++ ) egap1[j] = 'o';
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1420 for( j=0; j<clus2; j++ ) egap2[j] = 'o';
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1421 }
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1422 #if 0
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1423 {
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1424 fprintf( stderr, "kyokkaigap1(%d)=", cut1[i]-1 );
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1425 for( j=0; j<clus1; j++ )
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1426 fprintf( stderr, "%c", sgap1[j] );
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1427 fprintf( stderr, "=kyokkaigap1-start\n" );
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1428 }
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1429 {
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1430 fprintf( stderr, "kyokkaigap2(%d)=", cut2[i]-1 );
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1431 for( j=0; j<clus2; j++ )
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1432 fprintf( stderr, "%c", sgap2[j] );
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1433 fprintf( stderr, "=kyokkaigap2-start\n" );
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1434 }
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1435 {
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1436 fprintf( stderr, "kyokkaigap1(%d)=", cut1[i]-1 );
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1437 for( j=0; j<clus1; j++ )
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1438 fprintf( stderr, "%c", egap1[j] );
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1439 fprintf( stderr, "=kyokkaigap1-end\n" );
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1440 }
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1441 {
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1442 fprintf( stderr, "kyokkaigap2(%d)=", cut2[i]-1 );
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1443 for( j=0; j<clus2; j++ )
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1444 fprintf( stderr, "%c", egap2[j] );
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1445 fprintf( stderr, "=kyokkaigap2-end\n" );
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1446 }
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1447 #endif
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1448
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1449 #if DEBUG
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1450 fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
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1451 #else
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diff changeset
1452 #if KEIKA
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1453 fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
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1454 #endif
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1455 #endif
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1456 for( j=0; j<clus1; j++ )
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1457 {
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1458 strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
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1459 tmpres1[j][cut1[i+1]-cut1[i]] = 0;
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1460 }
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1461 if( kobetsubunkatsu && fftkeika ) commongappick( clus1, tmpres1 ); //dvtditr に呼ばれたとき fftkeika=1
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1462 // if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
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diff changeset
1463 for( j=0; j<clus2; j++ )
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1464 {
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1465 strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
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1466 tmpres2[j][cut2[i+1]-cut2[i]] = 0;
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1467 }
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1468 if( kobetsubunkatsu && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr に呼ばれたとき fftkeika=1
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1469 // if( kobetsubunkatsu ) commongappick( clus2, tmpres2 );
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1470
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1471 if( constraint )
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1472 {
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1473 fprintf( stderr, "Not supported\n" );
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1474 exit( 1 );
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1475 }
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1476 #if 0
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1477 fprintf( stderr, "i=%d, before alignment", i );
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1478 fprintf( stderr, "%4d\n", totallen );
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1479 fprintf( stderr, "\n\n" );
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1480 for( j=0; j<clus1; j++ )
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1481 {
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1482 fprintf( stderr, "%s\n", tmpres1[j] );
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1483 }
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1484 fprintf( stderr, "-------\n" );
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1485 for( j=0; j<clus2; j++ )
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1486 {
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1487 fprintf( stderr, "%s\n", tmpres2[j] );
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1488 }
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1489 #endif
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1490
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1491 #if 0
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1492 fprintf( stdout, "writing input\n" );
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1493 for( j=0; j<clus1; j++ )
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1494 {
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1495 fprintf( stdout, ">%d of GROUP1\n", j );
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1496 fprintf( stdout, "%s\n", tmpres1[j] );
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1497 }
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1498 for( j=0; j<clus2; j++ )
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1499 {
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1500 fprintf( stdout, ">%d of GROUP2\n", j );
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1501 fprintf( stdout, "%s\n", tmpres2[j] );
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1502 }
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1503 fflush( stdout );
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1504 #endif
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1505 switch( alg )
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1506 {
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1507 case( 'a' ):
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1508 totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
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1509 break;
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1510 case( 'M' ):
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diff changeset
1511 if( scoringmatrices ) // called by tditeration.c
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1512 totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
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1513 else
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1514 totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
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1515 // totalscore += MSalignmm( n_dis_consweight_multi, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
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1516 break;
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1517 case( 'A' ):
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1518 if( clus1 == 1 && clus2 == 1 )
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1519 {
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1520 totalscore += G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
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1521 }
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1522 else
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1523 {
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1524 if( scoringmatrices ) // called by tditeration.c
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1525 {
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1526 totalscore += A__align_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
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1527 }
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1528 else
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1529 totalscore += A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
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1530 }
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1531 break;
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1532 default:
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1533 fprintf( stderr, "alg = %c\n", alg );
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1534 ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
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1535 break;
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1536 }
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1537
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1538 #ifdef enablemultithread
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1539 if( chudanres && *chudanres )
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1540 {
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1541 // fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );
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1542 return( -1.0 );
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1543 }
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1544 #endif
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1545
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1546 nlen = strlen( tmpres1[0] );
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1547 if( totallen + nlen > alloclen )
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1548 {
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1549 fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
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1550 ErrorExit( "LENGTH OVER in Falign\n " );
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1551 }
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1552 for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
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1553 for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
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1554 totallen += nlen;
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diff changeset
1555 #if 0
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1556 fprintf( stderr, "$#####$$$$ i=%d", i );
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diff changeset
1557 fprintf( stderr, "%4d\n", totallen );
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1558 fprintf( stderr, "\n\n" );
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1559 for( j=0; j<clus1; j++ )
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1560 {
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1561 fprintf( stderr, "%s\n", tmpres1[j] );
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1562 }
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1563 fprintf( stderr, "-------\n" );
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1564 for( j=0; j<clus2; j++ )
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1565 {
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1566 fprintf( stderr, "%s\n", tmpres2[j] );
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1567 }
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1568 #endif
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1569 }
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1570 #if KEIKA
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1571 fprintf( stderr, "DP ... done \n" );
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1572 #endif
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1573
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1574 for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
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1575 for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
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1576 #if 0
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1577 for( j=0; j<clus1; j++ )
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1578 {
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1579 fprintf( stderr, "in Falign, %s\n", result1[j] );
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1580 }
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1581 fprintf( stderr, "- - - - - - - - - - -\n" );
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1582 for( j=0; j<clus2; j++ )
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1583 {
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1584 fprintf( stderr, "in Falign, %s\n", result2[j] );
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1585 }
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1586 #endif
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1587 return( totalscore );
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1588 }
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1589
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1590
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1591
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1592
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1593
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1594
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1595
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1596
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1597 /*
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1598 sakujo wo kentou (2010/10/05)
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1599 */
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1600 float Falign_udpari_long(
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1601 double **offsetmtx, double ***scoringmatrices,
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1602 double **n_dynamicmtx,
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1603 char **seq1, char **seq2,
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1604 double *eff1, double *eff2,
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1605 double **eff1s, double **eff2s,
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1606 int clus1, int clus2,
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1607 int alloclen, int *fftlog )
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1608 {
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1609 int i, j, k, l, m, maxk;
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1610 int nlen, nlen2, nlen4;
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1611 static TLS int prevalloclen = 0;
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1612 static TLS int crossscoresize = 0;
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1613 static TLS char **tmpseq1 = NULL;
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1614 static TLS char **tmpseq2 = NULL;
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1615 static TLS char **tmpptr1 = NULL;
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1616 static TLS char **tmpptr2 = NULL;
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1617 static TLS char **tmpres1 = NULL;
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1618 static TLS char **tmpres2 = NULL;
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1619 static TLS char **result1 = NULL;
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1620 static TLS char **result2 = NULL;
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1621 #if RND
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1622 static TLS char **rndseq1 = NULL;
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1623 static TLS char **rndseq2 = NULL;
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diff changeset
1624 #endif
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diff changeset
1625 static TLS Fukusosuu **seqVector1 = NULL;
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diff changeset
1626 static TLS Fukusosuu **seqVector2 = NULL;
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diff changeset
1627 static TLS Fukusosuu **naiseki = NULL;
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diff changeset
1628 static TLS Fukusosuu *naisekiNoWa = NULL;
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diff changeset
1629 static TLS double *soukan = NULL;
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diff changeset
1630 static TLS double **crossscore = NULL;
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diff changeset
1631 int nlentmp;
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diff changeset
1632 static TLS int *kouho = NULL;
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diff changeset
1633 static TLS Segment *segment = NULL;
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diff changeset
1634 static TLS Segment *segment1 = NULL;
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diff changeset
1635 static TLS Segment *segment2 = NULL;
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diff changeset
1636 static TLS Segment **sortedseg1 = NULL;
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diff changeset
1637 static TLS Segment **sortedseg2 = NULL;
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diff changeset
1638 static TLS int *cut1 = NULL;
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diff changeset
1639 static TLS int *cut2 = NULL;
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diff changeset
1640 static TLS char *sgap1, *egap1, *sgap2, *egap2;
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diff changeset
1641 static TLS int localalloclen = 0;
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diff changeset
1642 int lag;
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diff changeset
1643 int tmpint;
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diff changeset
1644 int count, count0;
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diff changeset
1645 int len1, len2;
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diff changeset
1646 int totallen;
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diff changeset
1647 float totalscore;
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diff changeset
1648 int nkouho = 0;
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diff changeset
1649 int headgp, tailgp;
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diff changeset
1650 // float dumfl = 0.0;
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1651
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1652 if( seq1 == NULL )
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diff changeset
1653 {
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diff changeset
1654 if( result1 )
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diff changeset
1655 {
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1656 // fprintf( stderr, "### Freeing localarrays in Falign\n" );
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diff changeset
1657 localalloclen = 0;
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diff changeset
1658 prevalloclen = 0;
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diff changeset
1659 crossscoresize = 0;
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parents:
diff changeset
1660 mymergesort( 0, 0, NULL );
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diff changeset
1661 alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
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diff changeset
1662 fft( 0, NULL, 1 );
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diff changeset
1663 A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
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diff changeset
1664 A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
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diff changeset
1665 G__align11( NULL, NULL, NULL, 0, 0, 0 );
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diff changeset
1666 blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
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diff changeset
1667 if( crossscore ) FreeDoubleMtx( crossscore );
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diff changeset
1668 crossscore = NULL; // reallocate sareru kanousei ga arunode.
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diff changeset
1669 FreeCharMtx( result1 ); result1 = NULL;
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parents:
diff changeset
1670 FreeCharMtx( result2 );
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diff changeset
1671 FreeCharMtx( tmpres1 );
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diff changeset
1672 FreeCharMtx( tmpres2 );
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parents:
diff changeset
1673 FreeCharMtx( tmpseq1 );
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parents:
diff changeset
1674 FreeCharMtx( tmpseq2 );
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parents:
diff changeset
1675 free( sgap1 );
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parents:
diff changeset
1676 free( egap1 );
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parents:
diff changeset
1677 free( sgap2 );
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parents:
diff changeset
1678 free( egap2 );
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parents:
diff changeset
1679 free( kouho );
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parents:
diff changeset
1680 free( cut1 );
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parents:
diff changeset
1681 free( cut2 );
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parents:
diff changeset
1682 free( tmpptr1 );
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parents:
diff changeset
1683 free( tmpptr2 );
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parents:
diff changeset
1684 free( segment );
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parents:
diff changeset
1685 free( segment1 );
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parents:
diff changeset
1686 free( segment2 );
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diff changeset
1687 free( sortedseg1 );
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parents:
diff changeset
1688 free( sortedseg2 );
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diff changeset
1689 if( !kobetsubunkatsu )
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diff changeset
1690 {
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diff changeset
1691 FreeFukusosuuMtx ( seqVector1 );
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parents:
diff changeset
1692 FreeFukusosuuMtx ( seqVector2 );
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diff changeset
1693 FreeFukusosuuVec( naisekiNoWa );
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parents:
diff changeset
1694 FreeFukusosuuMtx( naiseki );
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diff changeset
1695 FreeDoubleVec( soukan );
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diff changeset
1696 }
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diff changeset
1697 }
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diff changeset
1698 else
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diff changeset
1699 {
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1700 // fprintf( stderr, "Did not allocate localarrays in Falign\n" );
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1701 }
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diff changeset
1702
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1703 return( 0.0 );
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diff changeset
1704 }
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diff changeset
1705
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diff changeset
1706
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diff changeset
1707
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1708 len1 = strlen( seq1[0] );
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parents:
diff changeset
1709 len2 = strlen( seq2[0] );
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parents:
diff changeset
1710 nlentmp = MAX( len1, len2 );
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diff changeset
1711
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1712 nlen = 1;
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parents:
diff changeset
1713 while( nlentmp >= nlen ) nlen <<= 1;
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diff changeset
1714 #if 0
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1715 fprintf( stderr, "### nlen = %d\n", nlen );
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diff changeset
1716 #endif
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diff changeset
1717
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1718 nlen2 = nlen/2; nlen4 = nlen2 / 2;
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1719
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diff changeset
1720 #if 0
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1721 fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
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1722 fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
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diff changeset
1723 #endif
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1724
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1725 if( prevalloclen != alloclen ) // Falign_noudp mo kaeru
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1726 {
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1727 if( prevalloclen )
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diff changeset
1728 {
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1729 FreeCharMtx( result1 );
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parents:
diff changeset
1730 FreeCharMtx( result2 );
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parents:
diff changeset
1731 FreeCharMtx( tmpres1 );
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parents:
diff changeset
1732 FreeCharMtx( tmpres2 );
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diff changeset
1733 }
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1734 // fprintf( stderr, "\n\n\nreallocating ...\n" );
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diff changeset
1735 result1 = AllocateCharMtx( njob, alloclen );
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1736 result2 = AllocateCharMtx( njob, alloclen );
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1737 tmpres1 = AllocateCharMtx( njob, alloclen );
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diff changeset
1738 tmpres2 = AllocateCharMtx( njob, alloclen );
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diff changeset
1739 prevalloclen = alloclen;
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diff changeset
1740 }
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diff changeset
1741
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diff changeset
1742 if( !localalloclen )
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parents:
diff changeset
1743 {
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diff changeset
1744 sgap1 = AllocateCharVec( njob );
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nick
parents:
diff changeset
1745 egap1 = AllocateCharVec( njob );
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nick
parents:
diff changeset
1746 sgap2 = AllocateCharVec( njob );
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nick
parents:
diff changeset
1747 egap2 = AllocateCharVec( njob );
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nick
parents:
diff changeset
1748 kouho = AllocateIntVec( NKOUHO_LONG );
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nick
parents:
diff changeset
1749 cut1 = AllocateIntVec( MAXSEG );
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nick
parents:
diff changeset
1750 cut2 = AllocateIntVec( MAXSEG );
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parents:
diff changeset
1751 tmpptr1 = AllocateCharMtx( njob, 0 );
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parents:
diff changeset
1752 tmpptr2 = AllocateCharMtx( njob, 0 );
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diff changeset
1753 segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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parents:
diff changeset
1754 segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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diff changeset
1755 segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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diff changeset
1756 sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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diff changeset
1757 sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
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1758 if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
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1759 ErrorExit( "Allocation error\n" );
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1760
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1761 if ( scoremtx == -1 ) n20or4or2 = 1;
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diff changeset
1762 else if( fftscore ) n20or4or2 = 1;
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diff changeset
1763 else n20or4or2 = 20;
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1764 }
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diff changeset
1765 if( localalloclen < nlen )
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diff changeset
1766 {
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diff changeset
1767 if( localalloclen )
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1768 {
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diff changeset
1769 #if 1
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diff changeset
1770 if( !kobetsubunkatsu )
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1771 {
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diff changeset
1772 FreeFukusosuuMtx ( seqVector1 );
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parents:
diff changeset
1773 FreeFukusosuuMtx ( seqVector2 );
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diff changeset
1774 FreeFukusosuuVec( naisekiNoWa );
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diff changeset
1775 FreeFukusosuuMtx( naiseki );
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diff changeset
1776 FreeDoubleVec( soukan );
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1777 }
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diff changeset
1778 FreeCharMtx( tmpseq1 );
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diff changeset
1779 FreeCharMtx( tmpseq2 );
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diff changeset
1780 #endif
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diff changeset
1781 #if RND
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parents:
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1782 FreeCharMtx( rndseq1 );
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diff changeset
1783 FreeCharMtx( rndseq2 );
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diff changeset
1784 #endif
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diff changeset
1785 }
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diff changeset
1786
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diff changeset
1787
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diff changeset
1788 tmpseq1 = AllocateCharMtx( njob, nlen );
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diff changeset
1789 tmpseq2 = AllocateCharMtx( njob, nlen );
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diff changeset
1790 if( !kobetsubunkatsu )
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diff changeset
1791 {
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diff changeset
1792 naisekiNoWa = AllocateFukusosuuVec( nlen );
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diff changeset
1793 naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
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diff changeset
1794 seqVector1 = AllocateFukusosuuMtx( n20or4or2, nlen+1 );
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diff changeset
1795 seqVector2 = AllocateFukusosuuMtx( n20or4or2, nlen+1 );
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diff changeset
1796 soukan = AllocateDoubleVec( nlen+1 );
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1797 }
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diff changeset
1798 #if RND
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diff changeset
1799 rndseq1 = AllocateCharMtx( njob, nlen );
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1800 rndseq2 = AllocateCharMtx( njob, nlen );
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1801 for( i=0; i<njob; i++ )
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1802 {
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1803 generateRndSeq( rndseq1[i], nlen );
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1804 generateRndSeq( rndseq2[i], nlen );
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1805 }
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1806 #endif
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1807 localalloclen = nlen;
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1808 }
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1809
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1810 for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
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1811 for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
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1812
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1813 #if 0
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1814 fftfp = fopen( "input_of_Falign", "w" );
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1815 fprintf( fftfp, "nlen = %d\n", nlen );
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1816 fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
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1817 for( i=0; i<clus1; i++ )
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1818 fprintf( fftfp, "%s\n", seq1[i] );
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1819 fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
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1820 for( i=0; i<clus2; i++ )
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1821 fprintf( fftfp, "%s\n", seq2[i] );
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1822 fclose( fftfp );
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1823 system( "less input_of_Falign < /dev/tty > /dev/tty" );
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1824 #endif
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1825 if( !kobetsubunkatsu )
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1826 {
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1827 fprintf( stderr, " FFT ... " );
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1828
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1829 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
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1830 if( scoremtx == -1 )
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1831 {
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1832 for( i=0; i<clus1; i++ )
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1833 seq_vec_4( seqVector1[0], eff1[i], tmpseq1[i] );
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1834 }
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1835 else if( fftscore )
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1836 {
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1837 for( i=0; i<clus1; i++ )
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1838 {
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1839 #if 0
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1840 seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
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1841 seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
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1842 #else
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1843 seq_vec_5( seqVector1[0], polarity, volume, eff1[i], tmpseq1[i] );
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1844 #endif
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1845 }
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1846 }
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1847 else
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1848 {
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1849 for( i=0; i<clus1; i++ )
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1850 seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
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1851 }
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1852 #if RND
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1853 for( i=0; i<clus1; i++ )
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1854 {
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1855 vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
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1856 }
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1857 #endif
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1858 #if 0
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1859 fftfp = fopen( "seqVec", "w" );
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1860 fprintf( fftfp, "before transform\n" );
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1861 for( k=0; k<n20or4or2; k++ )
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1862 {
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1863 fprintf( fftfp, "nlen=%d\n", nlen );
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1864 fprintf( fftfp, "%c\n", amino[k] );
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1865 for( l=0; l<nlen; l++ )
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1866 fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
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1867 }
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1868 fclose( fftfp );
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1869 system( "less seqVec < /dev/tty > /dev/tty" );
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1870 #endif
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1871
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1872 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
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1873 if( scoremtx == -1 )
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1874 {
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1875 for( i=0; i<clus2; i++ )
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1876 seq_vec_4( seqVector2[0], eff2[i], tmpseq2[i] );
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1877 }
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1878 else if( fftscore )
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1879 {
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1880 for( i=0; i<clus2; i++ )
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1881 {
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1882 #if 0
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1883 seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
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1884 seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
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1885 #else
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1886 seq_vec_5( seqVector2[0], polarity, volume, eff2[i], tmpseq2[i] );
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1887 #endif
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1888 }
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1889 }
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1890 else
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1891 {
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1892 for( i=0; i<clus2; i++ )
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1893 seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
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1894 }
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1895 #if RND
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1896 for( i=0; i<clus2; i++ )
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1897 {
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1898 vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
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1899 }
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1900 #endif
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1901
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1902 #if 0
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1903 fftfp = fopen( "seqVec2", "w" );
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1904 fprintf( fftfp, "before fft\n" );
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1905 for( k=0; k<n20or4or2; k++ )
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1906 {
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1907 fprintf( fftfp, "%c\n", amino[k] );
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1908 for( l=0; l<nlen; l++ )
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1909 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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1910 }
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1911 fclose( fftfp );
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1912 system( "less seqVec2 < /dev/tty > /dev/tty" );
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1913 #endif
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1914
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1915 for( j=0; j<n20or4or2; j++ )
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1916 {
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1917 fft( nlen, seqVector2[j], 0 );
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1918 fft( nlen, seqVector1[j], 0 );
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1919 }
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1920 #if 0
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1921 fftfp = fopen( "seqVec2", "w" );
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1922 fprintf( fftfp, "#after fft\n" );
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1923 for( k=0; k<n20or4or2; k++ )
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1924 {
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1925 fprintf( fftfp, "#%c\n", amino[k] );
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1926 for( l=0; l<nlen; l++ )
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1927 fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
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1928 }
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1929 fclose( fftfp );
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1930 system( "less seqVec2 < /dev/tty > /dev/tty" );
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1931 #endif
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1932
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1933 for( k=0; k<n20or4or2; k++ )
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1934 {
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1935 for( l=0; l<nlen; l++ )
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1936 calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
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1937 }
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1938 for( l=0; l<nlen; l++ )
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1939 {
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1940 naisekiNoWa[l].R = 0.0;
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1941 naisekiNoWa[l].I = 0.0;
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1942 for( k=0; k<n20or4or2; k++ )
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1943 {
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1944 naisekiNoWa[l].R += naiseki[k][l].R;
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1945 naisekiNoWa[l].I += naiseki[k][l].I;
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1946 }
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1947 }
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1948
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1949 #if 0
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1950 fftfp = fopen( "naisekiNoWa", "w" );
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1951 fprintf( fftfp, "#Before fft\n" );
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1952 for( l=0; l<nlen; l++ )
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1953 fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
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1954 fclose( fftfp );
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1955 system( "less naisekiNoWa < /dev/tty > /dev/tty " );
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1956 #endif
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1957
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1958 fft( -nlen, naisekiNoWa, 0 );
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1959
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1960 for( m=0; m<=nlen2; m++ )
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1961 soukan[m] = naisekiNoWa[nlen2-m].R;
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1962 for( m=nlen2+1; m<nlen; m++ )
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1963 soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
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1964
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1965 #if 0
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1966 fftfp = fopen( "naisekiNoWa", "w" );
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1967 fprintf( fftfp, "#After fft\n" );
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1968 for( l=0; l<nlen; l++ )
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1969 fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
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1970 fclose( fftfp );
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1971 fftfp = fopen( "list.plot", "w" );
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1972 fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
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1973 fclose( fftfp );
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1974 system( "/usr/bin/gnuplot list.plot &" );
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1975 #endif
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1976 #if 0
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1977 fprintf( stderr, "soukan\n" );
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1978 for( l=0; l<nlen; l++ )
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1979 fprintf( stderr, "%d %f\n", l-nlen2, soukan[l] );
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1980 #if 0
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1981 fftfp = fopen( "list.plot", "w" );
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1982 fprintf( fftfp, "plot 'frt'\n pause +1" );
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1983 fclose( fftfp );
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1984 system( "/usr/bin/gnuplot list.plot" );
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1985 #endif
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1986 #endif
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1987
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1988
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1989 nkouho = getKouho( kouho, NKOUHO_LONG, soukan, nlen );
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1990
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1991 #if 0
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1992 for( i=0; i<nkouho; i++ )
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1993 {
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1994 fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
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1995 }
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1996 #endif
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1997 }
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1998
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1999 #if KEIKA
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2000 fprintf( stderr, "Searching anchors ... " );
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2001 #endif
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2002 count = 0;
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2003
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2004
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2005
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2006 #define CAND 0
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2007 #if CAND
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2008 fftfp = fopen( "cand", "w" );
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2009 fclose( fftfp );
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2010 #endif
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2011 if( kobetsubunkatsu )
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2012 {
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2013 maxk = 1;
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2014 kouho[0] = 0;
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2015 }
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2016 else
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2017 {
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2018 maxk = nkouho;
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2019 }
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2020
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2021 for( k=0; k<maxk; k++ )
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2022 {
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2023 lag = kouho[k];
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2024 if( lag <= -len1 || len2 <= lag ) continue;
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2025 // fprintf( stderr, "k=%d, lag=%d\n", k, lag );
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2026 zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
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2027 #if CAND
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2028 fftfp = fopen( "cand", "a" );
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2029 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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2030 fprintf( fftfp, "%s\n", tmpptr1[0] );
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2031 fprintf( fftfp, ">Candidate No.%d lag = %d\n", k+1, lag );
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2032 fprintf( fftfp, "%s\n", tmpptr2[0] );
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2033 fprintf( fftfp, ">\n", k+1, lag );
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2034 fclose( fftfp );
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2035 #endif
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2036
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2037 // fprintf( stderr, "lag = %d\n", lag );
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2038 tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
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2039 // fprintf( stderr, "lag = %d, %d found\n", lag, tmpint );
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2040
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2041 // if( lag == -50 ) exit( 1 );
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2042
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2043 if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
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2044
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2045 // fprintf( stderr, "##### k=%d / %d\n", k, maxk );
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2046 // if( tmpint == 0 ) break; // 060430 iinoka ? // 090530 yameta
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2047 while( tmpint-- > 0 )
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2048 {
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2049 #if 0
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2050 if( segment[count].end - segment[count].start < fftWinSize )
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2051 {
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2052 count++;
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2053 continue;
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2054 }
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2055 #endif
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2056 if( lag > 0 )
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2057 {
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2058 segment1[count].start = segment[count].start ;
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2059 segment1[count].end = segment[count].end ;
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2060 segment1[count].center = segment[count].center;
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2061 segment1[count].score = segment[count].score;
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2062
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2063 segment2[count].start = segment[count].start + lag;
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2064 segment2[count].end = segment[count].end + lag;
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2065 segment2[count].center = segment[count].center + lag;
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2066 segment2[count].score = segment[count].score ;
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2067 }
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2068 else
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2069 {
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2070 segment1[count].start = segment[count].start - lag;
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2071 segment1[count].end = segment[count].end - lag;
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2072 segment1[count].center = segment[count].center - lag;
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2073 segment1[count].score = segment[count].score ;
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2074
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2075 segment2[count].start = segment[count].start ;
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2076 segment2[count].end = segment[count].end ;
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2077 segment2[count].center = segment[count].center;
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2078 segment2[count].score = segment[count].score ;
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2079 }
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2080 #if 0
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2081 fprintf( stderr, "##### k=%d / %d\n", k, maxk );
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2082 fprintf( stderr, "anchor %d, score = %f\n", count, segment1[count].score );
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diff changeset
2083 fprintf( stderr, "in 1 %d\n", segment1[count].center );
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nick
parents:
diff changeset
2084 fprintf( stderr, "in 2 %d\n", segment2[count].center );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2085 #endif
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nick
parents:
diff changeset
2086 segment1[count].pair = &segment2[count];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2087 segment2[count].pair = &segment1[count];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2088 count++;
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nick
parents:
diff changeset
2089 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2090 fprintf( stderr, "count=%d\n", count );
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nick
parents:
diff changeset
2091 #endif
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nick
parents:
diff changeset
2092 }
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nick
parents:
diff changeset
2093 }
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nick
parents:
diff changeset
2094 #if 1
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nick
parents:
diff changeset
2095 if( !kobetsubunkatsu )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2096 fprintf( stderr, "done. (%d anchors) ", count );
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nick
parents:
diff changeset
2097 #endif
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nick
parents:
diff changeset
2098 if( !count && fftNoAnchStop )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2099 ErrorExit( "Cannot detect anchor!" );
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nick
parents:
diff changeset
2100 #if 0
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nick
parents:
diff changeset
2101 fprintf( stderr, "RESULT before sort:\n" );
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nick
parents:
diff changeset
2102 for( l=0; l<count+1; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2103 {
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nick
parents:
diff changeset
2104 fprintf( stderr, "cut[%d]=%d, ", l, segment1[l].center );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2105 fprintf( stderr, "%d score = %f\n", segment2[l].center, segment1[l].score );
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nick
parents:
diff changeset
2106 }
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nick
parents:
diff changeset
2107 #endif
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nick
parents:
diff changeset
2108
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2109 for( i=0; i<count; i++ )
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nick
parents:
diff changeset
2110 {
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nick
parents:
diff changeset
2111 sortedseg1[i] = &segment1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2112 sortedseg2[i] = &segment2[i];
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nick
parents:
diff changeset
2113 }
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nick
parents:
diff changeset
2114 #if 0
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nick
parents:
diff changeset
2115 tmpsort( count, sortedseg1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2116 tmpsort( count, sortedseg2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2117 qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2118 qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
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nick
parents:
diff changeset
2119 #else
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nick
parents:
diff changeset
2120 mymergesort( 0, count-1, sortedseg1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2121 mymergesort( 0, count-1, sortedseg2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2122 #endif
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nick
parents:
diff changeset
2123 for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2124 for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2125
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nick
parents:
diff changeset
2126
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nick
parents:
diff changeset
2127
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nick
parents:
diff changeset
2128 if( kobetsubunkatsu )
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nick
parents:
diff changeset
2129 {
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nick
parents:
diff changeset
2130 for( i=0; i<count; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2131 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2132 cut1[i+1] = sortedseg1[i]->center;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2133 cut2[i+1] = sortedseg2[i]->center;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2134 }
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nick
parents:
diff changeset
2135 cut1[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2136 cut2[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2137 cut1[count+1] = len1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2138 cut2[count+1] = len2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2139 count += 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2140 }
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nick
parents:
diff changeset
2141
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2142 else
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nick
parents:
diff changeset
2143 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2144 if( count < 5000 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2145 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2146 if( crossscoresize < count+2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2147 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2148 crossscoresize = count+2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2149 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2150 if( fftkeika ) fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2151 #endif
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nick
parents:
diff changeset
2152 if( crossscore ) FreeDoubleMtx( crossscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2153 crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2154 }
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nick
parents:
diff changeset
2155 for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2156 crossscore[i][j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2157 for( i=0; i<count; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2158 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2159 crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2160 cut1[i+1] = sortedseg1[i]->center;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2161 cut2[i+1] = sortedseg2[i]->center;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2162 }
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nick
parents:
diff changeset
2163
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2164 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2165 fprintf( stderr, "AFTER SORT\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2166 for( i=0; i<count+1; i++ ) fprintf( stderr, "%d, %d\n", cut1[i], cut2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2167 fprintf( stderr, "crossscore = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2168 for( i=0; i<count+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2169 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2170 for( j=0; j<count+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2171 fprintf( stderr, "%.0f ", crossscore[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2172 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2173 }
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nick
parents:
diff changeset
2174 #endif
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nick
parents:
diff changeset
2175
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2176 crossscore[0][0] = 10000000.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2177 cut1[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2178 cut2[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2179 crossscore[count+1][count+1] = 10000000.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2180 cut1[count+1] = len1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2181 cut2[count+1] = len2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2182 count += 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2183 count0 = count;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2184
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2185 // fprintf( stderr, "\n\n\ncalling blockAlign2\n\n\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2186 blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2187
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2188 // if( count-count0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2189 // fprintf( stderr, "%d unused anchors\n", count0-count );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2190
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2191 if( !kobetsubunkatsu && fftkeika )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2192 fprintf( stderr, "%d anchors found\n", count );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2193 if( fftkeika )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2194 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2195 if( count0 > count )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2196 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2197 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2198 fprintf( stderr, "\7 REPEAT!? \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2199 #else
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nick
parents:
diff changeset
2200 fprintf( stderr, "REPEAT!? \n" );
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nick
parents:
diff changeset
2201 #endif
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nick
parents:
diff changeset
2202 if( fftRepeatStop ) exit( 1 );
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nick
parents:
diff changeset
2203 }
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nick
parents:
diff changeset
2204 #if KEIKA
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nick
parents:
diff changeset
2205 else fprintf( stderr, "done\n" );
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nick
parents:
diff changeset
2206 #endif
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nick
parents:
diff changeset
2207 }
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nick
parents:
diff changeset
2208 }
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nick
parents:
diff changeset
2209
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nick
parents:
diff changeset
2210
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nick
parents:
diff changeset
2211 else
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nick
parents:
diff changeset
2212 {
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parents:
diff changeset
2213 fprintf( stderr, "\nMany anchors were found. The upper-level DP is skipped.\n\n" );
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nick
parents:
diff changeset
2214
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nick
parents:
diff changeset
2215 cut1[0] = 0;
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nick
parents:
diff changeset
2216 cut2[0] = 0;
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nick
parents:
diff changeset
2217 count0 = 0;
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nick
parents:
diff changeset
2218 for( i=0; i<count; i++ )
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nick
parents:
diff changeset
2219 {
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nick
parents:
diff changeset
2220 // fprintf( stderr, "i=%d, %d-%d ?\n", i, sortedseg1[i]->center, sortedseg1[i]->pair->center );
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nick
parents:
diff changeset
2221 if( sortedseg1[i]->center > cut1[count0]
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nick
parents:
diff changeset
2222 && sortedseg1[i]->pair->center > cut2[count0] )
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nick
parents:
diff changeset
2223 {
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nick
parents:
diff changeset
2224 count0++;
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nick
parents:
diff changeset
2225 cut1[count0] = sortedseg1[i]->center;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2226 cut2[count0] = sortedseg1[i]->pair->center;
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parents:
diff changeset
2227 }
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parents:
diff changeset
2228 else
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nick
parents:
diff changeset
2229 {
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nick
parents:
diff changeset
2230 if( i && sortedseg1[i]->score > sortedseg1[i-1]->score )
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nick
parents:
diff changeset
2231 {
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nick
parents:
diff changeset
2232 if( sortedseg1[i]->center > cut1[count0-1]
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nick
parents:
diff changeset
2233 && sortedseg1[i]->pair->center > cut2[count0-1] )
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nick
parents:
diff changeset
2234 {
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nick
parents:
diff changeset
2235 cut1[count0] = sortedseg1[i]->center;
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nick
parents:
diff changeset
2236 cut2[count0] = sortedseg1[i]->pair->center;
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nick
parents:
diff changeset
2237 }
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nick
parents:
diff changeset
2238 else
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nick
parents:
diff changeset
2239 {
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nick
parents:
diff changeset
2240 // count0--;
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parents:
diff changeset
2241 }
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nick
parents:
diff changeset
2242 }
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parents:
diff changeset
2243 }
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parents:
diff changeset
2244 }
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parents:
diff changeset
2245 // if( count-count0 )
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nick
parents:
diff changeset
2246 // fprintf( stderr, "%d anchors unused\n", count-count0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2247 cut1[count0+1] = len1;
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nick
parents:
diff changeset
2248 cut2[count0+1] = len2;
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nick
parents:
diff changeset
2249 count = count0 + 2;
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nick
parents:
diff changeset
2250 count0 = count;
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nick
parents:
diff changeset
2251
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nick
parents:
diff changeset
2252 }
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nick
parents:
diff changeset
2253 }
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nick
parents:
diff changeset
2254
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nick
parents:
diff changeset
2255 // exit( 0 );
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nick
parents:
diff changeset
2256
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nick
parents:
diff changeset
2257 #if 0
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nick
parents:
diff changeset
2258 fftfp = fopen( "fft", "a" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2259 fprintf( fftfp, "RESULT after sort:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2260 for( l=0; l<count; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2261 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2262 fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2263 fprintf( fftfp, "%d\n", segment2[l].center );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2264 }
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nick
parents:
diff changeset
2265 fclose( fftfp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2266 #endif
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nick
parents:
diff changeset
2267
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nick
parents:
diff changeset
2268 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2269 fprintf( stderr, "RESULT after blckalign:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2270 for( l=0; l<count+1; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2271 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2272 fprintf( stderr, "cut : %d %d\n", cut1[l], cut2[l] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2273 }
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nick
parents:
diff changeset
2274 #endif
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nick
parents:
diff changeset
2275
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2276 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2277 fprintf( trap_g, "Devided to %d segments\n", count-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2278 fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2279 #endif
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nick
parents:
diff changeset
2280
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2281 totallen = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2282 for( j=0; j<clus1; j++ ) result1[j][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2283 for( j=0; j<clus2; j++ ) result2[j][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2284 totalscore = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2285 *fftlog = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2286 for( i=0; i<count-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2287 {
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nick
parents:
diff changeset
2288 *fftlog += 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2289 if( i == 0 ) headgp = outgap; else headgp = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2290 if( i == count-2 ) tailgp = outgap; else tailgp = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2291
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2292 if( cut1[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2293 {
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nick
parents:
diff changeset
2294 // getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2295 // getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2296 getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2297 getkyokaigap( sgap2, tmpres2, nlen-1, clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2298 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2299 else
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nick
parents:
diff changeset
2300 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2301 for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2302 for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2303 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2304 if( cut1[i+1] != len1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2305 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2306 getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2307 getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2308 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2309 else
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nick
parents:
diff changeset
2310 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2311 for( j=0; j<clus1; j++ ) egap1[j] = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2312 for( j=0; j<clus2; j++ ) egap2[j] = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2313 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2314 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2315 fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2316 #else
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nick
parents:
diff changeset
2317 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2318 fprintf( stderr, "DP %05d / %05d \b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", i+1, count-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2319 #endif
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nick
parents:
diff changeset
2320 #endif
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nick
parents:
diff changeset
2321 for( j=0; j<clus1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2322 {
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nick
parents:
diff changeset
2323 strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2324 tmpres1[j][cut1[i+1]-cut1[i]] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2325 }
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nick
parents:
diff changeset
2326 if( kobetsubunkatsu && fftkeika ) commongappick( clus1, tmpres1 ); //dvtditr に呼ばれたとき fftkeika=1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2327 // if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2328 for( j=0; j<clus2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2329 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2330 // fprintf( stderr, "### cut2[i+1]-cut2[i] = %d\n", cut2[i+1]-cut2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2331 if( cut2[i+1]-cut2[i] <= 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2332 fprintf( stderr, "### cut2[i+1]=%d, cut2[i]=%d\n", cut2[i+1], cut2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2333 strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2334 tmpres2[j][cut2[i+1]-cut2[i]] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2335 }
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nick
parents:
diff changeset
2336 if( kobetsubunkatsu && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr に呼ばれたとき fftkeika=1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2337 // if( kobetsubunkatsu ) commongappick( clus2, tmpres2 );
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nick
parents:
diff changeset
2338
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nick
parents:
diff changeset
2339 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2340 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2341 fprintf( stderr, "Not supported\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2342 exit( 1 );
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nick
parents:
diff changeset
2343 }
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nick
parents:
diff changeset
2344 #if 0
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nick
parents:
diff changeset
2345 fprintf( stderr, "i=%d, before alignment", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2346 fprintf( stderr, "%4d\n", totallen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2347 fprintf( stderr, "\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2348 for( j=0; j<clus1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2349 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2350 fprintf( stderr, "%s\n", tmpres1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2351 }
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nick
parents:
diff changeset
2352 fprintf( stderr, "-------\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2353 for( j=0; j<clus2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2354 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2355 fprintf( stderr, "%s\n", tmpres2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2356 }
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nick
parents:
diff changeset
2357 #endif
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nick
parents:
diff changeset
2358
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nick
parents:
diff changeset
2359 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2360 fprintf( stdout, "writing input\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2361 for( j=0; j<clus1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2362 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2363 fprintf( stdout, ">%d of GROUP1\n", j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2364 fprintf( stdout, "%s\n", tmpres1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2365 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2366 for( j=0; j<clus2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2367 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2368 fprintf( stdout, ">%d of GROUP2\n", j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2369 fprintf( stdout, "%s\n", tmpres2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2370 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2371 fflush( stdout );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2372 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2373 switch( alg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2374 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2375 case( 'M' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2376 if( scoringmatrices ) // called by tditeration.c
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2377 totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2378 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2379 totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2380 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2381 default:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2382 fprintf( stderr, "alg = %c\n", alg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2383 ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2384 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2385 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2386
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2387 nlen = strlen( tmpres1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2388 if( totallen + nlen > alloclen )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2389 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2390 fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2391 ErrorExit( "LENGTH OVER in Falign\n " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2392 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2393 for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2394 for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2395 totallen += nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2396 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2397 fprintf( stderr, "i=%d", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2398 fprintf( stderr, "%4d\n", totallen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2399 fprintf( stderr, "\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2400 for( j=0; j<clus1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2401 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2402 fprintf( stderr, "%s\n", tmpres1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2403 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2404 fprintf( stderr, "-------\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2405 for( j=0; j<clus2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2406 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2407 fprintf( stderr, "%s\n", tmpres2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2408 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2409 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2410 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2411 #if KEIKA
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2412 fprintf( stderr, "DP ... done \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2413 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2414
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2415 for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2416 for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2417 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2418 for( j=0; j<clus1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2419 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2420 fprintf( stderr, "%s\n", result1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2421 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2422 fprintf( stderr, "- - - - - - - - - - -\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2423 for( j=0; j<clus2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2424 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2425 fprintf( stderr, "%s\n", result2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2426 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2427 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2428 return( totalscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2429 }