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annotate mafft/core/fftFunctions.c @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2
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3 #define SEGMENTSIZE 150
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4 #define TMPTMPTMP 0
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5
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6 #define DEBUG 0
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7
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8 void keika( char *str, int current, int all )
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9 {
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10 if( current == 0 )
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11 fprintf( stderr, "%s : ", str );
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12
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13 fprintf( stderr, "\b\b\b\b\b\b\b\b" );
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14 fprintf( stderr, "%3d /%3d", current+1, all+1 );
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15
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16 if( current+1 == all )
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17 fprintf( stderr, "\b\b\b\b\b\b\b\bdone. \n" );
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18 }
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19
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20 double maxItch( double *soukan, int size )
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21 {
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22 int i;
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23 double value = 0.0;
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24 double cand;
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25 for( i=0; i<size; i++ )
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26 if( ( cand = soukan[i] ) > value ) value = cand;
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27 return( value );
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28 }
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29
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30 void calcNaiseki( Fukusosuu *value, Fukusosuu *x, Fukusosuu *y )
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31 {
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32 value->R = x->R * y->R + x->I * y->I;
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33 value->I = -x->R * y->I + x->I * y->R;
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34 }
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35
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36 Fukusosuu *AllocateFukusosuuVec( int l1 )
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37 {
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38 Fukusosuu *value;
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39 value = (Fukusosuu *)calloc( l1, sizeof( Fukusosuu ) );
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40 if( !value )
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41 {
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42 fprintf( stderr, "Cannot allocate %d FukusosuuVec\n", l1 );
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43 return( NULL );
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44 }
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45 return( value );
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46 }
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47
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48 Fukusosuu **AllocateFukusosuuMtx( int l1, int l2 )
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49 {
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50 Fukusosuu **value;
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51 int j;
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52 // fprintf( stderr, "allocating %d x %d FukusosuuMtx\n", l1, l2 );
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53 value = (Fukusosuu **)calloc( l1+1, sizeof( Fukusosuu * ) );
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54 if( !value )
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55 {
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56 fprintf( stderr, "Cannot allocate %d x %d FukusosuuVecMtx\n", l1, l2 );
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57 exit( 1 );
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58 }
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59 for( j=0; j<l1; j++ )
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60 {
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61 value[j] = AllocateFukusosuuVec( l2 );
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62 if( !value[j] )
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63 {
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64 fprintf( stderr, "Cannot allocate %d x %d FukusosuuVecMtx\n", l1, l2 );
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65 exit( 1 );
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66 }
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67 }
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68 value[l1] = NULL;
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69 return( value );
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70 }
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71
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72 Fukusosuu ***AllocateFukusosuuCub( int l1, int l2, int l3 )
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73 {
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74 Fukusosuu ***value;
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75 int i;
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76 value = calloc( l1+1, sizeof( Fukusosuu ** ) );
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77 if( !value ) ErrorExit( "Cannot allocate Fukusosuu" );
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78 for( i=0; i<l1; i++ ) value[i] = AllocateFukusosuuMtx( l2, l3 );
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79 value[l1] = NULL;
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80 return( value );
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81 }
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82
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83 void FreeFukusosuuVec( Fukusosuu *vec )
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84 {
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85 free( (void *)vec );
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86 }
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87
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88 void FreeFukusosuuMtx( Fukusosuu **mtx )
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89 {
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90 int i;
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91
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92 for( i=0; mtx[i]; i++ )
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93 free( (void *)mtx[i] );
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94 free( (void *)mtx );
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95 }
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96
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97 int getKouho( int *kouho, int nkouho, double *soukan, int nlen2 )
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98 {
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99 int i, j;
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100 int nlen4 = nlen2 / 2;
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101 double max;
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102 double tmp;
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103 int ikouho = 0; // by D.Mathog, iinoka?
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104 for( j=0; j<nkouho; j++ )
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105 {
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106 max = -9999.9;
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107 for( i=0; i<nlen2; i++ )
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108 {
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109 if( ( tmp = soukan[i] ) > max )
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110 {
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111 ikouho = i;
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112 max = tmp;
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113 }
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114 }
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115 #if 0
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116 if( max < 0.15 )
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117 {
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118 break;
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119 }
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120 #endif
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121 #if 0
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122 fprintf( stderr, "Kouho No.%d, pos=%d, score=%f, lag=%d\n", j, ikouho, soukan[ikouho], ikouho-nlen4 );
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123 #endif
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124 soukan[ikouho] = -9999.9;
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125 kouho[j] = ( ikouho - nlen4 );
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126 }
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127 return( j );
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128 }
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129
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130 void zurasu2( int lag, int clus1, int clus2,
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131 char **seq1, char **seq2,
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132 char **aseq1, char **aseq2 )
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133 {
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134 int i;
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135 #if 0
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136 fprintf( stderr, "### lag = %d\n", lag );
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137 #endif
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138 if( lag > 0 )
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139 {
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140 for( i=0; i<clus1; i++ ) aseq1[i] = seq1[i];
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141 for( i=0; i<clus2; i++ ) aseq2[i] = seq2[i]+lag;
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142 }
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143 else
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144 {
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145 for( i=0; i<clus1; i++ ) aseq1[i] = seq1[i]-lag;
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146 for( i=0; i<clus2; i++ ) aseq2[i] = seq2[i];
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147 }
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148 }
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149
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150 void zurasu( int lag, int clus1, int clus2,
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151 char **seq1, char **seq2,
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152 char **aseq1, char **aseq2 )
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153 {
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154 int i;
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155 #if DEBUG
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156 fprintf( stderr, "lag = %d\n", lag );
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157 #endif
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158 if( lag > 0 )
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159 {
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160 for( i=0; i<clus1; i++ ) strcpy( aseq1[i], seq1[i] );
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161 for( i=0; i<clus2; i++ ) strcpy( aseq2[i], seq2[i]+lag );
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162 }
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163 else
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164 {
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165 for( i=0; i<clus1; i++ ) strcpy( aseq1[i], seq1[i]-lag );
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166 for( i=0; i<clus2; i++ ) strcpy( aseq2[i], seq2[i] );
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167 }
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168 }
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169
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170
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171 int alignableReagion( int clus1, int clus2,
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172 char **seq1, char **seq2,
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173 double *eff1, double *eff2,
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174 Segment *seg )
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175 {
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176 int i, j, k;
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177 int status, starttmp = 0; // by D.Mathog, a gess
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178 double score;
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179 int value = 0;
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180 int len, maxlen;
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181 int length = 0; // by D.Mathog, a gess
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182 static TLS double *stra = NULL;
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183 static TLS int alloclen = 0;
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184 double totaleff;
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185 double cumscore;
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186 static TLS double threshold;
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187 static TLS double *prf1 = NULL;
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188 static TLS double *prf2 = NULL;
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189 static TLS int *hat1 = NULL;
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190 static TLS int *hat2 = NULL;
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191 int pre1, pre2;
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192 #if 0
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193 char **seq1pt;
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194 char **seq2pt;
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195 double *eff1pt;
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196 double *eff2pt;
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197 #endif
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198
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199 #if 0
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200 fprintf( stderr, "### In alignableRegion, clus1=%d, clus2=%d \n", clus1, clus2 );
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201 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
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202 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
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203 fprintf( stderr, "eff1[0] = %f\n", eff1[0] );
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204 fprintf( stderr, "eff2[0] = %f\n", eff2[0] );
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205 #endif
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206
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207 if( clus1 == 0 )
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208 {
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209 if( stra ) FreeDoubleVec( stra ); stra = NULL;
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210 if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
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211 if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
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212 if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
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213 if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
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214 alloclen = 0;
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215 return( 0 );
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216 }
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217
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218 if( prf1 == NULL )
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219 {
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220 prf1 = AllocateDoubleVec( nalphabets );
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221 prf2 = AllocateDoubleVec( nalphabets );
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222 hat1 = AllocateIntVec( nalphabets+1 );
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223 hat2 = AllocateIntVec( nalphabets+1 );
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224 }
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225
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226 len = MIN( strlen( seq1[0] ), strlen( seq2[0] ) );
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227 maxlen = MAX( strlen( seq1[0] ), strlen( seq2[0] ) ) + fftWinSize;
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228 if( alloclen < maxlen )
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229 {
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230 if( alloclen )
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231 {
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232 FreeDoubleVec( stra );
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233 }
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234 else
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235 {
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236 threshold = (int)fftThreshold / 100.0 * 600.0 * fftWinSize;
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237 }
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238 stra = AllocateDoubleVec( maxlen );
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239 alloclen = maxlen;
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240 }
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241
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242
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243 totaleff = 0.0;
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244 for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ ) totaleff += eff1[i] * eff2[j];
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245 for( i=0; i<len; i++ )
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246 {
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247 /* make prfs */
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248 for( j=0; j<nalphabets; j++ )
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249 {
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250 prf1[j] = 0.0;
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251 prf2[j] = 0.0;
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252 }
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253 #if 0
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254 seq1pt = seq1;
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255 eff1pt = eff1;
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256 j = clus1;
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257 while( j-- ) prf1[amino_n[(*seq1pt++)[i]]] += *eff1pt++;
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258 #else
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259 for( j=0; j<clus1; j++ ) prf1[amino_n[(int)seq1[j][i]]] += eff1[j];
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260 #endif
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261 for( j=0; j<clus2; j++ ) prf2[amino_n[(int)seq2[j][i]]] += eff2[j];
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262
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263 /* make hats */
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264 pre1 = pre2 = nalphabets;
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265 for( j=25; j>=0; j-- )
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266 {
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267 if( prf1[j] )
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268 {
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269 hat1[pre1] = j;
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270 pre1 = j;
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271 }
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272 if( prf2[j] )
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273 {
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274 hat2[pre2] = j;
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275 pre2 = j;
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276 }
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277 }
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278 hat1[pre1] = -1;
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279 hat2[pre2] = -1;
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280
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281 /* make site score */
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282 stra[i] = 0.0;
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283 for( k=hat1[nalphabets]; k!=-1; k=hat1[k] )
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284 for( j=hat2[nalphabets]; j!=-1; j=hat2[j] )
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285 // stra[i] += n_dis[k][j] * prf1[k] * prf2[j];
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286 stra[i] += n_disFFT[k][j] * prf1[k] * prf2[j];
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287 stra[i] /= totaleff;
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288 }
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289
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290 (seg+0)->skipForeward = 0;
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291 (seg+1)->skipBackward = 0;
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292 status = 0;
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293 cumscore = 0.0;
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294 score = 0.0;
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295 for( j=0; j<fftWinSize; j++ ) score += stra[j];
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296
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297 for( i=1; i<len-fftWinSize; i++ )
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298 {
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299 score = score - stra[i-1] + stra[i+fftWinSize-1];
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300 #if TMPTMPTMP
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301 fprintf( stderr, "%d %10.0f ? %10.0f\n", i, score, threshold );
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302 #endif
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303
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304 if( score > threshold )
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305 {
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306 #if 0
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307 seg->start = i;
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308 seg->end = i;
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309 seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
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310 seg->score = score;
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311 status = 0;
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312 value++;
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313 #else
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314 if( !status )
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315 {
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316 status = 1;
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317 starttmp = i;
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318 length = 0;
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319 cumscore = 0.0;
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320 }
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321 length++;
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322 cumscore += score;
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323 #endif
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324 }
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325 if( score <= threshold || length > SEGMENTSIZE )
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326 {
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327 if( status )
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328 {
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329 if( length > fftWinSize )
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330 {
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331 seg->start = starttmp;
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332 seg->end = i;
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333 seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
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334 seg->score = cumscore;
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335 #if 0
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336 fprintf( stderr, "%d-%d length = %d, score = %f, value = %d\n", seg->start, seg->end, length, cumscore, value );
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337 #endif
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338 if( length > SEGMENTSIZE )
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339 {
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340 (seg+0)->skipForeward = 1;
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341 (seg+1)->skipBackward = 1;
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342 }
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343 else
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344 {
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345 (seg+0)->skipForeward = 0;
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346 (seg+1)->skipBackward = 0;
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347 }
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348 value++;
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349 seg++;
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350 }
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351 length = 0;
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352 cumscore = 0.0;
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353 status = 0;
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354 starttmp = i;
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355 if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
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356 }
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357 }
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358 }
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359 if( status && length > fftWinSize )
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360 {
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361 seg->end = i;
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362 seg->start = starttmp;
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363 seg->center = ( starttmp + i + fftWinSize ) / 2 ;
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364 seg->score = cumscore;
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365 #if 0
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366 fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
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367 #endif
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368 value++;
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369 }
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370 #if TMPTMPTMP
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371 exit( 0 );
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372 #endif
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373 // fprintf( stderr, "returning %d\n", value );
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374 return( value );
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375 }
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376
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377
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378 static int permit( Segment *seg1, Segment *seg2 )
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379 {
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380 return( 0 );
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381 if( seg1->end >= seg2->start ) return( 0 );
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382 if( seg1->pair->end >= seg2->pair->start ) return( 0 );
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383 else return( 1 );
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384 }
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385
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386 void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
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387 {
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388 int i, j, k, shift, cur1, cur2, count, klim;
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389 static TLS int crossscoresize = 0;
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390 static TLS int *result1 = NULL;
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391 static TLS int *result2 = NULL;
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392 static TLS int *ocut1 = NULL;
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393 static TLS int *ocut2 = NULL;
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394 double maximum;
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395 static TLS double **crossscore = NULL;
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396 static TLS int **track = NULL;
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397 static TLS double maxj, maxi;
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398 static TLS int pointj, pointi;
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399
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400 if( cut1 == NULL)
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401 {
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402 if( result1 )
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403 {
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404 if( result1 ) free( result1 ); result1 = NULL;
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405 if( result2 ) free( result2 ); result2 = NULL;
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406 if( ocut1 ) free( ocut1 ); ocut1 = NULL;
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407 if( ocut2 ) free( ocut2 ); ocut2 = NULL;
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408 if( track ) FreeIntMtx( track ); track = NULL;
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409 if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
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410 }
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411 crossscoresize = 0;
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412 return;
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413 }
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414
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415 if( result1 == NULL )
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416 {
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417 result1 = AllocateIntVec( MAXSEG );
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418 result2 = AllocateIntVec( MAXSEG );
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419 ocut1 = AllocateIntVec( MAXSEG );
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420 ocut2 = AllocateIntVec( MAXSEG );
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421 }
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422
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423 if( crossscoresize < *ncut+2 )
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424 {
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425 crossscoresize = *ncut+2;
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426 if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
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427 if( track ) FreeIntMtx( track );
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428 if( crossscore ) FreeDoubleMtx( crossscore );
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429 track = AllocateIntMtx( crossscoresize, crossscoresize );
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430 crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
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431 }
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432
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433 #if 0
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434 for( i=0; i<*ncut-2; i++ )
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435 fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
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436
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437 for( i=0; i<*ncut; i++ )
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438 fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
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439 for( i=0; i<*ncut; i++ )
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440 {
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441 for( j=0; j<*ncut; j++ )
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442 fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
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443 fprintf( stderr, "\n" );
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444 }
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445 #endif
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446
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447 for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
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448 crossscore[i][j] = ocrossscore[i][j];
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449 for( i=0; i<*ncut; i++ )
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450 {
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451 ocut1[i] = cut1[i];
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452 ocut2[i] = cut2[i];
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453 }
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454
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455 for( i=1; i<*ncut; i++ )
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456 {
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457 #if 0
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458 fprintf( stderr, "### i=%d/%d\n", i,*ncut );
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459 #endif
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460 for( j=1; j<*ncut; j++ )
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461 {
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462 pointi = 0; maxi = 0.0;
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463 klim = j-2;
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464 for( k=0; k<klim; k++ )
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465 {
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466 /*
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467 fprintf( stderr, "k=%d, i=%d\n", k, i );
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468 */
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469 if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
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470 if( crossscore[i-1][k] > maxj )
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471 {
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472 pointi = k;
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473 maxi = crossscore[i-1][k];
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474 }
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475 }
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diff changeset
476
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nick
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diff changeset
477 pointj = 0; maxj = 0.0;
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nick
parents:
diff changeset
478 klim = i-2;
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479 for( k=0; k<klim; k++ )
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480 {
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481 if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
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parents:
diff changeset
482 if( crossscore[k][j-1] > maxj )
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483 {
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484 pointj = k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
485 maxj = crossscore[k][j-1];
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diff changeset
486 }
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diff changeset
487 }
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diff changeset
488
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diff changeset
489 maxi += penalty;
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parents:
diff changeset
490 maxj += penalty;
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diff changeset
491
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diff changeset
492 maximum = crossscore[i-1][j-1];
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493 track[i][j] = 0;
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494
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495 if( maximum < maxi )
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496 {
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497 maximum = maxi ;
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498 track[i][j] = j - pointi;
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499 }
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500
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501 if( maximum < maxj )
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502 {
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503 maximum = maxj ;
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504 track[i][j] = pointj - i;
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505 }
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506
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507 crossscore[i][j] += maximum;
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508 }
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509 }
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diff changeset
510 #if 0
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511 for( i=0; i<*ncut; i++ )
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512 {
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513 for( j=0; j<*ncut; j++ )
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514 fprintf( stderr, "%3d ", track[i][j] );
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515 fprintf( stderr, "\n" );
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516 }
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diff changeset
517 #endif
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518
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nick
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diff changeset
519
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diff changeset
520 result1[MAXSEG-1] = *ncut-1;
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parents:
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521 result2[MAXSEG-1] = *ncut-1;
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522
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523 for( i=MAXSEG-1; i>=1; i-- )
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524 {
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diff changeset
525 cur1 = result1[i];
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parents:
diff changeset
526 cur2 = result2[i];
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parents:
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527 if( cur1 == 0 || cur2 == 0 ) break;
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diff changeset
528 shift = track[cur1][cur2];
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529 if( shift == 0 )
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530 {
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diff changeset
531 result1[i-1] = cur1 - 1;
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parents:
diff changeset
532 result2[i-1] = cur2 - 1;
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533 continue;
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534 }
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535 else if( shift > 0 )
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536 {
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537 result1[i-1] = cur1 - 1;
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538 result2[i-1] = cur2 - shift;
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539 }
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540 else if( shift < 0 )
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541 {
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542 result1[i-1] = cur1 + shift;
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parents:
diff changeset
543 result2[i-1] = cur2 - 1;
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544 }
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545 }
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546
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547 count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
548 for( j=i; j<MAXSEG; j++ )
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549 {
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550 if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
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551
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diff changeset
552 if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
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553 if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
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parents:
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554 count--;
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diff changeset
555
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parents:
diff changeset
556 cut1[count] = ocut1[result1[j]];
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parents:
diff changeset
557 cut2[count] = ocut2[result2[j]];
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diff changeset
558
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559 count++;
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560 }
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diff changeset
561
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562 *ncut = count;
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parents:
diff changeset
563 #if 0
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564 for( i=0; i<*ncut; i++ )
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parents:
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565 fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
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parents:
diff changeset
566 #endif
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diff changeset
567 }
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568
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569 void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
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parents:
diff changeset
570 // memory complexity = O(n^3), time complexity = O(n^2)
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571 {
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diff changeset
572 int i, j, shift, cur1, cur2, count;
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parents:
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573 static TLS int crossscoresize = 0;
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parents:
diff changeset
574 static TLS int jumpposi, *jumppos;
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parents:
diff changeset
575 static TLS double jumpscorei, *jumpscore;
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parents:
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576 static TLS int *result1 = NULL;
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parents:
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577 static TLS int *result2 = NULL;
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parents:
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578 static TLS int *ocut1 = NULL;
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parents:
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579 static TLS int *ocut2 = NULL;
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580 double maximum;
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parents:
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581 static TLS double **crossscore = NULL;
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parents:
diff changeset
582 static TLS int **track = NULL;
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parents:
diff changeset
583
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584 if( result1 == NULL )
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parents:
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585 {
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586 result1 = AllocateIntVec( MAXSEG );
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diff changeset
587 result2 = AllocateIntVec( MAXSEG );
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parents:
diff changeset
588 ocut1 = AllocateIntVec( MAXSEG );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
589 ocut2 = AllocateIntVec( MAXSEG );
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590 }
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591 if( crossscoresize < *ncut+2 )
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parents:
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592 {
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593 crossscoresize = *ncut+2;
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nick
parents:
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594 if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
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595 if( track ) FreeIntMtx( track );
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596 if( crossscore ) FreeDoubleMtx( crossscore );
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597 if( jumppos ) FreeIntVec( jumppos );
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598 if( jumpscore ) FreeDoubleVec( jumpscore );
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599 track = AllocateIntMtx( crossscoresize, crossscoresize );
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600 crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
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601 jumppos = AllocateIntVec( crossscoresize );
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602 jumpscore = AllocateDoubleVec( crossscoresize );
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603 }
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604
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605 #if 0
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606 for( i=0; i<*ncut-2; i++ )
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607 fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
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608
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609 for( i=0; i<*ncut; i++ )
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610 fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
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611 for( i=0; i<*ncut; i++ )
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612 {
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613 for( j=0; j<*ncut; j++ )
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614 fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
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615 fprintf( stderr, "\n" );
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616 }
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617 #endif
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618
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619 for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
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620 crossscore[i][j] = ocrossscore[i][j];
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621 for( i=0; i<*ncut; i++ )
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622 {
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623 ocut1[i] = cut1[i];
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624 ocut2[i] = cut2[i];
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625 }
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626 for( j=0; j<*ncut; j++ )
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627 {
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628 jumpscore[j] = -999.999;
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629 jumppos[j] = -1;
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630 }
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631
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632 for( i=1; i<*ncut; i++ )
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633 {
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634
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635 jumpscorei = -999.999;
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636 jumpposi = -1;
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637
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638 for( j=1; j<*ncut; j++ )
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639 {
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640 #if 1
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641 fprintf( stderr, "in blockalign3, ### i=%d, j=%d\n", i, j );
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642 #endif
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643
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644
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645 #if 0
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646 for( k=0; k<j-2; k++ )
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647 {
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648 /*
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649 fprintf( stderr, "k=%d, i=%d\n", k, i );
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650 */
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651 if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
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652 if( crossscore[i-1][k] > maxj )
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653 {
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654 pointi = k;
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655 maxi = crossscore[i-1][k];
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656 }
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657 }
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658
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659 pointj = 0; maxj = 0.0;
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660 for( k=0; k<i-2; k++ )
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661 {
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662 if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
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663 if( crossscore[k][j-1] > maxj )
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664 {
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665 pointj = k;
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666 maxj = crossscore[k][j-1];
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667 }
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668 }
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669
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670
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671 maxi += penalty;
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672 maxj += penalty;
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673 #endif
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674 maximum = crossscore[i-1][j-1];
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675 track[i][j] = 0;
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676
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677 if( maximum < jumpscorei && permit( seg1[jumpposi], seg1[i] ) )
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678 {
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679 maximum = jumpscorei;
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680 track[i][j] = j - jumpposi;
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681 }
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682
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683 if( maximum < jumpscore[j] && permit( seg2[jumppos[j]], seg2[j] ) )
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684 {
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685 maximum = jumpscore[j];
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686 track[i][j] = jumpscore[j] - i;
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687 }
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688
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689 crossscore[i][j] += maximum;
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690
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691 if( jumpscorei < crossscore[i-1][j] )
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692 {
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693 jumpscorei = crossscore[i-1][j];
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694 jumpposi = j;
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695 }
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696
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697 if( jumpscore[j] < crossscore[i][j-1] )
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698 {
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699 jumpscore[j] = crossscore[i][j-1];
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700 jumppos[j] = i;
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701 }
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702 }
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703 }
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704 #if 0
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705 for( i=0; i<*ncut; i++ )
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706 {
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707 for( j=0; j<*ncut; j++ )
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708 fprintf( stderr, "%3d ", track[i][j] );
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709 fprintf( stderr, "\n" );
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710 }
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711 #endif
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712
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713
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714 result1[MAXSEG-1] = *ncut-1;
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715 result2[MAXSEG-1] = *ncut-1;
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716
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717 for( i=MAXSEG-1; i>=1; i-- )
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718 {
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719 cur1 = result1[i];
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720 cur2 = result2[i];
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721 if( cur1 == 0 || cur2 == 0 ) break;
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722 shift = track[cur1][cur2];
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723 if( shift == 0 )
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724 {
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725 result1[i-1] = cur1 - 1;
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726 result2[i-1] = cur2 - 1;
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727 continue;
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728 }
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729 else if( shift > 0 )
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730 {
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731 result1[i-1] = cur1 - 1;
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732 result2[i-1] = cur2 - shift;
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733 }
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734 else if( shift < 0 )
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735 {
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736 result1[i-1] = cur1 + shift;
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737 result2[i-1] = cur2 - 1;
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738 }
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739 }
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740
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741 count = 0;
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742 for( j=i; j<MAXSEG; j++ )
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743 {
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744 if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
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745
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746 if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
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747 if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
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748 count--;
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749
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750 cut1[count] = ocut1[result1[j]];
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751 cut2[count] = ocut2[result2[j]];
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752
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753 count++;
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754 }
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755
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756 *ncut = count;
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757 #if 0
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758 for( i=0; i<*ncut; i++ )
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759 fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
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760 #endif
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761 }
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762