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annotate mafft/core/Galign11.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 #include "dp.h"
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3
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4 #define DEBUG 0
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5 #define XXXXXXX 0
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6 #define USE_PENALTY_EX 1
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7
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8 #if 1
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9 static void match_calc_mtx( double **mtx, float *match, char **s1, char **s2, int i1, int lgth2 )
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10 {
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11 char *seq2 = s2[0];
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12 double *doubleptr = mtx[(int)s1[0][i1]];
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13
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14 while( lgth2-- )
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15 *match++ = doubleptr[(int)*seq2++];
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16 }
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17 #else
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18 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
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19 {
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20 int j;
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21
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22 for( j=0; j<lgth2; j++ )
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23 match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
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24 }
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25 #endif
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26
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27 static float Atracking( float *lasthorizontalw, float *lastverticalw,
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28 char **seq1, char **seq2,
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29 char **mseq1, char **mseq2,
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30 int **ijp,
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31 int tailgp,
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32 int *warpis, int *warpjs, int warpbase )
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33 {
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34 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
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35 // char gap[] = "-";
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36 char *gap;
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37 gap = newgapstr;
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38 lgth1 = strlen( seq1[0] );
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39 lgth2 = strlen( seq2[0] );
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40 float wm;
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41
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42
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43 #if 0
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44 for( i=0; i<lgth1; i++ )
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45 {
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46 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
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47 }
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48 #endif
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49
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50 for( i=0; i<lgth1+1; i++ )
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51 {
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52 ijp[i][0] = i + 1;
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53 }
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54 for( j=0; j<lgth2+1; j++ )
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55 {
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56 ijp[0][j] = -( j + 1 );
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57 }
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58
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59 // if( tailgp == 1 || ijp[lgth1][lgth2] >= warpbase )
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60 if( tailgp == 1 )
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61 ;
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62 else
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63 {
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64 wm = lastverticalw[0];
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65 for( i=0; i<lgth1; i++ )
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66 {
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67 if( lastverticalw[i] >= wm )
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68 {
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69 wm = lastverticalw[i];
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70 iin = i; jin = lgth2-1;
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71 ijp[lgth1][lgth2] = +( lgth1 - i );
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72 }
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73 }
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74 for( j=0; j<lgth2; j++ )
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75 {
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76 if( lasthorizontalw[j] >= wm )
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77 {
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78 wm = lasthorizontalw[j];
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79 iin = lgth1-1; jin = j;
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80 ijp[lgth1][lgth2] = -( lgth2 - j );
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81 }
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82 }
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83 }
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84
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85
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86
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87 mseq1[0] += lgth1+lgth2;
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88 *mseq1[0] = 0;
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89 mseq2[0] += lgth1+lgth2;
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90 *mseq2[0] = 0;
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91
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92
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93
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94 iin = lgth1; jin = lgth2;
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95 limk = lgth1+lgth2 + 1;
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96 for( k=0; k<limk; k++ )
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97 {
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98 if( ijp[iin][jin] >= warpbase )
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99 {
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100 // fprintf( stderr, "WARP!\n" );
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101 ifi = warpis[ijp[iin][jin]-warpbase];
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102 jfi = warpjs[ijp[iin][jin]-warpbase];
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103 }
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104 else if( ijp[iin][jin] < 0 )
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105 {
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106 ifi = iin-1; jfi = jin+ijp[iin][jin];
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107 }
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108 else if( ijp[iin][jin] > 0 )
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109 {
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110 ifi = iin-ijp[iin][jin]; jfi = jin-1;
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111 }
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112 else
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113 {
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114 ifi = iin-1; jfi = jin-1;
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115 }
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116
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117 if( ifi == -warpbase && jfi == -warpbase )
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118 {
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119 l = iin;
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120 while( --l >= 0 )
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121 {
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122 *--mseq1[0] = seq1[0][l];
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123 *--mseq2[0] = *gap;
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124 k++;
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125 }
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126 l= jin;
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127 while( --l >= 0 )
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128 {
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129 *--mseq1[0] = *gap;
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130 *--mseq2[0] = seq2[0][l];
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131 k++;
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132 }
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133 break;
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134 }
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135 else
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136 {
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137 l = iin - ifi;
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138 while( --l > 0 )
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139 {
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140 *--mseq1[0] = seq1[0][ifi+l];
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141 *--mseq2[0] = *gap;
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142 k++;
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143 }
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144 l= jin - jfi;
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145 while( --l > 0 )
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146 {
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147 *--mseq1[0] = *gap;
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148 *--mseq2[0] = seq2[0][jfi+l];
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149 k++;
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150 }
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151 }
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152 if( iin <= 0 || jin <= 0 ) break;
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153 *--mseq1[0] = seq1[0][ifi];
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154 *--mseq2[0] = seq2[0][jfi];
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155 k++;
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156 iin = ifi; jin = jfi;
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157 }
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158
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159 // fprintf( stderr, "%s\n", mseq1[0] );
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160 // fprintf( stderr, "%s\n", mseq2[0] );
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161 return( 0.0 );
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162 }
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163
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164
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165 float G__align11( double **n_dynamicmtx, char **seq1, char **seq2, int alloclen, int headgp, int tailgp )
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166 {
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167 // int k;
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168 register int i, j;
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169 int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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170 int lastj;
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171 int lgth1, lgth2;
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172 int resultlen;
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173 float wm; /* int ?????? */
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174 float g;
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175 float *currentw, *previousw;
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176 float fpenalty = (float)penalty;
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177 float fpenalty_shift = (float)penalty_shift;
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178 float fpenalty_tmp;
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179 #if USE_PENALTY_EX
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180 float fpenalty_ex = (float)penalty_ex;
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181 #endif
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182 #if 1
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183 float *wtmp;
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184 int *ijppt;
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185 float *mjpt, *prept, *curpt;
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186 int *mpjpt;
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187 #endif
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188 static TLS float mi = 0.0;
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189 static TLS float *m = NULL;
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190 static TLS int **ijp = NULL;
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191 static TLS int mpi = 0;
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192 static TLS int *mp = NULL;
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193 static TLS float *w1 = NULL;
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194 static TLS float *w2 = NULL;
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195 static TLS float *match = NULL;
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196 static TLS float *initverticalw = NULL; /* kufuu sureba iranai */
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197 static TLS float *lastverticalw = NULL; /* kufuu sureba iranai */
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198 static TLS char **mseq1 = NULL;
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199 static TLS char **mseq2 = NULL;
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200 static TLS char **mseq = NULL;
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201 static TLS int **intwork = NULL;
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202 static TLS float **floatwork = NULL;
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203 static TLS int orlgth1 = 0, orlgth2 = 0;
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204 static TLS double **amino_dynamicmtx = NULL; // ??
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205
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206 int *warpis = NULL;
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207 int *warpjs = NULL;
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208 int *warpi = NULL;
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209 int *warpj = NULL;
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210 int *prevwarpi = NULL;
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211 int *prevwarpj = NULL;
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212 float *wmrecords = NULL;
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213 float *prevwmrecords = NULL;
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214 int warpn = 0;
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215 int warpbase;
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216 float curm = 0.0;
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217 float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
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218 int *warpipt, *warpjpt;
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219
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220
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221 if( seq1 == NULL )
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222 {
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223 if( orlgth1 > 0 && orlgth2 > 0 )
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224 {
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225 orlgth1 = 0;
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226 orlgth2 = 0;
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227 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
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228 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
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229 if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
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230 if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
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231 if( match ) FreeFloatVec( match ); match = NULL;
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232 if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
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233 if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
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234
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235 if( m ) FreeFloatVec( m ); m = NULL;
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236 if( mp ) FreeIntVec( mp ); mp = NULL;
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237
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238 if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
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239
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240
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241
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242 if( floatwork ) FreeFloatMtx( floatwork ); floatwork = NULL;
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243 if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
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244
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245 if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
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246 }
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247 orlgth1 = 0;
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248 orlgth2 = 0;
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249 return( 0.0 );
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250 }
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251
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252
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253
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254 lgth1 = strlen( seq1[0] );
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255 lgth2 = strlen( seq2[0] );
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256
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257 warpbase = lgth1 + lgth2;
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258 warpis = NULL;
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259 warpjs = NULL;
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260 warpn = 0;
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261 if( trywarp )
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262 {
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263 // fprintf( stderr, "IN G__align11\n" );
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264 if( headgp == 0 || tailgp == 0 )
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265 {
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266 fprintf( stderr, "At present, headgp and tailgp must be 1.\n" );
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267 exit( 1 );
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268 }
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269
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270 wmrecords = AllocateFloatVec( lgth2+1 );
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271 warpi = AllocateIntVec( lgth2+1 );
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272 warpj = AllocateIntVec( lgth2+1 );
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273 prevwmrecords = AllocateFloatVec( lgth2+1 );
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274 prevwarpi = AllocateIntVec( lgth2+1 );
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275 prevwarpj = AllocateIntVec( lgth2+1 );
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276 for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
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277 for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
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278 for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
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279 for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
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280 for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
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281 for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
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282 }
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283
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284 #if 0
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285 if( lgth1 <= 0 || lgth2 <= 0 )
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286 {
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287 fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
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288 }
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289 #endif
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290
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291 #if 1
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292 if( lgth1 == 0 && lgth2 == 0 )
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293 return( 0.0 );
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294
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295 if( lgth1 == 0 )
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296 {
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297 seq1[0][lgth2] = 0;
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298 while( lgth2 ) seq1[0][--lgth2] = *newgapstr;
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299 // fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
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300 return( 0.0 );
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301 }
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302
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303 if( lgth2 == 0 )
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304 {
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305 seq2[0][lgth1] = 0;
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306 while( lgth1 ) seq2[0][--lgth1] = *newgapstr;
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307 // fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
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308 return( 0.0 );
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309 }
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310 #endif
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311
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312
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313 wm = 0.0;
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314
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315 if( orlgth1 == 0 )
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316 {
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317 mseq1 = AllocateCharMtx( njob, 0 );
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318 mseq2 = AllocateCharMtx( njob, 0 );
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319 }
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320
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321
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322
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323 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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324 {
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325 int ll1, ll2;
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326
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327 if( orlgth1 > 0 && orlgth2 > 0 )
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328 {
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329 FreeFloatVec( w1 );
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330 FreeFloatVec( w2 );
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331 FreeFloatVec( match );
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332 FreeFloatVec( initverticalw );
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333 FreeFloatVec( lastverticalw );
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334
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335 FreeFloatVec( m );
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336 FreeIntVec( mp );
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337
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338 FreeCharMtx( mseq );
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339
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340
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341
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342 FreeFloatMtx( floatwork );
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343 FreeIntMtx( intwork );
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344 FreeDoubleMtx( amino_dynamicmtx );
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345 }
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346
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347 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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348 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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349
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350 #if DEBUG
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351 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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352 #endif
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353
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354 w1 = AllocateFloatVec( ll2+2 );
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355 w2 = AllocateFloatVec( ll2+2 );
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356 match = AllocateFloatVec( ll2+2 );
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357
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358 initverticalw = AllocateFloatVec( ll1+2 );
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359 lastverticalw = AllocateFloatVec( ll1+2 );
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360
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361 m = AllocateFloatVec( ll2+2 );
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362 mp = AllocateIntVec( ll2+2 );
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363
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364 mseq = AllocateCharMtx( njob, ll1+ll2 );
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365
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366
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367 floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
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368 intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
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369 amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
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370
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371 #if DEBUG
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372 fprintf( stderr, "succeeded\n" );
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373 #endif
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374
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375 orlgth1 = ll1 - 100;
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376 orlgth2 = ll2 - 100;
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377 }
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378 for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
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379 amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
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380
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381
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382 mseq1[0] = mseq[0];
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383 mseq2[0] = mseq[1];
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384
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385
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386 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
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387 {
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388 int ll1, ll2;
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389
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390 if( commonAlloc1 && commonAlloc2 )
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391 {
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392 FreeIntMtx( commonIP );
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393 }
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394
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395 ll1 = MAX( orlgth1, commonAlloc1 );
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396 ll2 = MAX( orlgth2, commonAlloc2 );
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397
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398 #if DEBUG
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399 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
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400 #endif
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401
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402 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
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403
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404 #if DEBUG
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405 fprintf( stderr, "succeeded\n\n" );
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406 #endif
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407
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408 commonAlloc1 = ll1;
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409 commonAlloc2 = ll2;
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410 }
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411 ijp = commonIP;
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412
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413
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414 #if 0
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415 for( i=0; i<lgth1; i++ )
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416 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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417 #endif
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418
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419 currentw = w1;
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420 previousw = w2;
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421
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422
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423 match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
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424 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
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425
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426 if( headgp == 1 )
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427 {
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428 for( i=1; i<lgth1+1; i++ )
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429 {
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430 initverticalw[i] += fpenalty;
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431 }
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432 for( j=1; j<lgth2+1; j++ )
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433 {
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434 currentw[j] += fpenalty;
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435 }
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436 }
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437
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438 for( j=1; j<lgth2+1; ++j )
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439 {
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440 m[j] = currentw[j-1]; mp[j] = 0;
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441 }
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442
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443 if( lgth2 == 0 )
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444 lastverticalw[0] = 0.0; // lgth2==0 no toki error
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445 else
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446 lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
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447
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448 if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
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449 lastj = lgth2+1;
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450
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451 #if XXXXXXX
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452 fprintf( stderr, "currentw = \n" );
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453 for( i=0; i<lgth1+1; i++ )
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454 {
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455 fprintf( stderr, "%5.2f ", currentw[i] );
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456 }
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457 fprintf( stderr, "\n" );
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458 fprintf( stderr, "initverticalw = \n" );
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459 for( i=0; i<lgth2+1; i++ )
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460 {
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461 fprintf( stderr, "%5.2f ", initverticalw[i] );
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462 }
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463 fprintf( stderr, "\n" );
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464 #endif
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465
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466 for( i=1; i<lasti; i++ )
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467 {
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468 wtmp = previousw;
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469 previousw = currentw;
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470 currentw = wtmp;
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471
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472 previousw[0] = initverticalw[i-1];
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473
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474 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
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475 #if XXXXXXX
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476 fprintf( stderr, "\n" );
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477 fprintf( stderr, "i=%d\n", i );
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478 fprintf( stderr, "currentw = \n" );
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479 for( j=0; j<lgth2; j++ )
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480 {
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481 fprintf( stderr, "%5.2f ", currentw[j] );
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482 }
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483 fprintf( stderr, "\n" );
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484 #endif
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485 #if XXXXXXX
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486 fprintf( stderr, "\n" );
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487 fprintf( stderr, "i=%d\n", i );
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488 fprintf( stderr, "currentw = \n" );
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489 for( j=0; j<lgth2; j++ )
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490 {
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491 fprintf( stderr, "%5.2f ", currentw[j] );
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492 }
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493 fprintf( stderr, "\n" );
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494 #endif
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495 currentw[0] = initverticalw[i];
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496
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497 mi = previousw[0]; mpi = 0;
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498
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499 ijppt = ijp[i] + 1;
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500 mjpt = m + 1;
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501 prept = previousw;
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502 curpt = currentw + 1;
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503 mpjpt = mp + 1;
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504 if( trywarp )
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505 {
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506 prevwmrecordspt = prevwmrecords;
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507 wmrecordspt = wmrecords+1;
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508 wmrecords1pt = wmrecords;
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509 warpipt = warpi + 1;
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510 warpjpt = warpj + 1;
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511 }
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512
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513 for( j=1; j<lastj; j++ )
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514 {
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diff changeset
515
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516 wm = *prept;
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517 *ijppt = 0;
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518
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519 #if 0
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520 fprintf( stderr, "%5.0f->", wm );
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521 #endif
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522 #if 0
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523 fprintf( stderr, "%5.0f?", g );
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524 #endif
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525 if( (g=mi+fpenalty) > wm )
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526 {
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527 wm = g;
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528 *ijppt = -( j - mpi );
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529 }
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530 if( (g=*prept) >= mi )
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531 {
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532 mi = g;
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533 mpi = j-1;
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534 }
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535 #if USE_PENALTY_EX
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536 mi += fpenalty_ex;
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537 #endif
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538
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539 #if 0
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540 fprintf( stderr, "%5.0f?", g );
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541 #endif
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542 if( (g=*mjpt + fpenalty) > wm )
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543 {
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544 wm = g;
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545 *ijppt = +( i - *mpjpt );
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546 }
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547 if( (g=*prept) >= *mjpt )
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548 {
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549 *mjpt = g;
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550 *mpjpt = i-1;
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551 }
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552 #if USE_PENALTY_EX
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553 m[j] += fpenalty_ex;
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554 #endif
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555 #if 1
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556 if( trywarp )
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557 {
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558 fpenalty_tmp = fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] );
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559 // fprintf( stderr, "fpenalty_shift = %f\n", fpenalty_tmp );
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560
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561 // fprintf( stderr, "\n\n\nwarp to %c-%c (%d-%d) from %c-%c (%d-%d) ? prevwmrecords[%d] = %f + %f <- wm = %f\n", seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], prevwarpi[j-1], prevwarpj[j-1], seq1[0][i], seq2[0][j], i, j, j, prevwmrecords[j-1], fpenalty_tmp, wm );
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562 // if( (g=prevwmrecords[j-1] + fpenalty_shift )> wm )
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563 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
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diff changeset
564 {
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565 // fprintf( stderr, "Yes! Warp!! from %d-%d (%c-%c) to %d-%d (%c-%c) fpenalty_tmp = %f! warpn = %d\n", i, j, seq1[0][i], seq2[0][j-1], prevwarpi[j-1], prevwarpj[j-1],seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], fpenalty_tmp, warpn );
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566 if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
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diff changeset
567 {
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568 *ijppt = warpbase + warpn - 1;
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569 }
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570 else
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571 {
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572 *ijppt = warpbase + warpn;
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573 warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
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574 warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
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575 warpis[warpn] = prevwarpi[j-1];
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576 warpjs[warpn] = prevwarpj[j-1];
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577 warpn++;
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diff changeset
578 }
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579 wm = g;
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diff changeset
580 }
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581 else
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diff changeset
582 {
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diff changeset
583 }
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diff changeset
584
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585 curm = *curpt + wm;
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parents:
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586
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587 // fprintf( stderr, "###### curm = %f at %c-%c, i=%d, j=%d\n", curm, seq1[0][i], seq2[0][j], i, j );
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diff changeset
588
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589 // fprintf( stderr, "copy from i, j-1? %f > %f?\n", wmrecords[j-1], curm );
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diff changeset
590 // if( wmrecords[j-1] > wmrecords[j] )
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diff changeset
591 if( *wmrecords1pt > *wmrecordspt )
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592 {
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593 // fprintf( stderr, "yes\n" );
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594 // wmrecords[j] = wmrecords[j-1];
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595 *wmrecordspt = *wmrecords1pt;
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596 // warpi[j] = warpi[j-1];
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597 // warpj[j] = warpj[j-1];
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598 *warpipt = *(warpipt-1);
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599 *warpjpt = *(warpjpt-1);
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600 // fprintf( stderr, "warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
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601 }
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602 // else
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603 // {
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604 // fprintf( stderr, "no\n" );
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605 // }
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606
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607 // fprintf( stderr, " curm = %f at %c-%c\n", curm, seq1[0][i], seq2[0][j] );
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608 // fprintf( stderr, " wmrecords[%d] = %f\n", j, wmrecords[j] );
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609 // fprintf( stderr, "replace?\n" );
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610
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611 // if( curm > wmrecords[j] )
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612 if( curm > *wmrecordspt )
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613 {
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614 // fprintf( stderr, "yes at %d-%d (%c-%c), replaced warp: warpi[j]=%d, warpj[j]=%d warpn=%d, wmrecords[j] = %f -> %f\n", i, j, seq1[0][i], seq2[0][j], i, j, warpn, wmrecords[j], curm );
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615 // wmrecords[j] = curm;
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616 *wmrecordspt = curm;
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617 // warpi[j] = i;
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618 // warpj[j] = j;
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619 *warpipt = i;
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620 *warpjpt = j;
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621 }
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622 // else
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623 // {
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624 // fprintf( stderr, "No! warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
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625 // }
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626 // fprintf( stderr, "%d-%d (%c-%c) curm = %5.0f, wmrecords[j]=%f\n", i, j, seq1[0][i], seq2[0][j], curm, wmrecords[j] );
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627 wmrecordspt++;
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628 wmrecords1pt++;
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629 warpipt++;
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630 warpjpt++;
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631 }
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632 #endif
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633
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634 *curpt++ += wm;
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635 ijppt++;
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636 mjpt++;
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637 prept++;
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638 mpjpt++;
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639 }
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640 lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
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641
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642 if( trywarp )
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643 {
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644 fltncpy( prevwmrecords, wmrecords, lastj );
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645 intncpy( prevwarpi, warpi, lastj );
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646 intncpy( prevwarpj, warpj, lastj );
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647 }
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648 }
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649
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650 if( trywarp )
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651 {
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652 // fprintf( stderr, "\nwm = %f\n", wm );
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653 // fprintf( stderr, "warpn = %d\n", warpn );
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654 free( wmrecords );
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655 free( prevwmrecords );
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656 free( warpi );
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657 free( warpj );
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658 free( prevwarpi );
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659 free( prevwarpj );
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660 }
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661
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662 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp, warpis, warpjs, warpbase );
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663 if( warpis ) free( warpis );
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664 if( warpjs ) free( warpjs );
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665
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666
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667 resultlen = strlen( mseq1[0] );
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668 if( alloclen < resultlen || resultlen > N )
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669 {
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670 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
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671 ErrorExit( "LENGTH OVER!\n" );
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672 }
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673
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674
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675 strcpy( seq1[0], mseq1[0] );
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676 strcpy( seq2[0], mseq2[0] );
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677 #if 0
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678 fprintf( stderr, "\n" );
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679 fprintf( stderr, ">\n%s\n", mseq1[0] );
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680 fprintf( stderr, ">\n%s\n", mseq2[0] );
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681 fprintf( stderr, "wm = %f\n", wm );
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682 #endif
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683
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684 return( wm );
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685 }
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686
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687 float G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char **seq1, char **seq2, int alloclen )
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688 /* warp mitaiou */
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689 {
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690 // int k;
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691 register int i, j;
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692 int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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693 int lgth1, lgth2;
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694 // int resultlen;
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695 float wm; /* int ?????? */
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696 float g;
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697 float *currentw, *previousw;
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698 float fpenalty = (float)penal;
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699 #if USE_PENALTY_EX
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700 float fpenalty_ex = (float)penal_ex;
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701 #endif
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702 #if 1
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703 float *wtmp;
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704 float *mjpt, *prept, *curpt;
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705 // int *mpjpt;
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706 #endif
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707 static TLS float mi, *m;
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708 static TLS float *w1, *w2;
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709 static TLS float *match;
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710 static TLS float *initverticalw; /* kufuu sureba iranai */
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711 static TLS float *lastverticalw; /* kufuu sureba iranai */
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712 static TLS int **intwork;
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713 static TLS float **floatwork;
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714 static TLS int orlgth1 = 0, orlgth2 = 0;
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715 static TLS double **amino_dynamicmtx;
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716
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717 if( seq1 == NULL )
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718 {
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719 if( orlgth1 > 0 && orlgth2 > 0 )
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720 {
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721 orlgth1 = 0;
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722 orlgth2 = 0;
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723 FreeFloatVec( w1 );
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724 FreeFloatVec( w2 );
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725 FreeFloatVec( match );
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726 FreeFloatVec( initverticalw );
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727 FreeFloatVec( lastverticalw );
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728 free( m );
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729
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730
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731 FreeFloatMtx( floatwork );
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732 FreeIntMtx( intwork );
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733 FreeDoubleMtx( amino_dynamicmtx );
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734 }
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735 return( 0.0 );
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736 }
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737
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738
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739 wm = 0.0;
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740
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741
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742
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743 lgth1 = strlen( seq1[0] );
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744 lgth2 = strlen( seq2[0] );
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745
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746
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747
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748 #if 0
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749 if( lgth1 <= 0 || lgth2 <= 0 )
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750 {
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751 fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
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752 }
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753 #endif
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754
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755 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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756 {
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757 int ll1, ll2;
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758
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759 if( orlgth1 > 0 && orlgth2 > 0 )
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760 {
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761 FreeFloatVec( w1 );
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762 FreeFloatVec( w2 );
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763 FreeFloatVec( match );
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764 FreeFloatVec( initverticalw );
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765 FreeFloatVec( lastverticalw );
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766
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767 FreeFloatVec( m );
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768
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769
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770
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771
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772 FreeFloatMtx( floatwork );
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773 FreeIntMtx( intwork );
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774
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775 FreeDoubleMtx( amino_dynamicmtx );
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776 }
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777
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778 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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779 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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780
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781 #if DEBUG
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782 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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783 #endif
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784
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785 w1 = AllocateFloatVec( ll2+2 );
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786 w2 = AllocateFloatVec( ll2+2 );
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787 match = AllocateFloatVec( ll2+2 );
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788
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789 initverticalw = AllocateFloatVec( ll1+2 );
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790 lastverticalw = AllocateFloatVec( ll1+2 );
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791
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792 m = AllocateFloatVec( ll2+2 );
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793
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794
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795
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796 floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
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797 intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
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798
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799
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800 amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
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801 #if DEBUG
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802 fprintf( stderr, "succeeded\n" );
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803 #endif
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804
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805 orlgth1 = ll1 - 100;
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806 orlgth2 = ll2 - 100;
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807 }
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808
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809
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810 for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
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811 amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
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812
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813
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814
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815
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816 #if 0
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817 for( i=0; i<lgth1; i++ )
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818 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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819 #endif
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820
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821 currentw = w1;
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822 previousw = w2;
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823
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824
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825 match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
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826
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827
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828 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
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829
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830 if( 1 ) // tsuneni outgap-1
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831 {
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832 for( i=1; i<lgth1+1; i++ )
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833 {
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834 initverticalw[i] += fpenalty;
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835 }
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836 for( j=1; j<lgth2+1; j++ )
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837 {
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838 currentw[j] += fpenalty;
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839 }
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840 }
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841
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842 for( j=1; j<lgth2+1; ++j )
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843 {
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844 m[j] = currentw[j-1];
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845 }
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846
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847 if( lgth2 == 0 )
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848 lastverticalw[0] = 0.0; // lgth2==0 no toki error
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849 else
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850 lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
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851
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852 if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap-1
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853
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854 #if XXXXXXX
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855 fprintf( stderr, "currentw = \n" );
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856 for( i=0; i<lgth1+1; i++ )
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857 {
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858 fprintf( stderr, "%5.2f ", currentw[i] );
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859 }
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860 fprintf( stderr, "\n" );
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861 fprintf( stderr, "initverticalw = \n" );
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862 for( i=0; i<lgth2+1; i++ )
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863 {
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864 fprintf( stderr, "%5.2f ", initverticalw[i] );
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865 }
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866 fprintf( stderr, "\n" );
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867 #endif
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868
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869 for( i=1; i<lasti; i++ )
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870 {
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871 wtmp = previousw;
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872 previousw = currentw;
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873 currentw = wtmp;
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874
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875 previousw[0] = initverticalw[i-1];
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876
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877 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
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878 #if XXXXXXX
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879 fprintf( stderr, "\n" );
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880 fprintf( stderr, "i=%d\n", i );
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881 fprintf( stderr, "currentw = \n" );
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882 for( j=0; j<lgth2; j++ )
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883 {
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884 fprintf( stderr, "%5.2f ", currentw[j] );
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885 }
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886 fprintf( stderr, "\n" );
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887 #endif
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888 #if XXXXXXX
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889 fprintf( stderr, "\n" );
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890 fprintf( stderr, "i=%d\n", i );
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891 fprintf( stderr, "currentw = \n" );
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892 for( j=0; j<lgth2; j++ )
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893 {
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894 fprintf( stderr, "%5.2f ", currentw[j] );
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895 }
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896 fprintf( stderr, "\n" );
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897 #endif
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898 currentw[0] = initverticalw[i];
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899
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900 mi = previousw[0];
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901
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902 mjpt = m + 1;
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903 prept = previousw;
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904 curpt = currentw + 1;
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905 for( j=1; j<lgth2+1; j++ )
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906 {
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907 wm = *prept;
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908
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909 #if 0
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910 fprintf( stderr, "%5.0f->", wm );
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911 #endif
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912 #if 0
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913 fprintf( stderr, "%5.0f?", g );
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914 #endif
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915 if( (g=mi+fpenalty) > wm )
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916 {
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917 wm = g;
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918 }
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919 if( (g=*prept) >= mi )
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920 {
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921 mi = g;
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922 }
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923 #if USE_PENALTY_EX
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924 mi += fpenalty_ex;
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925 #endif
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926
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927 #if 0
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928 fprintf( stderr, "%5.0f?", g );
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929 #endif
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930 if( (g=*mjpt + fpenalty) > wm )
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931 {
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932 wm = g;
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933 }
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934 if( (g=*prept) >= *mjpt )
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935 {
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936 *mjpt = g;
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937 }
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938 #if USE_PENALTY_EX
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939 m[j] += fpenalty_ex;
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940 #endif
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941
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942 #if 0
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943 fprintf( stderr, "%5.0f ", wm );
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944 #endif
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945 *curpt++ += wm;
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946 mjpt++;
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947 prept++;
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948 }
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949 lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
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950 }
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951
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952 #if 0
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953 fprintf( stderr, "\n" );
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954 fprintf( stderr, ">\n%s\n", mseq1[0] );
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955 fprintf( stderr, ">\n%s\n", mseq2[0] );
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956 fprintf( stderr, "wm = %f\n", wm );
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957 #endif
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958
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959 return( wm );
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960 }