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annotate mafft/core/Lalign11.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 DEBUG2 0
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6 #define XXXXXXX 0
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7 #define USE_PENALTY_EX 1
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8
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9
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10 static TLS int localstop; // 060910
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11
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12 #if 1
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13 static void match_calc_mtx( double **mtx, float *match, char **s1, char **s2, int i1, int lgth2 )
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14 {
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15 char *seq2 = s2[0];
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16 double *doubleptr = mtx[(int)s1[0][i1]];
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17
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18 while( lgth2-- )
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19 *match++ = doubleptr[(int)*seq2++];
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20 }
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21 #else
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22 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
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23 {
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24 int j;
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25
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26 for( j=0; j<lgth2; j++ )
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27 match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
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28 }
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29 #endif
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30
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31 #if 0
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32 static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
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33 {
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34 int j, k, l;
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35 float scarr[nalphabets];
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36 float **cpmxpd = floatwork;
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37 int **cpmxpdn = intwork;
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38 int count = 0;
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39
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40 if( initialize )
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41 {
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42 for( j=0; j<lgth2; j++ )
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43 {
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44 count = 0;
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45 for( l=0; l<nalphabets; l++ )
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46 {
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47 if( cpmx2[l][j] )
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48 {
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49 cpmxpd[count][j] = cpmx2[l][j];
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50 cpmxpdn[count][j] = l;
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51 count++;
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52 }
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53 }
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54 cpmxpdn[count][j] = -1;
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55 }
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56 }
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57
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58 for( l=0; l<nalphabets; l++ )
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59 {
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60 scarr[l] = 0.0;
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61 for( k=0; k<nalphabets; k++ )
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62 scarr[l] += n_dis[k][l] * cpmx1[k][i1];
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63 }
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64 #if 0 /* これを使うときはfloatworkのアロケートを逆にする */
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65 {
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66 float *fpt, **fptpt, *fpt2;
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67 int *ipt, **iptpt;
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68 fpt2 = match;
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69 iptpt = cpmxpdn;
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70 fptpt = cpmxpd;
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71 while( lgth2-- )
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72 {
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73 *fpt2 = 0.0;
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74 ipt=*iptpt,fpt=*fptpt;
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75 while( *ipt > -1 )
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76 *fpt2 += scarr[*ipt++] * *fpt++;
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77 fpt2++,iptpt++,fptpt++;
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78 }
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79 }
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80 #else
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81 for( j=0; j<lgth2; j++ )
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82 {
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83 match[j] = 0.0;
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84 for( k=0; cpmxpdn[k][j]>-1; k++ )
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85 match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
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86 }
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87 #endif
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88 }
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89 #endif
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90
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91 static float Ltracking( float *lasthorizontalw, float *lastverticalw,
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92 char **seq1, char **seq2,
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93 char **mseq1, char **mseq2,
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94 int **ijp, int *off1pt, int *off2pt, int endi, int endj,
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95 int *warpis, int *warpjs, int warpbase )
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96 {
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97 int i, j, l, iin, jin, lgth1, lgth2, k, limk;
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98 int ifi=0, jfi=0; // by D.Mathog, a guess
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99 // char gap[] = "-";
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100 char *gap;
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101 gap = newgapstr;
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102 lgth1 = strlen( seq1[0] );
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103 lgth2 = strlen( seq2[0] );
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104
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105 #if 0
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106 for( i=0; i<lgth1; i++ )
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107 {
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108 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
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109 }
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110 #endif
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111
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112 for( i=0; i<lgth1+1; i++ )
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113 {
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114 ijp[i][0] = localstop;
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115 }
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116 for( j=0; j<lgth2+1; j++ )
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117 {
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118 ijp[0][j] = localstop;
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119 }
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120
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121 mseq1[0] += lgth1+lgth2;
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122 *mseq1[0] = 0;
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123 mseq2[0] += lgth1+lgth2;
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124 *mseq2[0] = 0;
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125 iin = endi; jin = endj;
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126 limk = lgth1+lgth2;
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127 for( k=0; k<=limk; k++ )
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128 {
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129 if( ijp[iin][jin] >= warpbase )
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130 {
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131 // fprintf( stderr, "WARP!\n" );
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132 ifi = warpis[ijp[iin][jin]-warpbase];
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133 jfi = warpjs[ijp[iin][jin]-warpbase];
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134 }
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135 else if( ijp[iin][jin] < 0 )
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136 {
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137 ifi = iin-1; jfi = jin+ijp[iin][jin];
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138 }
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139 else if( ijp[iin][jin] > 0 )
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140 {
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141 ifi = iin-ijp[iin][jin]; jfi = jin-1;
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142 }
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143 else
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144 {
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145 ifi = iin-1; jfi = jin-1;
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146 }
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147
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148
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149 #if 1 // sentou de warp?
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150 if( ifi == -warpbase && jfi == -warpbase )
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151 {
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152 l = iin;
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153 while( --l >= 0 )
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154 {
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155 *--mseq1[0] = seq1[0][l];
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156 *--mseq2[0] = *gap;
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157 k++;
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158 }
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159 l= jin;
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160 while( --l >= 0 )
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161 {
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162 *--mseq1[0] = *gap;
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163 *--mseq2[0] = seq2[0][l];
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164 k++;
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165 }
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166 break;
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167 }
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168 else
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169 #endif
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170 {
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171 l = iin - ifi;
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172 while( --l > 0 )
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173 {
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174 *--mseq1[0] = seq1[0][ifi+l];
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175 *--mseq2[0] = *gap;
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176 k++;
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177 }
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178 l= jin - jfi;
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179 while( --l > 0 )
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180 {
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181 *--mseq1[0] = *gap;
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182 *--mseq2[0] = seq2[0][jfi+l];
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183 k++;
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184 }
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185 }
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186
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187
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188 if( iin <= 0 || jin <= 0 ) break;
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189 *--mseq1[0] = seq1[0][ifi];
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190 *--mseq2[0] = seq2[0][jfi];
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191 if( ijp[ifi][jfi] == localstop ) break;
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192 k++;
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193 iin = ifi; jin = jfi;
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194 }
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195 if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
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196 if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
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197
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198 // fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
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199 // fprintf( stderr, "\n" );
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200 // fprintf( stderr, "%s\n", mseq1[0] );
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201 // fprintf( stderr, "%s\n", mseq2[0] );
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202
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203
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204 return( 0.0 );
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205 }
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206
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207
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208 float L__align11( double **n_dynamicmtx, float scoreoffset, char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
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209 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
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210 {
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211 // int k;
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212 int i, j;
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213 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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214 int lgth1, lgth2;
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215 int resultlen;
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216 float wm = 0.0; /* int ?????? */
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217 float g;
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218 float *currentw, *previousw;
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219 #if 1
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220 float *wtmp;
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221 int *ijppt;
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222 float *mjpt, *prept, *curpt;
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223 int *mpjpt;
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224 #endif
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225 static TLS float mi, *m;
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226 static TLS int **ijp;
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227 static TLS int mpi, *mp;
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228 static TLS float *w1, *w2;
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229 static TLS float *match;
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230 static TLS float *initverticalw; /* kufuu sureba iranai */
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231 static TLS float *lastverticalw; /* kufuu sureba iranai */
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232 static TLS char **mseq1;
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233 static TLS char **mseq2;
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234 static TLS char **mseq;
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235 // static TLS int **intwork;
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236 // static TLS float **floatwork;
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237 static TLS int orlgth1 = 0, orlgth2 = 0;
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238 static TLS double **amino_dynamicmtx = NULL; // ??
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239 float maxwm;
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240 int endali = 0, endalj = 0; // by D.Mathog, a guess
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241 // int endali, endalj;
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242 float localthr = -offset + scoreoffset * 600; // 2013/12/13
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243 float localthr2 = -offset + scoreoffset * 600; // 2013/12/13
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244 // float localthr = -offset;
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245 // float localthr2 = -offset;
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246 float fpenalty = (float)penalty;
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247 float fpenalty_ex = (float)penalty_ex;
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248 float fpenalty_shift = (float)penalty_shift;
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249 float fpenalty_tmp; // atode kesu
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250
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251 int *warpis = NULL;
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252 int *warpjs = NULL;
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253 int *warpi = NULL;
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254 int *warpj = NULL;
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255 int *prevwarpi = NULL;
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256 int *prevwarpj = NULL;
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257 float *wmrecords = NULL;
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258 float *prevwmrecords = NULL;
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259 int warpn = 0;
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260 int warpbase;
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261 float curm = 0.0;
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262 float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
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263 int *warpipt, *warpjpt;
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264
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265
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266
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267 if( seq1 == NULL )
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268 {
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269 if( orlgth1 > 0 && orlgth2 > 0 )
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270 {
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271 orlgth1 = 0;
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272 orlgth2 = 0;
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273 free( mseq1 );
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274 free( mseq2 );
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275 FreeFloatVec( w1 );
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276 FreeFloatVec( w2 );
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277 FreeFloatVec( match );
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278 FreeFloatVec( initverticalw );
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279 FreeFloatVec( lastverticalw );
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280
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281 FreeFloatVec( m );
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282 FreeIntVec( mp );
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283
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284 FreeCharMtx( mseq );
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285 if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
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286
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287 }
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288 return( 0.0 );
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289 }
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290
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291
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292 if( orlgth1 == 0 )
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293 {
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294 mseq1 = AllocateCharMtx( njob, 0 );
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295 mseq2 = AllocateCharMtx( njob, 0 );
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296 }
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297
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298
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299 lgth1 = strlen( seq1[0] );
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300 lgth2 = strlen( seq2[0] );
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301
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302
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303 warpbase = lgth1 + lgth2;
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304 warpis = NULL;
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305 warpjs = NULL;
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306 warpn = 0;
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307 if( trywarp )
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308 {
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309 wmrecords = AllocateFloatVec( lgth2+1 );
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310 warpi = AllocateIntVec( lgth2+1 );
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311 warpj = AllocateIntVec( lgth2+1 );
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312 prevwmrecords = AllocateFloatVec( lgth2+1 );
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313 prevwarpi = AllocateIntVec( lgth2+1 );
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314 prevwarpj = AllocateIntVec( lgth2+1 );
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315 for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
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316 for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
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317 for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
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318 for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
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319 for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
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320 for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
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321 }
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322
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323
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324 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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325 {
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326 int ll1, ll2;
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327
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328 if( orlgth1 > 0 && orlgth2 > 0 )
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329 {
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330 FreeFloatVec( w1 );
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331 FreeFloatVec( w2 );
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332 FreeFloatVec( match );
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333 FreeFloatVec( initverticalw );
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334 FreeFloatVec( lastverticalw );
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335
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336 FreeFloatVec( m );
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337 FreeIntVec( mp );
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338
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339 FreeCharMtx( mseq );
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340 if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
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341
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342
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343 // FreeFloatMtx( floatwork );
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344 // FreeIntMtx( intwork );
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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
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370 #if DEBUG
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371 fprintf( stderr, "succeeded\n" );
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372 #endif
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373 amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
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374 orlgth1 = ll1 - 100;
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375 orlgth2 = ll2 - 100;
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376 }
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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 match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
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423
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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
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427 lasti = lgth2+1;
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428 for( j=1; j<lasti; ++j )
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429 {
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430 m[j] = currentw[j-1]; mp[j] = 0;
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431 #if 0
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432 if( m[j] < localthr ) m[j] = localthr2;
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433 #endif
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434 }
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435
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436 lastverticalw[0] = currentw[lgth2-1];
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437
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438 lasti = lgth1+1;
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439
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440 #if 0
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441 fprintf( stderr, "currentw = \n" );
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442 for( i=0; i<lgth1+1; i++ )
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443 {
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444 fprintf( stderr, "%5.2f ", currentw[i] );
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445 }
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446 fprintf( stderr, "\n" );
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447 fprintf( stderr, "initverticalw = \n" );
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448 for( i=0; i<lgth2+1; i++ )
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449 {
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450 fprintf( stderr, "%5.2f ", initverticalw[i] );
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451 }
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452 fprintf( stderr, "\n" );
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453 #endif
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454 #if DEBUG2
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455 fprintf( stderr, "\n" );
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456 fprintf( stderr, " " );
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457 for( j=0; j<lgth2; j++ )
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458 fprintf( stderr, "%c ", seq2[0][j] );
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459 fprintf( stderr, "\n" );
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460 #endif
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461
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462 localstop = lgth1+lgth2+1;
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463 maxwm = -999999999.9;
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464 #if DEBUG2
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465 fprintf( stderr, "\n" );
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466 fprintf( stderr, "%c ", seq1[0][0] );
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467
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468 for( j=0; j<lgth2+1; j++ )
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469 fprintf( stderr, "%5.0f ", currentw[j] );
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470 fprintf( stderr, "\n" );
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471 #endif
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472
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473 for( i=1; i<lasti; i++ )
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474 {
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475 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
476 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
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diff changeset
477 currentw = wtmp;
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nick
parents:
diff changeset
478
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diff changeset
479 previousw[0] = initverticalw[i-1];
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nick
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diff changeset
480
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
481 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
482 #if DEBUG2
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
483 fprintf( stderr, "%c ", seq1[0][i] );
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nick
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diff changeset
484 fprintf( stderr, "%5.0f ", currentw[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
485 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
486
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diff changeset
487 #if XXXXXXX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
488 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
489 fprintf( stderr, "i=%d\n", i );
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nick
parents:
diff changeset
490 fprintf( stderr, "currentw = \n" );
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491 for( j=0; j<lgth2; j++ )
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492 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
493 fprintf( stderr, "%5.2f ", currentw[j] );
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diff changeset
494 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
495 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
496 #endif
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diff changeset
497 #if XXXXXXX
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nick
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498 fprintf( stderr, "\n" );
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diff changeset
499 fprintf( stderr, "i=%d\n", i );
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500 fprintf( stderr, "currentw = \n" );
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parents:
diff changeset
501 for( j=0; j<lgth2; j++ )
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502 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
503 fprintf( stderr, "%5.2f ", currentw[j] );
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504 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
505 fprintf( stderr, "\n" );
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diff changeset
506 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
507 currentw[0] = initverticalw[i];
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nick
parents:
diff changeset
508
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diff changeset
509 mi = previousw[0]; mpi = 0;
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diff changeset
510
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nick
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diff changeset
511 #if 0
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512 if( mi < localthr ) mi = localthr2;
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diff changeset
513 #endif
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diff changeset
514
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diff changeset
515 ijppt = ijp[i] + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
516 mjpt = m + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
517 prept = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
518 curpt = currentw + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
519 mpjpt = mp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
520 lastj = lgth2+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
521
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
522 if( trywarp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
523 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
524 prevwmrecordspt = prevwmrecords;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
525 wmrecordspt = wmrecords+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
526 wmrecords1pt = wmrecords;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
527 warpipt = warpi + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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528 warpjpt = warpj + 1;
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529 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
530 for( j=1; j<lastj; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
531 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
532 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
533 *ijppt = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
534
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
535 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
536 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
537 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
538 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
539 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
540 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
541 if( (g=mi+fpenalty) > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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542 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
543 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
544 *ijppt = -( j - mpi );
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diff changeset
545 }
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diff changeset
546 if( *prept > mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
547 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
548 mi = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
549 mpi = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
550 }
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parents:
diff changeset
551
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
552 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
553 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
554 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
555
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
556 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
557 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
558 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
559 if( (g=*mjpt+fpenalty) > wm )
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nick
parents:
diff changeset
560 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
561 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
562 *ijppt = +( i - *mpjpt );
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diff changeset
563 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
564 if( *prept > *mjpt )
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nick
parents:
diff changeset
565 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
566 *mjpt = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
567 *mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
568 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
569 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
570 *mjpt += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
571 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
572
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
573 if( maxwm < wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
574 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
575 maxwm = wm;
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nick
parents:
diff changeset
576 endali = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
577 endalj = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
578 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
579 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
580 if( wm < localthr )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
581 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
582 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f, localthr = %f\n", i, j, *curpt, localthr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
583 *ijppt = localstop;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
584 wm = localthr2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
585 }
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nick
parents:
diff changeset
586 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
587 #if 0
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nick
parents:
diff changeset
588 fprintf( stderr, "%5.0f ", *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
589 #endif
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nick
parents:
diff changeset
590 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
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diff changeset
591 fprintf( stderr, "wm (%d,%d) = %5.0f\n", i, j, wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
592 // fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
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parents:
diff changeset
593 #endif
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parents:
diff changeset
594 if( trywarp )
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nick
parents:
diff changeset
595 {
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nick
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596 fpenalty_tmp = fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] );
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597 // fprintf( stderr, "fpenalty_shift = %f\n", fpenalty_tmp );
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598
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599 // 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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600 // if( (g=prevwmrecords[j-1] + fpenalty_shift )> wm )
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601 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
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602 {
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603 // 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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604 if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
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605 {
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606 *ijppt = warpbase + warpn - 1;
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607 }
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608 else
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609 {
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610 *ijppt = warpbase + warpn;
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611 warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
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612 warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
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613 warpis[warpn] = prevwarpi[j-1];
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614 warpjs[warpn] = prevwarpj[j-1];
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615 warpn++;
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616 }
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617 wm = g;
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618 }
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619 else
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620 {
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621 }
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622
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623 curm = *curpt + wm;
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624
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625 // 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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626
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627 // fprintf( stderr, "copy from i, j-1? %f > %f?\n", wmrecords[j-1], curm );
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628 // if( wmrecords[j-1] > wmrecords[j] )
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629 if( *wmrecords1pt > *wmrecordspt )
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630 {
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631 // fprintf( stderr, "yes\n" );
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632 // wmrecords[j] = wmrecords[j-1];
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633 *wmrecordspt = *wmrecords1pt;
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634 // warpi[j] = warpi[j-1];
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635 // warpj[j] = warpj[j-1];
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636 *warpipt = *(warpipt-1);
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637 *warpjpt = *(warpjpt-1);
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638 // fprintf( stderr, "warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
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639 }
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640 // else
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641 // {
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642 // fprintf( stderr, "no\n" );
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643 // }
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644
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645 // fprintf( stderr, " curm = %f at %c-%c\n", curm, seq1[0][i], seq2[0][j] );
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646 // fprintf( stderr, " wmrecords[%d] = %f\n", j, wmrecords[j] );
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647 // fprintf( stderr, "replace?\n" );
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648
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649 // if( curm > wmrecords[j] )
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650 if( curm > *wmrecordspt )
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651 {
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652 // 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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653 // wmrecords[j] = curm;
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654 *wmrecordspt = curm;
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655 // warpi[j] = i;
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656 // warpj[j] = j;
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657 *warpipt = i;
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658 *warpjpt = j;
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659 }
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660 // else
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661 // {
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662 // fprintf( stderr, "No! warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
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663 // }
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664 // 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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665 wmrecordspt++;
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666 wmrecords1pt++;
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667 warpipt++;
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668 warpjpt++;
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669 }
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670
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671 *curpt++ += wm;
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672 ijppt++;
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673 mjpt++;
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674 prept++;
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675 mpjpt++;
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676 }
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677 #if DEBUG2
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678 fprintf( stderr, "\n" );
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679 #endif
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680
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681 lastverticalw[i] = currentw[lgth2-1];
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682 if( trywarp )
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683 {
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684 fltncpy( prevwmrecords, wmrecords, lastj );
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685 intncpy( prevwarpi, warpi, lastj );
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686 intncpy( prevwarpj, warpj, lastj );
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687 }
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688
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689 }
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690 // fprintf( stderr, "\nwm = %f\n", wm );
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691 if( trywarp )
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692 {
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693 // if( warpn ) fprintf( stderr, "warpn = %d\n", warpn );
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694 free( wmrecords );
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695 free( prevwmrecords );
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696 free( warpi );
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697 free( warpj );
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698 free( prevwarpi );
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699 free( prevwarpj );
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700 }
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701
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702 #if 0
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703 fprintf( stderr, "maxwm = %f\n", maxwm );
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704 fprintf( stderr, "endali = %d\n", endali );
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705 fprintf( stderr, "endalj = %d\n", endalj );
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706 #endif
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707
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708 if( ijp[endali][endalj] == localstop )
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709 {
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710 strcpy( seq1[0], "" );
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711 strcpy( seq2[0], "" );
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712 *off1pt = *off2pt = 0;
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713 fprintf( stderr, "maxwm <- 0.0 \n" );
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714 return( 0.0 );
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715 }
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716
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717 Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj, warpis, warpjs, warpbase );
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718 if( warpis ) free( warpis );
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719 if( warpjs ) free( warpjs );
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720
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721
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722 resultlen = strlen( mseq1[0] );
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723 if( alloclen < resultlen || resultlen > N )
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724 {
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725 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
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726 ErrorExit( "LENGTH OVER!\n" );
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727 }
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728
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729
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730 strcpy( seq1[0], mseq1[0] );
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731 strcpy( seq2[0], mseq2[0] );
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732
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733 #if 0
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734 fprintf( stderr, "wm=%f\n", wm );
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735 fprintf( stderr, ">\n%s\n", mseq1[0] );
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736 fprintf( stderr, ">\n%s\n", mseq2[0] );
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737
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738 fprintf( stderr, "maxwm = %f\n", maxwm );
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739 fprintf( stderr, " wm = %f\n", wm );
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740 #endif
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741
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742 return( maxwm );
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743 }
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744
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745
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746 float L__align11_noalign( double **n_dynamicmtx, char **seq1, char **seq2 )
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747 // warp mitaiou
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748 {
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749 // int k;
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750 int i, j;
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751 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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752 int lgth1, lgth2;
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753 // int resultlen;
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754 float wm = 0.0; /* int ?????? */
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755 float g;
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756 float *currentw, *previousw;
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757 #if 1
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758 float *wtmp;
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759 // int *ijppt;
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760 float *mjpt, *prept, *curpt;
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761 // int *mpjpt;
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762 #endif
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763 static TLS float mi, *m;
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764 // static TLS int **ijp;
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765 // static TLS int mpi, *mp;
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766 static TLS float *w1, *w2;
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767 static TLS float *match;
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768 static TLS float *initverticalw; /* kufuu sureba iranai */
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769 static TLS float *lastverticalw; /* kufuu sureba iranai */
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770 // static TLS char **mseq1;
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771 // static TLS char **mseq2;
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772 // static TLS char **mseq;
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773 // static TLS int **intwork;
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774 // static TLS float **floatwork;
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775 static TLS int orlgth1 = 0, orlgth2 = 0;
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776 static TLS double **amino_dynamicmtx = NULL; // ??
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777 float maxwm;
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778 // int endali = 0, endalj = 0; // by D.Mathog, a guess
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779 // int endali, endalj;
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780 float localthr = -offset;
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781 float localthr2 = -offset;
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782 // float localthr = 100;
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783 // float localthr2 = 100;
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784 float fpenalty = (float)penalty;
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785 float fpenalty_ex = (float)penalty_ex;
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786
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787 if( seq1 == NULL )
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788 {
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789 if( orlgth1 > 0 && orlgth2 > 0 )
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790 {
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791 orlgth1 = 0;
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792 orlgth2 = 0;
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793 // free( mseq1 );
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794 // free( mseq2 );
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795 FreeFloatVec( w1 );
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796 FreeFloatVec( w2 );
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797 FreeFloatVec( match );
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798 FreeFloatVec( initverticalw );
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799 FreeFloatVec( lastverticalw );
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800
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801 FreeFloatVec( m );
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802 // FreeIntVec( mp );
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803
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804 // FreeCharMtx( mseq );
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805 if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
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806
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807 }
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808 return( 0.0 );
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809 }
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810
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811
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812 // if( orlgth1 == 0 )
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813 // {
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814 // mseq1 = AllocateCharMtx( njob, 0 );
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815 // mseq2 = AllocateCharMtx( njob, 0 );
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816 // }
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817
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818
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819 lgth1 = strlen( seq1[0] );
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820 lgth2 = strlen( seq2[0] );
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821
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822 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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823 {
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824 int ll1, ll2;
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825
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826 if( orlgth1 > 0 && orlgth2 > 0 )
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827 {
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828 FreeFloatVec( w1 );
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829 FreeFloatVec( w2 );
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830 FreeFloatVec( match );
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831 FreeFloatVec( initverticalw );
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832 FreeFloatVec( lastverticalw );
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833
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834 FreeFloatVec( m );
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835 // FreeIntVec( mp );
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836
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837 // FreeCharMtx( mseq );
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838
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839
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840
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841 // FreeFloatMtx( floatwork );
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842 // FreeIntMtx( intwork );
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843 if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
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844 }
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845
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846 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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847 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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848
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849 #if DEBUG
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850 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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851 #endif
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852
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853 w1 = AllocateFloatVec( ll2+2 );
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854 w2 = AllocateFloatVec( ll2+2 );
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855 match = AllocateFloatVec( ll2+2 );
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856
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857 initverticalw = AllocateFloatVec( ll1+2 );
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858 lastverticalw = AllocateFloatVec( ll1+2 );
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859
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860 m = AllocateFloatVec( ll2+2 );
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861 // mp = AllocateIntVec( ll2+2 );
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862
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863 // mseq = AllocateCharMtx( njob, ll1+ll2 );
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864
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865
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866 // floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
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867 // intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
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868
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869 #if DEBUG
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870 fprintf( stderr, "succeeded\n" );
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871 #endif
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872 amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
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873 orlgth1 = ll1 - 100;
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874 orlgth2 = ll2 - 100;
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875 }
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876
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877 for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
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878 amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
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879
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880
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881
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882 // mseq1[0] = mseq[0];
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883 // mseq2[0] = mseq[1];
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884
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885
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886 // if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
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887 // {
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888 // int ll1, ll2;
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889 //
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890 // if( commonAlloc1 && commonAlloc2 )
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891 // {
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892 // FreeIntMtx( commonIP );
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893 // }
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894 //
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895 // ll1 = MAX( orlgth1, commonAlloc1 );
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896 // ll2 = MAX( orlgth2, commonAlloc2 );
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897
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898 #if DEBUG
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899 // fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
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900 #endif
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901
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902 // commonIP = AllocateIntMtx( ll1+10, ll2+10 );
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903
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904 #if DEBUG
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905 // fprintf( stderr, "succeeded\n\n" );
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906 #endif
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907
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908 // commonAlloc1 = ll1;
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909 // commonAlloc2 = ll2;
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910 // }
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911 // ijp = commonIP;
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912
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913
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914 #if 0
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915 for( i=0; i<lgth1; i++ )
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916 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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917 #endif
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918
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919 currentw = w1;
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920 previousw = w2;
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921
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922 match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
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923
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924 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
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925
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926
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927 lasti = lgth2+1;
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928 for( j=1; j<lasti; ++j )
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929 {
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930 m[j] = currentw[j-1];
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931 // mp[j] = 0;
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932 #if 0
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933 if( m[j] < localthr ) m[j] = localthr2;
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934 #endif
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935 }
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936
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937 lastverticalw[0] = currentw[lgth2-1];
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938
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939 lasti = lgth1+1;
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940
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941 #if 0
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942 fprintf( stderr, "currentw = \n" );
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943 for( i=0; i<lgth1+1; i++ )
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944 {
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945 fprintf( stderr, "%5.2f ", currentw[i] );
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946 }
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947 fprintf( stderr, "\n" );
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948 fprintf( stderr, "initverticalw = \n" );
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949 for( i=0; i<lgth2+1; i++ )
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950 {
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951 fprintf( stderr, "%5.2f ", initverticalw[i] );
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952 }
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953 fprintf( stderr, "\n" );
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954 #endif
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955 #if DEBUG2
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956 fprintf( stderr, "\n" );
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957 fprintf( stderr, " " );
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958 for( j=0; j<lgth2; j++ )
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959 fprintf( stderr, "%c ", seq2[0][j] );
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960 fprintf( stderr, "\n" );
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961 #endif
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962
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963 localstop = lgth1+lgth2+1;
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964 maxwm = -999999999.9;
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965 #if DEBUG2
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966 fprintf( stderr, "\n" );
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967 fprintf( stderr, "%c ", seq1[0][0] );
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968
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969 for( j=0; j<lgth2+1; j++ )
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970 fprintf( stderr, "%5.0f ", currentw[j] );
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971 fprintf( stderr, "\n" );
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972 #endif
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973
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974 for( i=1; i<lasti; i++ )
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975 {
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976 wtmp = previousw;
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977 previousw = currentw;
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978 currentw = wtmp;
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979
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980 previousw[0] = initverticalw[i-1];
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981
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982 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
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983 #if DEBUG2
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984 fprintf( stderr, "%c ", seq1[0][i] );
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985 fprintf( stderr, "%5.0f ", currentw[0] );
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986 #endif
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987
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988 #if XXXXXXX
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989 fprintf( stderr, "\n" );
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990 fprintf( stderr, "i=%d\n", i );
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991 fprintf( stderr, "currentw = \n" );
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992 for( j=0; j<lgth2; j++ )
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993 {
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994 fprintf( stderr, "%5.2f ", currentw[j] );
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995 }
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996 fprintf( stderr, "\n" );
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997 #endif
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998 #if XXXXXXX
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999 fprintf( stderr, "\n" );
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1000 fprintf( stderr, "i=%d\n", i );
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1001 fprintf( stderr, "currentw = \n" );
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1002 for( j=0; j<lgth2; j++ )
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1003 {
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1004 fprintf( stderr, "%5.2f ", currentw[j] );
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1005 }
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1006 fprintf( stderr, "\n" );
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1007 #endif
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1008 currentw[0] = initverticalw[i];
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1009
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1010 mi = previousw[0];
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1011 // mpi = 0;
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1012
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1013 #if 0
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1014 if( mi < localthr ) mi = localthr2;
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1015 #endif
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1016
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1017 // ijppt = ijp[i] + 1;
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1018 mjpt = m + 1;
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1019 prept = previousw;
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1020 curpt = currentw + 1;
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1021 // mpjpt = mp + 1;
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1022 lastj = lgth2+1;
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1023 for( j=1; j<lastj; j++ )
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1024 {
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1025 wm = *prept;
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1026 // *ijppt = 0;
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1027
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1028 #if 0
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1029 fprintf( stderr, "%5.0f->", wm );
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1030 #endif
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1031 #if 0
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1032 fprintf( stderr, "%5.0f?", g );
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1033 #endif
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1034 if( (g=mi+fpenalty) > wm )
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1035 {
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1036 wm = g;
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1037 // *ijppt = -( j - mpi );
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1038 }
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1039 if( *prept > mi )
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1040 {
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1041 mi = *prept;
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1042 // mpi = j-1;
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1043 }
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1044
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1045 #if USE_PENALTY_EX
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1046 mi += fpenalty_ex;
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1047 #endif
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1048
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1049 #if 0
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1050 fprintf( stderr, "%5.0f?", g );
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1051 #endif
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1052 if( (g=*mjpt+fpenalty) > wm )
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1053 {
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1054 wm = g;
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1055 // *ijppt = +( i - *mpjpt );
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1056 }
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1057 if( *prept > *mjpt )
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1058 {
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1059 *mjpt = *prept;
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1060 // *mpjpt = i-1;
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1061 }
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1062 #if USE_PENALTY_EX
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1063 *mjpt += fpenalty_ex;
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1064 #endif
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1065
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1066 if( maxwm < wm )
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1067 {
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1068 maxwm = wm;
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1069 // endali = i;
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1070 // endalj = j;
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1071 }
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1072 #if 1
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1073 if( wm < localthr )
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1074 {
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1075 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
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1076 // *ijppt = localstop;
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1077 wm = localthr2;
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1078 }
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1079 #endif
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1080 #if 0
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1081 fprintf( stderr, "%5.0f ", *curpt );
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1082 #endif
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1083 #if DEBUG2
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1084 fprintf( stderr, "%5.0f ", wm );
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1085 // fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
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1086 #endif
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1087
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1088 *curpt++ += wm;
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1089 // ijppt++;
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1090 mjpt++;
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1091 prept++;
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1092 // mpjpt++;
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1093 }
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1094 #if DEBUG2
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1095 fprintf( stderr, "\n" );
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1096 #endif
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1097
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1098 lastverticalw[i] = currentw[lgth2-1];
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1099 }
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1100
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1101
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1102 #if 0
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1103 fprintf( stderr, "maxwm = %f\n", maxwm );
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1104 fprintf( stderr, "endali = %d\n", endali );
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1105 fprintf( stderr, "endalj = %d\n", endalj );
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1106 #endif
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1107
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1108
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1109 #if 0 // IRUKAMO!!!!
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1110 if( ijp[endali][endalj] == localstop )
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1111 {
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1112 strcpy( seq1[0], "" );
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1113 strcpy( seq2[0], "" );
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1114 *off1pt = *off2pt = 0;
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1115 fprintf( stderr, "maxwm <- 0.0 \n" );
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1116 return( 0.0 );
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1117 }
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1118 #else
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1119 if( maxwm < localthr )
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1120 {
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1121 fprintf( stderr, "maxwm <- 0.0 \n" );
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1122 return( 0.0 );
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1123 }
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1124 #endif
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1125
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1126 // Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj );
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1127
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1128
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1129 // resultlen = strlen( mseq1[0] );
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1130 // if( alloclen < resultlen || resultlen > N )
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1131 // {
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1132 // fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
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1133 // ErrorExit( "LENGTH OVER!\n" );
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1134 // }
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1135
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1136
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1137 // strcpy( seq1[0], mseq1[0] );
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1138 // strcpy( seq2[0], mseq2[0] );
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1139
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1140 #if 0
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1141 fprintf( stderr, "wm=%f\n", wm );
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1142 fprintf( stderr, ">\n%s\n", mseq1[0] );
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1143 fprintf( stderr, ">\n%s\n", mseq2[0] );
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1144
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1145 fprintf( stderr, "maxwm = %f\n", maxwm );
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1146 fprintf( stderr, " wm = %f\n", wm );
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1147 #endif
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1148
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1149 return( maxwm );
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1150 }