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annotate mafft/core/Salignmm.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 MACHIGAI 0
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5 #define OUTGAP0TRY 0
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6 #define DEBUG 0
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7 #define XXXXXXX 0
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8 #define USE_PENALTY_EX 1
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9 #define FASTMATCHCALC 1
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10 #define MCD 0
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11
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12
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13 static TLS float **impmtx = NULL;
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14 static TLS int impalloclen = 0;
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15 float imp_match_out_sc( int i1, int j1 )
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16 {
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17 // fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
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18 // fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
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19 return( impmtx[i1][j1] );
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20 }
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21
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22 static void imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
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23 {
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24 #if FASTMATCHCALC
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25 float *pt = impmtx[i1];
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26 int *gapmappt = gapmap2;
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27 while( lgth2-- )
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28 *imp++ += pt[*gapmappt++];
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29 #else
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30 int j;
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31 float *pt = impmtx[i1];
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32 for( j=0; j<lgth2; j++ )
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33 *imp++ += pt[gapmap2[j]];
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34 #endif
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35 }
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36
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37
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38 static void imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
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39 {
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40 #if FASTMATCHCALC
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41 int *gapmappt = gapmap1;
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42 while( lgth1-- )
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43 *imp++ += impmtx[*gapmappt++][j1];
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44 #else
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45 int i;
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46 for( i=0; i<lgth1; i++ )
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47 *imp++ += impmtx[gapmap1[i]][j1];
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48 #endif
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49 }
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50
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51 static void imp_match_out_vead( float *imp, int i1, int lgth2 )
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52 {
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53 #if FASTMATCHCALC
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54 float *pt = impmtx[i1];
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55 while( lgth2-- )
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56 *imp++ += *pt++;
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57 #else
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58 int j;
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59 float *pt = impmtx[i1];
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60 for( j=0; j<lgth2; j++ )
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61 *imp++ += pt[j];
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62 #endif
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63 }
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64 static void imp_match_out_vead_tate( float *imp, int j1, int lgth1 )
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65 {
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66 int i;
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67 for( i=0; i<lgth1; i++ )
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68 *imp++ += impmtx[i][j1];
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69 }
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70
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71 void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *pair )
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72 {
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73 foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, pair );
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74 }
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75
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76 void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
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77 {
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78 int i, j, k1, k2, tmpint, start1, start2, end1, end2;
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79 float effij;
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80 float effij_kozo;
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81 double effijx;
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82 char *pt, *pt1, *pt2;
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83 static TLS char *nocount1 = NULL;
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84 static TLS char *nocount2 = NULL;
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85 LocalHom *tmpptr;
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86
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87 if( seq1 == NULL )
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88 {
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89 if( impmtx ) FreeFloatMtx( impmtx );
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90 impmtx = NULL;
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91 if( nocount1 ) free( nocount1 );
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92 nocount1 = NULL;
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93 if( nocount2 ) free( nocount2 );
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94 nocount2 = NULL;
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95
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96 return;
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97 }
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98
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99 if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
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100 {
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101 if( impmtx ) FreeFloatMtx( impmtx );
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102 if( nocount1 ) free( nocount1 );
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103 if( nocount2 ) free( nocount2 );
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104 impalloclen = MAX( lgth1, lgth2 ) + 2;
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105 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
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106 nocount1 = AllocateCharVec( impalloclen );
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107 nocount2 = AllocateCharVec( impalloclen );
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108 }
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109
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110 for( i=0; i<lgth1; i++ )
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111 {
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112 for( j=0; j<clus1; j++ )
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113 if( seq1[j][i] == '-' ) break;
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114 if( j != clus1 ) nocount1[i] = 1;
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115 else nocount1[i] = 0;
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116 }
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117 for( i=0; i<lgth2; i++ )
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118 {
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119 for( j=0; j<clus2; j++ )
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120 if( seq2[j][i] == '-' ) break;
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121 if( j != clus2 ) nocount2[i] = 1;
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122 else nocount2[i] = 0;
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123 }
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124
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125 #if 0
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126 fprintf( stderr, "nocount2 =\n" );
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127 for( i = 0; i<impalloclen; i++ )
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128 {
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129 fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
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130 }
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131 #endif
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132
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133
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134
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135 #if 0
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136 fprintf( stderr, "eff1 in _init_strict = \n" );
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137 for( i=0; i<clus1; i++ )
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138 fprintf( stderr, "eff1[] = %f\n", eff1[i] );
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139 for( i=0; i<clus2; i++ )
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140 fprintf( stderr, "eff2[] = %f\n", eff2[i] );
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141 #endif
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142
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143 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
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144 impmtx[i][j] = 0.0;
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145 effijx = fastathreshold;
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146 for( i=0; i<clus1; i++ )
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147 {
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148 for( j=0; j<clus2; j++ )
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149 {
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150 effij = (float)( eff1[i] * eff2[j] * effijx );
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151 effij_kozo = (float)( eff1_kozo[i] * eff2_kozo[j] * effijx );
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152 tmpptr = localhom[i][j];
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153 while( tmpptr )
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154 {
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155 // fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
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156 // fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
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157 // fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
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158 // fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
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159 pt = seq1[i];
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160 tmpint = -1;
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161 while( *pt != 0 )
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162 {
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163 if( *pt++ != '-' ) tmpint++;
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164 if( tmpint == tmpptr->start1 ) break;
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165 }
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166 start1 = pt - seq1[i] - 1;
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167
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168 if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
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169 else
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170 {
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171 #if MACHIGAI
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172 while( *pt != 0 )
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173 {
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174 // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
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175 if( tmpint == tmpptr->end1 ) break;
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176 if( *pt++ != '-' ) tmpint++;
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177 }
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178 end1 = pt - seq1[i] - 0;
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179 #else
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180 while( *pt != 0 )
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181 {
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182 // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
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183 if( *pt++ != '-' ) tmpint++;
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184 if( tmpint == tmpptr->end1 ) break;
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185 }
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186 end1 = pt - seq1[i] - 1;
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187 #endif
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188 }
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189
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190 pt = seq2[j];
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191 tmpint = -1;
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192 while( *pt != 0 )
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193 {
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194 if( *pt++ != '-' ) tmpint++;
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195 if( tmpint == tmpptr->start2 ) break;
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196 }
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197 start2 = pt - seq2[j] - 1;
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198 if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
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199 else
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200 {
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201 #if MACHIGAI
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202 while( *pt != 0 )
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203 {
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204 if( tmpint == tmpptr->end2 ) break;
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205 if( *pt++ != '-' ) tmpint++;
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206 }
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207 end2 = pt - seq2[j] - 0;
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208 #else
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209 while( *pt != 0 )
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210 {
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211 if( *pt++ != '-' ) tmpint++;
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212 if( tmpint == tmpptr->end2 ) break;
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213 }
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214 end2 = pt - seq2[j] - 1;
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215 #endif
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216 }
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217 // fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
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218 // fprintf( stderr, "step 0\n" );
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219 if( end1 - start1 != end2 - start2 )
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220 {
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221 // fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
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222 }
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223
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224 #if 1
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225 k1 = start1; k2 = start2;
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226 pt1 = seq1[i] + k1;
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227 pt2 = seq2[j] + k2;
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228 while( *pt1 && *pt2 )
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229 {
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230 if( *pt1 != '-' && *pt2 != '-' )
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231 {
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232 // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
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233 // impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
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234 // impmtx[k1][k2] += tmpptr->importance * effij;
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235 // impmtx[k1][k2] += tmpptr->fimportance * effij;
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236 if( tmpptr->korh == 'k' )
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237 impmtx[k1][k2] += tmpptr->fimportance * effij_kozo;
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238 else
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239 impmtx[k1][k2] += tmpptr->fimportance * effij;
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240
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241 // fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
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242 // fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
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243 // fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
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244 k1++; k2++;
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245 pt1++; pt2++;
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246 }
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247 else if( *pt1 != '-' && *pt2 == '-' )
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248 {
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249 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
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250 k2++; pt2++;
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251 }
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252 else if( *pt1 == '-' && *pt2 != '-' )
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253 {
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254 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
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255 k1++; pt1++;
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256 }
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257 else if( *pt1 == '-' && *pt2 == '-' )
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258 {
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259 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
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260 k1++; pt1++;
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261 k2++; pt2++;
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262 }
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263 if( k1 > end1 || k2 > end2 ) break;
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264 }
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265 #else
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266 while( k1 <= end1 && k2 <= end2 )
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267 {
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268 fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
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269 if( !nocount1[k1] && !nocount2[k2] )
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270 {
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271 impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
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272 fprintf( stderr, "marked\n" );
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273 }
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274 else
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275 fprintf( stderr, "no count\n" );
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276 k1++; k2++;
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277 }
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278 #endif
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279 tmpptr = tmpptr->next;
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280 }
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281 }
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282 }
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283
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284 #if 0
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285 if( clus1 == 1 && clus2 == 1 )
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286 {
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287 fprintf( stderr, "writing impmtx\n" );
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288 fprintf( stderr, "\n" );
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289 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
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290 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
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291 fprintf( stderr, "impmtx = \n" );
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292 for( k2=0; k2<lgth2; k2++ )
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293 fprintf( stderr, "%6.3f ", (double)k2 );
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294 fprintf( stderr, "\n" );
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295 for( k1=0; k1<lgth1; k1++ )
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296 {
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297 fprintf( stderr, "%d ", k1 );
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298 for( k2=0; k2<30; k2++ )
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299 fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
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300 fprintf( stderr, "\n" );
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301 }
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302 // exit( 1 );
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303 }
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304 #endif
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305 }
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306
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307 #if 0
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308 void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
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309 {
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310 int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
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311 static TLS int impalloclen = 0;
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312 char *pt;
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313 int allgap;
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314 static TLS char *nocount1 = NULL;
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315 static TLS char *nocount2 = NULL;
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316
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317 if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
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318 {
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319 if( impmtx ) FreeFloatMtx( impmtx );
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320 if( nocount1 ) free( nocount1 );
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321 if( nocount2 ) free( nocount2 );
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322 impalloclen = MAX( lgth1, lgth2 ) + 2;
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323 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
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324 nocount1 = AllocateCharVec( impalloclen );
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325 nocount2 = AllocateCharVec( impalloclen );
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326 }
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327
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328 for( i=0; i<lgth1; i++ )
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329 {
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330 for( j=0; j<clus1; j++ )
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331 if( seq1[j][i] == '-' ) break;
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332 if( j != clus1 ) nocount1[i] = 1;
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333 else nocount1[i] = 0;
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334 }
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335 for( i=0; i<lgth2; i++ )
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336 {
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337 for( j=0; j<clus2; j++ )
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338 if( seq2[j][i] == '-' ) break;
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339 if( j != clus2 ) nocount2[i] = 1;
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340 else nocount2[i] = 0;
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341 }
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342
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343 #if 0
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344 fprintf( stderr, "nocount2 =\n" );
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345 for( i = 0; i<impalloclen; i++ )
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346 {
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347 fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
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348 }
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349 #endif
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350
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351 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
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352 impmtx[i][j] = 0;
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353 for( i=0; i<clus1; i++ )
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354 {
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355 fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
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356 for( j=0; j<clus2; j++ )
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357 {
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358 fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
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359 fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 );
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360 fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
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361 pt = seq1[i];
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362 tmpint = -1;
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363 while( *pt != 0 )
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364 {
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365 if( *pt++ != '-' ) tmpint++;
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366 if( tmpint == localhom[i][j]->start1 ) break;
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367 }
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368 start1 = pt - seq1[i] - 1;
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369
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370 while( *pt != 0 )
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371 {
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372 // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
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373 if( *pt++ != '-' ) tmpint++;
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374 if( tmpint == localhom[i][j]->end1 ) break;
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375 }
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376 end1 = pt - seq1[i] - 1;
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377
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378 pt = seq2[j];
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379 tmpint = -1;
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380 while( *pt != 0 )
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381 {
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382 if( *pt++ != '-' ) tmpint++;
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383 if( tmpint == localhom[i][j]->start2 ) break;
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384 }
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385 start2 = pt - seq2[j] - 1;
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386 while( *pt != 0 )
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387 {
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388 if( *pt++ != '-' ) tmpint++;
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389 if( tmpint == localhom[i][j]->end2 ) break;
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390 }
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391 end2 = pt - seq2[j] - 1;
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392 // fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
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393 k1 = start1;
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394 k2 = start2;
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395 fprintf( stderr, "step 0\n" );
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396 while( k1 <= end1 && k2 <= end2 )
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397 {
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398 #if 0
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399 if( !nocount1[k1] && !nocount2[k2] )
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400 impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
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401 k1++; k2++;
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402 #else
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403 if( !nocount1[k1] && !nocount2[k2] )
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404 impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
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405 k1++; k2++;
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406 #endif
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407 }
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408
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409 dif = ( end1 - start1 ) - ( end2 - start2 );
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410 fprintf( stderr, "dif = %d\n", dif );
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411 if( dif > 0 )
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412 {
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413 do
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414 {
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415 fprintf( stderr, "dif = %d\n", dif );
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416 k1 = start1;
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417 k2 = start2 - dif;
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418 while( k1 <= end1 && k2 <= end2 )
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419 {
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420 if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
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421 impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
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422 k1++; k2++;
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423 }
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424 }
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425 while( dif-- );
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426 }
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427 else
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428 {
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429 do
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430 {
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431 k1 = start1 + dif;
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432 k2 = start2;
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433 while( k1 <= end1 )
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434 {
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435 if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
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436 impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
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437 k1++; k2++;
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438 }
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439 }
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440 while( dif++ );
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441 }
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442 }
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443 }
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444 #if 0
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445 fprintf( stderr, "impmtx = \n" );
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446 for( k2=0; k2<lgth2; k2++ )
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447 fprintf( stderr, "%6.3f ", (double)k2 );
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448 fprintf( stderr, "\n" );
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449 for( k1=0; k1<lgth1; k1++ )
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450 {
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451 fprintf( stderr, "%d", k1 );
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452 for( k2=0; k2<lgth2; k2++ )
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453 fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
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454 fprintf( stderr, "\n" );
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455 }
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456 #endif
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457 }
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458 #endif
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459
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460 #if MCD
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461 static void match_calc_dynamicmtx( double **pairoffset, double **n_dynamicmtx, float *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, float **floatwork, int **intwork, int initialize, int flip )
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462 {
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463 // osoi!
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464 int i, j, k;
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465 int c1, c2;
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466 double po;
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467 // fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
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468 // fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
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469 // fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
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470 for( k=0; k<lgth2; k++ )
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471 {
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472 match[k] = 0.0;
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473 for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
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474 {
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475 if( flip ) po = pairoffset[j][i];
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476 else po = pairoffset[i][j];
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477 // if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
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478 c1 = amino_n[(int)seq1[i][i1]];
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479 c2 = amino_n[(int)seq2[j][k]];
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480 if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
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481 if( c1 < 0 || c2 < 0 ) continue;
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482 // fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
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483 if( flip )
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484 match[k] += ( n_dynamicmtx[c1][c2] + po * 600 ) * eff1[i] * eff2[j];
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485 else
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486 match[k] += ( n_dynamicmtx[c1][c2] + po * 600 ) * eff1[i] * eff2[j];
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487 // fprintf( stderr, "match[k] = %f\n", match[k] );
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488 // fprintf( stderr, "pairoffset[i][j] = %f\n", pairoffset[i][j] );
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489 }
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490 }
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491 // fprintf( stderr, "done\n" );
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492 return;
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493 }
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494 #endif
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495
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496 static void fillzero( float *s, int l )
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497 {
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498 while( l-- ) *s++ = 0.0;
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499 }
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500
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501 static void match_calc_add( double **scoreingmtx, float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
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502 {
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503 #if FASTMATCHCALC
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504 // fprintf( stderr, "\nmatch_calc... %d", i1 );
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505 int j, l;
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506 // float scarr[26];
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507 float **cpmxpd = floatwork;
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508 int **cpmxpdn = intwork;
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509 float *matchpt, *cpmxpdpt, **cpmxpdptpt;
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510 int *cpmxpdnpt, **cpmxpdnptpt;
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511 float *scarr;
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512 scarr = calloc( nalphabets, sizeof( float ) );
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513 if( initialize )
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514 {
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515 int count = 0;
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516 for( j=0; j<lgth2; j++ )
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517 {
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518 count = 0;
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519 for( l=0; l<nalphabets; l++ )
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520 {
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521 if( cpmx2[l][j] )
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522 {
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523 cpmxpd[j][count] = cpmx2[l][j];
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524 cpmxpdn[j][count] = l;
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525 count++;
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526 }
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527 }
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528 cpmxpdn[j][count] = -1;
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529 }
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530 }
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531
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532 {
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533 for( l=0; l<nalphabets; l++ )
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534 {
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535 scarr[l] = 0.0;
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536 for( j=0; j<nalphabets; j++ )
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537 // scarr[l] += n_dis[j][l] * cpmx1[j][i1];
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538 // scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
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539 scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1];
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540 }
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541 matchpt = match;
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542 cpmxpdnptpt = cpmxpdn;
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543 cpmxpdptpt = cpmxpd;
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544 while( lgth2-- )
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545 {
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546 // *matchpt = 0.0;
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547 cpmxpdnpt = *cpmxpdnptpt++;
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548 cpmxpdpt = *cpmxpdptpt++;
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549 while( *cpmxpdnpt>-1 )
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550 *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
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551 matchpt++;
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552 }
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553 }
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554 free( scarr );
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555 // fprintf( stderr, "done\n" );
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556 #else
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557 int j, k, l;
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558 // float scarr[26];
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559 float **cpmxpd = floatwork;
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560 int **cpmxpdn = intwork;
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561 float *scarr;
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562 scarr = calloc( nalphabets, sizeof( float ) );
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563 // simple
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564 if( initialize )
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565 {
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566 int count = 0;
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567 for( j=0; j<lgth2; j++ )
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568 {
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569 count = 0;
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570 for( l=0; l<nalphabets; l++ )
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571 {
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572 if( cpmx2[l][j] )
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573 {
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574 cpmxpd[count][j] = cpmx2[l][j];
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575 cpmxpdn[count][j] = l;
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576 count++;
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577 }
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578 }
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579 cpmxpdn[count][j] = -1;
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580 }
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581 }
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582 for( l=0; l<nalphabets; l++ )
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583 {
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584 scarr[l] = 0.0;
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585 for( k=0; k<nalphabets; k++ )
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586 // scarr[l] += n_dis[k][l] * cpmx1[k][i1];
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587 // scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
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588 scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1];
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589 }
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590 for( j=0; j<lgth2; j++ )
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591 {
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592 match[j] = 0.0;
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593 for( k=0; cpmxpdn[k][j]>-1; k++ )
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594 match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
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595 }
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596 free( scarr );
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597 #endif
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598 }
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599 static void match_calc( double **n_dynamicmtx, float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
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600 {
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601 #if FASTMATCHCALC
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602 // fprintf( stderr, "\nmatch_calc... %d", i1 );
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603 int j, l;
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604 // float scarr[26];
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605 float **cpmxpd = floatwork;
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606 int **cpmxpdn = intwork;
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607 float *matchpt, *cpmxpdpt, **cpmxpdptpt;
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608 int *cpmxpdnpt, **cpmxpdnptpt;
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609 float *scarr;
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610 scarr = calloc( nalphabets, sizeof( float ) );
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611 if( initialize )
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612 {
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613 int count = 0;
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614 for( j=0; j<lgth2; j++ )
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615 {
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616 count = 0;
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617 for( l=0; l<nalphabets; l++ )
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618 {
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619 if( cpmx2[l][j] )
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620 {
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621 cpmxpd[j][count] = cpmx2[l][j];
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622 cpmxpdn[j][count] = l;
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623 count++;
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624 }
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625 }
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626 cpmxpdn[j][count] = -1;
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627 }
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628 }
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629
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630 {
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631 for( l=0; l<nalphabets; l++ )
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632 {
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633 scarr[l] = 0.0;
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634 for( j=0; j<nalphabets; j++ )
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635 // scarr[l] += n_dis[j][l] * cpmx1[j][i1];
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636 // scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
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637 scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1];
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638 }
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639 matchpt = match;
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640 cpmxpdnptpt = cpmxpdn;
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641 cpmxpdptpt = cpmxpd;
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642 while( lgth2-- )
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643 {
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644 *matchpt = 0.0;
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645 cpmxpdnpt = *cpmxpdnptpt++;
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646 cpmxpdpt = *cpmxpdptpt++;
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647 while( *cpmxpdnpt>-1 )
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648 *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
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649 matchpt++;
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650 }
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651 }
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652 free( scarr );
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653 // fprintf( stderr, "done\n" );
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654 #else
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655 int j, k, l;
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656 // float scarr[26];
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657 float **cpmxpd = floatwork;
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658 int **cpmxpdn = intwork;
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659 float *scarr;
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660 scarr = calloc( nalphabets, sizeof( float ) );
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661 // simple
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662 if( initialize )
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663 {
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664 int count = 0;
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665 for( j=0; j<lgth2; j++ )
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666 {
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667 count = 0;
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668 for( l=0; l<nalphabets; l++ )
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669 {
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670 if( cpmx2[l][j] )
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671 {
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672 cpmxpd[count][j] = cpmx2[l][j];
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673 cpmxpdn[count][j] = l;
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674 count++;
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675 }
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676 }
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677 cpmxpdn[count][j] = -1;
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678 }
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679 }
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680 for( l=0; l<nalphabets; l++ )
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681 {
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682 scarr[l] = 0.0;
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683 for( k=0; k<nalphabets; k++ )
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684 // scarr[l] += n_dis[k][l] * cpmx1[k][i1];
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685 // scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
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686 scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1];
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687 }
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688 for( j=0; j<lgth2; j++ )
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689 {
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690 match[j] = 0.0;
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691 for( k=0; cpmxpdn[k][j]>-1; k++ )
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692 match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
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693 }
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nick
parents:
diff changeset
694 free( scarr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
695 #endif
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nick
parents:
diff changeset
696 }
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nick
parents:
diff changeset
697
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nick
parents:
diff changeset
698 static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
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nick
parents:
diff changeset
699 char **seq1, char **seq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
700 char **mseq1, char **mseq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
701 int **ijp, int icyc, int jcyc,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
702 int *warpis, int *warpjs, int warpbase )
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nick
parents:
diff changeset
703 {
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nick
parents:
diff changeset
704 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
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nick
parents:
diff changeset
705 float wm;
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nick
parents:
diff changeset
706 char *gaptable1, *gt1bk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
707 char *gaptable2, *gt2bk;
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nick
parents:
diff changeset
708 lgth1 = strlen( seq1[0] );
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nick
parents:
diff changeset
709 lgth2 = strlen( seq2[0] );
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nick
parents:
diff changeset
710 gt1bk = AllocateCharVec( lgth1+lgth2+1 );
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nick
parents:
diff changeset
711 gt2bk = AllocateCharVec( lgth1+lgth2+1 );
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nick
parents:
diff changeset
712
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nick
parents:
diff changeset
713 #if 0
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nick
parents:
diff changeset
714 for( i=0; i<lgth1; i++ )
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nick
parents:
diff changeset
715 {
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diff changeset
716 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
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parents:
diff changeset
717 }
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parents:
diff changeset
718 #endif
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parents:
diff changeset
719
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720 if( outgap == 1 )
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parents:
diff changeset
721 ;
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diff changeset
722 else
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parents:
diff changeset
723 {
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parents:
diff changeset
724 wm = lastverticalw[0];
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nick
parents:
diff changeset
725 for( i=0; i<lgth1; i++ )
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nick
parents:
diff changeset
726 {
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parents:
diff changeset
727 if( lastverticalw[i] >= wm )
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nick
parents:
diff changeset
728 {
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nick
parents:
diff changeset
729 wm = lastverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
730 iin = i; jin = lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
731 ijp[lgth1][lgth2] = +( lgth1 - i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
732 }
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parents:
diff changeset
733 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
734 for( j=0; j<lgth2; j++ )
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nick
parents:
diff changeset
735 {
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parents:
diff changeset
736 if( lasthorizontalw[j] >= wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
737 {
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parents:
diff changeset
738 wm = lasthorizontalw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
739 iin = lgth1-1; jin = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
740 ijp[lgth1][lgth2] = -( lgth2 - j );
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nick
parents:
diff changeset
741 }
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nick
parents:
diff changeset
742 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
743 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
744
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
745 for( i=0; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
746 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
747 ijp[i][0] = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
748 }
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nick
parents:
diff changeset
749 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
750 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
751 ijp[0][j] = -( j + 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
752 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
753
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
754 gaptable1 = gt1bk + lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
755 *gaptable1 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
756 gaptable2 = gt2bk + lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
757 *gaptable2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
758
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
759 iin = lgth1; jin = lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
760 limk = lgth1+lgth2 + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
761 *impwmpt = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
762 for( k=0; k<limk; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
763 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
764 if( ijp[iin][jin] >= warpbase )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
765 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
766 ifi = warpis[ijp[iin][jin]-warpbase];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
767 jfi = warpjs[ijp[iin][jin]-warpbase];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
768 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
769 else if( ijp[iin][jin] < 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
770 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
771 ifi = iin-1; jfi = jin+ijp[iin][jin];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
772 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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773 else if( ijp[iin][jin] > 0 )
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parents:
diff changeset
774 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
775 ifi = iin-ijp[iin][jin]; jfi = jin-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
776 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
777 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
778 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
779 ifi = iin-1; jfi = jin-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
780 }
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nick
parents:
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781 if( ifi == -warpbase && jfi == -warpbase )
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nick
parents:
diff changeset
782 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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783 l = iin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
784 while( --l >= 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
785 {
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parents:
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786 *--gaptable1 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
787 *--gaptable2 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
788 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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789 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
790 l= jin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
791 while( --l >= 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
792 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
793 *--gaptable1 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
794 *--gaptable2 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
795 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
796 break;
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nick
parents:
diff changeset
797 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
798 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
799 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
800 l = iin - ifi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
801 while( --l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
802 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
803 *--gaptable1 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
804 *--gaptable2 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
805 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
806 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
807 l= jin - jfi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
808 while( --l )
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nick
parents:
diff changeset
809 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
810 *--gaptable1 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
811 *--gaptable2 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
812 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
813 }
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nick
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814 }
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nick
parents:
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815 if( iin == lgth1 || jin == lgth2 )
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parents:
diff changeset
816 ;
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817 else
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818 {
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parents:
diff changeset
819 *impwmpt += imp_match_out_sc( iin, jin );
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nick
parents:
diff changeset
820
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821 // fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
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822 }
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823 if( iin <= 0 || jin <= 0 ) break;
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nick
parents:
diff changeset
824 *--gaptable1 = 'o';
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nick
parents:
diff changeset
825 *--gaptable2 = 'o';
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nick
parents:
diff changeset
826 k++;
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nick
parents:
diff changeset
827 iin = ifi; jin = jfi;
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nick
parents:
diff changeset
828 }
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nick
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diff changeset
829
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nick
parents:
diff changeset
830 for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
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nick
parents:
diff changeset
831 for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
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nick
parents:
diff changeset
832
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nick
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diff changeset
833 free( gt1bk );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
834 free( gt2bk );
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nick
parents:
diff changeset
835 }
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836
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nick
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diff changeset
837 static float Atracking( float *lasthorizontalw, float *lastverticalw,
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nick
parents:
diff changeset
838 char **seq1, char **seq2,
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nick
parents:
diff changeset
839 char **mseq1, char **mseq2,
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nick
parents:
diff changeset
840 int **ijp, int icyc, int jcyc,
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nick
parents:
diff changeset
841 int tailgp,
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nick
parents:
diff changeset
842 int *warpis, int *warpjs, int warpbase )
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843 {
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parents:
diff changeset
844 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
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nick
parents:
diff changeset
845 float wm;
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nick
parents:
diff changeset
846 char *gaptable1, *gt1bk;
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nick
parents:
diff changeset
847 char *gaptable2, *gt2bk;
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nick
parents:
diff changeset
848 lgth1 = strlen( seq1[0] );
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nick
parents:
diff changeset
849 lgth2 = strlen( seq2[0] );
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nick
parents:
diff changeset
850
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parents:
diff changeset
851 gt1bk = AllocateCharVec( lgth1+lgth2+1 );
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parents:
diff changeset
852 gt2bk = AllocateCharVec( lgth1+lgth2+1 );
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nick
parents:
diff changeset
853
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nick
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diff changeset
854 #if 0
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nick
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855 for( i=0; i<lgth1; i++ )
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856 {
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857 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
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858 }
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859 #endif
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860
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861 if( tailgp == 1 )
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862 ;
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863 else
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864 {
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865 wm = lastverticalw[0];
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nick
parents:
diff changeset
866 for( i=0; i<lgth1; i++ )
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867 {
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868 if( lastverticalw[i] >= wm )
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parents:
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869 {
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870 wm = lastverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
871 iin = i; jin = lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
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872 ijp[lgth1][lgth2] = +( lgth1 - i );
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873 }
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874 }
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875 for( j=0; j<lgth2; j++ )
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876 {
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877 if( lasthorizontalw[j] >= wm )
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parents:
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878 {
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879 wm = lasthorizontalw[j];
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nick
parents:
diff changeset
880 iin = lgth1-1; jin = j;
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nick
parents:
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881 ijp[lgth1][lgth2] = -( lgth2 - j );
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882 }
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diff changeset
883 }
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parents:
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884 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
885
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
886 for( i=0; i<lgth1+1; i++ )
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887 {
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888 ijp[i][0] = i + 1;
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889 }
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890 for( j=0; j<lgth2+1; j++ )
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891 {
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892 ijp[0][j] = -( j + 1 );
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893 }
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894
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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895 gaptable1 = gt1bk + lgth1+lgth2;
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parents:
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896 *gaptable1 = 0;
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parents:
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897 gaptable2 = gt2bk + lgth1+lgth2;
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898 *gaptable2 = 0;
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nick
parents:
diff changeset
899
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900 iin = lgth1; jin = lgth2;
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parents:
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901 limk = lgth1+lgth2 + 1;
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nick
parents:
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902 for( k=0; k<limk; k++ )
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903 {
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904 if( ijp[iin][jin] >= warpbase )
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905 {
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906 ifi = warpis[ijp[iin][jin]-warpbase];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
907 jfi = warpjs[ijp[iin][jin]-warpbase];
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908 }
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909 else if( ijp[iin][jin] < 0 )
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parents:
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910 {
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nick
parents:
diff changeset
911 ifi = iin-1; jfi = jin+ijp[iin][jin];
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parents:
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912 }
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913 else if( ijp[iin][jin] > 0 )
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parents:
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914 {
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915 ifi = iin-ijp[iin][jin]; jfi = jin-1;
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parents:
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916 }
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917 else
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918 {
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919 ifi = iin-1; jfi = jin-1;
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parents:
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920 }
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921
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922 if( ifi == -warpbase && jfi == -warpbase )
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923 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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924 l = iin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
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925 while( --l >= 0 )
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926 {
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parents:
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927 *--gaptable1 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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928 *--gaptable2 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
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929 k++;
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930 }
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931 l= jin;
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932 while( --l >= 0 )
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933 {
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934 *--gaptable1 = '-';
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935 *--gaptable2 = 'o';
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936 }
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937 break;
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938 }
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939 else
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940 {
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941 l = iin - ifi;
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942 while( --l )
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943 {
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944 *--gaptable1 = 'o';
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945 *--gaptable2 = '-';
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diff changeset
946 k++;
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947 }
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948 l= jin - jfi;
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949 while( --l )
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950 {
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951 *--gaptable1 = '-';
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952 *--gaptable2 = 'o';
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953 k++;
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954 }
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955 }
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956 if( iin <= 0 || jin <= 0 ) break;
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957 *--gaptable1 = 'o';
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958 *--gaptable2 = 'o';
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959 k++;
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960 iin = ifi; jin = jfi;
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961 }
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962
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963 for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
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964 for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
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965
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966 free( gt1bk );
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967 free( gt2bk );
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968
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969 return( 0.0 );
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970 }
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971
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972 float A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
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973 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
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974 {
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975 // int k;
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976 register int i, j;
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977 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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978 int lgth1, lgth2;
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979 int resultlen;
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980 float wm = 0.0; /* int ?????? */
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981 float g;
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982 float *currentw, *previousw;
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983 // float fpenalty = (float)penalty;
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984 #if USE_PENALTY_EX
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985 float fpenalty_ex = (float)penalty_ex;
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986 #endif
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987 #if 1
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988 float *wtmp;
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989 int *ijppt;
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990 float *mjpt, *prept, *curpt;
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991 int *mpjpt;
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992 #endif
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993 static TLS float mi, *m;
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994 static TLS int **ijp;
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995 static TLS int mpi, *mp;
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996 static TLS float *w1, *w2;
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997 static TLS float *match;
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998 static TLS float *initverticalw; /* kufuu sureba iranai */
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999 static TLS float *lastverticalw; /* kufuu sureba iranai */
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1000 static TLS char **mseq1;
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1001 static TLS char **mseq2;
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1002 static TLS char **mseq;
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1003 static TLS float *ogcp1;
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1004 static TLS float *ogcp2;
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1005 static TLS float *fgcp1;
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1006 static TLS float *fgcp2;
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1007 static TLS float **cpmx1;
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1008 static TLS float **cpmx2;
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1009 static TLS int **intwork;
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1010 static TLS float **floatwork;
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1011 static TLS int orlgth1 = 0, orlgth2 = 0;
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1012 static TLS float *gapfreq1;
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1013 static TLS float *gapfreq2;
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1014 float fpenalty = (float)penalty;
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1015 float fpenalty_shift = (float)penalty_shift;
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1016 float *fgcp2pt;
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1017 float *ogcp2pt;
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1018 float fgcp1va;
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1019 float ogcp1va;
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1020 float *gf2pt;
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1021 float *gf2ptpre;
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1022 float gf1va;
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1023 float gf1vapre;
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1024 float headgapfreq1;
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1025 float headgapfreq2;
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1026
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1027 int *warpis = NULL;
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1028 int *warpjs = NULL;
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1029 int *warpi = NULL;
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1030 int *warpj = NULL;
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1031 int *prevwarpi = NULL;
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1032 int *prevwarpj = NULL;
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1033 float *wmrecords = NULL;
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1034 float *prevwmrecords = NULL;
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1035 int warpn = 0;
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1036 int warpbase;
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1037 float curm = 0.0;
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1038 float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
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1039 int *warpipt, *warpjpt;
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1040
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1041
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1042 if( seq1 == NULL )
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1043 {
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1044 if( orlgth1 )
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1045 {
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1046 // fprintf( stderr, "## Freeing local arrays in A__align\n" );
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1047 orlgth1 = 0;
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1048 orlgth2 = 0;
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1049
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1050 imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
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1051
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1052 free( mseq1 );
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1053 free( mseq2 );
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1054 FreeFloatVec( w1 );
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1055 FreeFloatVec( w2 );
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1056 FreeFloatVec( match );
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1057 FreeFloatVec( initverticalw );
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1058 FreeFloatVec( lastverticalw );
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1059
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1060 FreeFloatVec( m );
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1061 FreeIntVec( mp );
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1062
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1063 FreeCharMtx( mseq );
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1064
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1065 FreeFloatVec( ogcp1 );
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1066 FreeFloatVec( ogcp2 );
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1067 FreeFloatVec( fgcp1 );
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1068 FreeFloatVec( fgcp2 );
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1069
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1070
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1071 FreeFloatMtx( cpmx1 );
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1072 FreeFloatMtx( cpmx2 );
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1073
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1074 FreeFloatVec( gapfreq1 );
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1075 FreeFloatVec( gapfreq2 );
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1076
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1077 FreeFloatMtx( floatwork );
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1078 FreeIntMtx( intwork );
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1079
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1080 }
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1081 else
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1082 {
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1083 // fprintf( stderr, "## Not allocated\n" );
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1084 }
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1085 return( 0.0 );
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1086 }
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1087
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1088
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1089 lgth1 = strlen( seq1[0] );
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1090 lgth2 = strlen( seq2[0] );
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1091 #if 0
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1092 if( lgth1 == 0 || lgth2 == 0 )
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1093 {
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1094 fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
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1095 }
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1096 #endif
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1097 if( lgth1 == 0 && lgth2 == 0 )
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1098 return( 0.0 );
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1099
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1100 if( lgth1 == 0 )
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1101 {
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1102 for( i=0; i<icyc; i++ )
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1103 {
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1104 j = lgth2;
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1105 seq1[i][j] = 0;
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1106 while( j ) seq1[i][--j] = *newgapstr;
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1107 // fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
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1108 }
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1109 return( 0.0 );
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1110 }
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1111
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1112 if( lgth2 == 0 )
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1113 {
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1114 for( i=0; i<jcyc; i++ )
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1115 {
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1116 j = lgth1;
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1117 seq2[i][j] = 0;
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1118 while( j ) seq2[i][--j] = *newgapstr;
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1119 // fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
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1120 }
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1121 return( 0.0 );
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1122 }
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1123
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1124 warpbase = lgth1 + lgth2;
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1125 warpis = NULL;
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1126 warpjs = NULL;
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1127 warpn = 0;
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1128
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1129
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1130
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1131 if( trywarp )
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1132 {
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1133 // fprintf( stderr, "IN A__align, penalty_shift = %d\n", penalty_shift );
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1134 if( headgp == 0 || tailgp == 0 )
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1135 {
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1136 fprintf( stderr, "At present, headgp and tailgp must be 1 to allow shift.\n" );
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1137 exit( 1 );
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1138 }
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1139 wmrecords = AllocateFloatVec( lgth2+1 );
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1140 warpi = AllocateIntVec( lgth2+1 );
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1141 warpj = AllocateIntVec( lgth2+1 );
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1142 prevwmrecords = AllocateFloatVec( lgth2+1 );
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1143 prevwarpi = AllocateIntVec( lgth2+1 );
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1144 prevwarpj = AllocateIntVec( lgth2+1 );
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1145 for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
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1146 for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
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1147 for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
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1148 for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
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1149 for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
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1150 for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
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1151 }
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1152
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1153
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1154 #if 0
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1155 fprintf( stderr, "#### eff in SA+++align\n" );
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1156 fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
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1157 fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
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1158 for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
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1159 fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
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1160 fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
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1161 for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
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1162 #endif
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1163 if( orlgth1 == 0 )
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1164 {
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1165 mseq1 = AllocateCharMtx( njob, 0 );
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1166 mseq2 = AllocateCharMtx( njob, 0 );
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1167 }
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1168
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1169
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1170
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1171 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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1172 {
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1173 int ll1, ll2;
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1174
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1175
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1176 if( orlgth1 > 0 && orlgth2 > 0 )
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1177 {
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1178 FreeFloatVec( w1 );
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1179 FreeFloatVec( w2 );
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1180 FreeFloatVec( match );
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1181 FreeFloatVec( initverticalw );
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1182 FreeFloatVec( lastverticalw );
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1183
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1184 FreeFloatVec( m );
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1185 FreeIntVec( mp );
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1186
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1187 FreeCharMtx( mseq );
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1188
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1189 FreeFloatVec( ogcp1 );
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1190 FreeFloatVec( ogcp2 );
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1191 FreeFloatVec( fgcp1 );
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1192 FreeFloatVec( fgcp2 );
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1193
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1194
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1195 FreeFloatMtx( cpmx1 );
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1196 FreeFloatMtx( cpmx2 );
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1197
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1198 FreeFloatVec( gapfreq1 );
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1199 FreeFloatVec( gapfreq2 );
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1200
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1201 FreeFloatMtx( floatwork );
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1202 FreeIntMtx( intwork );
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1203 }
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1204
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1205 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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1206 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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1207
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1208 #if DEBUG
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1209 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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1210 #endif
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1211
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1212 w1 = AllocateFloatVec( ll2+2 );
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1213 w2 = AllocateFloatVec( ll2+2 );
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1214 match = AllocateFloatVec( ll2+2 );
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1215
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1216 initverticalw = AllocateFloatVec( ll1+2 );
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1217 lastverticalw = AllocateFloatVec( ll1+2 );
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1218
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1219 m = AllocateFloatVec( ll2+2 );
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1220 mp = AllocateIntVec( ll2+2 );
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1221
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1222 mseq = AllocateCharMtx( njob, ll1+ll2 );
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1223
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1224 ogcp1 = AllocateFloatVec( ll1+2 );
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1225 ogcp2 = AllocateFloatVec( ll2+2 );
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1226 fgcp1 = AllocateFloatVec( ll1+2 );
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1227 fgcp2 = AllocateFloatVec( ll2+2 );
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1228
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1229 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
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1230 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
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1231
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1232 gapfreq1 = AllocateFloatVec( ll1+2 );
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1233 gapfreq2 = AllocateFloatVec( ll2+2 );
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1234
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1235 #if FASTMATCHCALC
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1236 floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
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1237 intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets+1 );
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1238 #else
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1239 floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
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1240 intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
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1241 #endif
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1242
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1243 #if DEBUG
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1244 fprintf( stderr, "succeeded\n" );
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1245 #endif
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1246
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1247 orlgth1 = ll1 - 100;
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1248 orlgth2 = ll2 - 100;
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1249 }
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1250
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1251
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1252 for( i=0; i<icyc; i++ )
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1253 {
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1254 mseq1[i] = mseq[i];
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1255 seq1[i][lgth1] = 0;
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1256 }
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1257 for( j=0; j<jcyc; j++ )
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1258 {
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1259 mseq2[j] = mseq[icyc+j];
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1260 seq2[j][lgth2] = 0;
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1261 }
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1262
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1263
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1264 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
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1265 {
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1266 int ll1, ll2;
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1267
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1268 if( commonAlloc1 && commonAlloc2 )
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1269 {
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1270 FreeIntMtx( commonIP );
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1271 }
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1272
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1273 ll1 = MAX( orlgth1, commonAlloc1 );
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1274 ll2 = MAX( orlgth2, commonAlloc2 );
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1275
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1276 #if DEBUG
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1277 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
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1278 #endif
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1279
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1280 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
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1281
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1282 #if DEBUG
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1283 fprintf( stderr, "succeeded\n\n" );
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1284 #endif
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1285
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1286 commonAlloc1 = ll1;
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1287 commonAlloc2 = ll2;
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1288 }
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1289 ijp = commonIP;
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1290
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1291 #if 0
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1292 {
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1293 float t = 0.0;
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1294 for( i=0; i<icyc; i++ )
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1295 t += eff1[i];
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1296 fprintf( stderr, "## totaleff = %f\n", t );
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1297 }
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1298 #endif
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1299
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1300 cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
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1301 cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
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1302
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1303 if( sgap1 )
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1304 {
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1305 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
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1306 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
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1307 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
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1308 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
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1309 outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
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1310 outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
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1311 outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
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1312 outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
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1313 }
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1314 else
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1315 {
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1316 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
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1317 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
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1318 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
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1319 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
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1320 headgapfreq1 = 0.0;
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1321 headgapfreq2 = 0.0;
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1322 gapfreq1[lgth1] = 0.0;
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1323 gapfreq2[lgth2] = 0.0;
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1324 }
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1325
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1326 if( legacygapcost == 0 )
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1327 {
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1328 gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
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1329 gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
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1330 for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
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1331 for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
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1332 headgapfreq1 = 1.0 - headgapfreq1;
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1333 headgapfreq2 = 1.0 - headgapfreq2;
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1334 }
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1335 else
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1336 {
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1337 for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
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1338 for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
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1339 headgapfreq1 = 1.0;
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1340 headgapfreq2 = 1.0;
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1341 }
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1342
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1343 #if 0
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1344 fprintf( stderr, "\ngapfreq1[] =" );
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1345 for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
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1346 fprintf( stderr, "\n" );
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1347
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1348 fprintf( stderr, "\ngapfreq2[] =" );
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1349 for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
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1350 fprintf( stderr, "\n" );
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1351 #endif
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1352
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1353
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1354 for( i=0; i<lgth1; i++ )
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1355 {
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1356 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
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1357 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
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1358 }
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1359
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1360 for( i=0; i<lgth2; i++ )
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1361 {
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1362 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
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1363 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
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1364 }
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1365 #if 0
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1366 for( i=0; i<lgth1; i++ )
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1367 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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1368 #endif
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1369
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1370 currentw = w1;
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1371 previousw = w2;
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1372
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1373 match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
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1374 if( localhom )
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1375 imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
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1376
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1377 match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
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1378 if( localhom )
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1379 imp_match_out_vead( currentw, 0, lgth2 ); // 060306
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1380 #if 0 // -> tbfast.c
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1381 if( localhom )
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1382 imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
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1383
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1384 #endif
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1385
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1386 if( headgp == 1 )
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1387 {
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1388 for( i=1; i<lgth1+1; i++ )
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1389 {
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1390 // initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
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1391 initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
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1392 }
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1393 for( j=1; j<lgth2+1; j++ )
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1394 {
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1395 // currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
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parents:
diff changeset
1396 currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
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1397 }
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diff changeset
1398 }
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diff changeset
1399 #if OUTGAP0TRY
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diff changeset
1400 else
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diff changeset
1401 {
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diff changeset
1402 fprintf( stderr, "offset = %d\n", offset );
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diff changeset
1403 for( j=1; j<lgth2+1; j++ )
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parents:
diff changeset
1404 currentw[j] -= offset * j / 2.0;
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parents:
diff changeset
1405 for( i=1; i<lgth1+1; i++ )
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nick
parents:
diff changeset
1406 initverticalw[i] -= offset * i / 2.0;
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diff changeset
1407 }
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diff changeset
1408 #endif
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diff changeset
1409 #if 0
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diff changeset
1410 fprintf( stderr, "\n " );
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1411 for( j=0; j<lgth2+1; j++ ) fprintf( stderr, " %c ", seq2[0][j] );
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nick
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diff changeset
1412 fprintf( stderr, "\n%c ", seq1[0][0] );
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1413 for( j=0; j<lgth2+1; j++ )
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1414 {
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1415 fprintf( stderr, "%5.0f ", currentw[j] );
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1416 }
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1417 fprintf( stderr, "\n" );
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diff changeset
1418 #endif
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diff changeset
1419
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diff changeset
1420
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1421 for( j=1; j<lgth2+1; ++j )
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1422 {
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diff changeset
1423 // m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
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parents:
diff changeset
1424 m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
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1425 }
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1426 if( lgth2 == 0 )
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nick
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diff changeset
1427 lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
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diff changeset
1428 else
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parents:
diff changeset
1429 lastverticalw[0] = currentw[lgth2-1];
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diff changeset
1430
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diff changeset
1431 if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
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nick
parents:
diff changeset
1432 lastj = lgth2+1;
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diff changeset
1433
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diff changeset
1434 #if XXXXXXX
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nick
parents:
diff changeset
1435 fprintf( stderr, "currentw = \n" );
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nick
parents:
diff changeset
1436 for( i=0; i<lgth1+1; i++ )
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diff changeset
1437 {
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diff changeset
1438 fprintf( stderr, "%5.2f ", currentw[i] );
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diff changeset
1439 }
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parents:
diff changeset
1440 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
1441 fprintf( stderr, "initverticalw = \n" );
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nick
parents:
diff changeset
1442 for( i=0; i<lgth2+1; i++ )
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diff changeset
1443 {
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diff changeset
1444 fprintf( stderr, "%5.2f ", initverticalw[i] );
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diff changeset
1445 }
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diff changeset
1446 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
1447 fprintf( stderr, "fcgp\n" );
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nick
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diff changeset
1448 for( i=0; i<lgth1; i++ )
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diff changeset
1449 fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
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diff changeset
1450 for( i=0; i<lgth2; i++ )
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diff changeset
1451 fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
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diff changeset
1452 #endif
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diff changeset
1453
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diff changeset
1454 for( i=1; i<lasti; i++ )
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diff changeset
1455 {
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diff changeset
1456
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diff changeset
1457 #ifdef enablemultithread
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diff changeset
1458 // fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
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nick
parents:
diff changeset
1459 if( chudanpt && *chudanpt != chudanref )
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diff changeset
1460 {
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diff changeset
1461 // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
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nick
parents:
diff changeset
1462 *chudanres = 1;
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nick
parents:
diff changeset
1463 return( -1.0 );
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diff changeset
1464 }
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diff changeset
1465 #endif
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diff changeset
1466 wtmp = previousw;
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parents:
diff changeset
1467 previousw = currentw;
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parents:
diff changeset
1468 currentw = wtmp;
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diff changeset
1469
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diff changeset
1470 previousw[0] = initverticalw[i-1];
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parents:
diff changeset
1471
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parents:
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1472 match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
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diff changeset
1473 #if XXXXXXX
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parents:
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1474 fprintf( stderr, "\n" );
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diff changeset
1475 fprintf( stderr, "i=%d\n", i );
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parents:
diff changeset
1476 fprintf( stderr, "currentw = \n" );
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diff changeset
1477 for( j=0; j<lgth2; j++ )
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diff changeset
1478 {
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diff changeset
1479 fprintf( stderr, "%5.2f ", currentw[j] );
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diff changeset
1480 }
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diff changeset
1481 fprintf( stderr, "\n" );
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diff changeset
1482 #endif
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diff changeset
1483 if( localhom )
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parents:
diff changeset
1484 {
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1485 // fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
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parents:
diff changeset
1486 #if 0
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diff changeset
1487 imp_match_out_vead( currentw, i, lgth2 );
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parents:
diff changeset
1488 #else
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diff changeset
1489 imp_match_out_vead( currentw, i, lgth2 );
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parents:
diff changeset
1490 #endif
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diff changeset
1491 }
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diff changeset
1492 #if XXXXXXX
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parents:
diff changeset
1493 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
1494 fprintf( stderr, "i=%d\n", i );
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nick
parents:
diff changeset
1495 fprintf( stderr, "currentw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1496 for( j=0; j<lgth2; j++ )
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nick
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diff changeset
1497 {
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diff changeset
1498 fprintf( stderr, "%5.2f ", currentw[j] );
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diff changeset
1499 }
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diff changeset
1500 fprintf( stderr, "\n" );
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parents:
diff changeset
1501 #endif
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diff changeset
1502 currentw[0] = initverticalw[i];
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nick
parents:
diff changeset
1503
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nick
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diff changeset
1504 #if 0
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nick
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diff changeset
1505 fprintf( stderr, "%c ", seq1[0][i] );
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nick
parents:
diff changeset
1506 for( j=0; j<lgth2+1; j++ )
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diff changeset
1507 {
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diff changeset
1508 fprintf( stderr, "%5.0f ", currentw[j] );
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nick
parents:
diff changeset
1509 }
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nick
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diff changeset
1510 fprintf( stderr, "\n" );
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parents:
diff changeset
1511 #endif
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diff changeset
1512
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diff changeset
1513 // mi = previousw[0] + ogcp2[1]; mpi = 0;
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parents:
diff changeset
1514 mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
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parents:
diff changeset
1515 ijppt = ijp[i] + 1;
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nick
parents:
diff changeset
1516 mjpt = m + 1;
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nick
parents:
diff changeset
1517 prept = previousw;
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parents:
diff changeset
1518 curpt = currentw + 1;
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nick
parents:
diff changeset
1519 mpjpt = mp + 1;
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nick
parents:
diff changeset
1520 fgcp2pt = fgcp2;
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nick
parents:
diff changeset
1521 ogcp2pt = ogcp2 + 1;
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nick
parents:
diff changeset
1522 fgcp1va = fgcp1[i-1];
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parents:
diff changeset
1523 ogcp1va = ogcp1[i];
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parents:
diff changeset
1524 gf1va = gapfreq1[i];
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nick
parents:
diff changeset
1525 gf1vapre = gapfreq1[i-1];
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parents:
diff changeset
1526 gf2pt = gapfreq2+1;
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nick
parents:
diff changeset
1527 gf2ptpre = gapfreq2;
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parents:
diff changeset
1528
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diff changeset
1529 if( trywarp )
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diff changeset
1530 {
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diff changeset
1531 prevwmrecordspt = prevwmrecords;
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parents:
diff changeset
1532 wmrecordspt = wmrecords+1;
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parents:
diff changeset
1533 wmrecords1pt = wmrecords;
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nick
parents:
diff changeset
1534 warpipt = warpi + 1;
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nick
parents:
diff changeset
1535 warpjpt = warpj + 1;
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parents:
diff changeset
1536 }
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diff changeset
1537
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diff changeset
1538
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diff changeset
1539 for( j=1; j<lastj; j++ )
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parents:
diff changeset
1540 {
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diff changeset
1541 #ifdef xxxenablemultithread
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parents:
diff changeset
1542 // fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
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parents:
diff changeset
1543 if( chudanpt && *chudanpt != chudanref )
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diff changeset
1544 {
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parents:
diff changeset
1545 // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
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nick
parents:
diff changeset
1546 *chudanres = 1;
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nick
parents:
diff changeset
1547 return( -1.0 );
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diff changeset
1548 }
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parents:
diff changeset
1549 #endif
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parents:
diff changeset
1550 wm = *prept;
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parents:
diff changeset
1551 *ijppt = 0;
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parents:
diff changeset
1552
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parents:
diff changeset
1553 #if 0
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parents:
diff changeset
1554 fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
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parents:
diff changeset
1555 fprintf( stderr, "%5.0f->", wm );
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parents:
diff changeset
1556 fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
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parents:
diff changeset
1557 #endif
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parents:
diff changeset
1558 if( (g=mi+*fgcp2pt*gf1va) > wm )
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parents:
diff changeset
1559 {
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parents:
diff changeset
1560 wm = g;
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parents:
diff changeset
1561 *ijppt = -( j - mpi );
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parents:
diff changeset
1562 // fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
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parents:
diff changeset
1563 }
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diff changeset
1564 if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
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parents:
diff changeset
1565 {
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diff changeset
1566 mi = g;
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parents:
diff changeset
1567 mpi = j-1;
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parents:
diff changeset
1568 }
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parents:
diff changeset
1569 #if USE_PENALTY_EX
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parents:
diff changeset
1570 mi += fpenalty_ex;
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parents:
diff changeset
1571 #endif
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diff changeset
1572
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diff changeset
1573 #if 0
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1574 fprintf( stderr, "%5.0f->", wm );
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parents:
diff changeset
1575 fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
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parents:
diff changeset
1576 #endif
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diff changeset
1577 if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
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parents:
diff changeset
1578 {
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parents:
diff changeset
1579 wm = g;
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parents:
diff changeset
1580 *ijppt = +( i - *mpjpt );
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parents:
diff changeset
1581 // fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
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parents:
diff changeset
1582 }
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diff changeset
1583 if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
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diff changeset
1584 {
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diff changeset
1585 *mjpt = g;
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parents:
diff changeset
1586 *mpjpt = i-1;
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parents:
diff changeset
1587 }
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diff changeset
1588 #if USE_PENALTY_EX
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1589 m[j] += fpenalty_ex;
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parents:
diff changeset
1590 #endif
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diff changeset
1591
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diff changeset
1592
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diff changeset
1593 if( trywarp )
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parents:
diff changeset
1594 {
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diff changeset
1595 #if USE_PENALTY_EX
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diff changeset
1596 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
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parents:
diff changeset
1597 #else
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diff changeset
1598 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
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diff changeset
1599 #endif
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diff changeset
1600 {
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diff changeset
1601 // fprintf( stderr, "WARP!!\n" );
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diff changeset
1602 if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
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diff changeset
1603 {
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1604 *ijppt = warpbase + warpn - 1;
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diff changeset
1605 }
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diff changeset
1606 else
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diff changeset
1607 {
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1608 *ijppt = warpbase + warpn;
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diff changeset
1609 warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
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diff changeset
1610 warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
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parents:
diff changeset
1611 warpis[warpn] = prevwarpi[j-1];
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parents:
diff changeset
1612 warpjs[warpn] = prevwarpj[j-1];
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parents:
diff changeset
1613 warpn++;
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diff changeset
1614 }
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diff changeset
1615 wm = g;
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parents:
diff changeset
1616 }
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diff changeset
1617
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diff changeset
1618 #if 0
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diff changeset
1619 fprintf( stderr, "%5.0f ", wm );
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parents:
diff changeset
1620 #endif
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diff changeset
1621 curm = *curpt + wm;
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diff changeset
1622
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1623 if( *wmrecords1pt > *wmrecordspt )
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parents:
diff changeset
1624 {
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1625 *wmrecordspt = *wmrecords1pt;
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1626 *warpipt = *(warpipt-1);
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1627 *warpjpt = *(warpjpt-1);
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1628 }
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1629 if( curm > *wmrecordspt )
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1630 {
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1631 *wmrecordspt = curm;
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1632 *warpipt = i;
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diff changeset
1633 *warpjpt = j;
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1634 }
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1635 wmrecordspt++;
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parents:
diff changeset
1636 wmrecords1pt++;
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parents:
diff changeset
1637 warpipt++;
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diff changeset
1638 warpjpt++;
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1639 }
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1640
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1641 *curpt++ += wm;
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nick
parents:
diff changeset
1642 ijppt++;
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parents:
diff changeset
1643 mjpt++;
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parents:
diff changeset
1644 prept++;
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diff changeset
1645 mpjpt++;
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nick
parents:
diff changeset
1646 fgcp2pt++;
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parents:
diff changeset
1647 ogcp2pt++;
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parents:
diff changeset
1648 gf2ptpre++;
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1649 gf2pt++;
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1650 }
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1651 lastverticalw[i] = currentw[lgth2-1];
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1652
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1653 if( trywarp )
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1654 {
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1655 fltncpy( prevwmrecords, wmrecords, lastj );
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parents:
diff changeset
1656 intncpy( prevwarpi, warpi, lastj );
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nick
parents:
diff changeset
1657 intncpy( prevwarpj, warpj, lastj );
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1658 }
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diff changeset
1659 }
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1660
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1661 if( trywarp )
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1662 {
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1663 // fprintf( stderr, "wm = %f\n", wm );
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parents:
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1664 // fprintf( stderr, "warpn = %d\n", warpn );
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1665 free( wmrecords );
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parents:
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1666 free( prevwmrecords );
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parents:
diff changeset
1667 free( warpi );
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parents:
diff changeset
1668 free( warpj );
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parents:
diff changeset
1669 free( prevwarpi );
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parents:
diff changeset
1670 free( prevwarpj );
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1671 }
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1672
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1673 #if OUTGAP0TRY
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1674 if( !outgap )
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1675 {
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1676 for( j=1; j<lgth2+1; j++ )
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1677 currentw[j] -= offset * ( lgth2 - j ) / 2.0;
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1678 for( i=1; i<lgth1+1; i++ )
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1679 lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
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1680 }
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1681 #endif
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1682
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1683 /*
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1684 fprintf( stderr, "\n" );
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1685 for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
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1686 fprintf( stderr, "#####\n" );
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diff changeset
1687 for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
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1688 fprintf( stderr, "====>" );
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parents:
diff changeset
1689 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
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1690 for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
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1691 */
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1692 if( localhom )
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1693 {
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1694 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
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1695 }
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1696 else
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1697 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
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1698
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1699 if( warpis ) free( warpis );
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1700 if( warpjs ) free( warpjs );
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1701
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1702 // fprintf( stderr, "### impmatch = %f\n", *impmatch );
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1703
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1704 resultlen = strlen( mseq1[0] );
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1705 if( alloclen < resultlen || resultlen > N )
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1706 {
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1707 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
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1708 ErrorExit( "LENGTH OVER!\n" );
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1709 }
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1710
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diff changeset
1711
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1712 for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
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1713 for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
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1714 #if 0
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1715 fprintf( stderr, "\n" );
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1716 for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
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1717 fprintf( stderr, "#####\n" );
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1718 for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
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1719 #endif
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1720
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1721 // fprintf( stderr, "wm = %f\n", wm );
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1722
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1723 return( wm );
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1724 }
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1725
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1726 float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 )
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1727 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
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1728 {
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1729 fprintf( stderr, "Unexpected error. Please contact kazutaka.katoh@aist.go.jp\n" );
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1730 exit( 1 );
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1731 }
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1732
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1733
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1734 float A__align_variousdist( double **pairoffset, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
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diff changeset
1735 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
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1736 {
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1737
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1738 // int k;
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diff changeset
1739 register int i, j, c;
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1740 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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1741 int lgth1, lgth2;
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1742 int resultlen;
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1743 float wm = 0.0; /* int ?????? */
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1744 float g;
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1745 float *currentw, *previousw;
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1746 // float fpenalty = (float)penalty;
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1747 #if USE_PENALTY_EX
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1748 float fpenalty_ex = (float)penalty_ex;
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1749 #endif
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1750 #if 1
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1751 float *wtmp;
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1752 int *ijppt;
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1753 float *mjpt, *prept, *curpt;
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1754 int *mpjpt;
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1755 #endif
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1756 static TLS float mi, *m;
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1757 static TLS int **ijp;
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1758 static TLS int mpi, *mp;
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1759 static TLS float *w1, *w2;
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1760 static TLS float *match;
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1761 static TLS float *initverticalw; /* kufuu sureba iranai */
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1762 static TLS float *lastverticalw; /* kufuu sureba iranai */
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1763 static TLS char **mseq1;
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1764 static TLS char **mseq2;
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1765 static TLS char **mseq;
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1766 static TLS float *ogcp1;
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1767 static TLS float *ogcp2;
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1768 static TLS float *fgcp1;
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1769 static TLS float *fgcp2;
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1770 static TLS float ***cpmx1s;
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1771 static TLS float ***cpmx2s;
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1772 static TLS int ***intwork;
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1773 static TLS float ***floatwork;
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1774 static TLS int orlgth1 = 0, orlgth2 = 0;
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1775 static TLS float *gapfreq1;
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1776 static TLS float *gapfreq2;
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1777 float fpenalty = (float)penalty;
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1778 float fpenalty_shift = (float)penalty_shift;
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1779 float *fgcp2pt;
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1780 float *ogcp2pt;
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1781 float fgcp1va;
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1782 float ogcp1va;
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1783 float *gf2pt;
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1784 float *gf2ptpre;
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1785 float gf1va;
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1786 float gf1vapre;
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1787 float headgapfreq1;
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1788 float headgapfreq2;
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1789
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1790 int *warpis = NULL;
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1791 int *warpjs = NULL;
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1792 int *warpi = NULL;
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1793 int *warpj = NULL;
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1794 int *prevwarpi = NULL;
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1795 int *prevwarpj = NULL;
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1796 float *wmrecords = NULL;
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1797 float *prevwmrecords = NULL;
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1798 int warpn = 0;
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1799 int warpbase;
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1800 float curm = 0.0;
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1801 float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
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1802 int *warpipt, *warpjpt;
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1803
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1804
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1805 if( seq1 == NULL )
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1806 {
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1807 if( orlgth1 )
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1808 {
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1809 // fprintf( stderr, "## Freeing local arrays in A__align\n" );
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1810 orlgth1 = 0;
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1811 orlgth2 = 0;
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1812
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1813 imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
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1814
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1815 free( mseq1 );
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1816 free( mseq2 );
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1817 FreeFloatVec( w1 );
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1818 FreeFloatVec( w2 );
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1819 FreeFloatVec( match );
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1820 FreeFloatVec( initverticalw );
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1821 FreeFloatVec( lastverticalw );
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1822
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1823 FreeFloatVec( m );
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1824 FreeIntVec( mp );
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1825
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1826 FreeCharMtx( mseq );
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1827
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1828 FreeFloatVec( ogcp1 );
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1829 FreeFloatVec( ogcp2 );
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1830 FreeFloatVec( fgcp1 );
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1831 FreeFloatVec( fgcp2 );
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1832
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1833
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1834 FreeFloatCub( cpmx1s );
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1835 FreeFloatCub( cpmx2s );
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1836
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1837 FreeFloatVec( gapfreq1 );
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1838 FreeFloatVec( gapfreq2 );
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1839
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1840 FreeFloatCub( floatwork );
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1841 FreeIntCub( intwork );
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1842
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1843 }
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1844 else
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1845 {
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1846 // fprintf( stderr, "## Not allocated\n" );
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1847 }
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1848 return( 0.0 );
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1849 }
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1850
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1851
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1852
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1853 // fprintf( stderr, "\npairoffset = \n" );
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1854 // for( i=0; i<icyc; i ++ ) for( j=0; j<jcyc; j ++ )
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1855 // fprintf( stderr, "%d-%d, %f\n", i, j, pairoffset[i][j] );
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1856
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1857 lgth1 = strlen( seq1[0] );
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1858 lgth2 = strlen( seq2[0] );
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1859 #if 0
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1860 if( lgth1 == 0 || lgth2 == 0 )
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1861 {
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1862 fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
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1863 }
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1864 #endif
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1865 if( lgth1 == 0 && lgth2 == 0 )
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1866 return( 0.0 );
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1867
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1868 if( lgth1 == 0 )
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1869 {
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1870 for( i=0; i<icyc; i++ )
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1871 {
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1872 j = lgth2;
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1873 seq1[i][j] = 0;
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1874 while( j ) seq1[i][--j] = *newgapstr;
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1875 // fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
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1876 }
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1877 return( 0.0 );
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1878 }
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1879
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1880 if( lgth2 == 0 )
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1881 {
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1882 for( i=0; i<jcyc; i++ )
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1883 {
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1884 j = lgth1;
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1885 seq2[i][j] = 0;
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1886 while( j ) seq2[i][--j] = *newgapstr;
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1887 // fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
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1888 }
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1889 return( 0.0 );
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1890 }
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1891
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1892 warpbase = lgth1 + lgth2;
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1893 warpis = NULL;
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1894 warpjs = NULL;
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1895 warpn = 0;
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1896
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1897 if( trywarp )
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1898 {
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1899 // fprintf( stderr, "In A__align_variousdist !!!!!\n" );
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1900 if( headgp == 0 || tailgp == 0 )
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1901 {
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1902 fprintf( stderr, "At present, headgp and tailgp must be 1.\n" );
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1903 exit( 1 );
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1904 }
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1905 wmrecords = AllocateFloatVec( lgth2+1 );
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1906 warpi = AllocateIntVec( lgth2+1 );
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1907 warpj = AllocateIntVec( lgth2+1 );
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1908 prevwmrecords = AllocateFloatVec( lgth2+1 );
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1909 prevwarpi = AllocateIntVec( lgth2+1 );
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1910 prevwarpj = AllocateIntVec( lgth2+1 );
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1911 for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
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1912 for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
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1913 for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
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1914 for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
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1915 for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
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1916 for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
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1917 }
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1918
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1919 #if 0
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1920 fprintf( stderr, "#### eff in SA+++align\n" );
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1921 fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
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1922 fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
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1923 for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
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1924 fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
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1925 fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
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1926 for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
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1927 #endif
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1928 if( orlgth1 == 0 )
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1929 {
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1930 mseq1 = AllocateCharMtx( njob, 0 );
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1931 mseq2 = AllocateCharMtx( njob, 0 );
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1932 }
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1933
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1934
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1935
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1936 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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1937 {
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1938 int ll1, ll2;
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1939
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1940
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1941 if( orlgth1 > 0 && orlgth2 > 0 )
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1942 {
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1943 FreeFloatVec( w1 );
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1944 FreeFloatVec( w2 );
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1945 FreeFloatVec( match );
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1946 FreeFloatVec( initverticalw );
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1947 FreeFloatVec( lastverticalw );
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1948
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1949 FreeFloatVec( m );
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1950 FreeIntVec( mp );
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1951
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1952 FreeCharMtx( mseq );
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1953
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1954 FreeFloatVec( ogcp1 );
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1955 FreeFloatVec( ogcp2 );
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1956 FreeFloatVec( fgcp1 );
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1957 FreeFloatVec( fgcp2 );
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1958
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1959
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1960 FreeFloatCub( cpmx1s );
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1961 FreeFloatCub( cpmx2s );
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1962
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1963 FreeFloatVec( gapfreq1 );
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1964 FreeFloatVec( gapfreq2 );
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1965
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1966 FreeFloatCub( floatwork );
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1967 FreeIntCub( intwork );
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1968 }
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1969
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1970 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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1971 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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1972
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1973 #if DEBUG
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1974 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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1975 #endif
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1976
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1977 w1 = AllocateFloatVec( ll2+2 );
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1978 w2 = AllocateFloatVec( ll2+2 );
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1979 match = AllocateFloatVec( ll2+2 );
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1980
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1981 initverticalw = AllocateFloatVec( ll1+2 );
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1982 lastverticalw = AllocateFloatVec( ll1+2 );
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1983
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1984 m = AllocateFloatVec( ll2+2 );
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1985 mp = AllocateIntVec( ll2+2 );
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1986
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1987 mseq = AllocateCharMtx( njob, ll1+ll2 );
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1988
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1989 ogcp1 = AllocateFloatVec( ll1+2 );
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1990 ogcp2 = AllocateFloatVec( ll2+2 );
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1991 fgcp1 = AllocateFloatVec( ll1+2 );
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1992 fgcp2 = AllocateFloatVec( ll2+2 );
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1993
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1994 cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
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1995 cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, ll2+2 );
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1996
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1997 gapfreq1 = AllocateFloatVec( ll1+2 );
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1998 gapfreq2 = AllocateFloatVec( ll2+2 );
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1999
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2000 floatwork = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
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2001 intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 );
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2002
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2003 #if DEBUG
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2004 fprintf( stderr, "succeeded\n" );
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2005 #endif
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2006
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2007 orlgth1 = ll1 - 100;
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2008 orlgth2 = ll2 - 100;
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2009 }
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2010
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2011
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2012 for( i=0; i<icyc; i++ )
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2013 {
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2014 mseq1[i] = mseq[i];
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2015 seq1[i][lgth1] = 0;
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2016 }
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2017 for( j=0; j<jcyc; j++ )
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2018 {
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2019 mseq2[j] = mseq[icyc+j];
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2020 seq2[j][lgth2] = 0;
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2021 }
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2022
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2023
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2024 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
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2025 {
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2026 int ll1, ll2;
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2027
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2028 if( commonAlloc1 && commonAlloc2 )
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2029 {
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2030 FreeIntMtx( commonIP );
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2031 }
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2032
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2033 ll1 = MAX( orlgth1, commonAlloc1 );
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2034 ll2 = MAX( orlgth2, commonAlloc2 );
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2035
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2036 #if DEBUG
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2037 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
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2038 #endif
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2039
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2040 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
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2041
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2042 #if DEBUG
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2043 fprintf( stderr, "succeeded\n\n" );
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2044 #endif
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2045
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2046 commonAlloc1 = ll1;
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2047 commonAlloc2 = ll2;
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2048 }
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2049 ijp = commonIP;
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2050
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2051 #if 0
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2052 {
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2053 float t = 0.0;
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2054 for( i=0; i<icyc; i++ )
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2055 t += eff1[i];
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2056 fprintf( stderr, "## totaleff = %f\n", t );
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2057 }
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2058 #endif
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2059
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2060 // cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
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2061 // cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
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2062 for( c=0; c<maxdistclass; c++ )
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2063 {
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2064 // fprintf( stderr, "c=%d\n", c );
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2065 cpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
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2066 cpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
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2067 }
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2068
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2069 if( sgap1 )
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2070 {
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2071 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
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2072 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
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2073 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
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2074 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
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2075 outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
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2076 outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
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2077 outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
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2078 outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
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2079 }
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2080 else
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2081 {
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2082 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
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2083 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
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2084 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
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2085 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
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2086 headgapfreq1 = 0.0;
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2087 headgapfreq2 = 0.0;
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2088 gapfreq1[lgth1] = 0.0;
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2089 gapfreq2[lgth2] = 0.0;
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2090 }
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2091
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2092 if( legacygapcost == 0 )
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2093 {
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2094 gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
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2095 gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
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2096 for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
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diff changeset
2097 for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
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diff changeset
2098 headgapfreq1 = 1.0 - headgapfreq1;
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2099 headgapfreq2 = 1.0 - headgapfreq2;
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2100 }
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2101 else
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2102 {
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2103 for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
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2104 for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
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2105 headgapfreq1 = 1.0;
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2106 headgapfreq2 = 1.0;
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2107 }
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2108
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2109 #if 0
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2110 fprintf( stderr, "\ngapfreq1[] =" );
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2111 for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
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2112 fprintf( stderr, "\n" );
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2113
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2114 fprintf( stderr, "\ngapfreq2[] =" );
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2115 for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
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2116 fprintf( stderr, "\n" );
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2117 #endif
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2118
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2119
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2120 for( i=0; i<lgth1; i++ )
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2121 {
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2122 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
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2123 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
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2124 }
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2125
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2126 for( i=0; i<lgth2; i++ )
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2127 {
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2128 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
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2129 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
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2130 }
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2131 #if 0
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2132 for( i=0; i<lgth1; i++ )
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2133 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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2134 #endif
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2135
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2136 currentw = w1;
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2137 previousw = w2;
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2138
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2139 // for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
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2140 // for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[j] = %s\n", seq2[j] );
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2141
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2142 #if MCD
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2143 match_calc_dynamicmtx( pairoffset, n_dynamicmtx, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, *floatwork, *intwork, 1, 1 );
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2144 // for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
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2145 #else
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2146 fillzero( initverticalw, lgth1 );
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2147 for( c=0; c<maxdistclass; c++ )
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2148 {
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2149 // fprintf( stderr, "c=%d matrices[c][W][W] = %f\n", c, matrices[c][amino_n['W']][amino_n['W']] );
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2150 // for( i=0; i<lgth1; i++ ) fprintf( stderr, "seq1[i] = %c, cpmx1s[c][3][%d] = %f\n", seq1[0][i], i, cpmx1s[c][3][i] );
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2151 // for( i=0; i<lgth2; i++ ) fprintf( stderr, "seq2[i] = %c, cpmx2s[c][3][%d] = %f\n", seq2[0][i], i, cpmx2s[c][3][i] );
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2152 match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, floatwork[c], intwork[c], 1 );
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2153 // for( i=0; i<lgth1; i++ ) fprintf( stderr, "c=%d, %d - %f\n", c, i, initverticalw[i] );
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diff changeset
2154 }
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2155 // for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
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2156 #endif
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2157
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2158 // exit( 1 );
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2159
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2160 if( localhom )
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2161 imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
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2162
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2163 #if MCD
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2164 match_calc_dynamicmtx( pairoffset, n_dynamicmtx, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, *floatwork, *intwork, 1, 0 );
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2165 // for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
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2166 // exit( 1 );
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2167 #else
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2168 fillzero( currentw, lgth2 );
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2169 for( c=0; c<maxdistclass; c++ )
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2170 match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], 0, lgth2, floatwork[c], intwork[c], 1 );
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2171 // for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
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2172 // exit( 1 );
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2173 #endif
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2174
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2175 if( localhom )
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2176 imp_match_out_vead( currentw, 0, lgth2 ); // 060306
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2177 #if 0 // -> tbfast.c
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2178 if( localhom )
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2179 imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
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2180
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2181 #endif
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2182
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2183 if( headgp == 1 )
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2184 {
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2185 for( i=1; i<lgth1+1; i++ )
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2186 {
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2187 // initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
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2188 initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
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2189 }
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2190 for( j=1; j<lgth2+1; j++ )
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2191 {
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2192 // currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
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2193 currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
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2194 }
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2195 }
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diff changeset
2196 #if OUTGAP0TRY
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diff changeset
2197 else
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diff changeset
2198 {
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nick
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diff changeset
2199 fprintf( stderr, "offset = %d\n", offset );
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nick
parents:
diff changeset
2200 for( j=1; j<lgth2+1; j++ )
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nick
parents:
diff changeset
2201 currentw[j] -= offset * j / 2.0;
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nick
parents:
diff changeset
2202 for( i=1; i<lgth1+1; i++ )
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nick
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diff changeset
2203 initverticalw[i] -= offset * i / 2.0;
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diff changeset
2204 }
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diff changeset
2205 #endif
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diff changeset
2206 #if 0
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diff changeset
2207 fprintf( stderr, "\n " );
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nick
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diff changeset
2208 for( j=0; j<lgth2+1; j++ ) fprintf( stderr, " %c ", seq2[0][j] );
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nick
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diff changeset
2209 fprintf( stderr, "\n%c ", seq1[0][0] );
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nick
parents:
diff changeset
2210 for( j=0; j<lgth2+1; j++ )
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diff changeset
2211 {
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diff changeset
2212 fprintf( stderr, "%5.0f ", currentw[j] );
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diff changeset
2213 }
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diff changeset
2214 fprintf( stderr, "\n" );
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diff changeset
2215 #endif
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diff changeset
2216
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diff changeset
2217
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diff changeset
2218 for( j=1; j<lgth2+1; ++j )
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diff changeset
2219 {
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diff changeset
2220 // m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
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parents:
diff changeset
2221 m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
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diff changeset
2222 }
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2223 if( lgth2 == 0 )
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nick
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diff changeset
2224 lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
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diff changeset
2225 else
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nick
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diff changeset
2226 lastverticalw[0] = currentw[lgth2-1];
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diff changeset
2227
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diff changeset
2228 if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
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nick
parents:
diff changeset
2229 lastj = lgth2+1;
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diff changeset
2230
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diff changeset
2231 #if XXXXXXX
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nick
parents:
diff changeset
2232 fprintf( stderr, "currentw = \n" );
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nick
parents:
diff changeset
2233 for( i=0; i<lgth1+1; i++ )
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diff changeset
2234 {
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nick
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diff changeset
2235 fprintf( stderr, "%5.2f ", currentw[i] );
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diff changeset
2236 }
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nick
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diff changeset
2237 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
2238 fprintf( stderr, "initverticalw = \n" );
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nick
parents:
diff changeset
2239 for( i=0; i<lgth2+1; i++ )
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diff changeset
2240 {
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diff changeset
2241 fprintf( stderr, "%5.2f ", initverticalw[i] );
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diff changeset
2242 }
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diff changeset
2243 fprintf( stderr, "\n" );
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parents:
diff changeset
2244 fprintf( stderr, "fcgp\n" );
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nick
parents:
diff changeset
2245 for( i=0; i<lgth1; i++ )
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nick
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diff changeset
2246 fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
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nick
parents:
diff changeset
2247 for( i=0; i<lgth2; i++ )
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nick
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diff changeset
2248 fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
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diff changeset
2249 #endif
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diff changeset
2250
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diff changeset
2251 for( i=1; i<lasti; i++ )
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diff changeset
2252 {
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nick
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diff changeset
2253
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diff changeset
2254 #ifdef enablemultithread
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nick
parents:
diff changeset
2255 // fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
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nick
parents:
diff changeset
2256 if( chudanpt && *chudanpt != chudanref )
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diff changeset
2257 {
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nick
parents:
diff changeset
2258 // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
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nick
parents:
diff changeset
2259 *chudanres = 1;
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nick
parents:
diff changeset
2260 return( -1.0 );
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diff changeset
2261 }
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parents:
diff changeset
2262 #endif
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nick
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diff changeset
2263 wtmp = previousw;
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nick
parents:
diff changeset
2264 previousw = currentw;
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nick
parents:
diff changeset
2265 currentw = wtmp;
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parents:
diff changeset
2266
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diff changeset
2267 previousw[0] = initverticalw[i-1];
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parents:
diff changeset
2268
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diff changeset
2269 #if MCD
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nick
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diff changeset
2270 match_calc_dynamicmtx( pairoffset, n_dynamicmtx, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, *floatwork, *intwork, 0, 0 );
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diff changeset
2271 #else
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diff changeset
2272 fillzero( currentw, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2273 for( c=0; c<maxdistclass; c++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2274 match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], i, lgth2, floatwork[c], intwork[c], 0 );
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diff changeset
2275 #endif
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diff changeset
2276 #if 0
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diff changeset
2277 if( i == 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2278 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2279 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2280 for( j=0; j<lgth2; j++ ) fprintf( stderr, "%d - %f\n", j, currentw[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2281 exit( 1 );
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diff changeset
2282 }
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diff changeset
2283 #endif
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diff changeset
2284
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diff changeset
2285 #if XXXXXXX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2286 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2287 fprintf( stderr, "i=%d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2288 fprintf( stderr, "currentw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2289 for( j=0; j<lgth2; j++ )
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2290 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2291 fprintf( stderr, "%5.2f ", currentw[j] );
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diff changeset
2292 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2293 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2294 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2295 if( localhom )
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parents:
diff changeset
2296 {
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diff changeset
2297 // fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
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parents:
diff changeset
2298 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2299 imp_match_out_vead( currentw, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2300 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
2301 imp_match_out_vead( currentw, i, lgth2 );
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parents:
diff changeset
2302 #endif
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nick
parents:
diff changeset
2303 }
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diff changeset
2304 #if XXXXXXX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
2305 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2306 fprintf( stderr, "i=%d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2307 fprintf( stderr, "currentw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2308 for( j=0; j<lgth2; j++ )
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diff changeset
2309 {
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nick
parents:
diff changeset
2310 fprintf( stderr, "%5.2f ", currentw[j] );
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nick
parents:
diff changeset
2311 }
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nick
parents:
diff changeset
2312 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
2313 #endif
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nick
parents:
diff changeset
2314 currentw[0] = initverticalw[i];
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nick
parents:
diff changeset
2315
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nick
parents:
diff changeset
2316 #if 0
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nick
parents:
diff changeset
2317 fprintf( stderr, "%c ", seq1[0][i] );
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nick
parents:
diff changeset
2318 for( j=0; j<lgth2+1; j++ )
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nick
parents:
diff changeset
2319 {
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nick
parents:
diff changeset
2320 fprintf( stderr, "%5.0f ", currentw[j] );
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diff changeset
2321 }
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nick
parents:
diff changeset
2322 fprintf( stderr, "\n" );
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parents:
diff changeset
2323 #endif
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nick
parents:
diff changeset
2324
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nick
parents:
diff changeset
2325 // mi = previousw[0] + ogcp2[1]; mpi = 0;
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nick
parents:
diff changeset
2326 mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
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nick
parents:
diff changeset
2327 ijppt = ijp[i] + 1;
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nick
parents:
diff changeset
2328 mjpt = m + 1;
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nick
parents:
diff changeset
2329 prept = previousw;
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nick
parents:
diff changeset
2330 curpt = currentw + 1;
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nick
parents:
diff changeset
2331 mpjpt = mp + 1;
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nick
parents:
diff changeset
2332 fgcp2pt = fgcp2;
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nick
parents:
diff changeset
2333 ogcp2pt = ogcp2 + 1;
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nick
parents:
diff changeset
2334 fgcp1va = fgcp1[i-1];
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nick
parents:
diff changeset
2335 ogcp1va = ogcp1[i];
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nick
parents:
diff changeset
2336 gf1va = gapfreq1[i];
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nick
parents:
diff changeset
2337 gf1vapre = gapfreq1[i-1];
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nick
parents:
diff changeset
2338 gf2pt = gapfreq2+1;
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nick
parents:
diff changeset
2339 gf2ptpre = gapfreq2;
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nick
parents:
diff changeset
2340
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nick
parents:
diff changeset
2341 if( trywarp )
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parents:
diff changeset
2342 {
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nick
parents:
diff changeset
2343 prevwmrecordspt = prevwmrecords;
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nick
parents:
diff changeset
2344 wmrecordspt = wmrecords+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2345 wmrecords1pt = wmrecords;
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nick
parents:
diff changeset
2346 warpipt = warpi + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2347 warpjpt = warpj + 1;
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nick
parents:
diff changeset
2348 }
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nick
parents:
diff changeset
2349
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nick
parents:
diff changeset
2350 for( j=1; j<lastj; j++ )
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nick
parents:
diff changeset
2351 {
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nick
parents:
diff changeset
2352 #ifdef xxxenablemultithread
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nick
parents:
diff changeset
2353 // fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
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nick
parents:
diff changeset
2354 if( chudanpt && *chudanpt != chudanref )
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nick
parents:
diff changeset
2355 {
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nick
parents:
diff changeset
2356 // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
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nick
parents:
diff changeset
2357 *chudanres = 1;
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nick
parents:
diff changeset
2358 return( -1.0 );
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nick
parents:
diff changeset
2359 }
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nick
parents:
diff changeset
2360 #endif
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nick
parents:
diff changeset
2361 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2362 *ijppt = 0;
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nick
parents:
diff changeset
2363
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nick
parents:
diff changeset
2364 #if 0
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nick
parents:
diff changeset
2365 fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2366 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2367 fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2368 #endif
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nick
parents:
diff changeset
2369 if( (g=mi+*fgcp2pt*gf1va) > wm )
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nick
parents:
diff changeset
2370 {
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nick
parents:
diff changeset
2371 wm = g;
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nick
parents:
diff changeset
2372 *ijppt = -( j - mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2373 // fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
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parents:
diff changeset
2374 }
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parents:
diff changeset
2375 if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
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nick
parents:
diff changeset
2376 {
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nick
parents:
diff changeset
2377 mi = g;
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nick
parents:
diff changeset
2378 mpi = j-1;
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nick
parents:
diff changeset
2379 }
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nick
parents:
diff changeset
2380 #if USE_PENALTY_EX
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nick
parents:
diff changeset
2381 mi += fpenalty_ex;
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nick
parents:
diff changeset
2382 #endif
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nick
parents:
diff changeset
2383
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nick
parents:
diff changeset
2384 #if 0
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nick
parents:
diff changeset
2385 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2386 fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
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parents:
diff changeset
2387 #endif
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nick
parents:
diff changeset
2388 if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
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nick
parents:
diff changeset
2389 {
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nick
parents:
diff changeset
2390 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2391 *ijppt = +( i - *mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2392 // fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
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parents:
diff changeset
2393 }
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nick
parents:
diff changeset
2394 if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2395 {
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nick
parents:
diff changeset
2396 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2397 *mpjpt = i-1;
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nick
parents:
diff changeset
2398 }
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nick
parents:
diff changeset
2399 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2400 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2401 #endif
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nick
parents:
diff changeset
2402 if( trywarp )
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nick
parents:
diff changeset
2403 {
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nick
parents:
diff changeset
2404 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2405 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2406 #else
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nick
parents:
diff changeset
2407 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2408 #endif
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nick
parents:
diff changeset
2409 {
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nick
parents:
diff changeset
2410 if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2411 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2412 *ijppt = warpbase + warpn - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2413 }
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nick
parents:
diff changeset
2414 else
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nick
parents:
diff changeset
2415 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2416 *ijppt = warpbase + warpn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2417 warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2418 warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2419 warpis[warpn] = prevwarpi[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2420 warpjs[warpn] = prevwarpj[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2421 warpn++;
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nick
parents:
diff changeset
2422 }
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nick
parents:
diff changeset
2423 wm = g;
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nick
parents:
diff changeset
2424 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2425 curm = *curpt + wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2426
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2427 if( *wmrecords1pt > *wmrecordspt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2428 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2429 *wmrecordspt = *wmrecords1pt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2430 *warpipt = *(warpipt-1);
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2431 *warpjpt = *(warpjpt-1);
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2432 }
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nick
parents:
diff changeset
2433 if( curm > *wmrecordspt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2434 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2435 *wmrecordspt = curm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2436 *warpipt = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2437 *warpjpt = j;
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nick
parents:
diff changeset
2438 }
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nick
parents:
diff changeset
2439 wmrecordspt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2440 wmrecords1pt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2441 warpipt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2442 warpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2443 }
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nick
parents:
diff changeset
2444
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nick
parents:
diff changeset
2445 #if 0
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nick
parents:
diff changeset
2446 fprintf( stderr, "%5.0f ", wm );
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nick
parents:
diff changeset
2447 #endif
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nick
parents:
diff changeset
2448 *curpt++ += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2449 ijppt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2450 mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2451 prept++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2452 mpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2453 fgcp2pt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2454 ogcp2pt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2455 gf2ptpre++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2456 gf2pt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2457
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2458 }
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nick
parents:
diff changeset
2459 lastverticalw[i] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2460
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2461 if( trywarp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2462 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2463 fltncpy( prevwmrecords, wmrecords, lastj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2464 intncpy( prevwarpi, warpi, lastj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2465 intncpy( prevwarpj, warpj, lastj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2466 }
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nick
parents:
diff changeset
2467 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2468 if( trywarp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2469 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2470 // fprintf( stderr, "wm = %f\n", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2471 // fprintf( stderr, "warpn = %d\n", warpn );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2472 free( wmrecords );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2473 free( prevwmrecords );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2474 free( warpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2475 free( warpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2476 free( prevwarpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2477 free( prevwarpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2478 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2479
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2480
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2481 #if OUTGAP0TRY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2482 if( !outgap )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2483 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2484 for( j=1; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2485 currentw[j] -= offset * ( lgth2 - j ) / 2.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2486 for( i=1; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2487 lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2488 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2489 #endif
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nick
parents:
diff changeset
2490
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2491 /*
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2492 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2493 for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2494 fprintf( stderr, "#####\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2495 for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2496 fprintf( stderr, "====>" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2497 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2498 for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2499 */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2500 if( localhom )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2501 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2502 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2503 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2504 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2505 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2506
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2507 if( warpis ) free( warpis );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2508 if( warpjs ) free( warpjs );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2509
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2510 // fprintf( stderr, "### impmatch = %f\n", *impmatch );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2511
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2512 resultlen = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2513 if( alloclen < resultlen || resultlen > N )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2514 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2515 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2516 ErrorExit( "LENGTH OVER!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2517 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2518
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2519
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2520 for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2521 for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2522 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2523 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2524 for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2525 fprintf( stderr, "#####\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2526 for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2527 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2528
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2529 // fprintf( stderr, "wm = %f\n", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2530
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2531 return( wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2532 }