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annotate mafft/core/suboptalign11.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2 #include "dp.h"
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3
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4 #define DEBUG 0
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5 #define DEBUG2 0
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6 #define XXXXXXX 0
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7 #define USE_PENALTY_EX 1
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8
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9 typedef struct _shuryoten
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10 {
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11 int i;
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12 int j;
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13 float wm;
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14 struct _shuryoten *next;
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15 struct _shuryoten *prev;
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16 } Shuryoten;
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17
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18
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19 static int localstop;
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20
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21 static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
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22 {
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23 Shuryoten *s1 = (Shuryoten *)s1_arg;
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24 Shuryoten *s2 = (Shuryoten *)s2_arg;
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25 if ( s1->wm > s2->wm ) return( -1 );
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26 else if ( s1->wm < s2->wm ) return( 1 );
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27 else return( 0 );
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28 }
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29
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30 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
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31 {
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32 int j;
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33
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34 for( j=0; j<lgth2; j++ )
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35 match[j] = amino_dis[(int)(*s1)[i1]][(int)(*s2)[j]];
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36 }
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37
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38 static float gentracking( int **used,
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39 char **seq1, char **seq2,
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40 char **mseq1, char **mseq2,
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41 float **cpmx1, float **cpmx2,
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42 int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
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43 {
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44 int l, iin, jin, lgth1, lgth2, k, limk;
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45 int ifi=0, jfi=0;
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46 // char gap[] = "-";
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47 char *gap;
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48 gap = newgapstr;
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49 static char *res1 = NULL, *res2 = NULL;
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50 char *mspt1, *mspt2;
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51 if( res1 == NULL )
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52 {
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53 res1 = (char *)calloc( N, sizeof( char ) );
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54 res2 = (char *)calloc( N, sizeof( char ) );
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55 }
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56
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57 lgth1 = strlen( seq1[0] );
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58 lgth2 = strlen( seq2[0] );
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59
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60 mspt1 = res1 + lgth1+lgth2;
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61 *mspt1 = 0;
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62 mspt2 = res2 + lgth1+lgth2;
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63 *mspt2 = 0;
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64 iin = endi; jin = endj;
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65
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66 limk = lgth1+lgth2;
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67 if( used[iin][jin] ) return( -1.0 );
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68 for( k=0; k<=limk; k++ )
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69 {
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70 ifi = ( ijpi[iin][jin] );
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71 jfi = ( ijpj[iin][jin] );
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72
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73 if( used[ifi][jfi] ) return( -1.0 );
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74
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75 l = iin - ifi;
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76 while( --l )
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77 {
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78 *--mspt1 = seq1[0][ifi+l];
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79 *--mspt2 = *gap;
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80 k++;
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81 }
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82 l= jin - jfi;
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83 while( --l )
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84 {
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85 *--mspt1 = *gap;
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86 *--mspt2 = seq2[0][jfi+l];
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87 k++;
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88 }
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89
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90 if( iin <= 0 || jin <= 0 ) break;
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91 *--mspt1 = seq1[0][ifi];
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92 *--mspt2 = seq2[0][jfi];
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93 if( ijpi[ifi][jfi] == localstop ) break;
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94 if( ijpj[ifi][jfi] == localstop ) break;
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95 k++;
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96 iin = ifi; jin = jfi;
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97 }
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98 if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
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99 if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
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100
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101 // fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
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102
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103 iin = endi; jin = endj;
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104 limk = lgth1+lgth2;
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105 for( k=0; k<=limk; k++ )
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106 {
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107 ifi = ( ijpi[iin][jin] );
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108 jfi = ( ijpj[iin][jin] );
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109
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110 used[ifi][jfi] = 1;
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111 if( iin <= 0 || jin <= 0 ) break;
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112 if( ijpi[ifi][jfi] == localstop ) break;
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113 if( ijpj[ifi][jfi] == localstop ) break;
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114
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115 k++;
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116 iin = ifi; jin = jfi;
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117 }
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118
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119
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120 strcpy( mseq1[0], mspt1 );
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121 strcpy( mseq2[0], mspt2 );
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122
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123 fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
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124
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125 return( 0.0 );
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126 }
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127
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128
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129 float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
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130 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
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131 {
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132 int k;
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133 static int **used;
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134 register int i, j;
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135 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
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136 int lgth1, lgth2;
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137 int resultlen;
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138 float wm = 0.0; // by D.Mathog,
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139 float g;
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140 float *currentw, *previousw;
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141 #if 1
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142 float *wtmp;
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143 int *ijpipt;
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144 int *ijpjpt;
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145 float *mjpt, *Mjpt, *prept, *curpt;
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146 int *mpjpt, *Mpjpt;
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147 #endif
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148 static float mi, *m;
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149 static float Mi, *largeM;
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150 static int **ijpi;
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151 static int **ijpj;
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152 static int mpi, *mp;
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153 static int Mpi, *Mp;
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154 static float *w1, *w2;
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155 // static float *match;
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156 static float *initverticalw; /* kufuu sureba iranai */
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157 static float *lastverticalw; /* kufuu sureba iranai */
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158 static char **mseq1;
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159 static char **mseq2;
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160 static float **cpmx1;
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161 static float **cpmx2;
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162 static int **intwork;
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163 static float **floatwork;
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164 static int orlgth1 = 0, orlgth2 = 0;
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165 float maxwm;
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166 float tbk;
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167 int tbki, tbkj;
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168 int endali, endalj;
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169 // float localthr = 0.0;
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170 // float localthr2 = 0.0;
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171 float fpenalty = (float)penalty;
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172 float fpenalty_OP = (float)penalty_OP;
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173 float fpenalty_ex = (float)penalty_ex;
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174 // float fpenalty_EX = (float)penalty_EX;
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175 float foffset = (float)offset;
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176 float localthr = -foffset;
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177 float localthr2 = -foffset;
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178 static Shuryoten *shuryo = NULL;
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179 int numshuryo;
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180 float minshuryowm = 0.0; // by D.Mathog
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181 int minshuryopos = 0; // by D.Mathog
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182 float resf;
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183
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184
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185 // fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
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186
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187 fprintf( stderr, "in suboptalign11\n" );
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188 if( !shuryo )
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189 {
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190 shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
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191 }
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192 for( i=0; i<100; i++ )
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193 {
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194 shuryo[i].i = -1;
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195 shuryo[i].j = -1;
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196 shuryo[i].wm = 0.0;
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197 }
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198 numshuryo = 0;
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199
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200 if( orlgth1 == 0 )
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201 {
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202 }
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203
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204
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205 lgth1 = strlen( seq1[0] );
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206 lgth2 = strlen( seq2[0] );
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207
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208 fprintf( stderr, "in suboptalign11 step 1\n" );
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209
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210 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
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211 {
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212 int ll1, ll2;
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213
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214 fprintf( stderr, "in suboptalign11 step 1.3\n" );
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215 if( orlgth1 > 0 && orlgth2 > 0 )
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216 {
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217 fprintf( stderr, "in suboptalign11 step 1.4\n" );
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218 FreeFloatVec( w1 );
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219 FreeFloatVec( w2 );
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220 // FreeFloatVec( match );
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221 FreeFloatVec( initverticalw );
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222 FreeFloatVec( lastverticalw );
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223 fprintf( stderr, "in suboptalign11 step 1.5\n" );
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224
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225 FreeFloatVec( m );
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226 FreeIntVec( mp );
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227 FreeFloatVec( largeM );
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228 FreeIntVec( Mp );
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229 fprintf( stderr, "in suboptalign11 step 1.6\n" );
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230
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231
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232 FreeFloatMtx( cpmx1 );
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233 FreeFloatMtx( cpmx2 );
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234
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235 fprintf( stderr, "in suboptalign11 step 1.7\n" );
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236 FreeFloatMtx( floatwork );
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237 FreeIntMtx( intwork );
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238 }
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239
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240 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
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241 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
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242
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243 #if DEBUG
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244 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
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245 #endif
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246
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247 w1 = AllocateFloatVec( ll2+2 );
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248 w2 = AllocateFloatVec( ll2+2 );
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249 // match = AllocateFloatVec( ll2+2 );
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250
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251 initverticalw = AllocateFloatVec( ll1+2 );
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252 lastverticalw = AllocateFloatVec( ll1+2 );
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253
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254 m = AllocateFloatVec( ll2+2 );
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255 mp = AllocateIntVec( ll2+2 );
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256 largeM = AllocateFloatVec( ll2+2 );
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257 Mp = AllocateIntVec( ll2+2 );
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258
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259 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
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260 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
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261
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262 floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
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263 intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
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264
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265 mseq1 = AllocateCharMtx( njob, ll1+ll2 );
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266 mseq2 = AllocateCharMtx( njob, ll1+ll2 );
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267
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268 #if DEBUG
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269 fprintf( stderr, "succeeded\n" );
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270 #endif
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271
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272 orlgth1 = ll1 - 100;
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273 orlgth2 = ll2 - 100;
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274 }
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275 fprintf( stderr, "in suboptalign11 step 1.6\n" );
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276
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277
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278
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279 fprintf( stderr, "in suboptalign11 step 2\n" );
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280
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281 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
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282 {
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283 int ll1, ll2;
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284
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285 if( commonAlloc1 && commonAlloc2 )
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286 {
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287 FreeIntMtx( commonIP );
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288 FreeIntMtx( commonJP );
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289 FreeIntMtx( used );
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290 }
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291
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292 ll1 = MAX( orlgth1, commonAlloc1 );
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293 ll2 = MAX( orlgth2, commonAlloc2 );
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294
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295 #if DEBUG
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296 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
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297 #endif
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298
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299 used = AllocateIntMtx( ll1+10, ll2+10 );
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300 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
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301 commonJP = AllocateIntMtx( ll1+10, ll2+10 );
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302
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303 #if DEBUG
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304 fprintf( stderr, "succeeded\n\n" );
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305 #endif
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306
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307 commonAlloc1 = ll1;
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308 commonAlloc2 = ll2;
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309 }
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310 ijpi = commonIP;
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311 ijpj = commonJP;
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312
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313
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314 #if 0
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315 for( i=0; i<lgth1; i++ )
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316 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
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317 #endif
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318
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319 fprintf( stderr, "in suboptalign11 step 3\n" );
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320 currentw = w1;
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321 previousw = w2;
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322
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323 match_calc( initverticalw, seq2, seq1, 0, lgth1 );
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324
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325 match_calc( currentw, seq1, seq2, 0, lgth2 );
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326
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327
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328 lasti = lgth2+1;
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329 for( j=1; j<lasti; ++j )
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330 {
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331 m[j] = currentw[j-1]; mp[j] = 0;
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332 largeM[j] = currentw[j-1]; Mp[j] = 0;
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333 }
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334
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335 lastverticalw[0] = currentw[lgth2-1];
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336
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337
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338 #if 0
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339 fprintf( stderr, "currentw = \n" );
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340 for( i=0; i<lgth1+1; i++ )
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341 {
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342 fprintf( stderr, "%5.2f ", currentw[i] );
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343 }
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344 fprintf( stderr, "\n" );
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345 fprintf( stderr, "initverticalw = \n" );
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346 for( i=0; i<lgth2+1; i++ )
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347 {
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348 fprintf( stderr, "%5.2f ", initverticalw[i] );
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349 }
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350 fprintf( stderr, "\n" );
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351 #endif
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352 #if DEBUG2
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353 fprintf( stderr, "\n" );
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354 fprintf( stderr, " " );
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355 for( j=0; j<lgth2+1; j++ )
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356 fprintf( stderr, "%c ", seq2[0][j] );
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357 fprintf( stderr, "\n" );
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358 #endif
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359
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360 localstop = lgth1+lgth2+1;
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361 maxwm = -999.9;
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362 endali = endalj = 0;
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363 #if DEBUG2
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364 fprintf( stderr, "\n" );
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365 fprintf( stderr, "%c ", seq1[0][0] );
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366
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367 for( j=0; j<lgth2+1; j++ )
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368 fprintf( stderr, "%5.0f ", currentw[j] );
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369 fprintf( stderr, "\n" );
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370 #endif
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371
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372 lasti = lgth1+1;
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373 for( i=1; i<lasti; i++ )
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374 {
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375 wtmp = previousw;
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376 previousw = currentw;
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377 currentw = wtmp;
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378
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379 previousw[0] = initverticalw[i-1];
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380
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381 match_calc( currentw, seq1, seq2, i, lgth2 );
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382 #if DEBUG2
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383 fprintf( stderr, "%c ", seq1[0][i] );
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384 fprintf( stderr, "%5.0f ", currentw[0] );
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385 #endif
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386
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387 #if XXXXXXX
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388 fprintf( stderr, "\n" );
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389 fprintf( stderr, "i=%d\n", i );
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390 fprintf( stderr, "currentw = \n" );
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391 for( j=0; j<lgth2; j++ )
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392 {
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393 fprintf( stderr, "%5.2f ", currentw[j] );
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394 }
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395 fprintf( stderr, "\n" );
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396 #endif
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397 #if XXXXXXX
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398 fprintf( stderr, "\n" );
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399 fprintf( stderr, "i=%d\n", i );
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400 fprintf( stderr, "currentw = \n" );
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401 for( j=0; j<lgth2; j++ )
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402 {
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403 fprintf( stderr, "%5.2f ", currentw[j] );
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404 }
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405 fprintf( stderr, "\n" );
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406 #endif
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407 currentw[0] = initverticalw[i];
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408
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409 mi = previousw[0]; mpi = 0;
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410 Mi = previousw[0]; Mpi = 0;
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411
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412 #if 0
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413 if( mi < localthr ) mi = localthr2;
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414 #endif
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415
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416 ijpipt = ijpi[i] + 1;
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417 ijpjpt = ijpj[i] + 1;
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418 mjpt = m + 1;
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419 Mjpt = largeM + 1;
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420 prept = previousw;
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421 curpt = currentw + 1;
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422 mpjpt = mp + 1;
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423 Mpjpt = Mp + 1;
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424 tbk = -999999.9;
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425 tbki = 0;
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426 tbkj = 0;
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427 lastj = lgth2+1;
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428 for( j=1; j<lastj; j++ )
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429 {
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430 wm = *prept;
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431 *ijpipt = i-1;
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432 *ijpjpt = j-1;
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433
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434
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435 // fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
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436 // fprintf( stderr, "wm=%f\n", wm );
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437 #if 0
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438 fprintf( stderr, "%5.0f->", wm );
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439 #endif
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440 g = mi + fpenalty;
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441 #if 0
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442 fprintf( stderr, "%5.0f?", g );
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443 #endif
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444 if( g > wm )
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445 {
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446 wm = g;
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447 // *ijpipt = i - 1;
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448 *ijpjpt = mpi;
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449 }
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450 g = *prept;
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451 if( g > mi )
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452 {
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453 mi = g;
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454 mpi = j-1;
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455 }
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456
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457 #if USE_PENALTY_EX
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458 mi += fpenalty_ex;
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459 #endif
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460
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461 #if 0
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462 fprintf( stderr, "%5.0f->", wm );
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463 #endif
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464 g = *mjpt + fpenalty;
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465 #if 0
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466 fprintf( stderr, "m%5.0f?", g );
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467 #endif
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468 if( g > wm )
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469 {
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470 wm = g;
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471 *ijpipt = *mpjpt;
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472 // *ijpjpt = j - 1;
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473 }
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474 g = *prept;
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475 if( g > *mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
476 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
477 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
478 *mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
479 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
480 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
481 *mjpt += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
482 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
483
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
484
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
485 g = tbk + fpenalty_OP;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
486 // g = tbk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
487 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
488 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
489 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
490 *ijpipt = tbki;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
491 *ijpjpt = tbkj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
492 // fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
493 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
494 g = Mi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
495 if( g > tbk )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
496 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
497 tbk = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
498 tbki = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
499 tbkj = Mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
500 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
501 g = *Mjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
502 if( g > tbk )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
503 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
504 tbk = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
505 tbki = *Mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
506 tbkj = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
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507 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
508 // tbk += fpenalty_EX;// + foffset;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
509
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
510 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
511 if( g > *Mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
512 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
513 *Mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
514 *Mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
515 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
516 // *Mjpt += fpenalty_EX;// + foffset;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
517
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
518 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
519 if( g > Mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
520 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
521 Mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
522 Mpi = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
523 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
524 // Mi += fpenalty_EX;// + foffset;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
525
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
526
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
527 // fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
528 // fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
529
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
530
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
531 if( maxwm < wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
532 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
533 maxwm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
534 endali = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
535 endalj = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
536 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
537
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
538 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
539 if( numshuryo < 100 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
540 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
541 shuryo[numshuryo].i = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
542 shuryo[numshuryo].j = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
543 shuryo[numshuryo].wm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
544
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
545 if( minshuryowm > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
546 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
547 minshuryowm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
548 minshuryopos = numshuryo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
549 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
550 numshuryo++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
551 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
552 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
553 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
554 if( wm > minshuryowm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
555 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
556 shuryo[minshuryopos].i = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
557 shuryo[minshuryopos].j = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
558 shuryo[minshuryopos].wm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
559 minshuryowm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
560 for( k=0; k<100; k++ ) // muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
561 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
562 if( shuryo[k].wm < minshuryowm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
563 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
564 minshuryowm = shuryo[k].wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
565 minshuryopos = k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
566 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
567 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
568 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
569 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
570 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
571 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
572 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
573 if( wm < localthr )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
574 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
575 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
576 *ijpipt = localstop;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
577 // *ijpjpt = localstop;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
578 wm = localthr2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
579 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
580 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
581 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
582 fprintf( stderr, "%5.0f ", *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
583 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
584 #if DEBUG2
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
585 fprintf( stderr, "%5.0f ", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
586 // fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
587 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
588
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
589 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
590 ijpipt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
591 ijpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
592 mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
593 Mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
594 prept++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
595 mpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
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596 Mpjpt++;
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597 curpt++;
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598 }
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599 #if DEBUG2
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600 fprintf( stderr, "\n" );
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601 #endif
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602
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603 lastverticalw[i] = currentw[lgth2-1];
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604 }
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605
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606 for( k=0; k<100; k++ )
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607 {
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608 fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
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609 }
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610
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611
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612 #if 1
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613 fprintf( stderr, "maxwm = %f\n", maxwm );
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614 fprintf( stderr, "endali = %d\n", endali );
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615 fprintf( stderr, "endalj = %d\n", endalj );
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616 #endif
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617
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618 qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
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619 for( k=0; k<100; k++ )
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620 {
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621 fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
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622 }
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623
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624
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625 lasti = lgth1+1;
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626 for( i=0; i<lasti; i++ )
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627 {
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628 ijpi[i][0] = localstop;
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629 ijpj[i][0] = localstop;
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630 }
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631 lastj = lgth2+1;
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632 for( j=0; j<lastj; j++ )
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633 {
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634 ijpi[0][j] = localstop;
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635 ijpj[0][j] = localstop;
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636 }
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637
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638 for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
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639
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640 for( k=0; k<numshuryo; k++ )
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641 {
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642 if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
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643 fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
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644 resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
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645 if( resf == -1.0 ) continue;
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646 putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
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647 #if 0
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648 fprintf( stderr, "\n" );
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649 fprintf( stderr, ">\n%s\n", mseq1[0] );
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650 fprintf( stderr, ">\n%s\n", mseq2[0] );
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651 #endif
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652 }
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653 for( i=0; i<20; i++ )
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654 {
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655 for( j=0; j<20; j++ )
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656 {
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657 fprintf( stderr, "%2d ", used[i][j] );
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658 }
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659 fprintf( stderr, "\n" );
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660 }
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661
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662
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663 // fprintf( stderr, "### impmatch = %f\n", *impmatch );
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664
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665 resultlen = strlen( mseq1[0] );
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666 if( alloclen < resultlen || resultlen > N )
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667 {
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668 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
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669 ErrorExit( "LENGTH OVER!\n" );
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670 }
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671
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672
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673
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674
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675
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676 return( wm );
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677 }
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678