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annotate mafft/core/iteration.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 /* iteration ( algorithm C ) */
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2 #include "mltaln.h"
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3
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4 #define DEBUG 0
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5
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6 static void Writeoptions( FILE *fp )
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7 {
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8 if( scoremtx == 1 )
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9 fprintf( fp, "Dayhoff( ... )\n" );
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10 else if( scoremtx == -1 )
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11 fprintf( fp, "DNA\n" );
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12 else if( scoremtx == 2 )
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13 fprintf( fp, "Miyata-Yasunaga\n" );
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14 else
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15 fprintf( fp, "JTT %dPAM\n", pamN );
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16
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17 if( scoremtx == 0 )
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18 fprintf( fp, "Gap Penalty = %+d, %+d\n", penalty, offset );
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19 else
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20 fprintf( fp, "Gap Penalty = %+d\n", penalty );
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21
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22 fprintf( fp, "marginal score to search : best - %f\n", cut );
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23 if( scmtd == 3 )
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24 fprintf( fp, "score of rnd or sco\n" );
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25 else if( scmtd == 4 )
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26 fprintf( fp, "score = sigma( score for a pair of homologous amino acids ) / ( number of amino acids pairs )\n" );
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27 else if( scmtd == 5 )
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28 fprintf( fp, "score : SP\n" );
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29 if( mix )
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30 fprintf( fp, "?\n" );
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31 else
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32 {
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33 if( weight == 2 )
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34 fprintf( fp, "weighted, geta2 = %f\n", geta2 );
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35 else if( weight == 3 )
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36 {
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37 if( scmtd == 4 )
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38 fprintf( fp, "reversely weighted in function 'align', unweighted in function 'score_calc'\n" );
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39 else
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40 fprintf( fp, "weighted like ClustalW," );
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41 }
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42 else
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43 fprintf( fp, "unweighted\n" );
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44 }
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45 if( weight && utree )
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46 {
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47 fprintf( fp, "using tree defined by the file hat2 with simplified UPG method\n" );
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48 }
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49 if( weight && !utree )
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50 fprintf( fp, "using temporary tree by simplified UPG method\n" );
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51 fprintf( fp, "Algorithm %c\n", alg );
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52 }
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53
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54
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55
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56
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57 char **align0( float *wm, char **aseq, char *seq, double effarr[M], int icyc, int ex )
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58 {
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59 char **result;
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60
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61 if( alg == 'B' )
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62 {
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63 ErrorExit( "Sorry!" );
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64 /*
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65 if( outgap == 0 )
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66 {
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67 result = alignm1_o( wm, aseq, seq, scmx, effarr, icyc, ex );
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68 }
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69 if( outgap == 1 )
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70 {
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71 result = alignm1( wm, aseq, seq, scmx, effarr, icyc, ex );
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72 }
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73 */
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74 }
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75 else if( alg == 'C' )
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76 {
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77 result = Calignm1( wm, aseq, seq, effarr, icyc, ex );
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78 }
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79 return( result );
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80 }
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81
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82
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83 double score_m_1_0( char **aseq, int locnjob, int s, double **eff, double effarr[M] )
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84 {
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85 double x;
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86
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87 if( alg == 'B' )
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88 {
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89 ErrorExit( "Sorry!" );
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90 }
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91 if( alg == 'C' )
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92 {
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93 x = Cscore_m_1( aseq, locnjob, s, eff );
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94 }
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95 fprintf( stderr, "in score_m_1_0 %f\n", x );
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96 return( x );
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97 }
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98
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99 int iteration( int locnjob, char name[M][B], int nlen[M], char **aseq, char **bseq, int ***topol, double **len, double **eff )
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100 {
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101 double tscore, mscore;
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102 int identity;
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103 static char *mseq1, **mseq2 = NULL;
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104 static char **result;
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105 int i, l;
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106 static double effarr[M];
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107 int s;
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108 int sss[2];
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109 char ou;
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110 int alloclen;
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111 int resultlen;
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112 int nlenmax0 = nlenmax;
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113 FILE *prep;
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114 char sai[M];
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115 char sai1[M];
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116 char sai2[M];
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117 #if 0
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118 double his[2][M][MAXITERATION/locnjob+1];
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119 #else
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120 double ***his;
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121 #endif
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122 int cyc[2];
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123 char shindou = 0;
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124 float wm;
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125 int returnvalue;
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126
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127 for( i=0; i<locnjob; i++ )
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128 {
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129 sai[i] = 1;
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130 sai1[i] = 1;
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131 sai2[i] = 2;
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132 }
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133 sai[locnjob] = sai1[locnjob] = sai2[locnjob] = 0;
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134
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135
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136 Writeoptions( trap_g );
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137
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138 his = AllocateDoubleCub( 2, M, MAXITERATION/locnjob+1 );
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139
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140 if( mseq2 == NULL )
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141 {
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142 alloclen = nlenmax * 2.0;
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143 AllocateTmpSeqs( &mseq2, &mseq1, alloclen );
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144 }
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145
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146 if( !tbitr && !tbweight )
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147 {
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148 writePre( locnjob, name, nlen, aseq, 0 );
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149
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150 #if 0
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151 prep = fopen( "best", "w" );
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152 Write( prep, locnjob, name, nlen, aseq );
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153 fclose( prep );
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154 #endif
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155 }
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156
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157
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158
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159
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160 treeconstruction( aseq, locnjob, topol, len, eff );
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161 tscore = score_calc0( aseq, locnjob, eff, 0 );
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162
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163 #if DEBUG
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164 fprintf( stderr, "eff mtx in iteration\n" );
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165 for( i=0; i<locnjob; i++ )
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166 {
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167 for( j=0; j<locnjob; j++ )
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168 {
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169 fprintf( stderr, "%5.3f ", eff[i][j] );
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170 }
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171 fprintf( stderr, "\n" );
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172 }
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173 #endif
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174
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175 fprintf( stderr, "\n" );
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176 if( disp )
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177 {
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178 fprintf( stderr, "aseq(initial)\n" );
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179 display( aseq, locnjob );
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180 }
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181 fprintf( stderr, "initial score = %f \n", tscore );
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182 fprintf( stderr, "\n" );
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183 for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
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184 mscore = tscore;
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185 srand( time(NULL) );
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186
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187 sss[1] = 0;
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188 sss[0] = locnjob-1;
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189 /*
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190 sss[0] = (int)( (float)locnjob/2.0 );
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191 */
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192 ou = 1;
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193 cyc[0] = 0; cyc[1] = 0;
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194
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195 for( s=-1, l=0; l<MAXITERATION; l++ )
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196 {
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197 int ss;
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198 double tmpscore, tmpscore1;
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199
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200 if( strlen( aseq[0] ) > nlenmax )
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201 nlenmax = strlen( aseq[0] );
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202
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203 /*
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204 s = ( int )( rnd() * locnjob );
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205 s++;
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206 if( s == locnjob ) s = 0;
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207 ou = 0;
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208 */
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209 if( ou == 0 )
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210 {
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211 ou = 1;
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212 s = sss[0];
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213 /*
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214 sss[0]++;
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215 if( sss[0] == locnjob )
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216 {
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217 sss[0] = 0;
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218 cyc[0]++;
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219 }
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220 */
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221 sss[0]--;
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222 if( sss[0] == -1 )
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223 {
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224 sss[0] = locnjob-1;
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225 cyc[0]++;
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226 }
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227 }
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228 else
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229 {
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230 ou = 0;
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231 s = sss[1];
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232 sss[1]++;
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233 if( sss[1] == locnjob )
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234 {
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235 sss[1] = 0;
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236 cyc[1]++;
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237 }
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238 }
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239 fprintf( trap_g, "%d ", weight );
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240
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241 /*
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242 for( i=0, count=0; i<strlen( aseq[s] ); i++ )
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243 {
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244 if( aseq[s][i] != '-' )
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245 {
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246 mseq1[count] = aseq[s][i];
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247 count++;
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248 }
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249 }
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250 mseq1[count] = 0;
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251 */
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252 gappick0( mseq1, aseq[s] );
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253
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254 if( checkC )
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255 tmpscore = score_m_1_0( aseq, locnjob, s, eff, effarr );
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256
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257 gappick( locnjob, s, aseq, mseq2, eff, effarr );
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258
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259 result = align0( &wm, mseq2, mseq1, effarr, locnjob-2, s );
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260 resultlen = strlen( result[0] );
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261 if( resultlen > alloclen )
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262 {
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263 if( resultlen > nlenmax0*3 || resultlen > N )
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264 {
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265 fprintf(stderr, "Error in main1\n");
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266 exit( 1 );
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267 }
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268 FreeTmpSeqs( mseq2, mseq1 );
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269 alloclen = strlen( result[0] ) * 2.0;
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270 fprintf( stderr, "\n\ntrying to allocate TmpSeqs\n\n" );
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271 AllocateTmpSeqs( &mseq2, &mseq1, alloclen );
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272 }
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273 for( i=0; i<locnjob; i++ ) strcpy( mseq2[i], result[i] );
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274
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275 if( checkC )
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276 fprintf( stderr, "wm in iteration == %f\n", wm );
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277
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278 strcpy( mseq1, mseq2[locnjob-1] );
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279 /*
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280 Write( stdout, locnjob, name, nlen, mseq2 );
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281 */
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282 for( i=locnjob-2; i>=s; i-- ) strcpy( mseq2[i+1], mseq2[i] );
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283 strcpy( mseq2[s], mseq1 );
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284 if( checkC )
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285 {
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286 tmpscore1= score_m_1_0( mseq2, locnjob, s, eff, effarr );
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287 fprintf( stderr, "pick up %d, before ALIGNM1 score_m_1_0 = %f\n", s+1, tmpscore );
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288 fprintf( stderr, "pick up %d, after ALIGNM1 score_m_1_0 = %f\n", s+1, tmpscore1 );
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289 if( tmpscore1 < tmpscore )
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290 {
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291 fprintf( stderr, "\7" );
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292 fprintf( trap_g, ">>>>>>>n\n" );
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293 }
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294 if( fabs( wm - tmpscore1 ) / wm > 0.001 )
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295 {
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296 fprintf( stderr, "\7sorry\n" );
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297 exit( 1 );
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298 }
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299 }
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300
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301 identity = !strcmp( mseq2[s], aseq[s] );
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302 if( s == locnjob - 1 ) ss = 0; else ss=s+1;
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303
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304 identity *= !strcmp( mseq2[ss], aseq[ss] );
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305
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306 if( !identity )
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307 {
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308 tmpscore = score_calc0( mseq2, locnjob, eff, s );
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309 }
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310 else tmpscore = tscore;
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311
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312 if( disp )
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313 {
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314 fprintf( stderr, "% 3d % 3d / the rest \n", l+1, s+1 );
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315 display( mseq2, locnjob );
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316 }
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317 fprintf( stderr, "% 3d % 3d / the rest \n", l+1, s+1 );
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318 fprintf( stderr, "score = %f mscore = %f ", tmpscore, mscore );
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319
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320 fprintf( trap_g, "%#4d %#4d / the rest ", l+1, s+1 );
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321 fprintf( trap_g, "score = %f mscore = %f ", tmpscore, mscore );
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322
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323 if( identity )
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324 {
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325 fprintf( stderr, "( identical )\n" );
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326 fprintf( trap_g, "( identical )\n" );
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327 sai[s] = 2;
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328 }
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329
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330 else if( tmpscore > mscore - cut )
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331 {
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332 fprintf( stderr, "accepted\n" );
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333 fprintf( trap_g, "accepted\n" );
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334 for( i=0; i<locnjob; i++ ) strcpy( aseq[i], mseq2[i] );
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335 strcpy( sai, sai1 ); /* kokoka ? */
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336 if( !tbitr && !tbweight )
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337 {
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338 writePre( locnjob, name, nlen, aseq, 0 );
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339 }
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340 strcpy( sai, sai1 );
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341 tscore = tmpscore;
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342 /*
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343 tscore = tmpscore = score_calc0( aseq, locnjob, eff, s ); * ? *
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344 */
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345 if( tmpscore > mscore )
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346 {
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347 for( i=0; i<locnjob; i++ ) strcpy( bseq[i], mseq2[i] );
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348 treeconstruction( bseq, locnjob, topol, len, eff );
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349 tscore = mscore = score_calc0( bseq, locnjob, eff, s );
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350 fprintf( trap_g, " -> %f\n", mscore );
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351 strcpy( sai, sai1 ); /* kokoka ? */
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352 #if 0
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353 if( !tbitr && !tbweight )
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354 { prep = fopen( "best", "w" );
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355 Write( prep, locnjob, name, nlen, bseq );
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356 fclose( prep );
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357 }
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358 #endif
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359 }
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360 }
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361
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362 else
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363 {
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364 if( tmpscore == tscore )
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365 {
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366 fprintf( stderr, "occational coincidence \n" );
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367 fprintf( trap_g, "occational coincidence\n" );
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368 }
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369 else
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370 {
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371 fprintf( stderr, "rejected\n" );
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372 fprintf( trap_g, "rejected\n" );
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373 }
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374 for( i=0; i<locnjob; i++ ) strcpy( aseq[i], bseq[i] );
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375 tscore = mscore;
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376 sai[s] = 2;
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377 }
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378
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379 /*
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380 prep = fopen( "cur", "w" );
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381 Write( prep, locnjob, name, nlen, mseq2 );
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382 fclose( prep );
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383 */
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384
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385 his[ou][s][cyc[ou]] = tmpscore;
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386 if( !strcmp( sai, sai2 ) )
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387 {
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388 returnvalue = 0;
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389 fprintf( trap_g, "converged\n" );
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390 break;
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391 }
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392 for( i=cyc[ou]-1; i>0; i-- )
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393 {
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394 if( tmpscore == his[ou][s][i] )
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395 {
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396 shindou = 1;
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397 break;
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398 }
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399 }
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400 fprintf( stderr, "\n" );
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401 if( shindou == 1 )
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402 {
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403 returnvalue = -1;
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404 fprintf( trap_g, "oscillating\n" );
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405 break;
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406 }
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407 }
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408 if( l == MAXITERATION ) returnvalue = -2;
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409 FreeDoubleCub( his );
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410 return( returnvalue );
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411 }
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412