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annotate mafft/core/addfunctions.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
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3
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4 void profilealignment2( int n0, int n2, char **aln0, char **aln2, int alloclen, char alg ) // n1 ha allgap
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5 {
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6 int i, newlen;
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7 double *effarr0, *effarr2;
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8 float dumfl;
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9 double eff;
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10 effarr0 = AllocateDoubleVec( n0 );
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11 effarr2 = AllocateDoubleVec( n2 );
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12
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13 // reporterr( "profilealignment!\n" );
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14
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15 commongappick( n0, aln0 );
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16 commongappick( n2, aln2 );
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17
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18 eff = 1.0 / (double)n0; for( i=0; i<n0; i++ ) effarr0[i] = eff;
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19 eff = 1.0 / (double)n2; for( i=0; i<n2; i++ ) effarr2[i] = eff;
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20
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21 newgapstr = "-";
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22 if( alg == 'M' )
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23 MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
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24 else
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25 A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
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26
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27 newlen = strlen( aln0[0] );
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28
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29 #if 0 // tabun hitsuyou
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30 for( j=0; j<newlen; j++ )
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31 {
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32 // fprintf( stderr, "j=%d\n", j );
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33 for( i=0; i<n0; i++ )
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34 {
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35 if( aln0[i][j] != '-' ) break;
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36 }
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37 if( i == n0 )
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38 {
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39 for( i=0; i<n1; i++ )
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40 {
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41 if( aln1[i][j] != '-' ) break;
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42 }
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43 }
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44 else i = -1;
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45
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46 if( i == n1 )
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47 {
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48 for( i=0; i<n1; i++ ) aln1[i][j] = '=';
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49 }
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50 }
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51 fprintf( stderr, "in profilealignment,\n" );
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52 for( i=0; i<n0; i++ ) fprintf( stderr, "\n>aln0[%d] = \n%s\n", i, aln0[i] );
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53 for( i=0; i<n1; i++ ) fprintf( stderr, "\n>aln1[%d] = \n%s\n", i, aln1[i] );
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54 for( i=0; i<n2; i++ ) fprintf( stderr, "\n>aln2[%d] = \n%s\n", i, aln2[i] );
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55 #endif
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56
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57 free( effarr0 );
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58 free( effarr2 );
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59 }
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60
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61 void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, char **aln2, int alloclen, char alg ) // n1 ha allgap
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62 {
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63 int i, j, newlen;
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64 double *effarr0, *effarr2;
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65 float dumfl;
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66 double eff;
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67 effarr0 = AllocateDoubleVec( n0 );
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68 effarr2 = AllocateDoubleVec( n2 );
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69
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70
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71 // reporterr( "profilealignment!\n" );
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72
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73 commongappick( n0, aln0 );
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74 commongappick( n2, aln2 );
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75
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76 eff = 1.0 / (double)n0; for( i=0; i<n0; i++ ) effarr0[i] = eff;
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77 eff = 1.0 / (double)n2; for( i=0; i<n2; i++ ) effarr2[i] = eff;
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78
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79 newgapstr = "-";
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80 if( alg == 'M' )
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81 MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
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82 else
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83 A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
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84
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85 newlen = strlen( aln0[0] );
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86
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87 for( i=0; i<newlen; i++ ) aln1[0][i] = '-';
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88 aln1[0][i] = 0;
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89 for( i=1; i<n1; i++ ) strcpy( aln1[i], aln1[0] );
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90
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91 for( j=0; j<newlen; j++ )
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92 {
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93 // fprintf( stderr, "j=%d\n", j );
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94 for( i=0; i<n0; i++ )
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95 {
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96 if( aln0[i][j] != '-' ) break;
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97 }
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98 if( i == n0 )
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99 {
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100 for( i=0; i<n1; i++ )
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101 {
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102 if( aln1[i][j] != '-' ) break;
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103 }
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104 }
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105 else i = -1;
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106
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107 if( i == n1 )
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108 {
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109 for( i=0; i<n1; i++ ) aln1[i][j] = '=';
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110 }
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111 }
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112 #if 0
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113 fprintf( stderr, "in profilealignment,\n" );
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114 for( i=0; i<n0; i++ ) fprintf( stderr, "\n>aln0[%d] = \n%s\n", i, aln0[i] );
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115 for( i=0; i<n1; i++ ) fprintf( stderr, "\n>aln1[%d] = \n%s\n", i, aln1[i] );
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116 for( i=0; i<n2; i++ ) fprintf( stderr, "\n>aln2[%d] = \n%s\n", i, aln2[i] );
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117 #endif
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118
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119 free( effarr0 );
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120 free( effarr2 );
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121 }
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122
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123 void eq2dashmatomete( char **s, int n )
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124 {
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125 int i, j;
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126 char sj;
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127
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128 for( j=0; (sj=s[0][j]); j++ )
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129 {
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130 if( sj == '=' )
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131 {
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132 for( i=0; i<n; i++ )
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133 {
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134 s[i][j] = '-';
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135 }
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136 }
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137 }
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138 }
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139
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140 void eq2dashmatometehayaku( char **s, int n )
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141 {
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142 int i, j, c;
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143 int *tobechanged;
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144 int len = strlen( s[0] );
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145
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146 tobechanged = calloc( len, sizeof( int ) );
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147 c = 0;
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148 for( j=0; j<len; j++ )
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149 {
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150 if( s[0][j] == '=' ) tobechanged[c++] = j;
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151 }
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152 tobechanged[c] = -1;
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153
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154 for( i=0; i<n; i++ )
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155 {
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156 for( c=0; (j=tobechanged[c])!=-1; c++ )
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157 s[i][j] = '-';
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158 }
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159 free( tobechanged );
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160 }
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161
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162 void eq2dash( char *s )
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163 {
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164 while( *s )
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165 {
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166 if( *s == '=' )
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167 {
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168 *s = '-';
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169 }
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170 s++;
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171 }
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172 }
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173
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174 void findnewgaps( int n, int rep, char **seq, int *gaplen )
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175 {
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176 int i, pos, len, len1;
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177
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178 len = strlen( seq[0] );
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179 // for( i=0; i<len; i++ ) gaplen[i] = 0; // calloc de shokika sareteirukara hontou ha iranai
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180 len1 = len + 1;
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181 for( i=0; i<len1; i++ ) gaplen[i] = 0; // reallo de shokika sareteirukara iru!
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182
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183 pos = 0;
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184 for( i=0; i<len; i++ )
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185 {
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186 if( seq[rep][i] == '=' )
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187 {
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188 // fprintf( stderr, "Newgap! pos = %d\n", pos );
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189 gaplen[pos]++;
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190 }
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191 else
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192 pos++;
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193 }
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194 }
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195
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196 void findcommongaps( int n, char **seq, int *gaplen )
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197 {
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198 int i, j, pos, len, len1;
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199 len = strlen( seq[0] );
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200 len1 = len+1;
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201
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202 // fprintf( stderr, "seq[0] = %s\n", seq[0] );
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203 for( i=0; i<len1; i++ ) gaplen[i] = 0;
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204
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205 pos = 0;
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206 for( i=0; i<len; i++ )
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207 {
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208 for( j=0; j<n; j++ )
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209 if( seq[j][i] != '-' ) break;
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210
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211 if( j == n ) gaplen[pos]++;
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212 else
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213 pos++;
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214 }
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215 #if 0
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216 for( i=0; i<pos; i++ )
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217 {
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218 fprintf( stderr, "vec[%d] = %d\n", i, gaplen[i] );
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219 }
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220 #endif
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221 }
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222
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223 void adjustgapmap( int newlen, int *gapmap, char *seq )
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224 {
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225 int j;
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226 int pos;
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227 int newlen1 = newlen+1;
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228 int *tmpmap;
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229
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230
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231 tmpmap = AllocateIntVec( newlen+2 );
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232 j = 0;
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233 pos = 0;
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234 while( *seq )
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235 {
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236 // fprintf( stderr, "j=%d *seq = %c\n", j, *seq );
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237 if( *seq++ == '=' )
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238 tmpmap[j++] = 0;
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239 else
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240 {
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241 tmpmap[j++] = gapmap[pos++];
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242 }
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243 }
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244 tmpmap[j++] = gapmap[pos];
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245
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246 for(j=0; j<newlen1; j++)
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247 gapmap[j] = tmpmap[j];
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248
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249 free( tmpmap );
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250 }
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251
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252 static void strncpy0( char *s1, char *s2, int n )
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253 {
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254 while( n-- ) *s1++ = *s2++;
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255 *s1 = 0;
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256 }
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257
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258 static int countnogaplen( int *gaplen, int *term )
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259 {
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260 int v = 0;
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261 while( gaplen < term )
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262 {
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263 if( *gaplen++ == 0 ) v++;
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264 else break;
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265 }
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266 return( v );
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267 }
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268
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269 void insertnewgaps( int njob, int *alreadyaligned, char **seq, int *ex1, int *ex2, int *gaplen, int *gapmap, int alloclen, char alg, char gapchar )
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270 {
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271 int *mar;
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272 char *gaps;
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273 char *cptr;
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274 int i, j, k, len, rep, len0, lp, blocklen;
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275 char **mseq2, **mseq0, **mseq1;
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276 char **aseq, *newchar;
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277 int ngroup2, ngroup0, ngroup1;
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278 int *list0, *list1, *list2;
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279 int posin12, gapshift, newpos;
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280 int mlen1, mlen0, mlen2;
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281 int tmptmptmpmark = 0;
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282
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283 mar = calloc( njob, sizeof( int ) );
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284 list0 = calloc( njob, sizeof( int ) );
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285 list1 = calloc( njob, sizeof( int ) );
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286 list2 = calloc( njob, sizeof( int ) );
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287
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288 for( i=0; i<njob; i++ ) mar[i] = 0;
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289 for( i=0; i<njob; i++ )
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290 {
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291 if( alreadyaligned[i]==0 ) mar[i] = 3;
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292 }
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293 for( i=0; (k=ex1[i])>-1; i++ )
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294 {
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295 mar[k] = 1;
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296 // fprintf( stderr, "excluding %d\n", ex1[i] );
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297 }
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298 for( i=0; (k=ex2[i])>-1; i++ )
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299 {
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300 mar[k] = 2;
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301 // fprintf( stderr, "excluding %d\n", ex2[i] );
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302 }
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303
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304 ngroup2 = ngroup1 = ngroup0 = 0;
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305 for( i=0; i<njob; i++ )
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306 {
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307 if( mar[i] == 2 )
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308 {
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309 list2[ngroup2] = i;
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310 ngroup2++;
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311 }
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312 if( mar[i] == 1 )
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313 {
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314 list1[ngroup1] = i;
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315 ngroup1++;
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316 }
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317 if( mar[i] == 0 )
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318 {
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319 list0[ngroup0] = i;
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320 // fprintf( stderr, "inserting new gaps to %d\n", i );
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321 ngroup0++;
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322 }
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323 }
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324 list0[ngroup0] = list1[ngroup1] = list2[ngroup2] = -1;
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325 if( ngroup0 == 0 )
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326 {
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327 // fprintf( stderr, "Nothing to do\n" );
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328 free( mar );
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329 free( list0 );
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330 free( list1 );
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331 free( list2 );
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332 return;
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333 }
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334
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335 for( i=0; i<njob; i++ ) if( mar[i] == 0 ) break;
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336 rep = i;
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337 len = strlen( seq[rep] );
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338 len0 = len+1;
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339
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340 //
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341 // if( i == njob )
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342 // {
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343 //// fprintf( stderr, "Nothing to do\n" );
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344 // free( mar );
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345 // return;
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346 // }
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347
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348 mseq2 = AllocateCharMtx( ngroup2, alloclen );
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349 mseq1 = AllocateCharMtx( ngroup1, alloclen );
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350 mseq0 = AllocateCharMtx( ngroup0, alloclen );
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351 aseq = AllocateCharMtx( njob, alloclen );
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352 gaps = calloc( alloclen, sizeof( char ) );
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353
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354
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355 for( i=0; i<njob; i++ ) aseq[i][0] = 0;
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356 newpos = 0;
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357 posin12 = 0;
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358 // fprintf( stderr, "\ngaplen[] = \n" );
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359 // for(i=0; i<len0; i++ ) fprintf( stderr, "%d ", gaplen[i] );
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360 // fprintf( stderr, "\n" );
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361
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362 for( j=0; j<len0; j++ )
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363 {
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364 // fprintf( stderr, "\nj=%d, gaplen[%d]=%d\n", j, j, gaplen[j] );
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365 if( gaplen[j] )
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366 {
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367 // fprintf( stderr, "j=%d GAP!\n", j );
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368 tmptmptmpmark = 1;
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369 for( i=0; i<ngroup0; i++ ) mseq0[i][0] = 0;
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370 for( i=0; i<ngroup1; i++ ) mseq1[i][0] = 0;
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371 for( i=0; i<ngroup2; i++ ) mseq2[i][0] = 0;
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372 mlen0 = mlen1 = mlen2 = 0;
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373
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374 gapshift = gaplen[j];
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375 cptr = gaps;
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376 while( gapshift-- ) *cptr++ = gapchar;
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377 *cptr = 0;
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378 gapshift = gaplen[j];
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379
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380 for( i=0; i<ngroup0; i++ ) strncpy0( mseq0[i]+mlen0, gaps, gapshift );
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381 for( i=0; i<ngroup1; i++ ) strncpy0( mseq1[i]+mlen1, seq[list1[i]]+posin12, gapshift );
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382 for( i=0; i<ngroup2; i++ ) strncpy0( mseq2[i]+mlen2, seq[list2[i]]+posin12, gapshift );
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383 posin12 += gapshift;
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384 mlen0 += gapshift;
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385 mlen1 += gapshift;
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386 mlen2 += gapshift;
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387
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388 gapshift = gapmap[posin12];
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389 // fprintf( stderr, "gapmap[%d] kouho = %d\n", posin12, gapmap[posin12] );
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390
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391
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392 for( i=0; i<ngroup0; i++ ) strncpy0( mseq0[i]+mlen0, seq[list0[i]]+j, gapshift );
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393 for( i=0; i<ngroup1; i++ ) strncpy0( mseq1[i]+mlen1, seq[list1[i]]+posin12, gapshift );
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394 for( i=0; i<ngroup2; i++ ) strncpy0( mseq2[i]+mlen2, seq[list2[i]]+posin12, gapshift );
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395 mlen0 += gapshift;
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396 mlen1 += gapshift;
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397 mlen2 += gapshift;
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398 #if 0
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399 for( i=0; i<ngroup0; i++ ) fprintf( stderr, "### mseq0[%d] = %s\n", i, mseq0[i] );
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400 for( i=0; i<ngroup1; i++ ) fprintf( stderr, "### mseq1[%d] = %s\n", i, mseq1[i] );
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401 for( i=0; i<ngroup2; i++ ) fprintf( stderr, "### mseq2[%d] = %s\n", i, mseq2[i] );
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402 #endif
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403
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404 if( gapshift )
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405 profilealignment( ngroup0, ngroup1, ngroup2, mseq0, mseq1, mseq2, alloclen, alg );
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406
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407 j += gapshift;
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408 posin12 += gapshift;
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409
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410 newpos = strlen( aseq[rep] ); // kufuu?
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411 for( i=0; i<ngroup0; i++ ) strcpy( aseq[list0[i]]+newpos, mseq0[i] );
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412 for( i=0; i<ngroup1; i++ ) strcpy( aseq[list1[i]]+newpos, mseq1[i] );
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413 for( i=0; i<ngroup2; i++ ) strcpy( aseq[list2[i]]+newpos, mseq2[i] );
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414
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415 // fprintf( stderr, "gapshift = %d\n", gapshift );
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416 }
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417 blocklen = 1 + countnogaplen( gaplen+j+1, gaplen+len0 );
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418 // fprintf( stderr, "\nj=%d, blocklen=%d, len0=%d\n", j, blocklen, len0 );
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419 // blocklen = 1;
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420 // if( tmptmptmpmark ) exit( 1 );
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421
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422 newpos = strlen( aseq[rep] );
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423
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424 #if 0
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425 for( i=0; i<ngroup0; i++ ) aseq[list0[i]][newpos] = seq[list0[i]][j];
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426 for( i=0; i<ngroup1; i++ ) aseq[list1[i]][newpos] = seq[list1[i]][posin12];
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427 for( i=0; i<ngroup2; i++ ) aseq[list2[i]][newpos] = seq[list2[i]][posin12];
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428 for( i=0; i<ngroup0; i++ ) aseq[list0[i]][newpos+1] = 0;
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429 for( i=0; i<ngroup1; i++ ) aseq[list1[i]][newpos+1] = 0;
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430 for( i=0; i<ngroup2; i++ ) aseq[list2[i]][newpos+1] = 0;
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431 #else
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432
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433 for( i=0; i<ngroup0; i++ )
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434 {
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435 lp = list0[i];
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436 newchar = aseq[lp] + newpos;
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437 strncpy0( newchar, seq[lp]+j, blocklen );
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438 }
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439 for( i=0; i<ngroup1; i++ )
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440 {
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441 lp = list1[i];
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442 newchar = aseq[lp] + newpos;
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443 strncpy0( newchar, seq[lp]+posin12, blocklen );
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444 }
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445 for( i=0; i<ngroup2; i++ )
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446 {
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447 lp = list2[i];
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448 newchar = aseq[lp] + newpos;
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449 strncpy0( newchar, seq[lp]+posin12, blocklen );
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450 }
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451 // fprintf( stderr, "### aseq[l0] = %s\n", aseq[list0[0]] );
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452 // fprintf( stderr, "### aseq[l1] = %s\n", aseq[list1[0]] );
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453 // fprintf( stderr, "### aseq[l2] = %s\n", aseq[list2[0]] );
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454 // exit( 1 );
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455 #endif
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456
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457 // fprintf( stderr, "j=%d -> %d\n", j, j+blocklen-1 );
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458 j += (blocklen-1);
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459
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460
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461 posin12 += (blocklen-1);
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462
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463
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464 posin12++;
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465 }
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466 #if 0
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467 fprintf( stderr, "\n" );
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468 fprintf( stderr, " seq[l0] = %s\n", seq[list0[0]] );
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469 fprintf( stderr, " seq[l1] = %s\n", seq[list1[0]] );
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470 fprintf( stderr, " seq[l2] = %s\n", seq[list2[0]] );
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471 fprintf( stderr, "=====>\n" );
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472 fprintf( stderr, "aseq[l0] = %s\n", aseq[list0[0]] );
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473 fprintf( stderr, "aseq[l1] = %s\n", aseq[list1[0]] );
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474 fprintf( stderr, "aseq[l2] = %s\n", aseq[list2[0]] );
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475 //if( tmptmptmpmark ) exit( 1 );
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476 #endif
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477
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478 // for( i=0; i<njob; i++ ) if( mar[i] != 3 ) strcpy( seq[i], aseq[i] );
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479 for( i=0; i<ngroup0; i++ ) strcpy( seq[list0[i]], aseq[list0[i]] );
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480 for( i=0; i<ngroup1; i++ ) strcpy( seq[list1[i]], aseq[list1[i]] );
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481 for( i=0; i<ngroup2; i++ ) strcpy( seq[list2[i]], aseq[list2[i]] );
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482
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483
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484 free( mar );
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485 free( gaps );
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486 free( list0 );
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487 free( list1 );
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488 free( list2 );
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489 FreeCharMtx( mseq2 );
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490 FreeCharMtx( mseq1 ); // ? added 2012/02/12
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491 FreeCharMtx( mseq0 );
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492 FreeCharMtx( aseq ); // ? added 2012/02/12
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493 }
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494
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495
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496 void restorecommongaps( int njob, char **seq, int *ex1, int *ex2, int *gaplen, int alloclen, char gapchar )
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497 {
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498 int *mar;
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499 char *tmpseq;
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500 char *cptr;
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501 int *iptr;
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502 int *tmpgaplen;
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503 int i, j, k, len, rep, len1, klim;
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504
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505 mar = calloc( njob, sizeof( int ) );
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506 tmpseq = calloc( alloclen, sizeof( char ) );
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507 tmpgaplen = calloc( alloclen, sizeof( int ) );
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508 // tmpseq = calloc( alloclen+2, sizeof( char ) );
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509 // tmpgaplen = calloc( alloclen+2, sizeof( int ) );
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510
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511
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512 for( i=0; i<njob; i++ ) mar[i] = 0;
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513 for( i=0; (k=ex1[i])>-1; i++ )
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514 {
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515 mar[k] = 1;
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516 // fprintf( stderr, "excluding %d\n", ex1[i] );
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517 }
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518 for( i=0; (k=ex2[i])>-1; i++ )
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519 {
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520 mar[k] = 1;
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521 // fprintf( stderr, "excluding %d\n", ex2[i] );
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522 }
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523
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524 for( i=0; i<njob; i++ )
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525 if( mar[i] ) break;
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526
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527 if( i == njob )
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528 {
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529 // fprintf( stderr, "Nothing to do\n" );
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530 free( mar );
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531 free( tmpseq );
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532 free( tmpgaplen );
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533 return;
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534 }
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535 rep = i;
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536 len = strlen( seq[rep] );
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537 len1 = len+1;
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538
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539
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540 for( i=0; i<njob; i++ )
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541 {
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542 if( mar[i] == 0 ) continue;
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543 cptr = tmpseq;
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544 for( j=0; j<len1; j++ )
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545 {
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546 klim = gaplen[j];
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547 // for( k=0; k<gaplen[j]; k++ )
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548 while( klim-- )
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549 *(cptr++) = gapchar; // ???
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550 *(cptr++) = seq[i][j];
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551 }
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552 *cptr = 0;
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553 strcpy( seq[i], tmpseq );
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554 }
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555
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556 iptr = tmpgaplen;
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557 for( j=0; j<len1; j++ )
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558 {
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559 *(iptr++) = gaplen[j];
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560 for( k=0; k<gaplen[j]; k++ )
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561 *(iptr++) = 0;
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562 }
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563 *iptr = -1;
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564
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565 iptr = tmpgaplen;
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566 while( *iptr != -1 ) *gaplen++ = *iptr++;
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567
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568 free( mar );
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569 free( tmpseq );
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570 free( tmpgaplen );
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571 }