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annotate mafft/core/mafft-profile.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
parents
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4
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5 #if DEBUG
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6 #include <time.h>
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7 #include <sys/time.h>
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8 #include <sys/resource.h>
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9 double getrusage_sec()
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10 {
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11 struct rusage t;
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12 struct timeval tv;
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13 getrusage(RUSAGE_SELF, &t);
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14 tv = t.ru_utime;
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15 return tv.tv_sec + (double)tv.tv_usec*1e-6;
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16 }
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17 #endif
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18
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19
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20 int intcmp( int *str1, int *str2 )
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21 {
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22 while( *str1 != -1 && *str2 != -1 )
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23 if( *str1++ != *str2++ ) return( 1 );
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24 if( *str1 != *str2 ) return( 1 );
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25 return( 0 );
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26 }
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27
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28 char **arguments( int argc, char *argv[] )
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29 {
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30 int c = 0;
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31
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32 fmodel = 0;
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33 nblosum = 62;
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34 calledByXced = 0;
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35 devide = 0;
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36 fftscore = 1;
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37 use_fft = 1;
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38 alg = 'A';
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39 weight = 0;
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40 utree = 1;
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41 tbutree = 0;
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42 refine = 0;
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43 check = 1;
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44 cut = 0.0;
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45 disp = 0;
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46 outgap = 0;
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47 mix = 0;
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48 tbitr = 0;
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49 scmtd = 5;
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50 tbweight = 0;
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51 tbrweight = 3;
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52 checkC = 0;
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53 scoremtx = 1;
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54 dorp = NOTSPECIFIED;
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55 ppenalty = NOTSPECIFIED;
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56 ppenalty_ex = NOTSPECIFIED;
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57 poffset = 0; // chokusetsu yobareru kara
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58 kimuraR = NOTSPECIFIED;
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59 pamN = NOTSPECIFIED;
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60 fftWinSize = NOTSPECIFIED;
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61 fftThreshold = NOTSPECIFIED;
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62 TMorJTT = JTT;
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63 treemethod = 'x';
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64
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65
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66 while( --argc > 0 && (*++argv)[0] == '-' )
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67 {
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68 while ( ( c = *++argv[0] ) )
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69 {
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70 switch( c )
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71 {
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72 case 'P':
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73 dorp = 'p';
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74 break;
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75 case 'D':
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76 dorp = 'd';
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77 break;
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78 case 'F':
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79 use_fft = 1;
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80 break;
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81 case 'N':
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82 use_fft = 0;
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83 break;
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84 case 'e':
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85 fftscore = 0;
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86 break;
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87 case 'Q':
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88 alg = 'Q';
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89 break;
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90 case 'A':
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91 alg = 'A';
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92 break;
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93 case 'M':
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94 alg = 'M';
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95 break;
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96 case 'd':
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97 disp = 1;
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98 break;
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99 case 'O':
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100 outgap = 0;
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101 break;
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102 case 'a':
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103 fmodel = 1;
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104 break;
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105 case 'u':
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106 tbrweight = 0;
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107 break;
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108 case 'z':
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109 fftThreshold = myatoi( *++argv );
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110 --argc;
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111 goto nextoption;
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112 case 'w':
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113 fftWinSize = myatoi( *++argv );
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114 --argc;
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115 goto nextoption;
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116 case 'Z':
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117 checkC = 1;
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118 break;
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119 case 'f':
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120 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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121 fprintf( stderr, "ppenalty = %d\n", ppenalty );
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122 --argc;
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123 goto nextoption;
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124 case 'g':
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125 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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126 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
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127 --argc;
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128 goto nextoption;
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129 case 'h':
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130 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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131 fprintf( stderr, "poffset = %d\n", poffset );
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132 --argc;
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133 goto nextoption;
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134 case 'k':
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135 kimuraR = myatoi( *++argv );
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136 fprintf( stderr, "kappa = %d\n", kimuraR );
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137 --argc;
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138 goto nextoption;
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139 case 'b':
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140 nblosum = myatoi( *++argv );
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141 scoremtx = 1;
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142 fprintf( stderr, "blosum %d\n", nblosum );
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143 --argc;
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144 goto nextoption;
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145 case 'j':
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146 pamN = myatoi( *++argv );
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147 scoremtx = 0;
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148 TMorJTT = JTT;
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149 fprintf( stderr, "jtt %d\n", pamN );
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150 --argc;
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151 goto nextoption;
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152 case 'm':
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153 pamN = myatoi( *++argv );
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154 scoremtx = 0;
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155 TMorJTT = TM;
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156 fprintf( stderr, "tm %d\n", pamN );
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157 --argc;
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158 goto nextoption;
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159 default:
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160 fprintf( stderr, "illegal option %c\n", c );
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161 argc = 0;
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162 break;
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163 }
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164 }
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165 nextoption:
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166 ;
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167 }
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168 if( argc != 2 )
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169 {
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170 fprintf( stderr, "options: Check source file ! %c ?\n", c );
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171 exit( 1 );
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172 }
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173 fprintf( stderr, "tbitr = %d, tbrweight = %d, tbweight = %d\n", tbitr, tbrweight, tbweight );
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174 // readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
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175 return( argv );
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176
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177 }
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178
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179 void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double **len, double *eff, int alloclen )
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180 {
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181 int i;
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182 int clus1, clus2;
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183 int s1, s2;
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184 float pscore;
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185 static char **name1, **name2;
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186 double *effarr = eff;
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187 double *effarr1 = NULL;
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188 double *effarr2 = NULL;
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189 static char *indication1, *indication2;
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190 float dumfl = 0.0;
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191 int intdum;
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192 #if DEBUG
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193 double time1, time2;
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194 #endif
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195
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196
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197 // fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize );
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198 // fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold );
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199
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200 if( effarr1 == NULL )
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201 {
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202 name1 = AllocateCharMtx( nseq1, B );
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203 name2 = AllocateCharMtx( nseq2, B );
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204 indication1 = AllocateCharVec( 150 );
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205 indication2 = AllocateCharVec( 150 );
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206 effarr1 = AllocateDoubleVec( njob );
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207 effarr2 = AllocateDoubleVec( njob );
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208 #if 0
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209 #else
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210 #endif
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211 }
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212
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213 for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
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214
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215
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216
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217 s1 = 0;
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218 s2 = nseq1;
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219 // fprintf( stdout, "nseq1 = %d\n", nseq1 );
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220
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221
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222
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223 clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
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224 clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
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225 /*
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226 fprintf( stderr, "before align all\n" );
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227 display( aseq, njob );
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228 fprintf( stderr, "\n" );
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229 fprintf( stderr, "before align 1 %s \n", indication1 );
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230 display( mseq1, clus1 );
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231 fprintf( stderr, "\n" );
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232 fprintf( stderr, "before align 2 %s \n", indication2 );
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233 display( mseq2, clus2 );
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234 fprintf( stderr, "\n" );
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235 */
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236
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237 commongappick( nseq1, mseq1 );
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238 commongappick( nseq2, mseq2 );
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239
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240
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241 #if DEBUG
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242 time1 = getrusage_sec();
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243 fprintf( stderr, "entering Falign\n" );
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244 #endif
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245 if( use_fft )
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246 {
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247 if( alg == 'M' )
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248 pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum );
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249 else
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250 pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
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251 }
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252 else
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253 {
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254 if( alg == 'M' )
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255 pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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256 else
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257 pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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258 }
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259 #if DEBUG
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260 time2 = getrusage_sec();
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261 fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 );
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262 fflush( stdout );
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263 #endif
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264
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265
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266 /*
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267 fprintf( stderr, "after align 1 %s \n", indication1 );
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268 display( mseq1, clus1 );
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269 fprintf( stderr, "\n" );
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270 fprintf( stderr, "after align 2 %s \n", indication2 );
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271 display( mseq2, clus2 );
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272 fprintf( stderr, "\n" );
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273 */
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274
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275 fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore );
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276 if( disp ) display( aseq, njob );
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277 fprintf( stderr, "\n" );
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278
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279 /*
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280 trap = fopen( "pre", "r+" );
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281 if( !trap ) ErrorExit( 1 );
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282 WriteGapFill( trap, njob, name, nlen, aseq );
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283 fclose( trap );
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284 fprintf( stdout, "nseq1 = %d\n", nseq1 );
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285 */
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286 }
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287
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288 static void WriteOptions( FILE *fp )
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289 {
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290 fprintf( fp, "tree-base method\n" );
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291 if( tbweight == 0 ) fprintf( fp, "unweighted\n" );
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292 else if( tbweight == 3 ) fprintf( fp, "reversely weighted\n" );
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293 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
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294 else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
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295 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
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296 else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
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297
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298 if( scoremtx )
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299 fprintf( fp, "Gap Penalty = %d, %d\n", penalty, offset );
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300 else
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301 fprintf( fp, "Gap Penalty = %d\n", penalty );
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302 }
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303
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304
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305 int main( int argc, char *argv[] )
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306 {
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307 char **argv2;
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308 static int *nlen;
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309 static char **name, **seq;
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310 static char **seq1, **seq2;
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311 static char **mseq1, **mseq2;
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312 static char **aseq;
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313 static char **bseq;
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314 static double **pscore;
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315 static double *eff;
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316 int i, j, len1, len2;
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317 static int ***topol;
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318 static double **len;
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319 FILE *gp1, *gp2;
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320 char c;
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321 int nlenmax1, nlenmax2, nseq1, nseq2;
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322 int alloclen;
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323
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324 argv2 = arguments( argc, argv );
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325
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326 fprintf( stderr, "####### in galn\n" );
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327
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328 initFiles();
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329
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330 fprintf( stderr, "file1 = %s\n", argv2[0] );
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331 fprintf( stderr, "file2 = %s\n", argv2[1] );
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332
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333 gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" );
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334 gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" );
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335
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336 #if 0
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337 PreRead( gp1, &nseq1, &nlenmax1 );
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338 PreRead( gp2, &nseq2, &nlenmax2 );
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339 #else
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340 getnumlen( gp1 );
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341 nseq1 = njob; nlenmax1 = nlenmax;
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342 getnumlen( gp2 );
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343 nseq2 = njob; nlenmax2 = nlenmax;
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344 #endif
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345
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346 njob = nseq1 + nseq2;
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347 nlenmax = MAX( nlenmax1, nlenmax2 );
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348
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349 rewind( gp1 );
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350 rewind( gp2 );
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351
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352
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353 name = AllocateCharMtx( njob, B );
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354 nlen = AllocateIntVec( njob );
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355 seq1 = AllocateCharMtx( nseq1, nlenmax*3 );
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356 seq2 = AllocateCharMtx( nseq2, nlenmax*3 );
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357 seq = AllocateCharMtx( njob, 1 );
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358 aseq = AllocateCharMtx( njob, nlenmax*3 );
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359 bseq = AllocateCharMtx( njob, nlenmax*3 );
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360 mseq1 = AllocateCharMtx( njob, 1 );
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361 mseq2 = AllocateCharMtx( njob, 1 );
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362 alloclen = nlenmax * 3;
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363
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364 topol = AllocateIntCub( njob, 2, njob );
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365 len = AllocateDoubleMtx( njob, 2 );
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366 pscore = AllocateDoubleMtx( njob, njob );
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367 eff = AllocateDoubleVec( njob );
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368
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369 #if 0
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370 njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 );
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371 njob=nseq1; FRead( gp1, name, nlen, seq1 );
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372 #else
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373 njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 );
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374 njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 );
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375 #endif
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376 njob = nseq1 + nseq2;
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377
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378
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379 #if 0 // CHUUI
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380 commongappick( nseq1, seq1 );
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381 commongappick( nseq2, seq2 );
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382 #endif
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383
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384 for( i=0; i<nseq1; i++ ) seq[i] = seq1[i];
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385 for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1];
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386 /*
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387 Write( stdout, njob, name, nlen, seq );
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388 */
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389
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390 constants( njob, seq );
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391
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392 WriteOptions( trap_g );
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393
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394 c = seqcheck( seq );
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395 if( c )
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396 {
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397 fprintf( stderr, "Illeagal character %c\n", c );
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398 exit( 1 );
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399 }
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400 for( i=1; i<nseq1; i++ )
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401 {
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402 if( nlen[i] != nlen[0] )
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403 ErrorExit( "group1 is not aligned." );
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404 }
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405 for( i=nseq1+1; i<njob; i++ )
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406 {
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407 if( nlen[i] != nlen[nseq1] )
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408 ErrorExit( "group2 is not aligned." );
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409 }
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410 if( tbutree == 0 )
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411 {
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412 for( i=0; i<nseq1; i++ )
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413 {
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414 for( j=i+1; j<nseq1; j++ )
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415 {
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416 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
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417 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
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418 }
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419 for( j=nseq1; j<njob; j++ )
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420 {
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421 pscore[i][j] = 3.0;
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422 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
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423 }
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424 }
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425 for( i=nseq1; i<njob-1; i++ )
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426 {
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427 for( j=i+1; j<njob; j++ )
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428 {
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429 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
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430 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
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431 }
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432 }
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433 // fprintf( stderr, "\n" );
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434
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435
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436 }
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437 else
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438 {
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439 fprintf( stderr, "Not supported\n" );
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440 exit( 1 );
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441 #if 0
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442 prep = fopen( "hat2", "r" );
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443 if( prep == NULL ) ErrorExit( "Make hat2." );
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444 readhat2( prep, njob, name, pscore );
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445 fclose( prep );
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446 #endif
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447 }
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448 fprintf( stderr, "Constructing dendrogram ... " );
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449 if( treemethod == 'x' )
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450 veryfastsupg( njob, pscore, topol, len );
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451 else
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452 ErrorExit( "Incorrect tree\n" );
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453 fprintf( stderr, "done.\n" );
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454
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455 if( tbrweight )
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456 {
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457 weight = 3;
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458 counteff_simple( njob, topol, len, eff );
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459 // for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] );
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460 }
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461 else
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462 {
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463 for( i=0; i<njob; i++ ) eff[i] = 1.0;
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464 }
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465
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466 len1 = strlen( seq[0] );
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467 len2 = strlen( seq[nseq1] );
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468 if( len1 > 30000 || len2 > 30000 )
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469 {
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470 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
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471 alg = 'M';
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472 }
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473
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474
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475
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476
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477 GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen );
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478
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479 #if 0
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480 writePre( njob, name, nlen, aseq, 1 );
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481 #else
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482 writeDataforgaln( stdout, njob, name, nlen, aseq );
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483 #endif
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484
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485 SHOWVERSION;
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486 return( 0 );
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487 }