| 1 | #include "mltaln.h" |
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| 2 | |
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| 3 | #define DEBUG 0 |
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| 4 | #define IODEBUG 0 |
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| 5 | #define SCOREOUT 1 |
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| 6 | #define TSUYOSAFACTOR 100 |
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| 7 | |
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| 8 | |
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| 9 | static int nhomologs; |
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| 10 | static int seedoffset; |
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| 11 | |
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| 12 | void strip( char *s ) |
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| 13 | { |
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| 14 | char *pt = s; |
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| 15 | while( *++pt ) |
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| 16 | if( *pt == '\n' ) *pt = 0; |
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| 17 | } |
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| 18 | |
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| 19 | |
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| 20 | void arguments( int argc, char *argv[] ) |
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| 21 | { |
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| 22 | int c; |
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| 23 | |
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| 24 | seedoffset = 0; |
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| 25 | nhomologs = 1; |
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| 26 | inputfile = NULL; |
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| 27 | fftkeika = 0; |
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| 28 | pslocal = -1000.0; |
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| 29 | constraint = 0; |
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| 30 | nblosum = 62; |
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| 31 | fmodel = 0; |
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| 32 | calledByXced = 0; |
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| 33 | devide = 0; |
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| 34 | use_fft = 0; |
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| 35 | fftscore = 1; |
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| 36 | fftRepeatStop = 0; |
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| 37 | fftNoAnchStop = 0; |
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| 38 | weight = 3; |
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| 39 | utree = 1; |
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| 40 | tbutree = 1; |
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| 41 | refine = 0; |
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| 42 | check = 1; |
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| 43 | cut = 0.0; |
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| 44 | disp = 0; |
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| 45 | outgap = 1; |
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| 46 | alg = 'A'; |
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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 | treemethod = 'x'; |
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| 54 | contin = 0; |
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| 55 | scoremtx = 1; |
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| 56 | kobetsubunkatsu = 0; |
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| 57 | divpairscore = 0; |
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| 58 | dorp = NOTSPECIFIED; |
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| 59 | ppenalty = NOTSPECIFIED; |
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| 60 | ppenalty_OP = NOTSPECIFIED; |
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| 61 | ppenalty_ex = NOTSPECIFIED; |
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| 62 | ppenalty_EX = NOTSPECIFIED; |
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| 63 | poffset = NOTSPECIFIED; |
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| 64 | kimuraR = NOTSPECIFIED; |
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| 65 | pamN = NOTSPECIFIED; |
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| 66 | geta2 = GETA2; |
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| 67 | fftWinSize = NOTSPECIFIED; |
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| 68 | fftThreshold = NOTSPECIFIED; |
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| 69 | |
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| 70 | while( --argc > 0 && (*++argv)[0] == '-' ) |
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| 71 | { |
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| 72 | while ( ( c = *++argv[0] ) ) |
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| 73 | { |
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| 74 | switch( c ) |
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| 75 | { |
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| 76 | case 'i': |
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| 77 | inputfile = *++argv; |
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| 78 | fprintf( stderr, "seed = %s\n", inputfile ); |
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| 79 | --argc; |
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| 80 | goto nextoption; |
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| 81 | case 't': |
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| 82 | nhomologs = atoi( *++argv ); |
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| 83 | fprintf( stderr, "nhomologs = %d\n", nhomologs ); |
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| 84 | --argc; |
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| 85 | goto nextoption; |
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| 86 | case 'o': |
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| 87 | seedoffset = atoi( *++argv ); |
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| 88 | fprintf( stderr, "seedoffset = %d\n", seedoffset ); |
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| 89 | --argc; |
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| 90 | goto nextoption; |
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| 91 | case 'D': |
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| 92 | dorp = 'd'; |
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| 93 | break; |
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| 94 | case 'P': |
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| 95 | dorp = 'p'; |
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| 96 | break; |
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| 97 | default: |
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| 98 | fprintf( stderr, "illegal option %c\n", c ); |
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| 99 | argc = 0; |
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| 100 | break; |
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| 101 | } |
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| 102 | } |
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| 103 | nextoption: |
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| 104 | ; |
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| 105 | } |
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| 106 | if( argc == 1 ) |
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| 107 | { |
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| 108 | cut = atof( (*argv) ); |
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| 109 | argc--; |
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| 110 | } |
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| 111 | if( argc != 0 ) |
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| 112 | { |
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| 113 | fprintf( stderr, "options: Check source file !\n" ); |
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| 114 | exit( 1 ); |
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| 115 | } |
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| 116 | if( tbitr == 1 && outgap == 0 ) |
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| 117 | { |
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| 118 | fprintf( stderr, "conflicting options : o, m or u\n" ); |
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| 119 | exit( 1 ); |
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| 120 | } |
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| 121 | if( alg == 'C' && outgap == 0 ) |
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| 122 | { |
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| 123 | fprintf( stderr, "conflicting options : C, o\n" ); |
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| 124 | exit( 1 ); |
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| 125 | } |
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| 126 | } |
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| 127 | |
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| 128 | int countamino( char *s, int end ) |
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| 129 | { |
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| 130 | int val = 0; |
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| 131 | while( end-- ) |
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| 132 | if( *s++ != '-' ) val++; |
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| 133 | return( val ); |
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| 134 | } |
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| 135 | |
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| 136 | static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen ) |
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| 137 | { |
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| 138 | int i, j; |
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| 139 | FILE *hat3p; |
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| 140 | float pscore = 0.0; // by D.Mathog |
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| 141 | static double *effarr1 = NULL; |
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| 142 | static double *effarr2 = NULL; |
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| 143 | char *aseq; |
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| 144 | static char **pseq; |
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| 145 | LocalHom **localhomtable, *tmpptr; |
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| 146 | double tsuyosa; |
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| 147 | |
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| 148 | if( nhomologs < 1 ) nhomologs = 1; // tsuyosa=0.0 wo sakeru |
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| 149 | tsuyosa = (double)nhomologs * nhomologs * TSUYOSAFACTOR; |
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| 150 | fprintf( stderr, "tsuyosa = %f\n", tsuyosa ); |
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| 151 | localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) ); |
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| 152 | for( i=0; i<njob; i++) |
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| 153 | { |
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| 154 | localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) ); |
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| 155 | for( j=0; j<njob; j++) |
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| 156 | { |
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| 157 | localhomtable[i][j].start1 = -1; |
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| 158 | localhomtable[i][j].end1 = -1; |
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| 159 | localhomtable[i][j].start2 = -1; |
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| 160 | localhomtable[i][j].end2 = -1; |
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| 161 | localhomtable[i][j].opt = -1.0; |
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| 162 | localhomtable[i][j].next = NULL; |
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| 163 | } |
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| 164 | } |
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| 165 | |
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| 166 | if( effarr1 == NULL ) |
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| 167 | { |
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| 168 | effarr1 = AllocateDoubleVec( njob ); |
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| 169 | effarr2 = AllocateDoubleVec( njob ); |
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| 170 | pseq = AllocateCharMtx( 2, 0 ); |
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| 171 | aseq = AllocateCharVec( nlenmax*9+1 ); |
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| 172 | #if 0 |
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| 173 | #else |
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| 174 | #endif |
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| 175 | } |
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| 176 | |
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| 177 | #if 0 |
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| 178 | fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold ); |
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| 179 | #endif |
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| 180 | |
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| 181 | #if 0 |
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| 182 | for( i=0; i<njob; i++ ) |
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| 183 | fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] ); |
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| 184 | #endif |
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| 185 | |
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| 186 | |
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| 187 | // writePre( njob, name, nlen, aseq, 0 ); |
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| 188 | |
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| 189 | hat3p = fopen( "hat3", "w" ); |
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| 190 | if( !hat3p ) ErrorExit( "Cannot open hat3." ); |
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| 191 | fprintf( stderr, "\n" ); |
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| 192 | for( i=0; i<njob-1; i++ ) |
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| 193 | { |
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| 194 | for( j=i+1; j<njob; j++ ) |
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| 195 | { |
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| 196 | pseq[0] = seq[i]; |
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| 197 | pseq[1] = seq[j]; |
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| 198 | |
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| 199 | if( strlen( pseq[0] ) != strlen( pseq[1] ) ) |
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| 200 | { |
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| 201 | fprintf( stderr, "## ERROR ###\n" ); |
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| 202 | fprintf( stderr, "Not aligned, %s - %s\n", name[i], name[j] ); |
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| 203 | fprintf( stderr, "## ERROR ###\n" ); |
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| 204 | exit( 1 ); |
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| 205 | } |
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| 206 | |
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| 207 | |
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| 208 | fprintf( stderr, "adding %d-%d\r", i, j ); |
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| 209 | putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) ); |
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| 210 | for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) |
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| 211 | { |
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| 212 | if( tmpptr->opt == -1.0 ) continue; |
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| 213 | if( tmpptr->start1 == -1 ) continue; |
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| 214 | fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d k\n", i+seedoffset, j+seedoffset, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 ); |
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| 215 | } |
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| 216 | } |
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| 217 | } |
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| 218 | fprintf( stderr, "\n" ); |
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| 219 | fclose( hat3p ); |
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| 220 | |
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| 221 | #if DEBUG |
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| 222 | fprintf( stderr, "calling FreeLocalHomTable\n" ); |
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| 223 | #endif |
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| 224 | FreeLocalHomTable( localhomtable, njob ); |
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| 225 | #if DEBUG |
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| 226 | fprintf( stderr, "done. FreeLocalHomTable\n" ); |
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| 227 | #endif |
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| 228 | } |
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| 229 | |
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| 230 | static void WriteOptions( FILE *fp ) |
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| 231 | { |
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| 232 | |
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| 233 | if( dorp == 'd' ) fprintf( fp, "DNA\n" ); |
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| 234 | else |
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| 235 | { |
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| 236 | if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN ); |
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| 237 | else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum ); |
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| 238 | else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" ); |
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| 239 | } |
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| 240 | fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 ); |
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| 241 | if( use_fft ) fprintf( fp, "FFT on\n" ); |
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| 242 | |
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| 243 | fprintf( fp, "tree-base method\n" ); |
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| 244 | if( tbrweight == 0 ) fprintf( fp, "unweighted\n" ); |
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| 245 | else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" ); |
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| 246 | if( tbitr || tbweight ) |
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| 247 | { |
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| 248 | fprintf( fp, "iterate at each step\n" ); |
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| 249 | if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" ); |
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| 250 | if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" ); |
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| 251 | if( tbweight ) fprintf( fp, " weighted\n" ); |
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| 252 | fprintf( fp, "\n" ); |
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| 253 | } |
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| 254 | |
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| 255 | fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 ); |
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| 256 | |
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| 257 | if( alg == 'a' ) |
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| 258 | fprintf( fp, "Algorithm A\n" ); |
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| 259 | else if( alg == 'A' ) |
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| 260 | fprintf( fp, "Algorithm A+\n" ); |
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| 261 | else if( alg == 'S' ) |
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| 262 | fprintf( fp, "Apgorithm S\n" ); |
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| 263 | else if( alg == 'C' ) |
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| 264 | fprintf( fp, "Apgorithm A+/C\n" ); |
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| 265 | else |
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| 266 | fprintf( fp, "Unknown algorithm\n" ); |
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| 267 | |
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| 268 | if( treemethod == 'x' ) |
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| 269 | fprintf( fp, "Tree = UPGMA (3).\n" ); |
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| 270 | else if( treemethod == 's' ) |
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| 271 | fprintf( fp, "Tree = UPGMA (2).\n" ); |
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| 272 | else if( treemethod == 'p' ) |
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| 273 | fprintf( fp, "Tree = UPGMA (1).\n" ); |
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| 274 | else |
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| 275 | fprintf( fp, "Unknown tree.\n" ); |
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| 276 | |
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| 277 | if( use_fft ) |
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| 278 | { |
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| 279 | fprintf( fp, "FFT on\n" ); |
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| 280 | if( dorp == 'd' ) |
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| 281 | fprintf( fp, "Basis : 4 nucleotides\n" ); |
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| 282 | else |
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| 283 | { |
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| 284 | if( fftscore ) |
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| 285 | fprintf( fp, "Basis : Polarity and Volume\n" ); |
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| 286 | else |
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| 287 | fprintf( fp, "Basis : 20 amino acids\n" ); |
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| 288 | } |
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| 289 | fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold ); |
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| 290 | fprintf( fp, "window size of anchors = %dsites\n", fftWinSize ); |
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| 291 | } |
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| 292 | else |
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| 293 | fprintf( fp, "FFT off\n" ); |
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| 294 | fflush( fp ); |
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| 295 | } |
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| 296 | |
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| 297 | |
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| 298 | int main( int argc, char *argv[] ) |
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| 299 | { |
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| 300 | static int nlen[M]; |
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| 301 | static char **name, **seq; |
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| 302 | static char **bseq; |
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| 303 | static double *eff; |
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| 304 | int i; |
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| 305 | char c; |
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| 306 | int alloclen; |
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| 307 | FILE *infp; |
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| 308 | |
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| 309 | arguments( argc, argv ); |
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| 310 | |
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| 311 | if( inputfile ) |
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| 312 | { |
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| 313 | infp = fopen( inputfile, "r" ); |
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| 314 | if( !infp ) |
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| 315 | { |
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| 316 | fprintf( stderr, "Cannot open %s\n", inputfile ); |
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| 317 | exit( 1 ); |
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| 318 | } |
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| 319 | } |
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| 320 | else |
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| 321 | infp = stdin; |
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| 322 | |
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| 323 | getnumlen( infp ); |
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| 324 | rewind( infp ); |
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| 325 | |
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| 326 | if( njob < 2 ) |
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| 327 | { |
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| 328 | fprintf( stderr, "At least 2 sequences should be input!\n" |
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| 329 | "Only %d sequence found.\n", njob ); |
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| 330 | exit( 1 ); |
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| 331 | } |
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| 332 | |
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| 333 | name = AllocateCharMtx( njob, B+1 ); |
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| 334 | seq = AllocateCharMtx( njob, nlenmax*9+1 ); |
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| 335 | bseq = AllocateCharMtx( njob, nlenmax*9+1 ); |
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| 336 | alloclen = nlenmax*9; |
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| 337 | |
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| 338 | eff = AllocateDoubleVec( njob ); |
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| 339 | |
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| 340 | #if 0 |
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| 341 | Read( name, nlen, seq ); |
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| 342 | #else |
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| 343 | readData_pointer( infp, name, nlen, seq ); |
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| 344 | #endif |
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| 345 | fclose( infp ); |
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| 346 | |
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| 347 | constants( njob, seq ); |
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| 348 | |
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| 349 | #if 0 |
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| 350 | fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset ); |
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| 351 | #endif |
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| 352 | |
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| 353 | initSignalSM(); |
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| 354 | |
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| 355 | initFiles(); |
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| 356 | |
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| 357 | WriteOptions( trap_g ); |
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| 358 | |
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| 359 | c = seqcheck( seq ); |
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| 360 | if( c ) |
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| 361 | { |
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| 362 | fprintf( stderr, "Illeagal character %c\n", c ); |
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| 363 | exit( 1 ); |
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| 364 | } |
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| 365 | |
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| 366 | // writePre( njob, name, nlen, seq, 0 ); |
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| 367 | |
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| 368 | for( i=0; i<njob; i++ ) eff[i] = 1.0; |
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| 369 | |
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| 370 | |
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| 371 | for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] ); |
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| 372 | |
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| 373 | |
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| 374 | // for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, bseq[i] ); // CHUUI!! |
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| 375 | for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, seq[i] ); |
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| 376 | |
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| 377 | pairalign( name, nlen, seq, eff, alloclen ); |
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| 378 | |
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| 379 | fprintf( trap_g, "done.\n" ); |
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| 380 | #if DEBUG |
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| 381 | fprintf( stderr, "closing trap_g\n" ); |
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| 382 | #endif |
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| 383 | fclose( trap_g ); |
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| 384 | |
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| 385 | #if IODEBUG |
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| 386 | fprintf( stderr, "OSHIMAI\n" ); |
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| 387 | #endif |
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| 388 | SHOWVERSION; |
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| 389 | return( 0 ); |
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| 390 | } |
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