+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- calledByXced = 0;
- devide = 0;
- use_fft = 0;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'C';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- ppenalty = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- scoremtx = NOTSPECIFIED;
-
- while( --argc > 0 && (*++argv)[0] == '-' )
- {
- while ( (c = *++argv[0]) )
- {
- switch( c )
- {
- case 'f':
- ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "ppenalty = %d\n", ppenalty );
- --argc;
- goto nextoption;
- case 'g':
- ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
- --argc;
- goto nextoption;
- case 'h':
- poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "poffset = %d\n", poffset );
- --argc;
- goto nextoption;
- case 'D':
- scoremtx = -1;
- break;
- case 'P':
- scoremtx = 0;
- break;
- case 'i':
- contin = 1;
- break;
- case 'e':
- fftscore = 0;
- break;
- case 'O':
- fftNoAnchStop = 1;
- break;
- case 'R':
- fftRepeatStop = 1;
- break;
- case 'Q':
- calledByXced = 1;
- break;
- case 's':
- treemethod = 's';
- break;
- case 'x':
- treemethod = 'x';
- break;
- case 'p':
- treemethod = 'p';
- break;
- case 'a':
- alg = 'a';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'S':
- alg = 'S';
- break;
- case 'C':
- alg = 'C';
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'v':
- tbrweight = 3;
- break;
- case 'd':
- disp = 1;
- break;
- case 'o':
- outgap = 0;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
- case 'Z':
- checkC = 1;
- break;
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc == 1 )
- {
- cut = atof( (*argv) );
- argc--;
- }
- if( argc != 0 )
- {
- fprintf( stderr, "options: Check source file !\n" );
- exit( 1 );
- }
- if( tbitr == 1 && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : o, m or u\n" );
- exit( 1 );
- }
- if( alg == 'C' && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : C, o\n" );
- exit( 1 );
- }
- readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
-}
-
-
-void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
-{
- int i, j, l;
- int clus1, clus2;
- int s1, s2, r1, r2;
- float pscore;
- static char *indication1, *indication2;
- static char **name1, **name2;
- static double **partialmtx = NULL;
- static int ***partialtopol = NULL;
- static double **partiallen = NULL;
- static double **partialeff = NULL;
- static double *effarr = NULL;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
-#if 0
- char pair[njob][njob];
-#else
- static char **pair;
-#endif
- if( partialtopol == NULL )
- {
- partialmtx = AllocateDoubleMtx( njob, njob );
- partialtopol = AllocateIntCub( njob, 2, njob );
- partialeff = AllocateDoubleMtx( njob, njob );
- partiallen = AllocateDoubleMtx( njob, 2 );
- effarr = AllocateDoubleVec( njob );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( njob*3+100 );
- indication2 = AllocateCharVec( njob*3+100 );
- name1 = AllocateCharMtx( njob, B+1 );
- name2 = AllocateCharMtx( njob, B+1 );
-#if 0
-#else
- pair = AllocateCharMtx( njob, njob );
-#endif
- }
-
- if( checkC )
- for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
-
- for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
- for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
-
- if( checkC )
- for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
-
- writePre( njob, name, nlen, aseq, 0 );
-
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
- for( i=0; i<njob; i++ ) pair[i][i] = 1;
- for( l=0; l<njob-1; l++ )
- {
- s1 = topol[l][0][0];
- for( i=0; (r1=topol[l][0][i])>-1; i++ )
- if( pair[s1][r1] != 1 ) exit( 1 );
- s2 = topol[l][1][0];
- for( i=0; (r2=topol[l][1][i])>-1; i++ )
- if( pair[s2][r2] != 1 ) exit( 1 );
-
- clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
- clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
- fprintf( trap_g, "\nSTEP-%d\n", l );
- fprintf( trap_g, "group1 = %s\n", indication1 );
- fprintf( trap_g, "group2 = %s\n", indication2 );
-
- fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
- fprintf( stderr, "group1 = %.66s", indication1 );
- if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, "\n" );
-
- if( checkC )
- for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-/*
- fprintf( stderr, "before align all\n" );
- display( aseq, njob );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
- pscore = Fgetlag( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
-
- for( i=0; (r2=topol[l][1][i])>-1; i++ )
- {
- pair[s1][r2] = 1;
- pair[s2][r2] = 0;
- }
-
- writePre( njob, name, nlen, aseq, 0 );
-
- if( disp ) display( aseq, njob );
- fprintf( stderr, "\n" );
-
- }
-}
-
-static void WriteOptions( FILE *fp )
-{
- fprintf( fp, "tree-base method\n" );
- if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
- if( tbitr || tbweight )
- {
- fprintf( fp, "iterate at each step\n" );
- if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
- if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
- if( tbweight ) fprintf( fp, " weighted\n" );
- fprintf( fp, "\n" );
- }
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
-
- if( scoremtx == 0 || scoremtx == -1 )
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- else
- fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Apgorithm A+\n" );
- else if( alg == 'S' )
- fprintf( fp, "Apgorithm S\n" );
- else if( alg == 'C' )
- fprintf( fp, "Apgorithm A+/C\n" );
- else
- fprintf( fp, "Unknown algorithm\n" );
-
- if( treemethod == 'x' )
- fprintf( fp, "Tree = UPGMA (3).\n" );
- else if( treemethod == 's' )
- fprintf( fp, "Tree = UPGMA (2).\n" );
- else if( treemethod == 'p' )
- fprintf( fp, "Tree = UPGMA (1).\n" );
- else
- fprintf( fp, "Unknown tree.\n" );
-
- if( use_fft )
- {
- fprintf( fp, "FFT on\n" );
- if( scoremtx == -1 )
- fprintf( fp, "Basis : 4 nucleotides\n" );
- else
- {
- if( fftscore )
- fprintf( fp, "Basis : Polarity and Volume\n" );
- else
- fprintf( fp, "Basis : 20 amino acids\n" );
- }
- fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
- fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
- }
- else
- fprintf( fp, "FFT off\n" );
- fflush( fp );
-}
-
-
-int main( int argc, char *argv[] )
-{
- static int nlen[M];
- static char **name, **seq;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static double **pscore;
- static double **eff;
- static double **node0, **node1;
- int i, j;
- static int ***topol;
- static double **len;
- FILE *prep;
- char c;
- int alloclen;
-
- arguments( argc, argv );
- getnumlen( stdin );
- rewind( stdin );
-
- name = AllocateCharMtx( njob, B+1 );
- seq = AllocateCharMtx( njob, nlenmax*5+1 );
- aseq = AllocateCharMtx( njob, nlenmax*5+1 );
- bseq = AllocateCharMtx( njob, nlenmax*5+1 );
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- alloclen = nlenmax*5;
-
- topol = AllocateIntCub( njob, 2, njob );
- len = AllocateDoubleMtx( njob, 2 );
- pscore = AllocateDoubleMtx( njob, njob );
- eff = AllocateDoubleMtx( njob, njob );
- node0 = AllocateDoubleMtx( njob, njob );
- node1 = AllocateDoubleMtx( njob, njob );
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData_pointer( stdin, name, nlen, seq );
-#endif
-
- constants( njob, seq );
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illeagal character %c\n", c );
- exit( 1 );
- }
-
- writePre( njob, name, nlen, seq, 0 );
-
- if( tbutree == 0 )
- {
- for( i=1; i<njob; i++ )
- {
- if( nlen[i] != nlen[0] )
- {
- fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
- exit( 1 );
- }
- }
- for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
- {
- /*
- pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
- */
- pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
- }
- }
- else
- {
- fprintf( stderr, "Loading 'hat2' ... " );
- prep = fopen( "hat2", "r" );
- if( prep == NULL ) ErrorExit( "Make hat2." );
- readhat2_pointer( prep, njob, name, pscore );
- fclose( prep );
- fprintf( stderr, "done.\n" );
-
-#if 0
- prep = fopen( "hat2_check", "w" );
- WriteHat2( prep, njob, name, pscore );
- fclose( prep );
-#endif
-
- }
-
- fprintf( stderr, "Constructing dendrogram ... " );
- if( treemethod == 'x' )
- supg( njob, pscore, topol, len );
- else if( treemethod == 's' )
- spg( njob, pscore, topol, len );
- else if( treemethod == 'p' )
- upg2( njob, pscore, topol, len );
- else
- ErrorExit( "Incorrect tree\n" );
- fprintf( stderr, "done.\n" );
-
- countnode( njob, topol, node0 );
- if( tbrweight )
- {
- weight = 3;
- utree = 0; counteff( njob, topol, len, eff ); utree = 1;
- }
- else
- {
- for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
- }
-
-
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
- treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
-
- fprintf( trap_g, "done\n" );
- fclose( trap_g );
-
- writePre( njob, name, nlen, aseq, !contin );
- writeData_pointer( stdout, njob, name, nlen, aseq );
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
- SHOWVERSION;
- return( 0 );
-}