+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- thrinter = 1.0;
- inputfile = NULL;
- fftkeika = 0;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- 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 = 'A';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- scoremtx = 1;
- kobetsubunkatsu = 0;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- TMorJTT = JTT;
-
- while( --argc > 0 && (*++argv)[0] == '-' )
- {
- while ( c = *++argv[0] )
- {
- switch( c )
- {
- case 'i':
- inputfile = *++argv;
- fprintf( stderr, "inputfile = %s\n", inputfile );
- --argc;
- goto nextoption;
- 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 'k':
- kimuraR = atoi( *++argv );
- fprintf( stderr, "kimuraR = %d\n", kimuraR );
- --argc;
- goto nextoption;
- case 'b':
- nblosum = atoi( *++argv );
- scoremtx = 1;
- fprintf( stderr, "blosum %d\n", nblosum );
- --argc;
- goto nextoption;
- case 'j':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = JTT;
- fprintf( stderr, "jtt %d\n", pamN );
- --argc;
- goto nextoption;
- case 'm':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = TM;
- fprintf( stderr, "tm %d\n", pamN );
- --argc;
- goto nextoption;
- case 'l':
- fastathreshold = atof( *++argv );
- constraint = 2;
- fprintf( stderr, "weighti = %f\n", fastathreshold );
- --argc;
- goto nextoption;
- case 'c':
- thrinter = atof( *++argv );
- fprintf( stderr, "thrinter %f\n", thrinter );
- --argc;
- goto nextoption;
-#if 0
- case 'm':
- fmodel = 1;
- break;
-#endif
- case 'r':
- fmodel = -1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- 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':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- 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 );
- }
-}
-
-
-void treebase( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double *effarr, int alloclen, LocalHom **localhomtable )
-{
- int i, j, l;
- int clus1, clus2;
- int s1, s2, r1, r2;
- float pscore, tscore;
- static char *indication1, *indication2;
- FILE *trap;
- static char name1[M][B], name2[M][B];
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- static LocalHom ***localhomshrink = NULL;
- float dumfl = 0.0;
- double total;
-
-
- if( effarr1 == NULL )
- {
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
-#if 0
-#else
- if( constraint )
- {
- localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
- for( i=0; i<njob; i++)
- localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- }
-#endif
- }
-
-#if 0
- fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
- for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
-
- if( constraint )
- calcimportance( njob, effarr, aseq, localhomtable );
-
-
- writePre( njob, name, nlen, aseq, 0 );
-
- tscore = 0.0;
- for( l=0; l<njob-1; l++ )
- {
-
- clus1 = fastconjuction( topol[l][0], aseq, mseq1, effarr1, effarr, name, name1, indication1 );
- clus2 = fastconjuction( topol[l][1], 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 );
-
-#if 1
- fprintf( stderr, "STEP %d /%d\r", l+1, njob-1 );
-#else
- 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" );
-#endif
-// for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-
- if( constraint )
- {
- fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-// fprintf( stderr, "localhomshrink =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
-// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
-// fprintf( stderr, "after weight =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
- }
-
-/*
- 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" );
-*/
-
- if( constraint == 2 )
- {
- imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &dumfl );
- }
- else if( use_fft )
- {
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- }
- else
- {
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- break;
- case( 'A' ):
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl );
- break;
- case ( 'C' ):
- if( outgap && ( clus1 == 1 && clus2 != 1 || clus1 != 1 && clus2 == 1 ) )
- {
- pscore = translate_and_Calign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- }
- else
- {
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl );
- }
- break;
- default:
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f\n", pscore );
-#endif
- tscore += pscore;
-/*
- fprintf( stderr, "after align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "after align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
- writePre( njob, name, nlen, aseq, 0 );
-
- if( disp ) display( aseq, njob );
- }
-#if SCOREOUT
- fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
-#endif
-}
-
-static void WriteOptions( FILE *fp )
-{
-
- if( dorp == 'd' ) fprintf( fp, "DNA\n" );
- else
- {
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- }
- fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- if( use_fft ) fprintf( fp, "FFT on\n" );
-
- 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" );
- }
-
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm 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( dorp == 'd' )
- 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[M][B], **seq;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static double **iscore;
- static double *eff;
- int i, j;
- int identity;
- static int ***topol;
- static double **len;
- FILE *prep;
- FILE *infp;
- FILE *hat3p;
- FILE *orderfp;
- char c;
- int alloclen;
- double total;
- LocalHom **localhomtable;
- LocalHom *tmpptr;
-
- arguments( argc, argv );
-
- if( inputfile )
- {
- infp = fopen( inputfile, "r" );
- if( !infp )
- {
- fprintf( stderr, "Cannot open %s\n", inputfile );
- exit( 1 );
- }
- }
- else
- infp = stdin;
-
-
- getnumlen( infp );
- rewind( infp );
-
- if( njob < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
-
- seq = AllocateCharMtx( njob, nlenmax*9+1 );
- aseq = AllocateCharMtx( njob, nlenmax*9+1 );
- bseq = AllocateCharMtx( njob, nlenmax*9+1 );
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- alloclen = nlenmax*9;
-
- topol = AllocateIntCub( njob, 2, njob );
- len = AllocateDoubleMtx( njob, 2 );
- iscore = AllocateDoubleMtx( njob, njob );
- eff = AllocateDoubleVec( njob );
- if( constraint )
- {
- localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- for( i=0; i<njob; i++)
- {
- localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
- for( j=0; j<njob; j++)
- {
- localhomtable[i][j].nokori = 0;
- localhomtable[i][j].start1 = -1;
- localhomtable[i][j].end1 = -1;
- localhomtable[i][j].start2 = -1;
- localhomtable[i][j].end2 = -1;
- localhomtable[i][j].overlapaa = -1.0;
- localhomtable[i][j].opt = -1.0;
- localhomtable[i][j].importance = -1.0;
- localhomtable[i][j].next = NULL;
- localhomtable[i][j].extended = -1;
- localhomtable[i][j].last = localhomtable[i]+j;
- }
- }
-
- fprintf( stderr, "Loading 'hat3' ... " );
- prep = fopen( "hat3", "r" );
- if( prep == NULL ) ErrorExit( "Make hat3." );
- readlocalhomtable2( prep, njob, localhomtable );
- fclose( prep );
- fprintf( stderr, "done.\n" );
-
-#if 0
- for( i=0; i<njob; i++ )
- for( j=0; j<njob; j++ )
- fprintf( stderr, "[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
-#endif
-
-// outlocalhom( localhomtable, njob );
-
- }
-
-
-
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData( infp, name, nlen, seq );
-#endif
- fclose( infp );
-
- 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] );
- */
- iscore[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( prep, njob, name, iscore );
- fclose( prep );
- fprintf( stderr, "done.\n" );
-
-#if 0
- prep = fopen( "hat2_check", "w" );
- WriteHat2( prep, njob, name, pscore );
- fclose( prep );
-#endif
-
- }
-
-#if 0
- for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
- iscore[j][i] = iscore[i][j];
-#endif
-
- fprintf( stderr, "Constructing dendrogram ... " );
- if( treemethod == 'x' )
- veryfastsupg( njob, iscore, topol, len );
- else if( treemethod == 's' )
- spg( njob, iscore, topol, len );
- else if( treemethod == 'p' )
- upg2( njob, iscore, topol, len );
- else
- ErrorExit( "Incorrect tree\n" );
- fprintf( stderr, "done.\n" );
-
- orderfp = fopen( "order", "w" );
- if( !orderfp )
- {
- fprintf( stderr, "Cannot open 'order'\n" );
- exit( 1 );
- }
- for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
- {
- fprintf( orderfp, "%d\n", j );
- }
- for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
- {
- fprintf( orderfp, "%d\n", j );
- }
- fclose( orderfp );
-
-
-// countnode( njob, topol, node0 );
- if( tbrweight )
- {
- weight = 3;
-#if 0
- utree = 0; counteff( njob, topol, len, eff ); utree = 1;
-#else
- counteff_simple( njob, topol, len, eff );
-#endif
- }
- else
- {
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
- }
-
- if( constraint )
- {
-#if 1
- if( thrinter > 0.0 )
- {
- fprintf( stderr, "Extending localhom ... " );
- extendlocalhom2( njob, localhomtable, iscore );
- fprintf( stderr, "done.\n" );
-// job de watteoku
- for( i=0; i<njob-1; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- if( i == j ) continue;
- if( localhomtable[i][j]->opt == -1.0 ) continue;
- for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
- tmpptr->opt /= njob;
- }
- }
- }
-#endif
-// resetlocalhom( njob, localhomtable ); // chuui !!!
-#if 1
- fprintf( stderr, "##### writing hat4, nlenmax = %d\n", nlenmax );
- hat3p = fopen( "hat4", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat4." );
- for( i=0; i<njob-1; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- if( i == j ) continue;
- for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p nokori=%d ext=%d\n", i, j, tmpptr->overlapaa, tmpptr->opt * 5.8 / 600, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next, tmpptr->nokori, tmpptr->extended );
- fflush( hat3p );
- if( tmpptr->opt == -1.0 ) continue;
- }
- }
- }
- fclose( hat3p );
- fprintf( stderr, "done.\n" );
-#endif
- }
-
- FreeDoubleMtx( len );
- FreeDoubleMtx( iscore );
-
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
- treebase( name, nlen, bseq, aseq, mseq1, mseq2, topol, eff, alloclen, localhomtable );
-
-
-#if 0
- if( constraint )
- {
- LocalHom *tmppt1, *tmppt2;
- for( i=0; i<njob; i++)
- {
- for( j=0; j<njob; j++)
- {
- tmppt1 = localhomtable[i]+j;
- while( tmppt2 = tmppt1->next )
- {
- free( (void *)tmppt1 );
- tmppt1 = tmppt2;
- }
- free( (void *)tmppt1 );
- }
- free( (void *)(localhomtable[i]+j) );
- }
- free( (void *)localhomtable );
- }
-#endif
-
- fprintf( trap_g, "done.\n" );
- fclose( trap_g );
-
- writePre( njob, name, nlen, aseq, !contin );
-#if 0
- writeData( stdout, njob, name, nlen, aseq );
-#endif
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
-
- if( constraint ) FreeLocalHomTable( localhomtable, njob );
-
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff