+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-#define END_OF_VEC -1
-
-
-void arguments()
-{
- int c;
-
- inputfile = NULL;
- fftkeika = 0;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- calledByXced = 0;
- devide = 0;
- use_fft = 1;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'M';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- kobetsubunkatsu = 0;
- makedistmtx = 1;
- ppenalty = -1530;
- ppenalty_ex = NOTSPECIFIED;
- poffset = -123;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- TMorJTT = JTT;
-}
-
-static int maxl;
-static int tsize;
-
-void seq_grp_nuc( int *grp, char *seq )
-{
- int tmp;
- while( *seq )
- {
- tmp = amino_grp[*seq++];
- if( tmp < 4 )
- *grp++ = tmp;
- else
- fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
- }
- *grp = END_OF_VEC;
-}
-
-void seq_grp( int *grp, char *seq )
-{
- int tmp;
- while( *seq )
- {
- tmp = amino_grp[*seq++];
- if( tmp < 6 )
- *grp++ = tmp;
- else
- fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
- }
- *grp = END_OF_VEC;
-}
-
-void makecompositiontable_p( short *table, int *pointt )
-{
- int point;
-
- while( ( point = *pointt++ ) != END_OF_VEC )
- table[point]++;
-}
-
-int commonsextet_p( short *table, int *pointt )
-{
- int value = 0;
- short tmp;
- int point;
- static short *memo = NULL;
- static int *ct = NULL;
- static int *cp;
-
- if( !memo )
- {
- memo = calloc( tsize, sizeof( short ) );
- if( !memo ) ErrorExit( "Cannot allocate memo\n" );
- ct = calloc( MIN( maxl, tsize )+1, sizeof( int ) );
- if( !ct ) ErrorExit( "Cannot allocate memo\n" );
- }
-
- cp = ct;
- while( ( point = *pointt++ ) != END_OF_VEC )
- {
- tmp = memo[point]++;
- if( tmp < table[point] )
- value++;
- if( tmp == 0 ) *cp++ = point;
- }
- *cp = END_OF_VEC;
-
- cp = ct;
- while( *cp != END_OF_VEC )
- memo[*cp++] = 0;
-
- return( value );
-}
-
-void makepointtable_nuc( int *pointt, int *n )
-{
- int point;
- register int *p;
-
- p = n;
- point = *n++ * 1024;
- point += *n++ * 256;
- point += *n++ * 64;
- point += *n++ * 16;
- point += *n++ * 4;
- point += *n++;
- *pointt++ = point;
-
- while( *n != END_OF_VEC )
- {
- point -= *p++ * 1024;
- point *= 4;
- point += *n++;
- *pointt++ = point;
- }
- *pointt = END_OF_VEC;
-}
-
-void makepointtable( int *pointt, int *n )
-{
- int point;
- register int *p;
-
- p = n;
- point = *n++ * 7776;
- point += *n++ * 1296;
- point += *n++ * 216;
- point += *n++ * 36;
- point += *n++ * 6;
- point += *n++;
- *pointt++ = point;
-
- while( *n != END_OF_VEC )
- {
- point -= *p++ * 7776;
- point *= 6;
- point += *n++;
- *pointt++ = point;
- }
- *pointt = END_OF_VEC;
-}
-
-void treebase( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double *effarr, int alloclen )
-{
- 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;
- float dumfl = 0.0;
- double total;
- int intdum;
-
-
- if( effarr1 == NULL )
- {
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
- }
-
-#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] );
-
-
-
-// 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( stderr, "STEP %d /%d\r", l+1, njob-1 );
-// 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" );
-// 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" );
-*/
-
- if( use_fft )
- {
- if( alg == 'M' )
- pscore = Falign_noudp( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
- else
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
- }
- else
- {
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- break;
- case( 'M' ):
- pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
- break;
- case( 'A' ):
- if( clus1 == 1 && clus2 == 1 )
- {
- pscore = G__align11( mseq1, mseq2, alloclen );
- }
- else
- {
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- }
- 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 );
-// fprintf( stderr, "\n" );
- }
-#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 disttbfast( char **in, int nlen[M], char name[M][B] )
-{
- static char **seq;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static int **pscore;
- static double *eff;
- int i, j;
- int identity;
- static int ***topol;
- static double **len;
- FILE *prep;
- FILE *infp;
- char c;
- int alloclen;
- double total;
-
- FILE *fp;
- FILE *orderfp;
- int *grpseq;
- char *tmpseq;
- int **pointt;
- double **mtx;
- double **mtx2;
- int score0;
- static short *table1;
- char b[B];
-
- arguments();
-
- if( njob < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
-
- seq = in;
- 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 = AllocateIntMtx( njob, njob );
- eff = AllocateDoubleVec( njob );
-
-
-
- constants( njob, seq );
-
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illeagal character %c\n", c );
- exit( 1 );
- }
-
- fprintf( stderr, "\n" );
-
-// writePre( njob, name, nlen, seq, 0 );
- if( makedistmtx )
- {
- fprintf( stderr, "Making a distance matrix ..\n" );
-
- tmpseq = AllocateCharVec( nlenmax+1 );
- grpseq = AllocateIntVec( nlenmax+1 );
- pointt = AllocateIntMtx( njob, nlenmax+1 );
- mtx = AllocateDoubleMtx( njob, njob );
- if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
- else tsize = (int)pow( 6, 6 );
-
- maxl = 0;
- for( i=0; i<njob; i++ )
- {
- gappick0( tmpseq, seq[i] );
- nlen[i] = strlen( tmpseq );
- if( nlen[i] < 6 )
- {
- fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
- exit( 1 );
- }
- if( nlen[i] > maxl ) maxl = nlen[i];
- if( dorp == 'd' ) /* nuc */
- {
- seq_grp_nuc( grpseq, tmpseq );
- makepointtable_nuc( pointt[i], grpseq );
- }
- else /* amino */
- {
- seq_grp( grpseq, tmpseq );
- makepointtable( pointt[i], grpseq );
- }
- }
- for( i=0; i<njob; i++ )
- {
- table1 = calloc( tsize, sizeof( short ) );
- if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
- if( i % 10 == 0 )
- {
- fprintf( stderr, "%#4d / %#4d\r", i+1, njob );
- }
- makecompositiontable_p( table1, pointt[i] );
-
- for( j=i; j<njob; j++ )
- {
- mtx[i][j] = commonsextet_p( table1, pointt[j] );
- }
- free( table1 );
- }
- for( i=0; i<njob; i++ )
- {
- score0 = mtx[i][i];
- for( j=0; j<njob; j++ )
- pscore[i][j] = (int)( ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3 * INTMTXSCALE + 0.5 );
- }
- for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
- {
- pscore[i][j] = MIN( pscore[i][j], pscore[j][i] );
- }
-
- if( disopt )
- {
- for( i=0; i<njob; i++ )
- {
- sprintf( b, "=lgth = %#04d", nlen[i] );
- strins( b, name[i] );
- }
- }
- FreeDoubleMtx( mtx );
- free( tmpseq );
- free( grpseq );
- FreeIntMtx( pointt );
- fprintf( stderr, "\ndone.\n\n" );
- }
- else 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] = (int)( substitution_hosei( seq[i], seq[j] ) * INTMTXSCALE + 0.5 );
- }
- }
- else
- {
-#if 1
- fprintf( stderr, "Loading 'hat2' ... " );
- prep = fopen( "hat2", "r" );
- if( prep == NULL ) ErrorExit( "Make hat2." );
- readhat2_int( prep, njob, name, pscore );
- fclose( prep );
- fprintf( stderr, "done.\n" );
-#endif
- }
-#if 0
- prep = fopen( "hat2_check", "w" );
- WriteHat2_int( prep, njob, name, pscore );
- fclose( prep );
-#endif
-
- fprintf( stderr, "Constructing dendrogram ... " );
- if( treemethod == 'x' )
- {
- veryfastsupg_int( njob, pscore, topol, len );
- }
- else
- ErrorExit( "Incorrect tree\n" );
- fprintf( stderr, "\ndone.\n\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 );
-
-
- for( i=0; i<njob; i++ )
- {
- len[i][0] /= INTMTXSCALE;
- len[i][1] /= INTMTXSCALE;
- }
-
- 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;
- }
-
-
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
- FreeIntMtx( pscore );
- FreeDoubleMtx( len );
- fprintf( stderr, "Progressive alignment ... \n" );
- treebase( name, nlen, bseq, aseq, mseq1, mseq2, topol, eff, alloclen );
- fprintf( stderr, "\ndone.\n\n" );
-
-#if DEBUG
- fprintf( stderr, "writing alignment to stdout\n" );
-#endif
-
-
- for( i=0; i<njob; i++ ) strcpy( seq[i], aseq[i] );
-
- fprintf( stderr, "mafft v%s\n", VERSION );
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff