+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-
-#if DEBUG
-#include <time.h>
-#include <sys/time.h>
-#include <sys/resource.h>
-double getrusage_sec()
-{
- struct rusage t;
- struct timeval tv;
- getrusage(RUSAGE_SELF, &t);
- tv = t.ru_utime;
- return tv.tv_sec + (double)tv.tv_usec*1e-6;
-}
-#endif
-
-
-int intcmp( int *str1, int *str2 )
-{
- while( *str1 != -1 && *str2 != -1 )
- if( *str1++ != *str2++ ) return( 1 );
- if( *str1 != *str2 ) return( 1 );
- return( 0 );
-}
-
-char **arguments( int argc, char *argv[] )
-{
- int c = 0;
-
- fmodel = 0;
- nblosum = 62;
- calledByXced = 0;
- devide = 0;
- fftscore = 1;
- use_fft = 1;
- alg = 'A';
- weight = 0;
- utree = 1;
- tbutree = 0;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 0;
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- scoremtx = 1;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- poffset = 0; // chokusetsu yobareru kara
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- TMorJTT = JTT;
- treemethod = 'x';
-
-
- while( --argc > 0 && (*++argv)[0] == '-' )
- {
- while ( ( c = *++argv[0] ) )
- {
- switch( c )
- {
- case 'P':
- dorp = 'p';
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'N':
- use_fft = 0;
- break;
- case 'e':
- fftscore = 0;
- break;
- case 'Q':
- alg = 'Q';
- break;
- case 'H':
- alg = 'H';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'M':
- alg = 'M';
- break;
- case 'd':
- disp = 1;
- break;
- case 'O':
- outgap = 0;
- break;
- case 'a':
- fmodel = 1;
- break;
- case 'u':
- tbrweight = 0;
- break;
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'Z':
- checkC = 1;
- break;
- 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, "kappa = %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;
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc != 2 )
- {
- fprintf( stderr, "options: Check source file ! %c ?\n", c );
- exit( 1 );
- }
- fprintf( stderr, "tbitr = %d, tbrweight = %d, tbweight = %d\n", tbitr, tbrweight, tbweight );
-// readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
- return( argv );
-
-}
-
-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 )
-{
- int i;
- int clus1, clus2;
- int s1, s2;
- float pscore;
- static char **name1, **name2;
- double *effarr = eff;
- double *effarr1 = NULL;
- double *effarr2 = NULL;
- static char *indication1, *indication2;
- float dumfl = 0.0;
- int intdum;
-#if DEBUG
- double time1, time2;
-#endif
-
-
-// fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize );
-// fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold );
-
- if( effarr1 == NULL )
- {
- name1 = AllocateCharMtx( nseq1, B );
- name2 = AllocateCharMtx( nseq2, B );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
-#if 0
-#else
-#endif
- }
-
- for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
-
-
-
- s1 = 0;
- s2 = nseq1;
-// fprintf( stdout, "nseq1 = %d\n", nseq1 );
-
-
-
- clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
- clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
-/*
- 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( alg == 'Q' )
- fprintf( stderr, "before realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
- else if( alg == 'H' )
- fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-
- commongappick( nseq1, mseq1 );
- commongappick( nseq2, mseq2 );
-
-
-#if DEBUG
- time1 = getrusage_sec();
- fprintf( stderr, "entering Falign\n" );
-#endif
- if( use_fft )
- {
- if( alg == 'M' )
- pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
- else
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
- }
- else
- {
- if( alg == 'M' )
- pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- else if( alg == 'H' )
- pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- else if( alg == 'Q' )
- pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- else
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- }
-#if DEBUG
- time2 = getrusage_sec();
- fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 );
- fflush( stdout );
-#endif
-
- if( alg == 'H' )
- fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
- else if( alg == 'Q' )
- fprintf( stderr, "after realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-
-
-/*
- 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" );
-*/
-
- fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore );
- if( disp ) display( aseq, njob );
- fprintf( stderr, "\n" );
-
-/*
- trap = fopen( "pre", "r+" );
- if( !trap ) ErrorExit( 1 );
- WriteGapFill( trap, njob, name, nlen, aseq );
- fclose( trap );
- fprintf( stdout, "nseq1 = %d\n", nseq1 );
-*/
-}
-
-static void WriteOptions( FILE *fp )
-{
- fprintf( fp, "tree-base method\n" );
- if( tbweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbweight == 3 ) fprintf( fp, "reversely weighted\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 )
- fprintf( fp, "Gap Penalty = %d, %d\n", penalty, offset );
- else
- fprintf( fp, "Gap Penalty = %d\n", penalty );
-}
-
-
-int main( int argc, char *argv[] )
-{
- char **argv2;
- static int *nlen;
- static char **name, **seq;
- static char **seq1, **seq2;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static double **pscore;
- static double *eff;
- int i, j, len1, len2;
- static int ***topol;
- static double **len;
- FILE *gp1, *gp2;
- char c;
- int nlenmax1, nlenmax2, nseq1, nseq2;
- int alloclen;
-
- argv2 = arguments( argc, argv );
-
- fprintf( stderr, "####### in galn\n" );
-
- initFiles();
-
- fprintf( stderr, "file1 = %s\n", argv2[0] );
- fprintf( stderr, "file2 = %s\n", argv2[1] );
-
- gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" );
- gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" );
-
-#if 0
- PreRead( gp1, &nseq1, &nlenmax1 );
- PreRead( gp2, &nseq2, &nlenmax2 );
-#else
- getnumlen( gp1 );
- nseq1 = njob; nlenmax1 = nlenmax;
- getnumlen( gp2 );
- nseq2 = njob; nlenmax2 = nlenmax;
-#endif
-
- njob = nseq1 + nseq2;
- nlenmax = MAX( nlenmax1, nlenmax2 );
-
- rewind( gp1 );
- rewind( gp2 );
-
-
- name = AllocateCharMtx( njob, B );
- nlen = AllocateIntVec( njob );
- seq1 = AllocateCharMtx( nseq1, nlenmax*3 );
- seq2 = AllocateCharMtx( nseq2, nlenmax*3 );
- seq = AllocateCharMtx( njob, 1 );
- aseq = AllocateCharMtx( njob, nlenmax*3 );
- bseq = AllocateCharMtx( njob, nlenmax*3 );
- mseq1 = AllocateCharMtx( njob, 1 );
- mseq2 = AllocateCharMtx( njob, 1 );
- alloclen = nlenmax * 3;
-
- topol = AllocateIntCub( njob, 2, njob );
- len = AllocateDoubleMtx( njob, 2 );
- pscore = AllocateDoubleMtx( njob, njob );
- eff = AllocateDoubleVec( njob );
-
-#if 0
- njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 );
- njob=nseq1; FRead( gp1, name, nlen, seq1 );
-#else
- njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 );
- njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 );
-#endif
- njob = nseq1 + nseq2;
-
-
-#if 0 // CHUUI
- commongappick( nseq1, seq1 );
- commongappick( nseq2, seq2 );
-#endif
-
- for( i=0; i<nseq1; i++ ) seq[i] = seq1[i];
- for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1];
-/*
- Write( stdout, njob, name, nlen, seq );
-*/
-
- constants( njob, seq );
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illeagal character %c\n", c );
- exit( 1 );
- }
- for( i=1; i<nseq1; i++ )
- {
- if( nlen[i] != nlen[0] )
- ErrorExit( "group1 is not aligned." );
- }
- for( i=nseq1+1; i<njob; i++ )
- {
- if( nlen[i] != nlen[nseq1] )
- ErrorExit( "group2 is not aligned." );
- }
- if( tbutree == 0 )
- {
- for( i=0; i<nseq1; i++ )
- {
- for( j=i+1; j<nseq1; j++ )
- {
- pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
-// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
- }
- for( j=nseq1; j<njob; j++ )
- {
- pscore[i][j] = 3.0;
-// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
- }
- }
- for( i=nseq1; i<njob-1; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
-// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
- }
- }
-// fprintf( stderr, "\n" );
-
-
- }
- else
- {
- fprintf( stderr, "Not supported\n" );
- exit( 1 );
-#if 0
- prep = fopen( "hat2", "r" );
- if( prep == NULL ) ErrorExit( "Make hat2." );
- readhat2( prep, njob, name, pscore );
- fclose( prep );
-#endif
- }
- fprintf( stderr, "Constructing dendrogram ... " );
- if( treemethod == 'x' )
- veryfastsupg( njob, pscore, topol, len );
- else
- ErrorExit( "Incorrect tree\n" );
- fprintf( stderr, "done.\n" );
-
- if( tbrweight )
- {
- weight = 3;
- counteff_simple( njob, topol, len, eff );
-// for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] );
- }
- else
- {
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
- }
-
- len1 = strlen( seq[0] );
- len2 = strlen( seq[nseq1] );
- if( len1 > 30000 || len2 > 30000 )
- {
- fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
- alg = 'M';
- }
-
-
-
-
- GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen );
-
-#if 0
- writePre( njob, name, nlen, aseq, 1 );
-#else
- writeDataforgaln( stdout, njob, name, nlen, aseq );
-#endif
-
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff