--- /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