diff mafft/core/mafft-profile.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/mafft-profile.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,487 @@
+#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 '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 = myatoi( *++argv );
+					--argc;
+					goto nextoption;
+				case 'w':
+					fftWinSize = myatoi( *++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 = myatoi( *++argv );
+                    fprintf( stderr, "kappa = %d\n", kimuraR );
+                    --argc;
+                    goto nextoption;
+				case 'b':
+					nblosum = myatoi( *++argv );
+					scoremtx = 1;
+					fprintf( stderr, "blosum %d\n", nblosum );
+					--argc;
+					goto nextoption;
+				case 'j':
+					pamN = myatoi( *++argv );
+					scoremtx = 0;
+					TMorJTT = JTT;
+					fprintf( stderr, "jtt %d\n", pamN );
+					--argc;
+					goto nextoption;
+				case 'm':
+					pamN = myatoi( *++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" );
+*/
+
+	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( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum );
+		else
+			pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+	}
+	else
+	{
+		if( alg == 'M' )
+			pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+		else
+			pscore = A__align( n_dis_consweight_multi, 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
+
+	
+/*
+	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 );
+}