diff mafft/core/getlag.c @ 18:e4d75f9efb90 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/getlag.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,461 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+	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 = 'C';
+    mix = 0;
+	tbitr = 0;
+	scmtd = 5;
+	tbweight = 0;
+	tbrweight = 3;
+	checkC = 0;
+	treemethod = 'x';
+	contin = 0;
+	ppenalty = NOTSPECIFIED;
+	ppenalty_ex = NOTSPECIFIED;
+	poffset = NOTSPECIFIED;
+	kimuraR = NOTSPECIFIED;
+	pamN = NOTSPECIFIED;
+	geta2 = GETA2;
+	scoremtx = NOTSPECIFIED;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+	{
+        while ( (c = *++argv[0]) )
+		{
+            switch( c )
+            {
+				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 'D':
+					scoremtx = -1;
+					break;
+				case 'P':
+					scoremtx = 0;
+					break;
+				case 'i':
+					contin = 1;
+					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':
+					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 );
+	}
+	readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
+}
+
+
+void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
+{
+	int i, j, l;
+	int clus1, clus2;
+	int s1, s2, r1, r2;
+	float pscore;
+	static char *indication1, *indication2;
+	static char **name1, **name2;
+	static double **partialmtx = NULL;
+	static int ***partialtopol = NULL;
+	static double **partiallen = NULL;
+	static double **partialeff = NULL;
+	static double *effarr = NULL;
+	static double *effarr1 = NULL;
+	static double *effarr2 = NULL;
+#if 0
+	char pair[njob][njob];
+#else
+	static char **pair;
+#endif
+	if( partialtopol == NULL ) 
+	{
+		partialmtx = AllocateDoubleMtx( njob, njob );
+		partialtopol = AllocateIntCub( njob, 2, njob );
+		partialeff = AllocateDoubleMtx( njob, njob );
+		partiallen = AllocateDoubleMtx( njob, 2 );
+		effarr = AllocateDoubleVec( njob );
+		effarr1 = AllocateDoubleVec( njob );
+		effarr2 = AllocateDoubleVec( njob );
+		indication1 = AllocateCharVec( njob*3+100 );
+		indication2 = AllocateCharVec( njob*3+100 );
+		name1 = AllocateCharMtx( njob, B+1 );
+		name2 = AllocateCharMtx( njob, B+1 );
+#if 0
+#else
+		pair = AllocateCharMtx( njob, njob );
+#endif
+	}
+
+	if( checkC )
+		for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
+
+	for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
+	for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+	if( checkC )
+		for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
+
+	writePre( njob, name, nlen, aseq, 0 );
+
+	for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+	for( i=0; i<njob; i++ ) pair[i][i] = 1;
+	for( l=0; l<njob-1; l++ )
+	{
+		s1 = topol[l][0][0];
+		for( i=0; (r1=topol[l][0][i])>-1; i++ ) 
+			if( pair[s1][r1] != 1 ) exit( 1 );
+		s2 = topol[l][1][0];
+		for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
+			if( pair[s2][r2] != 1 ) exit( 1 );
+
+		clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
+		clus2 = conjuction( pair, s2, 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 );
+
+		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" );
+
+		if( checkC )
+			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" );
+*/
+
+		pscore = Fgetlag( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+
+		for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
+		{
+			pair[s1][r2] = 1;
+			pair[s2][r2] = 0;
+		}
+
+		writePre( njob, name, nlen, aseq, 0 );
+
+		if( disp ) display( aseq, njob );
+		fprintf( stderr, "\n" );
+
+	}
+}
+
+static void WriteOptions( FILE *fp )
+{
+	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" );
+	}
+	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 == 0 || scoremtx == -1 )
+        fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+    else
+        fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
+
+	if( alg == 'a' )
+		fprintf( fp, "Algorithm A\n" );
+	else if( alg == 'A' ) 
+		fprintf( fp, "Apgorithm 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( scoremtx == -1 )
+            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, **seq;
+	static char **mseq1, **mseq2;
+	static char **aseq;
+	static char **bseq;
+	static double **pscore;
+	static double **eff;
+	static double **node0, **node1;
+	int i, j;
+	static int ***topol;
+	static double **len;
+	FILE *prep;
+	char c;
+	int alloclen;
+
+	arguments( argc, argv );
+	getnumlen( stdin );
+	rewind( stdin );
+
+	name = AllocateCharMtx( njob, B+1 );
+	seq = AllocateCharMtx( njob, nlenmax*5+1 );
+	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 = AllocateDoubleMtx( njob, njob );
+	eff = AllocateDoubleMtx( njob, njob );
+	node0 = AllocateDoubleMtx( njob, njob );
+	node1 = AllocateDoubleMtx( njob, njob );
+
+#if 0
+	Read( name, nlen, seq );
+#else
+	readData_pointer( stdin, name, nlen, seq );
+#endif
+
+	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] );
+		*/
+			pscore[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_pointer( prep, njob, name, pscore );
+		fclose( prep );
+		fprintf( stderr, "done.\n" );
+
+#if 0
+		prep = fopen( "hat2_check", "w" );
+		WriteHat2( prep, njob, name, pscore );
+		fclose( prep );
+#endif
+
+	}
+
+	fprintf( stderr, "Constructing dendrogram ... " );
+	if( treemethod == 'x' )
+		supg( njob, pscore, topol, len );
+	else if( treemethod == 's' )
+		spg( njob, pscore, topol, len );
+	else if( treemethod == 'p' )
+		upg2( njob, pscore, topol, len );
+	else 
+		ErrorExit( "Incorrect tree\n" );
+	fprintf( stderr, "done.\n" );
+
+	countnode( njob, topol, node0 );
+	if( tbrweight )
+	{
+		weight = 3; 
+		utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+	}
+	else
+	{
+		for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
+	}
+
+
+	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+	treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
+
+	fprintf( trap_g, "done\n" );
+	fclose( trap_g );
+
+	writePre( njob, name, nlen, aseq, !contin );
+	writeData_pointer( stdout, njob, name, nlen, aseq );
+#if IODEBUG
+	fprintf( stderr, "OSHIMAI\n" );
+#endif
+	SHOWVERSION;
+	return( 0 );
+}