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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/setcore.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,503 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+
+double corethr;
+int coreext;
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+	fftkeika = 1;
+	constraint = 0;
+	nblosum = 62;
+	fmodel = 0;
+	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 = 'A';
+    mix = 0;
+	tbitr = 0;
+	scmtd = 5;
+	tbweight = 0;
+	tbrweight = 3;
+	checkC = 0;
+	treemethod = 'x';
+	contin = 0;
+	scoremtx = 0;
+	kobetsubunkatsu = 0;
+	dorp = NOTSPECIFIED;
+	ppenalty = NOTSPECIFIED;
+	ppenalty_ex = NOTSPECIFIED;
+	poffset = NOTSPECIFIED;
+	kimuraR = NOTSPECIFIED;
+	pamN = NOTSPECIFIED;
+	geta2 = GETA2;
+	fftWinSize = NOTSPECIFIED;
+	fftThreshold = NOTSPECIFIED;
+	corethr = .5;
+	coreext = 0;
+
+    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 'k':
+					kimuraR = myatoi( *++argv );
+					fprintf( stderr, "kimuraR = %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;
+					fprintf( stderr, "jtt %d\n", pamN );
+					--argc;
+					goto nextoption;
+				case 'l':
+					fastathreshold = atof( *++argv );
+					constraint = 2;
+					fprintf( stderr, "weighti = %f\n", fastathreshold );
+					--argc;
+					goto nextoption;
+				case 'i':
+					corethr = atof( *++argv );
+					fprintf( stderr, "corethr = %f\n", corethr );
+					--argc;
+					goto nextoption;
+				case 'm':
+					fmodel = 1;
+					break;
+				case 'c':
+					coreext = 1;
+					break;
+				case 'r':
+					fmodel = -1;
+					break;
+				case 'D':
+					dorp = 'd';
+					break;
+				case 'P':
+					dorp = 'p';
+					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':
+					fftThreshold = myatoi( *++argv );
+					--argc; 
+					goto nextoption;
+				case 'w':
+					fftWinSize = myatoi( *++argv );
+					--argc;
+					goto nextoption;
+				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 );
+	}
+}
+
+
+
+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 main( int argc, char *argv[] )
+{
+	static int  nlen[M];	
+	static char **name, **seq;
+	static char **oseq;
+	static double **pscore;
+	static double *eff;
+	static double **node0, **node1;
+	static double *gapc;
+	static double *avgap;
+	double tmpavgap;
+	int i, j, m, goffset;
+	static int ***topol;
+	static double **len;
+	FILE *prep;
+	char c;
+	int corestart, coreend;
+	int alloclen;
+	int winsize;
+	char *pt, *ot;
+	double gapmin;
+
+	arguments( argc, argv );
+
+	getnumlen( stdin );
+	rewind( stdin );
+
+	if( njob < 2 )
+	{
+		fprintf( stderr, "At least 2 sequences should be input!\n"
+						 "Only %d sequence found.\n", njob ); 
+		exit( 1 );
+	}
+
+	seq = AllocateCharMtx( njob, nlenmax*9+1 );
+	name = AllocateCharMtx( njob, B+1 );
+	oseq = AllocateCharMtx( njob, nlenmax*9+1 );
+	alloclen = nlenmax*9;
+
+	topol = AllocateIntCub( njob, 2, njob );
+	len = AllocateDoubleMtx( njob, 2 );
+	pscore = AllocateDoubleMtx( njob, njob );
+	eff = AllocateDoubleVec( njob );
+	node0 = AllocateDoubleMtx( njob, njob );
+	node1 = AllocateDoubleMtx( njob, njob );
+	gapc = AllocateDoubleVec( alloclen );
+	avgap = AllocateDoubleVec( alloclen );
+
+#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; 
+#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<nlenmax; i++ )
+	{
+		gapc[i] = 0.0;
+		for( j=0; j<njob; j++ )
+		{
+			if( seq[j][i] == '-' ) gapc[i] += eff[j];
+		}
+	}
+
+	gapmin = 1.0;
+	winsize = fftWinSize;
+	goffset = winsize/2;
+	tmpavgap = 0.0;
+	corestart = coreend = -1;
+	for( i=0; i<winsize; i++ )
+	{
+		tmpavgap += gapc[i];
+	}
+	for( i=winsize; i<nlenmax; i++ )
+	{
+		m = i - goffset;
+		avgap[m] = tmpavgap / winsize;
+//		fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
+		if( avgap[m] < corethr )
+		{
+			if( corestart == -1 )
+				corestart = i - winsize;
+//			fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
+			if( avgap[m] < gapmin )
+			{ 
+				gapmin = avgap[m];
+			}
+			coreend = i;
+		}
+		tmpavgap -= gapc[i-winsize];
+		tmpavgap += gapc[i];
+	}
+	if( corestart == -1 || coreend == -1 )
+	{
+		corestart = 0;
+		coreend = nlenmax-1;
+	}
+
+	for( i=0; i<njob; i++ )
+	{
+		pt = oseq[i];
+		m = winsize;
+		while( m-- ) *pt++ = '-';
+		for( j=corestart; j<=coreend; j++ )
+			*pt++ = seq[i][j];
+		m = winsize;
+		while( m-- ) *pt++ = '-';
+		*pt = 0;
+
+		ot = oseq[i]+winsize-1;
+		pt = seq[i]+corestart-1;
+		if( coreext ) m = winsize;
+		else m = 0;
+		while( m && --pt > seq[i] )
+			if( *pt != '-' )
+			{
+				*ot-- = *pt;
+				m--;
+			}
+
+		ot = oseq[i]+winsize+coreend-corestart+1;
+		pt = seq[i]+coreend;
+		if( coreext ) m = winsize;
+		else m = 0;
+		while( m && *(++pt) )
+		{
+			if( *pt != '-' ) 
+			{
+				*ot++ = *pt;
+				m--;
+			}
+		}
+		fprintf( stdout, ">%s\n", name[i] );
+		fprintf( stdout, "%s\n", oseq[i] );
+	}
+
+	exit( 1 );
+
+	SHOWVERSION;
+	return( 0 );
+}