X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2Fpair2hat3s.c;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2Fpair2hat3s.c;h=0000000000000000000000000000000000000000;hb=fb21789ba11ae9b9f6abed1b01d4542e54abfe34;hp=e6e76f5f2bcfbba3638f2a7338596ff7502725b7;hpb=7d68cf3489c816b2ed7afb1925a6de2168eccf4a;p=jabaws.git

diff --git a/website/archive/binaries/mac/src/mafft/core/pair2hat3s.c b/website/archive/binaries/mac/src/mafft/core/pair2hat3s.c
deleted file mode 100644
index e6e76f5..0000000
--- a/website/archive/binaries/mac/src/mafft/core/pair2hat3s.c
+++ /dev/null
@@ -1,467 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 1
-#define TSUYOSAFACTOR 100
-
-
-static char *pairfile;
-static int nhomologs;
-
-void strip( char *s )
-{
-	char *pt = s;
-	while( *++pt )
-		if( *pt == '\n' ) *pt = 0;
-}
-
-int searchused( char *q, char **keys, int n )
-{
-	int i;
-	for( i=0; i<n; i++ )
-	{
-//		fprintf( stderr, "%s ? %s\n", q, names[i] );
-		if( !strcmp( q, keys[i] ) ) return( i );
-	}
-	return( -1 );
-}
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-	nhomologs = 2;
-	inputfile = NULL;
-	pairfile = NULL;
-	fftkeika = 0;
-	pslocal = -1000.0;
-	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 = 1;
-	kobetsubunkatsu = 0;
-	divpairscore = 0;
-	dorp = NOTSPECIFIED;
-	ppenalty = NOTSPECIFIED;
-	ppenalty_OP = NOTSPECIFIED;
-	ppenalty_ex = NOTSPECIFIED;
-	ppenalty_EX = NOTSPECIFIED;
-	poffset = NOTSPECIFIED;
-	kimuraR = NOTSPECIFIED;
-	pamN = NOTSPECIFIED;
-	geta2 = GETA2;
-	fftWinSize = NOTSPECIFIED;
-	fftThreshold = NOTSPECIFIED;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-	{
-        while ( ( c = *++argv[0] ) )
-		{
-            switch( c )
-            {
-				case 'i':
-					inputfile = *++argv;
-					fprintf( stderr, "inputfile = %s\n", inputfile );
-					--argc;
-					goto nextoption;
-				case 'p':
-					pairfile = *++argv;
-					fprintf( stderr, "pairfile = %s\n", pairfile );
-					--argc;
-					goto nextoption;
-				case 't':
-					nhomologs = atoi( *++argv );
-					fprintf( stderr, "nhomologs = %d\n", nhomologs );
-					--argc;
-					goto nextoption;
-				case 'D':
-					dorp = 'd';
-					break;
-				case 'P':
-					dorp = 'p';
-					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 );
-	}
-}
-
-int countamino( char *s, int end )
-{
-	int val = 0;
-	while( end-- )
-		if( *s++ != '-' ) val++;
-	return( val );
-}
-
-static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
-{
-	FILE *tmpfp;
-	static char dumm1[B], dumm0[B];
-	int i, j;
-	char *res;
-	FILE *hat3p;
-	static double *effarr1 = NULL;
-	static double *effarr2 = NULL;
-	static char **pseq;
-	LocalHom **localhomtable, *tmpptr;
-	float pscore = 0.0; // by D.Mathog, aguess
-	char *aseq = NULL; // by D.Mathog
-	char **usedseqs = NULL; // by D.Mathog
-	char **usednames = NULL; // by D.Mathog
-	int nused;
-	double tsuyosa;
-
-	tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
-	fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
-	localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
-	for( i=0; i<njob; i++)
-	{
-		localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
-		for( j=0; j<njob; j++)
-		{
-			localhomtable[i][j].start1 = -1;
-			localhomtable[i][j].end1 = -1;
-			localhomtable[i][j].start2 = -1; 
-			localhomtable[i][j].end2 = -1; 
-			localhomtable[i][j].opt = -1.0;
-			localhomtable[i][j].next = NULL;
-		}
-	}
-
-	if( effarr1 == NULL ) 
-	{
-		effarr1 = AllocateDoubleVec( njob );
-		effarr2 = AllocateDoubleVec( njob );
-		pseq = AllocateCharMtx( 2, nlenmax*9+1 );
-		aseq = AllocateCharVec( nlenmax*9+1 );
-		usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
-		usednames = AllocateCharMtx( njob, B );
-#if 0
-#else
-#endif
-	}
-
-#if 0
-	fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
-	for( i=0; i<njob; i++ )
-		fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-
-//	writePre( njob, name, nlen, aseq, 0 );
-
-	fprintf( stderr, "opening %s\n", pairfile  );
-	tmpfp = fopen( pairfile, "r" );
-	if( !tmpfp )
-	{
-		fprintf( stderr, "Cannot open %s\n", pairfile );
-		exit( 1 );
-	}
-	searchKUorWA( tmpfp );
-	hat3p = fopen( "hat3", "w" );
-	if( !hat3p ) ErrorExit( "Cannot open hat3." );
-	nused = 0;
-	while( 1 )
-	{
-		res = fgets( dumm0, B-1, tmpfp );
-		strip( dumm0 );
-		if( res == NULL )
-		{
-			break;
-		}
-		load1SeqWithoutName_new( tmpfp, pseq[0] );
-		gappick0( aseq, pseq[0] );
-		i =  searchused( aseq, usedseqs, nused );
-		if( i == -1 )
-		{
-			strcpy( usednames[nused], dumm0+1 );
-			strcpy( usedseqs[nused], aseq );
-			i = nused;
-			nused++;
-		}
-		fprintf( stderr, "i = %d\n", i );
-
-		res = fgets( dumm1, B-1, tmpfp );
-		strip( dumm1 );
-		if( res == NULL )
-		{
-			fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
-			exit( 1 );
-		}
-		load1SeqWithoutName_new( tmpfp, pseq[1] );
-		gappick0( aseq, pseq[1] );
-		j =  searchused( aseq, usedseqs, nused );
-		if( j == -1 )
-		{
-			strcpy( usednames[nused], dumm1+1 );
-			strcpy( usedseqs[nused], aseq );
-			j = nused;
-			nused++;
-		}
-		fprintf( stderr, "j = %d\n", j );
-
-		if( strlen( pseq[0] ) != strlen( pseq[1] ) )
-		{
-			fprintf( stderr, "Not aligned,  %s - %s\n", dumm0, dumm1 );
-			exit( 1 );
-		}
-
-
-		fprintf( stderr, "adding %d-%d\n", i, j );
-		putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
-		for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
-		{
-			if( tmpptr->opt == -1.0 ) continue;
-			fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next ); 
-		}
-	}
-	fclose( tmpfp );
-	fclose( hat3p );
-
-	for( i=0; i<nused; i++ )
-		fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
-
-
-#if 0
-	fprintf( stderr, "##### writing hat3\n" );
-	hat3p = fopen( "hat3", "w" );
-	if( !hat3p ) ErrorExit( "Cannot open hat3." );
-	ilim = njob-1;	
-	for( i=0; i<ilim; i++ ) 
-	{
-		for( j=i+1; j<njob; j++ )
-		{
-			for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
-			{
-				if( tmpptr->opt == -1.0 ) continue;
-				fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next ); 
-			}
-		}
-	}
-	fclose( hat3p );
-#endif
-#if DEBUG
-	fprintf( stderr, "calling FreeLocalHomTable\n" );
-#endif
-	FreeLocalHomTable( localhomtable, njob );
-#if DEBUG
-	fprintf( stderr, "done. FreeLocalHomTable\n" );
-#endif
-}
-
-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[M][B], **seq;
-	static char **bseq;
-	static double *eff;
-	int i;
-	char c;
-	int alloclen;
-	FILE *infp;
-
-	arguments( argc, argv );
-
-	if( inputfile )
-	{
-		infp = fopen( inputfile, "r" );
-		if( !infp )
-		{
-			fprintf( stderr, "Cannot open %s\n", inputfile );
-			exit( 1 );
-		}
-	}
-	else
-		infp = stdin;
-
-	if( !pairfile )
-	{
-		fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
-		exit( 1 );
-	}
-
-	getnumlen( infp );
-	rewind( infp );
-
-	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 );
-	bseq = AllocateCharMtx( njob, nlenmax*9+1 );
-	alloclen = nlenmax*9;
-
-	eff = AllocateDoubleVec( njob );
-
-#if 0
-	Read( name, nlen, seq );
-#else
-	readData( infp, name, nlen, seq );
-#endif
-	fclose( infp );
-
-	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 );
-
-	for( i=0; i<njob; i++ ) eff[i] = 1.0;
-
-
-	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
-
-	pairalign( name, nlen, bseq, eff, alloclen );
-
-	fprintf( trap_g, "done.\n" );
-#if DEBUG
-	fprintf( stderr, "closing trap_g\n" );
-#endif
-	fclose( trap_g );
-
-#if IODEBUG
-	fprintf( stderr, "OSHIMAI\n" );
-#endif
-	SHOWVERSION;
-	return( 0 );
-}