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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/restoreu.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,260 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *alignmentfile;
+
+static void fillorichar( int nseq, int *oripos, char **a, char **s )
+{
+	int i;
+	char *pta, *pts;
+	for( i=0; i<nseq; i++ )
+	{
+		pta = a[i];
+		pts = s[oripos[i]];
+		while( *pta )
+		{
+			if( *pta != '-' ) *pta = *pts++;
+			if( *pta++ == 0 )
+			{
+				fprintf( stderr, "ERROR!!\n" );
+				fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+				exit( 1 );
+			}
+		}
+		if( *pts != 0 )
+		{
+			fprintf( stderr, "ERROR!!\n" );
+			fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+			exit( 1 );
+		}
+	}
+}
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+	{
+        while ( (c = *++argv[0]) )
+		{
+            switch( c )
+            {
+				case 'i':
+					inputfile = *++argv;
+					--argc;
+					goto nextoption;
+				case 'a':
+					alignmentfile = *++argv;
+					--argc;
+					goto nextoption;
+                default:
+                    fprintf( stderr, "illegal option %c\n", c );
+                    argc = 0;
+                    break;
+            }
+		}
+		nextoption:
+			;
+	}
+    if( argc != 0 ) 
+    {
+        fprintf( stderr, "options: Check source file !\n" );
+        exit( 1 );
+    }
+}
+
+
+
+int main( int argc, char *argv[] )
+{
+	FILE *infp;
+	FILE *alfp;
+	char **name;
+	char **aname;
+	char **oname;
+	char **seq;
+	char **aseq;
+	int *nlen;
+	int *oripos;
+	char *npt, *npt0, *npt2, *pt, *pt2;
+	int i, o, prelen;
+	int nlenmin;
+	int njobs, njoba;
+
+	arguments( argc, argv );
+
+	if( inputfile )
+	{
+		infp = fopen( inputfile, "r" );
+		if( !infp )
+		{
+			fprintf( stderr, "Cannot open %s\n", inputfile );
+			exit( 1 );
+		}
+	}
+	else
+		infp = stdin;
+
+	if( alignmentfile )
+	{
+		alfp = fopen( alignmentfile, "r" );
+		if( !alfp )
+		{
+			fprintf( stderr, "Cannot open %s\n", alignmentfile );
+			exit( 1 );
+		}
+	}
+	else
+	{
+		fprintf( stderr, "No alignment is given.\n" );
+		exit( 1 );
+	}
+	
+	dorp = NOTSPECIFIED;
+	getnumlen_casepreserve( infp, &nlenmin );
+	njobs = njob;
+//	fprintf( stderr, "in infp, %d x %d - %d %c\n", njob, nlenmin, nlenmax, dorp );
+
+	seq = AllocateCharMtx( njob, nlenmax+1 );
+	name = AllocateCharMtx( njob, B+1 );
+	nlen = AllocateIntVec( njob );
+	oripos = AllocateIntVec( njob );
+	readData_pointer_casepreserve( infp, name, nlen, seq );
+
+	dorp = NOTSPECIFIED;
+	getnumlen( alfp );
+	njoba = njob;
+//	fprintf( stderr, "in alfp, %d x %d %c\n", njob, nlenmax, dorp );
+	aseq = AllocateCharMtx( njob, nlenmax+1 );
+	aname = AllocateCharMtx( njob, B+1 );
+	oname = AllocateCharMtx( njob, B+1 );
+	readData_pointer( alfp, aname, nlen, aseq );
+
+	for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
+
+	if( njoba != njobs )
+	{
+		fprintf( stderr, "ERROR!!\n" );
+		fprintf( stderr, "In input file,\n" );
+		fprintf( stderr, "njob = %d\n", njobs );
+		fprintf( stderr, "but in alignment file,\n" );
+		fprintf( stderr, "njob = %d\n", njoba );
+		exit( 1 );
+	}
+
+	for( i=0; i<njob; i++ )
+	{
+#if 0
+		if( strstr( aname[i], "_seed_" ) )
+		{
+			npt2 = aname[i] + 7;
+			strcpy( oname[i], "=_seed_" );
+		}
+		else
+		{
+			npt2 = aname[i] + 1;
+			strcpy( oname[i], "=" );
+		}
+
+		fprintf( stderr, "npt2 = %s\n", npt2 );
+
+		o = oripos[i] = atoi( npt2 );
+		npt = strstr( npt2, "_oe_" );
+		if( npt == NULL )
+		{
+			fprintf( stderr, "Format error!\n" );
+			exit( 1 );
+		}
+		npt += 4;
+		strcat( oname[i], npt+1 );
+#endif
+		npt0 = strstr( aname[i], "_os_" );
+		if( npt0 == NULL )
+		{
+			fprintf( stderr, "Format error!\n" );
+			exit( 1 );
+		}
+		npt2 = npt0 + 4;
+		o = oripos[i] = atoi( npt2 );
+
+		npt = strstr( aname[i], "_oe_" );
+		if( npt == NULL )
+		{
+			fprintf( stderr, "Format error!\n" );
+			exit( 1 );
+		}
+		npt += 4;
+
+		pt2 = npt;
+		pt = npt2 - 4;
+		while( *pt ) *pt++ = *pt2++; // okashii
+
+		prelen = npt0-aname[i];
+		strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
+		strcat( oname[i], npt0 );
+
+#if 0
+		pt = strstr( aname[i], "_numo_e" );
+		if( pt ) pt += 8;
+		else pt = aname[i] + 1;
+
+		if( strstr( pt, "_seed_" ) ) pt += 6;
+
+		fprintf( stderr, "pt = :%s:\n", pt );
+
+#endif
+//		fprintf( stderr, "npt0 = :%s:\n", npt0 );
+//
+//		reporterr( "oname[i] = %s\n", oname[i] );
+//		reporterr( "aname[i] = %s\n", aname[i] );
+//		reporterr( " name[i] = %s\n",  name[i] );
+
+//		fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
+//		fprintf( stderr, "pt = :%s:\n", pt );
+//		fprintf( stderr, "oname[i] = :%s:\n", oname[i] );
+//		fprintf( stderr, "name[o] = :%s:\n", name[o] );
+
+		if( strncmp( npt0, name[o]+1, 10 ) )
+		{
+			fprintf( stderr, "ERROR!!\n" );
+			fprintf( stderr, "In input file,\n" );
+			fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+			fprintf( stderr, "but in alignment file,\n" );
+			fprintf( stderr, "oname[%d] = %s\n", i, oname[i] );
+			fprintf( stderr, "npt0 = %s\n", npt0 );
+			fprintf( stderr, "prelen = %d\n", prelen );
+			fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+			exit( 1 );
+		}
+#if 0
+		else
+		{
+			fprintf( stderr, "OK!!\n" );
+			fprintf( stderr, "In input file,\n" );
+			fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+			fprintf( stderr, "and in alignment file,\n" );
+			fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+			fprintf( stderr, "\n" );
+		}
+#endif
+	}
+//	fprintf( stderr, "seq[0] = %s\n", seq[0] );
+//	fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
+
+	fillorichar( njob, oripos, aseq, seq );
+
+
+	writeData_pointer( stdout, njob, oname, nlen, aseq );
+
+	FreeCharMtx( seq );
+	FreeCharMtx( aseq );
+	FreeCharMtx( name );
+	FreeCharMtx( aname );
+	FreeCharMtx( oname );
+	free( nlen );
+	free( oripos );
+
+	return( 0 );
+}