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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/interface.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,144 @@
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include "mafft.h"
+
+int report( int status, int progress, char *message )
+{
+	fprintf( stderr, "status = %d\n", status );
+	fprintf( stderr, "progress = %d / 100\n", progress );
+	fprintf( stderr, "message = %s\n", message );
+	return( 0 );
+}
+
+int chudan( int status, int progress, char *message )
+{
+	fprintf( stderr, "status = %d\n", status );
+	fprintf( stderr, "progress = %d / 100\n", progress );
+	fprintf( stderr, "message = %s\n", message );
+	return( 2 );
+}
+int main( void )
+{
+	int i;
+	int argc;
+	char **argv;
+	char **seq;
+	char **name;
+	char *message;
+	int res;
+	int n, l, mlen;
+
+//	printf( "This is interface.\n" );
+
+
+	l = 10000;	
+	n = 130;
+	seq = (char **)calloc( n, sizeof( char * ) );
+	name = (char **)calloc( n, sizeof( char * ) );
+	for( i=0; i<n; i++ ) seq[i] = calloc( l+1, sizeof( char ) );
+	for( i=0; i<n; i++ ) name[i] = calloc( 100, sizeof( char ) );
+
+	for( i=0; i<10; i++ )
+	{
+		strcpy( name[i*13+0], "name0" );
+		strcpy( name[i*13+1], "name1" );
+		strcpy( name[i*13+2], "name2" );
+		strcpy( name[i*13+3], "name3" );
+		strcpy( name[i*13+4], "name4" );
+		strcpy( name[i*13+5], "name5" );
+		strcpy( name[i*13+6], "name6" );
+		strcpy( name[i*13+7], "name7" );
+		strcpy( name[i*13+8], "name8" );
+		strcpy( name[i*13+9], "name9" );
+		strcpy( name[i*13+10], "name10" );
+		strcpy( name[i*13+11], "name11" );
+		strcpy( name[i*13+12], "name12" );
+
+
+		strcpy( seq[i*13+0], "TAATTAAAGGGCCGTGGTATACTGACCATGCGAAGGTAGCATAATCATTAGCCTTTTGATTTGAGGCTGGAATGAATGGTTTGACGAGAGATGGTCTGTCTCTTCGATTAAATTGAAGTTAATCTTTAAGTGAAAAAGCTTAAATGTACTTGGAGGGCGATAAGACCCTATAGATCTTTACATTTAATTCTTTTGTCTTGCGGTAGGTAATTAGACAGAGTAAAACAATGTTCGGTTGGGGCGACGGTAAGAACAGAATAAACACTTACAACATAAACACATCAATAAATGACCATTGATCCTTAGATGAATAAAGACCAAGTTACCTTAGGGATAACAGCGTAATTCTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-------------------" );
+		strcpy( seq[i*13+1], "GTGTTGAAGGGCCGCGGTATTTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTCGAATGAATGGTTGGACGAAAAACACACTGTTTCAGACAAAGAATTTGAATTTAACTTTTAAGTGAAAAGGCTTAAATGAATTAAAAAGACGATAAGACCCTATAAATCTTTACATTATGTTTTGTATTTTTAAAGTTGTTGTGTATTAAAAAGAAATATAAAGTAGATGTTGTGTTGGGGCAACGATAATATAATAAGATTAGCTGTTGGTAAAATTAAACAAATGTGTTTGTTAGGAGTAGTTAGATCCTTTTTAGAGATTTAAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCTTATCGAAGAAAAAGATTGCGACCTCGATG" );
+		strcpy( seq[i*13+2], "ATATTGAAGGGCCGCGGTATTTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGGAGGCTCGTATGAAAGGTCGAACGAGTGATAGACTGTCTCAGCAAAAAAAAAATTGAACTTAACTTTAAAGTGAAAAGGCTTTAATATTTCAGAAAGACGATAAGACCCTATAAATCTTCACACCACCTTTTATACTAAGCCAATCTGTTTGTATAAGGAGAAGTATAAAAAACGTGTTTTGTTGGGGCAACAAAGATATAATTAAATAACTGTTTTAATTTTAAAACAAAAATTTTTGAAAATAAATTGATCCTCTCTAAAGATTAAAAGATCAAGTTACTTTAGGGATAACAGCGTCATTTTTCTTGAGAGTTCCCATCGAAAGAAAAGTTTGCGACCTCGATG---" );
+		strcpy( seq[i*13+3], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGTTTATAAGTGAATGATATATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAGTTTAAATACAATAATCATTGCTTAATATAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
+		strcpy( seq[i*13+4], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGCTTATAAGTGTATAAGAAATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAATTTAAATACAATAATCATTGCTTAATACAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
+		strcpy( seq[i*13+5], "ATATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAATTGTATAAAATATTAAATTTGTAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATTTATTAAATCCAGTAATTATTGATTAATAAAATTGATCCTTGAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
+		strcpy( seq[i*13+6], "ATATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGAATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATTAAAAAGACGATAAGACCCTATAAATCTTAACAATAAATAGACTTTATATTTTAATTTATAAGTGTGTAAGGTATAAATTTTATAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATATATTATATCCAATAATTGTTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
+		strcpy( seq[i*13+7], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTATATAAAATATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAGTAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
+		strcpy( seq[i*13+8], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTGTATAAAGTATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
+		strcpy( seq[i*13+9], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCGTCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAAGTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTGAATCAATGATTGTTGATTAATGTGGTTGATCCTTTAAGAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
+		strcpy( seq[i*13+10], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTAAATCAATAGTTGTTGATTAATATAGTTGATCCTTTAAAAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
+		strcpy( seq[i*13+11], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAACTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
+		strcpy( seq[i*13+12], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
+
+	}
+
+	argc = 20;
+	argv = (char **)calloc( argc, sizeof( char * ) );
+	for( i=0; i<argc; i++ ) argv[i] = calloc( 100, sizeof( char ) );
+	strcpy( argv[0], "disttbfast" );
+	strcpy( argv[1], "-W" );
+	strcpy( argv[2], "6" );
+	strcpy( argv[3], "-b" );
+	strcpy( argv[4], "62" );
+	strcpy( argv[5], "-Q" );
+	strcpy( argv[6], "100" );
+	strcpy( argv[7], "-h" );
+	strcpy( argv[8], "0" );
+	strcpy( argv[9], "-F" );
+	strcpy( argv[10], "-X" );
+	strcpy( argv[11], "-s" );
+	strcpy( argv[12], "0.0" );
+	strcpy( argv[13], "-f" );
+	strcpy( argv[14], "-1.53" );
+	strcpy( argv[15], "-C" );
+	strcpy( argv[16], "0" );
+	strcpy( argv[17], "-D" );  // Necessary. DNA -> -D; Protein -> -P
+	strcpy( argv[18], "-I" ); // --add
+	strcpy( argv[19], "2" ); // --add
+
+#if 0
+	mlen = 5000;
+	message = (char *)calloc( mlen+1, sizeof( char ) );
+
+	fprintf( stderr, "first run\n" );
+	res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
+	fprintf( stderr, "second run\n" );
+	res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
+	fprintf( stderr, "third run\n" );
+	res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
+
+	fprintf( stderr, "\n\n\nmessage in interface = :%s:\n", message );
+	free( message );
+#else
+	fprintf( stderr, "first run\n" );
+	res = disttbfast( n, l, name, seq, argc, argv, report );
+	fprintf( stderr, "second run\n" );
+	res = disttbfast( n, l, name, seq, argc, argv, chudan );
+//	fprintf( stderr, "third run\n" );
+//	res = disttbfast( n, l, name, seq, argc, argv, report );
+#endif
+
+	if( res == GUI_LENGTHOVER )
+	{
+		fprintf( stderr, "length over!" );
+	}
+	else
+	{
+		fprintf( stderr, "res = %d\n", res );
+		fprintf( stdout, "Output:\n" );
+		for( i=0; i<n; i++ ) 
+			fprintf( stdout, "%s\n", seq[i] );
+	}
+	fprintf( stderr, "argv = \n" );
+	for( i=0; i<argc; i++ )
+		fprintf( stderr, "%s ", argv[i] );
+	fprintf( stderr, "\n" );
+	
+	for( i=0; i<n; i++ ) free( seq[i] );
+	free( seq );
+	for( i=0; i<n; i++ ) free( name[i] );
+	free( name );
+	for( i=0; i<argc; i++ ) free( argv[i] );
+	free( argv );
+
+}