From: martinahansen Date: Wed, 10 Sep 2008 11:16:25 +0000 (+0000) Subject: added copyright to c stuff X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=d13a9479f997dc2ce7357faa1687b3db4b6b1bd0;p=biopieces.git added copyright to c stuff git-svn-id: http://biopieces.googlecode.com/svn/trunk@254 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/code_c/Maasha/src/Makefile b/code_c/Maasha/src/Makefile index c96912a..527b6ea 100644 --- a/code_c/Maasha/src/Makefile +++ b/code_c/Maasha/src/Makefile @@ -1,3 +1,5 @@ +# Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved + CC = gcc # Cflags = -Wall -Werror Cflags = -Wall -Werror -g -pg # for gprof diff --git a/code_c/Maasha/src/bipartite_scan.c b/code_c/Maasha/src/bipartite_scan.c index f4fc865..34fe55f 100644 --- a/code_c/Maasha/src/bipartite_scan.c +++ b/code_c/Maasha/src/bipartite_scan.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "filesys.h" diff --git a/code_c/Maasha/src/inc/bits.h b/code_c/Maasha/src/inc/bits.h index a72297c..440a548 100644 --- a/code_c/Maasha/src/inc/bits.h +++ b/code_c/Maasha/src/inc/bits.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #define BITS_IN_BYTE 8 #define BYTE_ON 255 diff --git a/code_c/Maasha/src/inc/common.h b/code_c/Maasha/src/inc/common.h index 6be9b1d..83360ff 100644 --- a/code_c/Maasha/src/inc/common.h +++ b/code_c/Maasha/src/inc/common.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + /* Including standard libraries */ #include #include diff --git a/code_c/Maasha/src/inc/fasta.h b/code_c/Maasha/src/inc/fasta.h index 68f0bed..cae2b5e 100644 --- a/code_c/Maasha/src/inc/fasta.h +++ b/code_c/Maasha/src/inc/fasta.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #define FASTA_BUFFER 1024 /* Count all entries in a FASTA file given a file pointer. */ diff --git a/code_c/Maasha/src/inc/filesys.h b/code_c/Maasha/src/inc/filesys.h index 733308a..42749e4 100644 --- a/code_c/Maasha/src/inc/filesys.h +++ b/code_c/Maasha/src/inc/filesys.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + //#define FILE_BUFFER_SIZE 64 * 1024 #define FILE_BUFFER_SIZE 1 diff --git a/code_c/Maasha/src/inc/hash.h b/code_c/Maasha/src/inc/hash.h index 34e1cb8..bd96c26 100644 --- a/code_c/Maasha/src/inc/hash.h +++ b/code_c/Maasha/src/inc/hash.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + /* Structure of a generic hash element. */ struct _hash_elem { diff --git a/code_c/Maasha/src/inc/list.h b/code_c/Maasha/src/inc/list.h index 5558575..27886d8 100644 --- a/code_c/Maasha/src/inc/list.h +++ b/code_c/Maasha/src/inc/list.h @@ -1,4 +1,4 @@ - +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ /* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> STRUCTURE DECLARATIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/ diff --git a/code_c/Maasha/src/inc/mem.h b/code_c/Maasha/src/inc/mem.h index 3c83c41..cc0dde6 100644 --- a/code_c/Maasha/src/inc/mem.h +++ b/code_c/Maasha/src/inc/mem.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + /* Get a pointer with a given size of allocated memory. */ void *mem_get( size_t size ); diff --git a/code_c/Maasha/src/inc/seq.h b/code_c/Maasha/src/inc/seq.h index 2cbc659..2f9cc7a 100644 --- a/code_c/Maasha/src/inc/seq.h +++ b/code_c/Maasha/src/inc/seq.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + /* Macro to test if a given char is sequence (DNA, RNA, Protein, indels. brackets, etc ). */ #define isseq( x ) ( x > 32 && x < 127 ) ? 1 : 0 diff --git a/code_c/Maasha/src/inc/strings.h b/code_c/Maasha/src/inc/strings.h index fa14686..61c72ca 100644 --- a/code_c/Maasha/src/inc/strings.h +++ b/code_c/Maasha/src/inc/strings.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + /* Remove the last char from a string. Returns the length of the chopped string.*/ size_t chop( char *string ); diff --git a/code_c/Maasha/src/inc/ucsc.h b/code_c/Maasha/src/inc/ucsc.h index 752b012..64e92d0 100644 --- a/code_c/Maasha/src/inc/ucsc.h +++ b/code_c/Maasha/src/inc/ucsc.h @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #define BED_BUFFER 1024 struct bed_entry3 diff --git a/code_c/Maasha/src/lib/Makefile b/code_c/Maasha/src/lib/Makefile index 5f60845..1cd39f8 100644 --- a/code_c/Maasha/src/lib/Makefile +++ b/code_c/Maasha/src/lib/Makefile @@ -1,3 +1,5 @@ +# Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved + CC = gcc # Cflags = -Wall -Werror Cflags = -Wall -Werror -g -pg # gprof diff --git a/code_c/Maasha/src/lib/bits.c b/code_c/Maasha/src/lib/bits.c index ffe6e4f..fcceafe 100644 --- a/code_c/Maasha/src/lib/bits.c +++ b/code_c/Maasha/src/lib/bits.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "bits.h" diff --git a/code_c/Maasha/src/lib/common.c b/code_c/Maasha/src/lib/common.c index b93220d..41dc8c2 100644 --- a/code_c/Maasha/src/lib/common.c +++ b/code_c/Maasha/src/lib/common.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "list.h" #include "mem.h" diff --git a/code_c/Maasha/src/lib/fasta.c b/code_c/Maasha/src/lib/fasta.c index 50c0cbb..f079afc 100644 --- a/code_c/Maasha/src/lib/fasta.c +++ b/code_c/Maasha/src/lib/fasta.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "filesys.h" diff --git a/code_c/Maasha/src/lib/filesys.c b/code_c/Maasha/src/lib/filesys.c index 4cbbec2..b31509e 100644 --- a/code_c/Maasha/src/lib/filesys.c +++ b/code_c/Maasha/src/lib/filesys.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "filesys.h" diff --git a/code_c/Maasha/src/lib/hash.c b/code_c/Maasha/src/lib/hash.c index e3727b2..e4484bc 100644 --- a/code_c/Maasha/src/lib/hash.c +++ b/code_c/Maasha/src/lib/hash.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "hash.h" diff --git a/code_c/Maasha/src/lib/list.c b/code_c/Maasha/src/lib/list.c index 93b91c8..cbd61c6 100644 --- a/code_c/Maasha/src/lib/list.c +++ b/code_c/Maasha/src/lib/list.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "list.h" diff --git a/code_c/Maasha/src/lib/mem.c b/code_c/Maasha/src/lib/mem.c index 6f5211d..d7bea0a 100644 --- a/code_c/Maasha/src/lib/mem.c +++ b/code_c/Maasha/src/lib/mem.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" diff --git a/code_c/Maasha/src/lib/seq.c b/code_c/Maasha/src/lib/seq.c index ac8ba17..b796034 100644 --- a/code_c/Maasha/src/lib/seq.c +++ b/code_c/Maasha/src/lib/seq.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "seq.h" diff --git a/code_c/Maasha/src/lib/strings.c b/code_c/Maasha/src/lib/strings.c index a75298e..6219d36 100644 --- a/code_c/Maasha/src/lib/strings.c +++ b/code_c/Maasha/src/lib/strings.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "strings.h" diff --git a/code_c/Maasha/src/lib/ucsc.c b/code_c/Maasha/src/lib/ucsc.c index 92ec4d9..9231069 100644 --- a/code_c/Maasha/src/lib/ucsc.c +++ b/code_c/Maasha/src/lib/ucsc.c @@ -1,7 +1,10 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "ucsc.h" + void bed_get_entry( FILE *fp, struct bed_entry3 *bed, int cols ) { /* Martin A. Hansen, June 2008 */ @@ -26,96 +29,3 @@ void bed_get_entry( FILE *fp, struct bed_entry3 *bed, int cols ) } -void bed_split( char *string, struct bed_entry12 *bed, int cols ) -{ - int i; - int field_num; - int offset; - char *new_line; - int new_line_pos; - char *pt; - int pos; - int field_seps[ cols ]; - int field_len; - char *field; - - if ( ( new_line = memchr( string, '\n', 1024 ) ) != NULL ) { - new_line_pos = new_line - string; - } else { - abort(); - } - - field_num = 0; - offset = 0; - - for ( i = 0; i < cols; i++ ) - { - if ( ( pt = memchr( &string[ offset ], '\t', new_line_pos - offset ) ) != NULL ) - { - pos = pt - string; - - pos = MIN( pos, new_line_pos ); - - field_seps[ field_num ] = pos; - - field_num++; - } - else - { - abort(); - } - - offset += pos + 1; - } - - offset = 0; - - for ( i = 0; i < cols; i++ ) - { - field_len = field_seps[ i ] - offset; - - field = mem_get( field_len ); - - field[ field_len ] = '\0'; - - memcpy( field, &string[ offset ], field_len ); - - if ( i == 0 ) { - bed->chr = mem_clone( ( char * ) field, field_len ); - } else if ( i == 1 ) { - bed->chr_beg = strtod( field, &pt ); - } else if ( i == 2 ) { - bed->chr_end = strtod( field, &pt ); - } else if ( i == 3 ) { - bed->q_id = mem_clone( ( char * ) field, field_len ); - } else if ( i == 4 ) { -// bed->score = strtof( field, &pt ); - } else if ( i == 5 ) { - bed->strand = field[ 0 ]; - } else if ( i == 6 ) { - bed->thick_beg = strtod( field, &pt ); - } else if ( i == 7 ) { - bed->thick_end = strtod( field, &pt ); - } else if ( i == 8 ) { - bed->itemrgb = mem_clone( ( char * ) field, field_len ); - } else if ( i == 9 ) { - bed->blockcount = strtod( field, &pt ); - } else if ( i == 10 ) { - bed->blocksizes = mem_clone( ( char * ) field, field_len ); - } else if ( i == 11 ) { - bed->q_begs = mem_clone( ( char * ) field, field_len ); - } - - if ( pt == NULL ) { - abort(); - } - - offset = field_seps[ i ] + 1; - } - - printf( "chr ->%s\n", bed->chr ); - printf( "chr_beg->%u\n", bed->chr_beg ); - printf( "chr_end->%u\n", bed->chr_end ); -} - - diff --git a/code_c/Maasha/src/repeat-O-matic.c b/code_c/Maasha/src/repeat-O-matic.c index 8d1f1e7..5f430d3 100644 --- a/code_c/Maasha/src/repeat-O-matic.c +++ b/code_c/Maasha/src/repeat-O-matic.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include #include "common.h" #include "mem.h" diff --git a/code_c/Maasha/src/test.c b/code_c/Maasha/src/test.c index 431d7da..a316c2a 100644 --- a/code_c/Maasha/src/test.c +++ b/code_c/Maasha/src/test.c @@ -1,88 +1,79 @@ -#include "common.h" -#include "filesys.h" -#include "fasta.h" +#include +#include -int main( int argc, char *argv[] ) -{ - char *file; - FILE *fp; - char chr[ 10 ]; - int chr_beg; - int chr_end; - - file = argv[ 1 ]; - - fp = read_open( file ); - - fscanf( "%s\t%d\t%d", fp, chr, chr_beg, chr_end ); - - printf( "CHR: %s CHR_BEG: %d CHR_END: %d\n", chr, chr_beg, chr_end ); - - close_stream( fp ); - - return 0; -} - - -double average( int num, ... ) -{ - /* Martin A. Hansen, July 2008 */ - - /* Example of varable length argument list usage. */ - - /* Requires '#include ' */ - - double sum = 0; - int x = 0; - - va_list arguments; - va_start( arguments, num ); - - for ( x = 0; x < num; x++ ) - { - sum += va_arg( arguments, double ); - } - - va_end( arguments ); - - return sum / num; -} - - - -/* - -int main( int argc, char *argv[] ) +int main() { - char *file; - FILE *fp; - struct seq_entry *entry = NULL; - int count; - - count = 0; - - file = argv[ 1 ]; + char str[] = "ABCDEFGHIJKLMNOPQRSTUVXYZ"; + int i = 0; + char *pt1 = NULL; + int size = 4; + char word[ size ]; - fp = read_open( file ); - while ( ( fasta_get_entry( fp, entry ) ) != FALSE ) + for ( i = size, pt1 = &str[ size ]; i < 10; i++, *( pt1++ ) ) { - printf( "seq_name: %s\n", entry->seq_name ); - -// mem_free( entry->seq_name ); -// mem_free( entry->seq ); -// entry = NULL; - - count++; + printf( "char: %s\n", pt1 ); +// printf( "word: %s\n", &pt[ i ] ); } - printf( "count: %d\n", count ); - - close_stream( fp ); - - return 0; + return EXIT_SUCCESS; } -*/ +//double average( int num, ... ) +//{ +// /* Martin A. Hansen, July 2008 */ +// +// /* Example of varable length argument list usage. */ +// +// /* Requires '#include ' */ +// +// double sum = 0; +// int x = 0; +// +// va_list arguments; +// +// va_start( arguments, num ); +// +// for ( x = 0; x < num; x++ ) +// { +// sum += va_arg( arguments, double ); +// } +// +// va_end( arguments ); +// +// return sum / num; +//} + + +//int main( int argc, char *argv[] ) +//{ +// char *file; +// FILE *fp; +// struct seq_entry *entry = NULL; +// int count; +// +// count = 0; +// +// file = argv[ 1 ]; +// +// fp = read_open( file ); +// +// while ( ( fasta_get_entry( fp, entry ) ) != FALSE ) +// { +// printf( "seq_name: %s\n", entry->seq_name ); +// +//// mem_free( entry->seq_name ); +//// mem_free( entry->seq ); +//// entry = NULL; +// +// count++; +// } +// +// printf( "count: %d\n", count ); +// +// close_stream( fp ); +// +// return 0; +//} diff --git a/code_c/Maasha/src/test/Makefile b/code_c/Maasha/src/test/Makefile index 283030d..01ee878 100644 --- a/code_c/Maasha/src/test/Makefile +++ b/code_c/Maasha/src/test/Makefile @@ -1,3 +1,5 @@ +# Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved + CC = gcc Cflags = -Wall -Werror -g -pg # for gprof @@ -9,7 +11,7 @@ LIB = -lm $(LIB_DIR)*.o all: test -test: test_bits test_common test_fasta test_filesys test_hash test_list test_mem test_seq test_strings +test: test_bits test_common test_fasta test_filesys test_hash test_list test_mem test_ucsc test_seq test_strings test_bits: test_bits.c $(LIB_DIR)bits.c $(CC) $(Cflags) $(INC) $(LIB) test_bits.c -o test_bits @@ -32,6 +34,9 @@ test_list: test_list.c $(LIB_DIR)list.c test_mem: test_mem.c $(LIB_DIR)mem.c $(CC) $(Cflags) $(INC) $(LIB) test_mem.c -o test_mem +test_ucsc: test_ucsc.c $(LIB_DIR)ucsc.c + $(CC) $(Cflags) $(INC) $(LIB) test_ucsc.c -o test_ucsc + test_seq: test_seq.c $(LIB_DIR)seq.c $(CC) $(Cflags) $(INC) $(LIB) test_seq.c -o test_seq @@ -46,5 +51,6 @@ clean: rm test_hash rm test_list rm test_mem + rm test_ucsc rm test_seq rm test_strings diff --git a/code_c/Maasha/src/test/test_bits.c b/code_c/Maasha/src/test/test_bits.c index ac1a54e..6a5e356 100644 --- a/code_c/Maasha/src/test/test_bits.c +++ b/code_c/Maasha/src/test/test_bits.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "bits.h" diff --git a/code_c/Maasha/src/test/test_common.c b/code_c/Maasha/src/test/test_common.c index 29656b9..e132baa 100644 --- a/code_c/Maasha/src/test/test_common.c +++ b/code_c/Maasha/src/test/test_common.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" static void test_true(); diff --git a/code_c/Maasha/src/test/test_fasta.c b/code_c/Maasha/src/test/test_fasta.c index 0560b7f..f991cc0 100644 --- a/code_c/Maasha/src/test/test_fasta.c +++ b/code_c/Maasha/src/test/test_fasta.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "filesys.h" #include "mem.h" diff --git a/code_c/Maasha/src/test/test_filesys.c b/code_c/Maasha/src/test/test_filesys.c index c75c6d4..fc327b0 100644 --- a/code_c/Maasha/src/test/test_filesys.c +++ b/code_c/Maasha/src/test/test_filesys.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "filesys.h" diff --git a/code_c/Maasha/src/test/test_hash.c b/code_c/Maasha/src/test/test_hash.c index d4a5041..51a981e 100644 --- a/code_c/Maasha/src/test/test_hash.c +++ b/code_c/Maasha/src/test/test_hash.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "hash.h" diff --git a/code_c/Maasha/src/test/test_list.c b/code_c/Maasha/src/test/test_list.c index d4e5551..f7660e1 100644 --- a/code_c/Maasha/src/test/test_list.c +++ b/code_c/Maasha/src/test/test_list.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" #include "list.h" diff --git a/code_c/Maasha/src/test/test_mem.c b/code_c/Maasha/src/test/test_mem.c index b5dbd65..8b1d545 100644 --- a/code_c/Maasha/src/test/test_mem.c +++ b/code_c/Maasha/src/test/test_mem.c @@ -1,3 +1,5 @@ +/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */ + #include "common.h" #include "mem.h" diff --git a/code_c/Maasha/src/testall.pl b/code_c/Maasha/src/testall.pl index 09b1a1b..818648c 100755 --- a/code_c/Maasha/src/testall.pl +++ b/code_c/Maasha/src/testall.pl @@ -14,7 +14,6 @@ $test_dir = "test"; test_list test_mem test_seq - test_sort test_strings );