From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 5 Sep 2008 03:13:04 +0000 (+0000)
Subject: added unit test to mem.c
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=520a9d9960231ce3a5e4b78f8a5101b12f8a124b;p=biopieces.git

added unit test to mem.c

git-svn-id: http://biopieces.googlecode.com/svn/trunk@245 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_c/Maasha/src/test/test_mem.c b/code_c/Maasha/src/test/test_mem.c
index 7327587..6f4f541 100644
--- a/code_c/Maasha/src/test/test_mem.c
+++ b/code_c/Maasha/src/test/test_mem.c
@@ -43,15 +43,21 @@ void test_mem_get_zero()
 {
     fprintf( stderr, "   Testing mem_get_zero ... " );
 
-    size_t  i   = 0;
-    size_t  len = 5555;
-    char   *pt  = mem_get_zero( len );
+    size_t  i    = 0;
+    size_t  len  = 5555;
+    char   *pt1  = mem_get_zero( sizeof( char ) * len );
+    uint   *pt2  = mem_get_zero( sizeof( uint ) * len );
 
-    for ( i = 0; i <= len; i++ ) {
-        assert( pt[ i ] == '\0' );
+    for ( i = 0; i <= ( sizeof( char ) * len ); i++ ) {
+        assert( pt1[ i ] == '\0' );
     }
 
-    mem_free( ( void * ) &pt );
+    for ( i = 0; i <= ( sizeof( char ) * len ); i++ ) {
+        assert( pt2[ i ] == '\0' );
+    }
+
+    mem_free( ( void * ) &pt1 );
+    mem_free( ( void * ) &pt2 );
 
     fprintf( stderr, "OK\n" );
 }
diff --git a/code_c/Maasha/src/tetra_count.c b/code_c/Maasha/src/tetra_count.c
deleted file mode 100644
index 7113c00..0000000
--- a/code_c/Maasha/src/tetra_count.c
+++ /dev/null
@@ -1,92 +0,0 @@
-#include "common.h"
-#include "filesys.h"
-#include "mem.h"
-#include "seq.h"
-#include "fasta.h"
-
-/*
- *  bipartite_scan locates motivs consisting of two blocks of tetra nucleotides seperated by 
- *  a distance between 0 and 256 bases. This is done by converting the tetra nucleotide blocks
- *  into 2-bits per base thus using the first 16 bits of a unsigned int (which is 32 bits). The
- *  remaning 16 bits exactly holds the distance (binary) between the blocks (using 9 bits for 256).
- *  For example in the following sequence the two tetra nucletotide blocks (in capital letters)
- *  are sepetarated by 13 bases:
- *
- *  tatagtacgttATCGatgagctagctgtTGCAgtgtgatac
- *
- *  Thus the resulting parts of the count block will look like this:
- *
- *  ATCG=00110110 TGCA=11100100 and 13=000001101 (using A=00 T=11 C=01 and G=10).
- *
- *  And the resulting bipartite block is then: 00110110111001000000011010000000
- *  The remainin 7 bits are unused.
- *
- *  The biparite block can then be used as an index in an unsigned int array that holds the count
- *  of all different bipartite blocks found in a sequence or list of sequnces (all genomes!).
- *
- *  Rescanning the sequences locating the bipartite blocks of interest allows location of the
- *  exact motif positions.
- * 
- * */
-
-#define BLOCK_SIZE  4
-#define MAX_SPACE   256
-//#define ARRAY_SIZE  ( 1 << 30 )
-#define ARRAY_SIZE  30
-#define WINDOW_SIZE ( ( 2 * BLOCK_SIZE ) + MAX_SPACE )
-
-#define add_A( c )             /* add 00 on the rightmost two bits of c (i. e. do nothing). */
-#define add_T( c ) ( c |= 3 )  /* add 11 on the rightmost two bits of c. */
-#define add_C( c ) ( c |= 1 )  /* add 01 on the rightmost two bits of c. */
-#define add_G( c ) ( c |= 2 )  /* add 10 on the rightmost two bits of c. */
-
-void bipartite_scan_file( char *file, uint **bipartite_array_ppt, seq_entry **entry_ppt );
-void bipartite_scan_entry( uint *bipartite_array, seq_entry *entry );
-
-int main( int argc, char *argv[] )
-{
-    int        i               = 0;
-    uint      *bipartite_array = NULL;
-    seq_entry *entry           = NULL;
-
-    bipartite_array = mem_get_zero( sizeof( uint ) * ARRAY_SIZE );
-
-    seq_new( &entry, MAX_SEQ_NAME, MAX_SEQ );
-
-    for ( i = 1; i < argc; i++ )
-    {
-        bipartite_scan_file( argv[ i ], &bipartite_array, &entry );
-    }
-
-    seq_destroy( entry );
-
-    mem_free( &bipartite_array );
-
-    return EXIT_SUCCESS;
-}
-
-
-void bipartite_scan_file( char *file, uint **bipartite_array_ppt, seq_entry **entry_ppt )
-{
-    /* Martin A. Hansen, September 2008. */
-
-    uint      *bipartite_array = *bipartite_array_ppt;
-    seq_entry *entry           = *entry_ppt;
-    FILE      *fp              = NULL;
-
-    fp = read_open( file );
-
-    while ( ( fasta_get_entry( fp, &entry ) != FALSE ) ) {
-        bipartite_scan_entry( bipartite_array, entry );
-    }
-
-    close_stream( fp );
-}
-
-
-void bipartite_scan_entry( uint *bipartite_array, seq_entry *entry )
-{
-    /* Martin A. Hansen, September 2008. */
-
-    fasta_put_entry( entry );
-}