From e218a67243de12cad6ca3456717824aaeb5f6de6 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Tue, 27 Oct 2009 09:29:47 +0000
Subject: [PATCH] redo recomp function to be much simpler.
---
src/zmapUtils/zmapDNA.c | 75 +++++++++++++++++------------------------
1 file changed, 30 insertions(+), 45 deletions(-)
diff --git a/src/zmapUtils/zmapDNA.c b/src/zmapUtils/zmapDNA.c
index 13e183e6c..5a357df88 100755
--- a/src/zmapUtils/zmapDNA.c
+++ b/src/zmapUtils/zmapDNA.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapDNA.h
* HISTORY:
- * Last edited: Apr 21 14:31 2008 (rds)
+ * Last edited: Oct 27 09:29 2009 (edgrif)
* Created: Fri Oct 6 11:41:38 2006 (edgrif)
- * CVS info: $Id: zmapDNA.c,v 1.5 2008-04-21 15:25:47 rds Exp $
+ * CVS info: $Id: zmapDNA.c,v 1.6 2009-10-27 09:29:47 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -273,60 +273,45 @@ GList *zMapDNAFindAllMatches(char *dna, char *query, ZMapStrand strand, int from
}
-/* Reverse complement the DNA. This function is fast enough for now, if it proves too slow
- * then rewrite it !
+
+
+
+/* Reverse complement the DNA. Probably this is about as good as one can do....
*
- * It works by starting at each end and swopping the bases and then complementing the bases
- * so that the whole thing is done in place.
+ * It works by reading in towards the middle and at each position, reading
+ * the base, complementing it and then putting it back at the mirror position,
+ * i.e. the whole thing is done in place. (if there is a middle base it is done
+ * twice)
* */
void zMapDNAReverseComplement(char *sequence, int length)
{
- char *s, *e ;
+ static char rev[256] = {'\0'} ;
+ char *s_ptr, *e_ptr ;
int i ;
- for (s = sequence, e = (sequence + length - 1), i = 0 ;
- i < length / 2 ;
- s++, e--, i++)
- {
- char tmp ;
+ /* could be done at compile time for max efficiency but not portable (EBCDIC ??). */
+ rev['a'] = 't' ;
+ rev['t'] = 'a' ;
+ rev['c'] = 'g' ;
+ rev['g'] = 'c' ;
- tmp = *s ;
- *s = *e ;
- *e = tmp ;
- switch (*s)
- {
- case 'a':
- *s = 't' ;
- break ;
- case 't':
- *s = 'a' ;
- break ;
- case 'c':
- *s = 'g' ;
- break ;
- case 'g':
- *s = 'c' ;
- break ;
- }
+ for (s_ptr = sequence, e_ptr = (sequence + length - 1), i = 0 ;
+ i < (length + 1) / 2 ;
+ s_ptr++, e_ptr--, i++)
+ {
+ char s, e ;
- switch (*e)
- {
- case 'a':
- *e = 't' ;
- break ;
- case 't':
- *e = 'a' ;
- break ;
- case 'c':
- *e = 'g' ;
- break ;
- case 'g':
- *e = 'c' ;
- break ;
- }
+ s = rev[*s_ptr] ;
+ e = rev[*e_ptr] ;
+
+ *s_ptr = e ;
+ *e_ptr = s ;
}
return ;
}
+
+
+
--
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