src/inc/fuzzyFind.h 1.20

Index: src/inc/fuzzyFind.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/fuzzyFind.h,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/inc/fuzzyFind.h	27 Mar 2007 23:21:25 -0000	1.19
+++ src/inc/fuzzyFind.h	21 Aug 2009 18:41:34 -0000	1.20
@@ -219,8 +219,16 @@
  * score of alignment. */
 
 /************* lib/fuzzyShow - display alignments. ****************/
 
+void ffShowSideBySide(FILE *f, struct ffAli *leftAli, DNA *needle, int needleNumOffset,
+		      DNA *haystack, int hayNumOffset, int haySize, int hayOffStart, int hayOffEnd,
+		      int blockMaxGap, boolean rcHaystack, boolean initialNewline);
+/* Print HTML side-by-side alignment of needle and haystack (no title or labels) to f.
+ * {hay,needle}NumOffset are the coords at which the DNA sequence begins.
+ * hayOff{Start,End} are the range of coords *relative to hayNumOffset* to which the 
+ * alignment display will be clipped -- pass in {0,haySize} for no clipping. */
+
 int ffShAliPart(FILE *f, struct ffAli *aliList, 
     char *needleName, DNA *needle, int needleSize, int needleNumOffset,
     char *haystackName, DNA *haystack, int haySize, int hayNumOffset,
     int blockMaxGap, boolean rcNeedle, boolean rcHaystack,