From 78d59935ce316b285060e4fa6b83f8bd7ffa18b3 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 30 Oct 2006 11:36:26 +0000
Subject: [PATCH] we did not set blixem offset param correctly, we do now.
---
src/zmapWindow/zmapWindowCallBlixem.c | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/src/zmapWindow/zmapWindowCallBlixem.c b/src/zmapWindow/zmapWindowCallBlixem.c
index 7827f5f22..33a9bd713 100755
--- a/src/zmapWindow/zmapWindowCallBlixem.c
+++ b/src/zmapWindow/zmapWindowCallBlixem.c
@@ -31,9 +31,9 @@
*
* Exported functions: see zmapWindow_P.h
* HISTORY:
- * Last edited: Oct 13 17:14 2006 (edgrif)
+ * Last edited: Oct 30 11:35 2006 (edgrif)
* Created: Tue May 9 14:30 2005 (rnc)
- * CVS info: $Id: zmapWindowCallBlixem.c,v 1.23 2006-10-16 10:52:51 edgrif Exp $
+ * CVS info: $Id: zmapWindowCallBlixem.c,v 1.24 2006-10-30 11:36:26 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -72,7 +72,7 @@ typedef struct BlixemDataStruct
ZMapWindow window;
FooCanvasItem *item ;
ZMapFeature feature ;
-
+ ZMapFeatureBlock block ;
/* Used for processing individual features. */
ZMapFeatureType required_feature_type ; /* specifies what type of feature
@@ -132,6 +132,7 @@ gboolean zmapWindowCallBlixem(ZMapWindow window, FooCanvasItem *item, gboolean o
status = FALSE;
err_msg = "No DNA attached to feature's parent so cannot call blixem." ;
}
+ blixem_data.block = block ;
if (status)
status = getUserPrefs(&blixem_data) ;
@@ -306,7 +307,7 @@ static char *buildParamString(blixemData blixem_data)
int start;
int scope = 40000; /* set from user prefs */
int x1, x2;
- int offset ;
+ int offset, origin ;
if (blixem_data->Scope > 0)
scope = blixem_data->Scope ;
@@ -332,9 +333,13 @@ static char *buildParamString(blixemData blixem_data)
start = x1 - blixem_data->min - 30 ;
- /* Offset is "- 1" because blixem needs to use it literally as an offset and not as an
- * absolute position. */
- offset = blixem_data->min - 1 ;
+ /* Offset is "+ 2" because acedb uses seq_length + 1 for revcomp for its own obsure reasons and blixem
+ * has inherited this. I don't know why but don't want to change anything in blixem. */
+ if (blixem_data->window->revcomped_features)
+ origin = blixem_data->block->block_to_sequence.q2 + 2 ;
+ else
+ origin = 1 ;
+ offset = blixem_data->min - origin ;
if (feature->feature.homol.type == ZMAPHOMOL_X_HOMOL) /* protein */
--
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