From c0265db4a5d30effbbe9fa8fe89b581d29cfafef Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 14 Jul 2004 13:07:42 +0000
Subject: [PATCH] Add parent length and name to feature context, required for
mapping
---
src/include/ZMap/zmapFeature.h | 7 +++++--
src/zmapGFF/zmapGFF2parser.c | 11 +++++++----
2 files changed, 12 insertions(+), 6 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 821baffaa..ea66145b5 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -25,9 +25,9 @@
* Description: Data structures describing a genetic feature.
*
* HISTORY:
- * Last edited: Jul 14 10:53 2004 (edgrif)
+ * Last edited: Jul 14 14:01 2004 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.5 2004-07-14 12:54:31 edgrif Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.6 2004-07-14 13:07:42 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -221,6 +221,9 @@ typedef struct ZMapFeatureSetStruct_
typedef struct ZMapFeatureContextStruct_
{
char *sequence ; /* The sequence to be displayed. */
+ char *parent ; /* Name of parent, not be needed ? */
+ int parent_length ; /* Length in bases of parent. */
+
ZMapMapBlockStruct sequence_to_parent ; /* Shows how this sequence maps to its
ultimate parent. */
ZMapMapBlockStruct features_to_sequence ; /* Shows how these features map to the
diff --git a/src/zmapGFF/zmapGFF2parser.c b/src/zmapGFF/zmapGFF2parser.c
index 35ba96552..3c7b0630b 100755
--- a/src/zmapGFF/zmapGFF2parser.c
+++ b/src/zmapGFF/zmapGFF2parser.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapGFF.h
* HISTORY:
- * Last edited: Jul 14 11:45 2004 (edgrif)
+ * Last edited: Jul 14 14:04 2004 (edgrif)
* Created: Fri May 28 14:25:12 2004 (edgrif)
- * CVS info: $Id: zmapGFF2parser.c,v 1.7 2004-07-14 12:53:44 edgrif Exp $
+ * CVS info: $Id: zmapGFF2parser.c,v 1.8 2004-07-14 13:07:42 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -228,12 +228,12 @@ ZMapFeatureContext zmapGFFGetFeatures(ZMapGFFParser parser)
* We assume that we only ask for complete clones....
* */
{
- int tmp_start = 100000 ;
+ int tmp_pad = 100000 ;
int clone_length = parser->features_end - parser->features_start + 1 ;
feature_context->sequence_to_parent.c1 = parser->features_start ;
feature_context->sequence_to_parent.c2 = parser->features_end ;
- feature_context->sequence_to_parent.p1 = tmp_start ;
+ feature_context->sequence_to_parent.p1 = tmp_pad ;
feature_context->sequence_to_parent.p2
= feature_context->sequence_to_parent.p1 + clone_length ;
@@ -241,6 +241,9 @@ ZMapFeatureContext zmapGFFGetFeatures(ZMapGFFParser parser)
feature_context->features_to_sequence.p2 = parser->features_end ;
feature_context->features_to_sequence.c1 = parser->features_start ;
feature_context->features_to_sequence.c2 = parser->features_end ;
+
+ feature_context->parent_length = feature_context->sequence_to_parent.p2 + tmp_pad ;
+ feature_context->parent = "chromsome_99" ;
}
g_datalist_init(&(feature_context->features)) ;
--
GitLab