From 81bb48179ab3ef66f3b6147b2dc82e9e1a413094 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 7 Sep 2009 09:37:52 +0000
Subject: [PATCH] there were several places where pointers to lists were used
when it should have been copies of the whole list. Add some mem debug code.
---
src/zmapFeature/zmapFeature.c | 72 +++++++++++++++++++++++++++--------
1 file changed, 56 insertions(+), 16 deletions(-)
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index f06a316a6..e205fa360 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -1,4 +1,3 @@
-
/* File: zmapFeatures.c
* Author: Ed Griffiths (edgrif@sanger.ac.uk)
* Copyright (c) 2006: Genome Research Ltd.
@@ -28,9 +27,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Sep 4 12:02 2009 (edgrif)
+ * Last edited: Sep 7 10:36 2009 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.116 2009-09-04 11:05:02 edgrif Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.117 2009-09-07 09:37:52 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -162,7 +161,7 @@ static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
char **error_out) ;
static void addFeatureModeCB(gpointer key, gpointer data, gpointer user_data) ;
-
+static void logMemCalls(gboolean alloc, ZMapFeatureAny feature_any) ;
@@ -174,6 +173,9 @@ static gboolean destroy_debug_G = FALSE;
/* Currently if we use this we get seg faults so we must not be cleaning up properly somewhere... */
static gboolean USE_SLICE_ALLOC = TRUE ;
+static gboolean LOG_MEM_CALLS = FALSE ;
+
+
#ifdef FEATURES_NEED_MAGIC
ZMAP_MAGIC_NEW(feature_magic_G, ZMapFeatureAnyStruct) ;
@@ -368,6 +370,9 @@ ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotif
new_feature_any = g_memdup(orig_feature_any, bytes) ;
+ logMemCalls(TRUE, new_feature_any) ;
+
+
/* We DO NOT copy children or parents... */
new_feature_any->parent = NULL ;
if (new_feature_any->struct_type != ZMAPFEATURE_STRUCT_FEATURE)
@@ -1462,6 +1467,7 @@ ZMapFeatureContextMergeCode zMapFeatureContextMerge(ZMapFeatureContext *merged_c
{
/* Here we need to merge for all alignments and all blocks.... */
MergeContextDataStruct merge_data = {NULL} ;
+ GList *copy_features ;
/* Note we make the diff context point at the feature list and styles of the new context,
@@ -1478,8 +1484,12 @@ ZMapFeatureContextMergeCode zMapFeatureContextMerge(ZMapFeatureContext *merged_c
merge_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK ;
merge_data.new_features = FALSE ;
+
+ /* THIS LOOKS SUSPECT...WHY ISN'T THE NAMES LIST COPIED FROM NEW_CONTEXT....*/
+ copy_features = g_list_copy(new_context->feature_set_names) ;
current_context->feature_set_names = g_list_concat(current_context->feature_set_names,
- new_context->feature_set_names);
+ copy_features) ;
+
if (merge_debug_G)
zMapLogWarning("%s", "merging ...");
@@ -1567,6 +1577,7 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
char *diff_context_string = NULL;
ZMapFeatureContext current_context ;
ZMapFeatureContext diff_context ;
+ GList *copy_list ;
zMapAssert(current_context_inout && remove_context && diff_context_out) ;
@@ -1575,16 +1586,29 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
diff_context = zMapFeatureContextCreate(NULL, 0, 0, NULL);
diff_context->diff_context = TRUE;
diff_context->elements_to_destroy = g_hash_table_new_full(NULL, NULL, NULL, destroyFeatureAny);
- diff_context->feature_set_names = remove_context->feature_set_names;
+
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+
+ /* WHY IS THIS DONE TWICE....??? */
+
+ /* TRY COPYING THE LIST.... */
+ diff_context->feature_set_names = g_list_copy(remove_context->feature_set_names) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
merge_data.view_context = current_context;
merge_data.iteration_context = remove_context;
merge_data.diff_context = diff_context;
merge_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK;
- diff_context->feature_set_names = remove_context->feature_set_names;
+
+ /* LOOKS SUSPECT...SHOULD BE COPIED....*/
+ diff_context->feature_set_names = g_list_copy(remove_context->feature_set_names) ;
+
+ copy_list = g_list_copy(remove_context->feature_set_names) ;
current_context->feature_set_names = g_list_concat(current_context->feature_set_names,
- remove_context->feature_set_names);
+ copy_list) ;
/* Set the original and unique ids so that the context passes the feature validity checks */
diff_context_string = g_strdup_printf("%s vs %s\n",
@@ -1747,16 +1771,9 @@ static void destroyFeatureAny(gpointer data)
if (feature_any->struct_type != ZMAPFEATURE_STRUCT_FEATURE)
g_hash_table_destroy(feature_any->children) ;
- {
- char *func ;
- if (USE_SLICE_ALLOC)
- func = "g_slice_free1" ;
- else
- func = "g_free" ;
+ logMemCalls(FALSE, feature_any) ;
- zMapLogWarning("%s: %s at %p\n", func, zMapFeatureStructType2Str(feature_any->struct_type), feature_any) ;
- }
memset(feature_any, (char )0, nbytes); /* Make sure mem for struct is useless. */
if (USE_SLICE_ALLOC)
@@ -2553,6 +2570,8 @@ static ZMapFeatureAny featureAnyCreateFeature(ZMapFeatureStructType struct_type,
feature_any->struct_type = struct_type ;
+ logMemCalls(TRUE, feature_any) ;
+
if (struct_type != ZMAPFEATURE_STRUCT_CONTEXT)
feature_any->parent = parent ;
@@ -2794,3 +2813,24 @@ gboolean zMapFeatureAnyHasMagic(ZMapFeatureAny feature_any)
return has_magic;
}
+
+
+
+static void logMemCalls(gboolean alloc, ZMapFeatureAny feature_any)
+{
+ char *func ;
+
+ if (LOG_MEM_CALLS)
+ {
+ if (USE_SLICE_ALLOC && alloc)
+ func = "g_slice_alloc0" ;
+ else if (USE_SLICE_ALLOC && !alloc)
+ func = "g_slice_free1" ;
+ else
+ func = "BAD_FUNC" ;
+
+ zMapLogWarning("%s: %s at %p\n", func, zMapFeatureStructType2Str(feature_any->struct_type), feature_any) ;
+ }
+
+ return ;
+}
--
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