From d2152510ff6c4a6ef845cfd61d347113e6cdebc1 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Tue, 7 Nov 2006 11:56:16 +0000
Subject: [PATCH] add code to support a slop factor for perfect gapped aligns.
---
src/zmapFeature/zmapFeature.c | 75 ++++++++++++++++++++++++++++++++---
1 file changed, 69 insertions(+), 6 deletions(-)
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index e5804c5e8..4ee9671cd 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Oct 6 10:53 2006 (edgrif)
+ * Last edited: Nov 6 16:05 2006 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.44 2006-10-06 10:16:31 edgrif Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.45 2006-11-07 11:56:16 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -96,6 +96,8 @@ static void removeNotFreeFeature(GQuark key_id, gpointer data, gpointer user_dat
static void destroyFeatureSet(gpointer data) ;
static void removeNotFreeFeatureSet(GQuark key_id, gpointer data, gpointer user_data) ;
+static gboolean checkForPerfectAlign(GArray *gaps, unsigned int align_error) ;
+
/* !
@@ -473,7 +475,7 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
int query_start, int query_end,
GArray *gaps)
{
- gboolean result = FALSE ;
+ gboolean result = TRUE ; /* Not used at the moment. */
zMapAssert(feature && feature->type == ZMAPFEATURE_ALIGNMENT) ;
@@ -484,10 +486,15 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
feature->feature.homol.y2 = query_end ;
if (gaps)
- feature->feature.homol.align = gaps ;
-
- result = TRUE ;
+ {
+ zMapFeatureSortGaps(gaps) ;
+ feature->feature.homol.align = gaps ;
+
+ feature->feature.homol.flags.perfect = checkForPerfectAlign(feature->feature.homol.align,
+ feature->style->align_error) ;
+ }
+
return result ;
}
@@ -1479,3 +1486,59 @@ static void doNewFeatures(GQuark key_id, gpointer data, gpointer user_data)
}
+/* Returns TRUE if the target blocks match coords are within align_error bases of each other, if
+ * there are less than two blocks then FALSE is returned.
+ *
+ * Sometimes, for reasons I don't understand, its possible to have two butting matches, i.e. they
+ * should really be one continuous match. It may be that this happens at a clone boundary, I don't
+ * try to correct this because really its a data entry problem.
+ *
+ * */
+static gboolean checkForPerfectAlign(GArray *gaps, unsigned int align_error)
+{
+ gboolean perfect_align = FALSE ;
+ int i ;
+ ZMapAlignBlock align, last_align ;
+
+ if (gaps->len > 1)
+ {
+ perfect_align = TRUE ;
+ last_align = &g_array_index(gaps, ZMapAlignBlockStruct, 0) ;
+
+ for (i = 1 ; i < gaps->len ; i++)
+ {
+ int prev_end, curr_start ;
+
+ align = &g_array_index(gaps, ZMapAlignBlockStruct, i) ;
+
+
+ /* The gaps array gets sorted by target coords, this can have the effect of reversing
+ the order of the query coords if the match is to the reverse strand of the target sequence. */
+ if (align->q2 < last_align->q1)
+ {
+ prev_end = align->q2 ;
+ curr_start = last_align->q1 ;
+ }
+ else
+ {
+ prev_end = last_align->q2 ;
+ curr_start = align->q1 ;
+ }
+
+
+ /* The "- 1" is because the default align_error is zero, i.e. zero _missing_ bases,
+ which is true when sub alignment follows on directly from the next. */
+ if ((curr_start - prev_end - 1) <= align_error)
+ {
+ last_align = align ;
+ }
+ else
+ {
+ perfect_align = FALSE ;
+ break ;
+ }
+ }
+ }
+
+ return perfect_align ;
+}
--
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