From 62a95fb3406aa98450369513bfd824c996dee201 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Mon, 8 Feb 2010 18:13:23 +0000
Subject: [PATCH] restored partial sequence display (not starting from 1)
---
src/include/ZMap/zmapFeature.h | 42 ++++++-
src/zmapFeature/zmapFeatureContext.c | 42 +++----
src/zmapFeature/zmapFeature_P.h | 24 ++--
src/zmapServer/pipe/pipeServer.c | 43 ++++---
src/zmapServer/zmapServerProtocolHandler.c | 16 ++-
src/zmapWindow/zmapWindowDrawFeatures.c | 140 ++++++++++++++++-----
src/zmapWindow/zmapWindowFeature.c | 9 +-
src/zmapWindow/zmapWindowItemFactory.c | 51 ++++++--
src/zmapWindow/zmapWindowNavigator.c | 5 +-
src/zmapWindow/zmapWindowState.c | 35 ++++--
10 files changed, 295 insertions(+), 112 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 8a46de481..d9d8ce795 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Feb 5 11:25 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.169 2010-02-05 11:44:21 edgrif Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.170 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -185,6 +185,38 @@ typedef struct
} ZMapMapBlockStruct, *ZMapMapBlock ;
+/*
+ * Sequences and Block Coordinates
+ *
+ * In the context of displaying a single align with a single block,
+ * given a chromosome and a sequence from that to look at *we have:
+ *
+ * 1 X chromosome bases
+ * ============================= ZMapFeatureContext.parent_span.x1/x1
+ *
+ * 1 Y our sequence
+ * ===================== ZMapFeatureContext.sequence_to_parent
+ * p1,p2 = 1,X and c1,c2 = 1,Y
+ *
+ * S E displayed block
+ * ============ ZMapFeatureBlockStruct.block_to_sequence
+ * q1,q2 = 1,Y and t1,t2 = S,E
+ * q_strand, t_strand
+ *
+ * We should always have parent_span set up, if not specified then it will be set to 1,Y.
+ * ZMap will always be run using a sequence of 1,Y; it will never start from a coordinate not equal to 1.
+ * Y may be specified as 0 in various places which signifies 'the end'.
+ *
+ * Start and end coordinates may be specified by command line args, from the main window,
+ * from a GFF file header, from other servers (eg ACEDB, DAS) and these will refer to the block
+ * coordinates not the sequence.
+ *
+ * Reverse complementing is a process that applies to blocks and this involves transforming
+ * the coordinates S,E in the context of the containing sequence 1,Y
+ */
+
+
+
/* DO THESE STRUCTS NEED TO BE EXPOSED ? PROBABLY NOT....TO HIDE THEM WOULD REQUIRE
@@ -269,9 +301,7 @@ typedef struct ZMapFeatureContextStruct_
GQuark parent_name ; /* Name of parent sequence
(== sequence_name if no parent). */
-
- int length ; /* total length of sequence. */
-
+// int length ; /* total length of sequence. */
@@ -922,7 +952,7 @@ gboolean zMapFeatureListForeachDumperDestroy(gpointer dumper_data);
gboolean zMapFeatureGetFeatureListExtent(GList *feature_list, int *start_out, int *end_out);
-void zMapFeature3FrameTranslationRevComp(ZMapFeatureSet feature_set, int origin);
+//void zMapFeature3FrameTranslationRevComp(ZMapFeatureSet feature_set, RevCompData cb_data); mh17: moved to zmapFeature_P.h
char *zMapFeature3FrameTranslationFeatureName(ZMapFeatureSet feature_set, ZMapFrame frame);
void zMapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_set);
gboolean zMapFeature3FrameTranslationCreateSet(ZMapFeatureBlock block, ZMapFeatureSet *set_out);
@@ -974,7 +1004,7 @@ ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
void zMapFeature3FrameTranslationSetCreateFeatures(ZMapFeatureSet feature_set,
ZMapFeatureTypeStyle style);
-void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, int origin);
+
GArray *zMapFeatureAnyAsXMLEvents(ZMapFeatureAny feature_any,
/* ZMapFeatureXMLType xml_type */
diff --git a/src/zmapFeature/zmapFeatureContext.c b/src/zmapFeature/zmapFeatureContext.c
index f09224e79..0e05e4e5b 100755
--- a/src/zmapFeature/zmapFeatureContext.c
+++ b/src/zmapFeature/zmapFeatureContext.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Nov 30 16:23 2009 (edgrif)
* Created: Tue Jan 17 16:13:12 2006 (edgrif)
- * CVS info: $Id: zmapFeatureContext.c,v 1.49 2009-12-02 16:30:04 edgrif Exp $
+ * CVS info: $Id: zmapFeatureContext.c,v 1.50 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -47,12 +47,6 @@
#define ZMAP_CONTEXT_EXEC_RECURSE_OK (ZMAP_CONTEXT_EXEC_STATUS_OK | ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE)
#define ZMAP_CONTEXT_EXEC_RECURSE_FAIL (~ ZMAP_CONTEXT_EXEC_RECURSE_OK)
-typedef struct
-{
- GData *styles ;
- int end ;
-} RevCompDataStruct, *RevCompData ;
-
typedef struct
{
/* Input dna string, note that start != 1 where we are looking at a sub-part of an assembly
@@ -80,12 +74,12 @@ typedef struct
}ContextExecuteStruct, *ContextExecute;
-static void revCompFeature(ZMapFeature feature, int end_coord);
+static void revCompFeature(ZMapFeature feature, int start_coord, int end_coord);
static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
gpointer data,
gpointer user_data,
char **error_out);
-static void revcompSpan(GArray *spans, int seq_end) ;
+static void revcompSpan(GArray *spans, int start_coord, int seq_end) ;
static char *fetchBlockDNAPtr(ZMapFeatureAny feature, ZMapFeatureBlock *block_out) ;
static gboolean coordsInBlock(ZMapFeatureBlock block, int *start_out, int *end_out) ;
@@ -135,9 +129,11 @@ void zMapFeatureReverseComplement(ZMapFeatureContext context, GData *styles)
cb_data.styles = styles ;
+printf("\nReverseComplement\n");
/* Get this first...Then swop */
- cb_data.end = context->sequence_to_parent.c2 ;
- zmapFeatureSwop(Coord, context->sequence_to_parent.p1, context->sequence_to_parent.p2) ;
+ // mh17: this should really be block->block_to_sequence.q1,q2
+ cb_data.start = context->sequence_to_parent.c1 ;
+ cb_data.end = context->sequence_to_parent.c2 ;
/* Because this doesn't allow for execution at context level ;( */
zMapFeatureContextExecute((ZMapFeatureAny)context,
@@ -859,7 +855,7 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
zMapDNAReverseComplement(feature_block->sequence.sequence, feature_block->sequence.length) ;
}
- zmapFeatureRevComp(Coord, cb_data->end,
+ zmapFeatureRevComp(Coord, cb_data->start, cb_data->end,
feature_block->block_to_sequence.t1,
feature_block->block_to_sequence.t2) ;
}
@@ -872,7 +868,7 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
/* Now redo the 3 frame translations from the dna (if they exist). */
if(feature_set->original_id == g_quark_from_string(ZMAP_FIXED_STYLE_3FT_NAME))
- zMapFeature3FrameTranslationSetRevComp(feature_set, cb_data->end);
+ zMapFeature3FrameTranslationSetRevComp(feature_set, cb_data);
}
break;
case ZMAPFEATURE_STRUCT_FEATURE:
@@ -881,7 +877,7 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
feature_ft = (ZMapFeature)feature_any;
- revCompFeature(feature_ft, cb_data->end);
+ revCompFeature(feature_ft, cb_data->start, cb_data->end);
break;
}
@@ -896,7 +892,7 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
return status;
}
-static void revcompSpan(GArray *spans, int seq_end)
+static void revcompSpan(GArray *spans, int seq_start, int seq_end)
{
int i ;
@@ -906,7 +902,7 @@ static void revcompSpan(GArray *spans, int seq_end)
span = &g_array_index(spans, ZMapSpanStruct, i) ;
- zmapFeatureRevComp(Coord, seq_end, span->x1, span->x2) ;
+ zmapFeatureRevComp(Coord, seq_start, seq_end, span->x1, span->x2) ;
}
@@ -914,11 +910,11 @@ static void revcompSpan(GArray *spans, int seq_end)
}
-static void revCompFeature(ZMapFeature feature, int end_coord)
+static void revCompFeature(ZMapFeature feature, int start_coord, int end_coord)
{
zMapAssert(feature);
- zmapFeatureRevComp(Coord, end_coord, feature->x1, feature->x2) ;
+ zmapFeatureRevComp(Coord, start_coord, end_coord, feature->x1, feature->x2) ;
if (feature->strand == ZMAPSTRAND_FORWARD)
feature->strand = ZMAPSTRAND_REVERSE ;
@@ -929,13 +925,13 @@ static void revCompFeature(ZMapFeature feature, int end_coord)
&& (feature->feature.transcript.exons || feature->feature.transcript.introns))
{
if (feature->feature.transcript.exons)
- revcompSpan(feature->feature.transcript.exons, end_coord) ;
+ revcompSpan(feature->feature.transcript.exons, start_coord, end_coord) ;
if (feature->feature.transcript.introns)
- revcompSpan(feature->feature.transcript.introns, end_coord) ;
+ revcompSpan(feature->feature.transcript.introns, start_coord, end_coord) ;
if(feature->feature.transcript.flags.cds)
- zmapFeatureRevComp(Coord, end_coord,
+ zmapFeatureRevComp(Coord, start_coord, end_coord,
feature->feature.transcript.cds_start,
feature->feature.transcript.cds_end);
}
@@ -950,7 +946,7 @@ static void revCompFeature(ZMapFeature feature, int end_coord)
align = &g_array_index(feature->feature.homol.align, ZMapAlignBlockStruct, i) ;
- zmapFeatureRevComp(Coord, end_coord, align->t1, align->t2) ;
+ zmapFeatureRevComp(Coord, start_coord, end_coord, align->t1, align->t2) ;
}
zMapFeatureSortGaps(feature->feature.homol.align) ;
@@ -958,7 +954,7 @@ static void revCompFeature(ZMapFeature feature, int end_coord)
else if (feature->type == ZMAPSTYLE_MODE_ASSEMBLY_PATH)
{
if (feature->feature.assembly_path.path)
- revcompSpan(feature->feature.assembly_path.path, end_coord) ;
+ revcompSpan(feature->feature.assembly_path.path, start_coord, end_coord) ;
}
return ;
diff --git a/src/zmapFeature/zmapFeature_P.h b/src/zmapFeature/zmapFeature_P.h
index 0a609172f..3d45a3605 100755
--- a/src/zmapFeature/zmapFeature_P.h
+++ b/src/zmapFeature/zmapFeature_P.h
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: May 10 08:06 2007 (edgrif)
* Created: Wed Nov 24 11:01:24 2004 (edgrif)
- * CVS info: $Id: zmapFeature_P.h,v 1.5 2007-05-30 14:05:52 edgrif Exp $
+ * CVS info: $Id: zmapFeature_P.h,v 1.6 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_P_H
@@ -46,20 +46,29 @@ typedef struct
} ZMapFeatureStr2EnumStruct, *ZMapFeatureStr2Enum ;
+// mh17: needed in zmapFeature3Frame.c as well as FeatureContext.c
+typedef struct
+{
+ GData *styles ;
+ int start;
+ int end ;
+} RevCompDataStruct, *RevCompData ;
+
#define zmapFeatureSwop(TYPE, FIRST, SECOND) \
{ TYPE tmp = (FIRST) ; (FIRST) = (SECOND) ; (SECOND) = tmp ; }
-#define zmapFeatureInvert(COORD, SEQ_END) \
+#define zmapFeatureInvert(COORD, SEQ_START, SEQ_END) \
(COORD) = (SEQ_END) - (COORD) + 1
-#define zmapFeatureRevComp(TYPE, SEQ_END, COORD_1, COORD_2) \
- { \
- zmapFeatureSwop(TYPE, COORD_1, COORD_2) ; \
- zmapFeatureInvert(COORD_1, SEQ_END) ; \
- zmapFeatureInvert(COORD_2, SEQ_END) ; \
+//
+#define zmapFeatureRevComp(TYPE, SEQ_START, SEQ_END, COORD_1, COORD_2) \
+ { \
+ zmapFeatureSwop(TYPE, COORD_1, COORD_2) ; \
+ zmapFeatureInvert(COORD_1, SEQ_START, SEQ_END) ; \
+ zmapFeatureInvert(COORD_2, SEQ_START, SEQ_END) ; \
}
@@ -71,6 +80,7 @@ gboolean zmapStr2Enum(ZMapFeatureStr2Enum type_table, char *type_str, int *type_
ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotify destroy_cb) ;
+void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, RevCompData cb_data);
#endif /* !ZMAP_FEATURE_P_H */
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index a7bf8654c..d0f031048 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -34,7 +34,7 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: 2009-11-26 12:02:40 (mh17)
- * CVS info: $Id: pipeServer.c,v 1.15 2010-01-27 15:03:03 mh17 Exp $
+ * CVS info: $Id: pipeServer.c,v 1.16 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -897,7 +897,7 @@ static ZMapServerResponseType destroyConnection(void *server_in)
-/*
+/*
* --------------------- Internal routines. ---------------------
*/
@@ -915,24 +915,32 @@ static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header)
* are several streams.... */
feature_context->parent_name = feature_context->sequence_name ;
- feature_context->parent_span.x1 = header->features_start ;
- feature_context->parent_span.x2 = header->features_end ;
-
/* I don't like having to do this right down here but user is allowed to specify "0" for
* end coord meaning "to the end of the sequence" and this is where we know the end... */
- if(feature_block->block_to_sequence.t1 == 0) // in case seq range not pre-specified, don't anchor to 1
+
+ // refer to comment in zmapFeature.h 'Sequences and Block Coordinates'
+ // NB at time of writing parent_span not always initialised
+ feature_context->parent_span.x1 = 1;
+ if(feature_context->parent_span.x2 < header->features_end)
+ feature_context->parent_span.x2 = header->features_end ;
+
+ // seq coords from parent sequence
+ feature_context->sequence_to_parent.p1 = header->features_start;
+ feature_context->sequence_to_parent.p2 = header->features_end;
+
+ // seq coords for our sequence based from 1
+ feature_context->sequence_to_parent.c1 = feature_block->block_to_sequence.q1 = 1;
+ feature_context->sequence_to_parent.c2 = feature_block->block_to_sequence.q2
+ = header->features_end;
+
+ if(feature_block->block_to_sequence.t1 == 0)
+ {
feature_block->block_to_sequence.t1 = header->features_start ;
- if (feature_block->block_to_sequence.t2 == 0)
feature_block->block_to_sequence.t2 = header->features_end ;
-
- feature_context->sequence_to_parent.p1 = feature_context->sequence_to_parent.c1
- = feature_block->block_to_sequence.q1 = feature_block->block_to_sequence.t1 ;
+ }
- feature_context->sequence_to_parent.p2 = feature_context->sequence_to_parent.c2
- = feature_block->block_to_sequence.q2 = feature_block->block_to_sequence.t2 ;
+// feature_context->length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1 + 1;
- feature_context->length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1 + 1;
-
return ;
}
@@ -1012,9 +1020,10 @@ static gboolean sequenceRequest(PipeServer server, ZMapGFFParser parser, GString
/* The caller may only want a small part of the features in the stream so we set the
* feature start/end from the block, not the gff stream start/end. */
zMapGFFSetFeatureClipCoords(parser,
- feature_block->block_to_sequence.q1,
- feature_block->block_to_sequence.q2) ;
-
+ feature_block->block_to_sequence.t1,
+ feature_block->block_to_sequence.t2) ;
+ zMapGFFSetFeatureClip(parser,GFF_CLIP_ALL); // mh17: needs config added to server stanza
+
first = TRUE ;
do
{
diff --git a/src/zmapServer/zmapServerProtocolHandler.c b/src/zmapServer/zmapServerProtocolHandler.c
index c00a89ee0..eced6763c 100755
--- a/src/zmapServer/zmapServerProtocolHandler.c
+++ b/src/zmapServer/zmapServerProtocolHandler.c
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Jan 14 10:26 2010 (edgrif)
* Created: Thu Jan 27 13:17:43 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocolHandler.c,v 1.53 2010-01-14 13:31:52 edgrif Exp $
+ * CVS info: $Id: zmapServerProtocolHandler.c,v 1.54 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -458,11 +458,15 @@ if(*slave_data) zMapLogMessage("req %s/%s %d",server->url->protocol,server->url-
zMapAssert(g_hash_table_size(blocks) == 1) ;
block = (ZMapFeatureBlock)(zMap_g_hash_table_nth(blocks, 0)) ;
- block->block_to_sequence.q1 = block->block_to_sequence.t1
- = context->context->sequence_to_parent.c1 ;
- block->block_to_sequence.q2 = block->block_to_sequence.t2
- = context->context->sequence_to_parent.c2 ;
-
+ if(!block->block_to_sequence.t2)
+ {
+ // mh17: this happens before getFeatures? which is where the data gets set
+ // adding the if has no effect of course
+ block->block_to_sequence.q1 = block->block_to_sequence.t1
+ = context->context->sequence_to_parent.c1 ;
+ block->block_to_sequence.q2 = block->block_to_sequence.t2
+ = context->context->sequence_to_parent.c2 ;
+ }
block->block_to_sequence.q_strand = block->block_to_sequence.t_strand = ZMAPSTRAND_FORWARD ;
}
diff --git a/src/zmapWindow/zmapWindowDrawFeatures.c b/src/zmapWindow/zmapWindowDrawFeatures.c
index ffcc65dc8..c86161896 100755
--- a/src/zmapWindow/zmapWindowDrawFeatures.c
+++ b/src/zmapWindow/zmapWindowDrawFeatures.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 28 01:16 2010 (roy)
* Created: Thu Jul 29 10:45:00 2004 (rnc)
- * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.262 2010-01-27 12:38:31 rds Exp $
+ * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.263 2010-02-08 18:13:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -48,7 +48,7 @@
#define SCALEBAR_OFFSET 0.0
#define SCALEBAR_WIDTH 50.0
-
+#define MH17_REVCOMP_DEBUG 1
/* parameters passed between the various functions drawing the features on the canvas, it's
* simplest to cache the current stuff as we go otherwise the code becomes convoluted by having
@@ -69,7 +69,7 @@ typedef struct _ZMapCanvasDataStruct
* ORDERING/PLACEMENT MECHANISM.... */
/* Records current positional information. */
double curr_x_offset ;
- //double curr_y_offset ;
+// double curr_y_offset ;
/* Records current canvas item groups, these are the direct parent groups of the display
@@ -175,6 +175,8 @@ static FooCanvasGroup *separatorGetFeatureSetColumn(ZMapWindowContainerStrand se
ZMapFeatureSet feature_set);
+static gboolean contextGetMasterAlignSpan(ZMapFeatureContext context,int *start,int *end);
+
extern GTimer *view_timer_G ;
static gboolean window_draw_context_debug_G = FALSE;
@@ -234,8 +236,8 @@ void zmapWindowDrawFeatures(ZMapWindow window,
FooCanvasItem *tmp_item = NULL;
gboolean debug_containers = FALSE, root_created = FALSE;
double x, y;
- double ix1, ix2, iy1, iy2; /* initial root_group coords */
-
+// double ix1, ix2, iy1, iy2; /* initial root_group coords */
+ int seq_start,seq_end;
zMapPrintTimer(NULL, "About to create canvas features") ;
@@ -261,24 +263,36 @@ void zmapWindowDrawFeatures(ZMapWindow window,
/* Must be reset each time because context will change as features get merged in. */
window->feature_context = full_context ;
+#ifdef SHOW_PARENT_SPAN
+ //original code, window based from 1
window->seq_start = full_context->sequence_to_parent.c1 ;
window->seq_end = full_context->sequence_to_parent.c2 ;
+#else
+ // we want to display just the data in our block, not the surrounding sequence
+ contextGetMasterAlignSpan(full_context,&seq_start,&seq_end);
+ window->seq_start = seq_start;
+ window->seq_end = seq_end;
+#endif
+
window->seqLength = zmapWindowExt(window->seq_start, window->seq_end) ;
- /* Set the origin used for displaying coords....
+ /* Set the origin used for displaying coords....
+ * which must refer to the parent span to allow reverse strand coords to be calculated.
* The "+ 2" is because we have to go from sequence_start == 1 to sequence_start == -1
* which is a shift of 2. */
if (window->display_forward_coords)
{
if (window->revcomped_features)
- window->origin = window->seq_end + 2 ;
+ window->origin = full_context->sequence_to_parent.c2 + 2 ;
else
- window->origin = 1 ;
+ window->origin = 1;
zmapWindowRulerCanvasSetOrigin(window->ruler, window->origin) ;
}
-
+#ifdef MH17_REVCOMP_DEBUG
+ printf("drawFeatures window: %f-%f, %d, %d\n",window->seq_start,window->seq_end,window->origin,window->revcomped_features);
+#endif
zmapWindowZoomControlInitialise(window); /* Sets min/max/zf */
@@ -286,7 +300,7 @@ void zmapWindowDrawFeatures(ZMapWindow window,
zmapWindowLongItemSetMaxZoom(window->long_items, zMapWindowGetZoomMax(window)) ;
- window->min_coord = window->seq_start ;
+ window->min_coord = window->seq_start;
window->max_coord = window->seq_end ;
zmapWindowSeq2CanExt(&(window->min_coord), &(window->max_coord)) ;
@@ -306,7 +320,9 @@ void zmapWindowDrawFeatures(ZMapWindow window,
/* I have no idea why, but... */
/* Get the current scroll region */
- zmapWindowGetScrollRegion(window, &ix1, &iy1, &ix2, &iy2);
+
+// mh17: these are not used at all
+// zmapWindowGetScrollRegion(window, &ix1, &iy1, &ix2, &iy2);
if((tmp_item = zmapWindowFToIFindItemFull(window->context_to_item,
0, 0, 0, ZMAPSTRAND_NONE, ZMAPFRAME_NONE, 0)))
@@ -333,7 +349,7 @@ void zmapWindowDrawFeatures(ZMapWindow window,
&(window->colour_root),
&(window->canvas_border));
- zmapWindowContainerGroupBackgroundSize(root_group, window->max_coord);
+ zmapWindowContainerGroupBackgroundSize(root_group, window->max_coord - window->min_coord);
g_signal_connect(G_OBJECT(root_group), "destroy", G_CALLBACK(containerDestroyCB), window) ;
@@ -1345,6 +1361,23 @@ static gboolean pick_forward_reverse_columns(ZMapWindow window,
return found_one;
}
+static gboolean contextGetMasterAlignSpan(ZMapFeatureContext context,int *start,int *end)
+{
+ gboolean res = TRUE;
+ GHashTable *blocks = context->master_align->blocks ;
+ ZMapFeatureBlock block ;
+
+ // refer to RT 158542
+ zMapAssert(g_hash_table_size(blocks) == 1) ; // (currently we only ever have one)
+
+ block = (ZMapFeatureBlock)(zMap_g_hash_table_nth(blocks, 0)) ;
+ if(start) *start = block->block_to_sequence.t1;
+ if(end) *end = block->block_to_sequence.t2;
+
+ return(res);
+}
+
+
static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
gpointer data,
gpointer user_data,
@@ -1389,18 +1422,25 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
ZMapWindowContainerGroup align_parent;
FooCanvasItem *align_hash_item;
double x, y;
+ int start,end;
feature_align = (ZMapFeatureAlignment)feature_any;
-
+#ifdef MH17_REVCOMP_DEBUG
+ printf("drawFeatures align");
+#endif
/* record the full_context current align, not the diff align which will get destroyed! */
canvas_data->curr_alignment = zMapFeatureContextGetAlignmentByID(canvas_data->full_context,
feature_any->unique_id) ;
- /* THIS MUST GO.t...because we will have aligns that .sigh.do not start at 0 one day.... */
+ /* THIS MUST GO....because we will have aligns that .sigh.do not start at 0 one day.... */
/* Always reset the aligns to start at y = 0. */
//canvas_data->curr_y_offset = 0.0 ;
x = canvas_data->curr_x_offset ;
- y = canvas_data->full_context->sequence_to_parent.c1 ;
+// y = canvas_data->full_context->sequence_to_parent.c1 ;
+ contextGetMasterAlignSpan(canvas_data->full_context,&start,&end); // else we get everything offset by the start coord
+ y = start;
+// canvas_data->curr_y_offset = start ;
+
my_foo_canvas_item_w2i(FOO_CANVAS_ITEM(canvas_data->curr_root_group), &x, &y) ;
if ((align_hash_item = zmapWindowFToIFindItemFull(window->context_to_item,
@@ -1460,21 +1500,27 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
gboolean block_created = FALSE;
feature_block = (ZMapFeatureBlock)feature_any;
+#ifdef MH17_REVCOMP_DEBUG
+printf("\ndrawFeatures block %d-%d",feature_block->block_to_sequence.t1,feature_block->block_to_sequence.t2);
+#endif
/* record the full_context current block, not the diff block which will get destroyed! */
canvas_data->curr_block = zMapFeatureAlignmentGetBlockByID(canvas_data->curr_alignment,
feature_block->unique_id);
/* Always set y offset to be top of current block. */
- // canvas_data->curr_y_offset = feature_block->block_to_sequence.t1 ;
+// canvas_data->curr_y_offset = feature_block->block_to_sequence.t1 ;
if ((block_hash_item = zmapWindowFToIFindItemFull(window->context_to_item,
canvas_data->curr_alignment->unique_id,
feature_block->unique_id, 0, ZMAPSTRAND_NONE,
ZMAPFRAME_NONE, 0)))
{
- zMapAssert(ZMAP_IS_CONTAINER_GROUP(block_hash_item));
+ zMapAssert(ZMAP_IS_CONTAINER_GROUP(block_hash_item));
block_parent = (ZMapWindowContainerGroup)(block_hash_item);
+#ifdef MH17_REVCOMP_DEBUG
+ printf(" old");
+#endif
}
else
{
@@ -1488,6 +1534,9 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
G_CALLBACK(containerDestroyCB),
window) ;
block_created = TRUE;
+#ifdef MH17_REVCOMP_DEBUG
+ printf(" new");
+#endif
zmapWindowContainerBlockAugment((ZMapWindowContainerBlock)block_parent,
canvas_data->curr_block) ;
@@ -1557,8 +1606,8 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
zmapWindowContainerStrandAugment((ZMapWindowContainerStrand)reverse_group, ZMAPSTRAND_REVERSE);
- zmapWindowContainerGroupBackgroundSize(reverse_group,
- (double)feature_block->block_to_sequence.t2);
+ zmapWindowContainerGroupBackgroundSize(reverse_group,
+ (double)(feature_block->block_to_sequence.t2 - feature_block->block_to_sequence.t1));
g_signal_connect(G_OBJECT(zmapWindowContainerGetBackground(reverse_group)),
"event", G_CALLBACK(strandBoundingBoxEventCB),
@@ -1571,15 +1620,16 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
if ((block_created == TRUE) ||
(strand_separator = (ZMapWindowContainerGroup)zmapWindowContainerBlockGetContainerSeparator(container_block)) == NULL)
+
{
- strand_separator = zmapWindowContainerGroupCreate(canvas_data->curr_block_group,
+ strand_separator = zmapWindowContainerGroupCreate(canvas_data->curr_block_group,
ZMAPCONTAINER_LEVEL_STRAND,
window->config.column_spacing,
&(window->colour_separator),
&(canvas_data->window->canvas_border));
- zmapWindowContainerStrandSetAsSeparator((ZMapWindowContainerStrand)strand_separator);
- zmapWindowContainerGroupBackgroundSize(strand_separator,
- (double)feature_block->block_to_sequence.t2);
+ zmapWindowContainerStrandSetAsSeparator((ZMapWindowContainerStrand)strand_separator);
+ zmapWindowContainerGroupBackgroundSize(strand_separator,
+ (double) (feature_block->block_to_sequence.t2 - feature_block->block_to_sequence.t1));
}
if ((block_created == TRUE) ||
@@ -1592,8 +1642,8 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
&(canvas_data->window->canvas_border));
zmapWindowContainerStrandAugment((ZMapWindowContainerStrand)forward_group, ZMAPSTRAND_FORWARD);
- zmapWindowContainerGroupBackgroundSize(forward_group,
- (double)feature_block->block_to_sequence.t2);
+ zmapWindowContainerGroupBackgroundSize(forward_group,
+ (double)(feature_block->block_to_sequence.t2 - feature_block->block_to_sequence.t1));
g_signal_connect(G_OBJECT(zmapWindowContainerGetBackground(forward_group)),
"event", G_CALLBACK(strandBoundingBoxEventCB),
@@ -1627,6 +1677,9 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
* copy of the view context's feature set. It should also get
* destroyed with the diff context, so be warned. */
feature_set = (ZMapFeatureSet)feature_any;
+#ifdef MH17_REVCOMP_DEBUG
+printf("drawFeatures set %s",feature_set->description);
+#endif
if (feature_set_matches_frame_drawing_mode(window, canvas_data, canvas_data->curr_set,
&frame_start, &frame_end))
@@ -1650,6 +1703,10 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
zMapWindowContainerFeatureSetMarkUnsorted(ZMAP_CONTAINER_FEATURESET(tmp_forward));
if(tmp_reverse)
zMapWindowContainerFeatureSetMarkUnsorted(ZMAP_CONTAINER_FEATURESET(tmp_reverse));
+#ifdef MH17_REVCOMP_DEBUG
+ printf("\nFeatures...\n");
+#endif
+
zmapWindowDrawFeatureSet(window,
canvas_data->styles,
@@ -1670,7 +1727,7 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
break;
}
- case ZMAPFEATURE_STRUCT_INVALID:
+ case ZMAPFEATURE_STRUCT_INVALID:
default:
{
status = ZMAP_CONTEXT_EXEC_STATUS_ERROR;
@@ -1678,6 +1735,10 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
break;
}
}
+#ifdef MH17_REVCOMP_DEBUG
+ if(feature_type != ZMAPFEATURE_STRUCT_FEATURE)
+ printf(" -> status %s\n",status == ZMAP_CONTEXT_EXEC_STATUS_OK ? "OK" : "error");
+#endif
return status;
}
@@ -1841,7 +1902,7 @@ static FooCanvasGroup *createColumnFull(ZMapWindowContainerFeatures parent_group
zmapWindowContainerGroupChildRedrawRequired(container, FALSE) ;
/* Make sure group covers whole span in y direction. */
- zmapWindowContainerGroupBackgroundSize(container, bot) ;
+ zmapWindowContainerGroupBackgroundSize(container, bot-top) ;
/* THIS WOULD ALL GO IF WE DIDN'T ADD EMPTY COLS...... */
/* We can't set the ITEM_FEATURE_DATA as we don't have the feature set at this point.
@@ -1914,7 +1975,9 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
FooCanvasItem *feature_item ;
ZMapFeatureTypeStyle style ;
-
+#ifdef MH17_REVCOMP_DEBUG
+ printf("ProcessFeature %d-%d ",feature->x1,feature->x2);
+#endif
/* Do some filtering on frame and strand */
/* Find out which strand group the feature should be displayed in. */
@@ -1924,15 +1987,25 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
* curr_forward_col or curr_reverse_col */
if ((display_strand == ZMAPSTRAND_FORWARD && !(featureset_data->curr_forward_col))
|| (display_strand == ZMAPSTRAND_REVERSE && !(featureset_data->curr_reverse_col)))
+ {
+#ifdef MH17_REVCOMP_DEBUG
+ printf("wrong strand 1\n");
+#endif
return ;
-
+ }
+
/* If we are doing frame specific display then don't display the feature if its the wrong
* frame or its on the reverse strand and we aren't displaying reverse strand frames. */
if (featureset_data->frame != ZMAPFRAME_NONE
&& (featureset_data->frame != zmapWindowFeatureFrame(feature)
|| (!(window->show_3_frame_reverse) && display_strand == ZMAPSTRAND_REVERSE)))
+ {
+#ifdef MH17_REVCOMP_DEBUG
+ printf("wrong strand 2\n");
+#endif
return ;
-
+ }
+
/* Get the correct column to draw into... */
if (display_strand == ZMAPSTRAND_FORWARD)
{
@@ -1946,6 +2019,9 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
featureset_data->feature_count++;
style = zMapFindStyle(featureset_data->styles, feature->style_id) ;
+#ifdef MH17_REVCOMP_DEBUG
+ if(!style) printf("no style 1 ");
+#endif
if(style)
style = zmapWindowContainerFeatureSetStyleFromStyle((ZMapWindowContainerFeatureSet)column_group, style) ;
@@ -1954,6 +2030,10 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
g_quark_to_string(feature->style_id),
g_quark_to_string(feature->original_id));
+#ifdef MH17_REVCOMP_DEBUG
+ if(!style) printf("no style 2");
+ printf("\n");
+#endif
if(style)
feature_item = zmapWindowFeatureDraw(window, style, (FooCanvasGroup *)column_group, feature) ;
else
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index b8b97eb29..ddb5ff038 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Jan 22 11:23 2010 (edgrif)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.172 2010-01-22 13:53:15 edgrif Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.173 2010-02-08 18:13:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -52,6 +52,8 @@
#define PFETCH_FAILED_PREFIX "PFetch failed:"
#define PFETCH_TITLE_FORMAT "ZMap - pfetch \"%s\""
+#define MH17_REVCOMP_DEBUG 1
+
enum
{
ITEM_MENU_INVALID,
@@ -502,7 +504,6 @@ FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
ZMapFeatureBlock block ;
ZMapFeatureSet set ;
-
/* Users will often not want to see what is on the reverse strand, style specifies what should
* be shown. */
if ((zMapStyleIsStrandSpecific(style)) &&
@@ -510,6 +511,10 @@ FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
{
return NULL ;
}
+#ifdef MH17_REVCOMP_DEBUG
+ printf("FeatureDraw %d-%d\n",feature->x1,feature->x2);
+#endif
+
/* These should be parameters, rather than continually fetch them, caller will almost certainly know these! */
set = (ZMapFeatureSet)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
diff --git a/src/zmapWindow/zmapWindowItemFactory.c b/src/zmapWindow/zmapWindowItemFactory.c
index 20d1ee0e7..ee94e53f7 100755
--- a/src/zmapWindow/zmapWindowItemFactory.c
+++ b/src/zmapWindow/zmapWindowItemFactory.c
@@ -30,9 +30,11 @@
* HISTORY:
* Last edited: Jan 17 10:28 2010 (edgrif)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.c,v 1.73 2010-01-22 17:33:53 mh17 Exp $
+ * CVS info: $Id: zmapWindowItemFactory.c,v 1.74 2010-02-08 18:13:24 mh17 Exp $
*-------------------------------------------------------------------
*/
+
+#define MH17_REVCOMP_DEBUG 1
#include <math.h>
#include <string.h>
@@ -285,12 +287,16 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
ZMapFeatureTypeStyle style = NULL;
ZMapStyleMode style_mode = ZMAPSTYLE_MODE_INVALID ;
gboolean no_points_in_block = TRUE;
- /* check here before they get called. I'd prefer to only do this
- * once per factory rather than once per Run! */
+#if MH17_REVCOMP_DEBUG
+ printf("run_single ");
+#endif
+ /* check here before they get called. I'd prefer to only do this
+ * once per factory rather than once per Run! */
zMapAssert(factory->user_funcs &&
factory->user_funcs->top_item_created);
+
#ifndef RDS_REMOVED_STATS
// ZMapWindowItemFeatureSetData set_data = NULL;
@@ -329,13 +335,17 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
if (zMapStyleIsStrandSpecific(style)
&& (feature->strand == ZMAPSTRAND_REVERSE && !zMapStyleIsShowReverseStrand(style)))
+ {
+#if MH17_REVCOMP_DEBUG
+ printf("not reverse\n");
+#endif
goto undrawn;
-
+ }
/* Note: for object to _span_ "width" units, we start at zero and end at "width". */
limits[0] = 0.0;
- limits[1] = (double)(block->block_to_sequence.q1);
+ limits[1] = (double)(block->block_to_sequence.t1);
limits[2] = zMapStyleGetWidth(style);
- limits[3] = (double)(block->block_to_sequence.q2);
+ limits[3] = (double)(block->block_to_sequence.t2);
/* Set these to this for normal main window use. */
points[0] = 0.0;
@@ -346,8 +356,13 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
/* inline static void normalSizeReq(ZMapFeature f, ... ){ return ; } */
/* inlined this should be nothing most of the time, question is can it be inlined?? */
if((no_points_in_block = (factory->user_funcs->feature_size_request)(feature, &limits[0], &points[0], factory->user_data)) == TRUE)
+ {
+#if MH17_REVCOMP_DEBUG
+ printf("no points in block\n");
+#endif
goto undrawn;
-
+ }
+
style_mode = zMapStyleGetMode(style) ;
@@ -374,6 +389,9 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
break;
}
+#if MH17_REVCOMP_DEBUG
+ printf("not reverse\n");
+#endif
case ZMAPSTYLE_MODE_ALIGNMENT:
{
@@ -540,6 +558,9 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
if(factory->ftoi_hash)
{
+#ifdef MH17_REVCOMP_DEBUG
+ printf("FToIAddFeature %d-%d\n",feature->x1,feature->x2);
+#endif
status = zmapWindowFToIAddFeature(factory->ftoi_hash,
align->unique_id,
block->unique_id,
@@ -547,6 +568,12 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
strand, frame,
feature->unique_id, item) ;
}
+ else
+ {
+#if MH17_REVCOMP_DEBUG
+ printf("ho hash\n");
+#endif
+ }
status = (factory->user_funcs->top_item_created)(item, context, align, block, set, feature, factory->user_data);
@@ -554,9 +581,19 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
return_item = item;
}
+ else
+ {
+#if MH17_REVCOMP_DEBUG
+ printf("no item\n");
+#endif
+ }
+
}
else
{
+#if MH17_REVCOMP_DEBUG
+ printf("unknown type\n");
+#endif
zMapLogFatal("Feature %s is of unknown type: %d\n",
(char *)g_quark_to_string(feature->original_id), feature->type) ;
}
diff --git a/src/zmapWindow/zmapWindowNavigator.c b/src/zmapWindow/zmapWindowNavigator.c
index ce763db87..b7674e0bc 100755
--- a/src/zmapWindow/zmapWindowNavigator.c
+++ b/src/zmapWindow/zmapWindowNavigator.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jan 23 22:54 2010 (roy)
* Created: Wed Sep 6 11:22:24 2006 (rds)
- * CVS info: $Id: zmapWindowNavigator.c,v 1.57 2010-01-24 10:23:57 rds Exp $
+ * CVS info: $Id: zmapWindowNavigator.c,v 1.58 2010-02-08 18:13:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -1006,7 +1006,8 @@ static void createColumnCB(gpointer data, gpointer user_data)
container_background = zmapWindowContainerGetBackground(draw_data->container_feature_set);
zmapWindowContainerGroupBackgroundSize(draw_data->container_feature_set,
- draw_data->current_block->block_to_sequence.t2 * draw_data->navigate->scaling_factor);
+ (draw_data->current_block->block_to_sequence.t2 - draw_data->current_block->block_to_sequence.t1)
+ * draw_data->navigate->scaling_factor);
/* scale doesn't need this. */
if(set_id != g_quark_from_string(ZMAP_FIXED_STYLE_SCALE_NAME))
diff --git a/src/zmapWindow/zmapWindowState.c b/src/zmapWindow/zmapWindowState.c
index d329c1dd0..efdab4ebc 100755
--- a/src/zmapWindow/zmapWindowState.c
+++ b/src/zmapWindow/zmapWindowState.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jan 22 12:12 2010 (edgrif)
* Created: Mon Jun 11 09:49:16 2007 (rds)
- * CVS info: $Id: zmapWindowState.c,v 1.24 2010-01-22 13:56:24 edgrif Exp $
+ * CVS info: $Id: zmapWindowState.c,v 1.25 2010-02-08 18:13:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -417,13 +417,28 @@ gboolean zmapWindowStateGetScrollRegion(ZMapWindowState state,
/* INTERNAL */
-static void rev_comp_about_origin(int origin, double *a, double *b)
+static void rev_comp_region(ZMapWindow window, double *a, double *b)
{
- double tp; /* temp */
+/*
+ * rev comp'd coords are based on sequence end (the new origin)
+ * these are displayed as -ve numbers via some calcultions in zmapWindowUtils.c
+ */
+ ZMapMapBlock p2s;
+
+ /* RevComp applies to a block not a window or featurecontext
+ * but for the momwnt we only handle one align and one block
+ * So we can get the block query sequence coord from here as
+ * they are the same as the sequence_to_parent child coordinates
+ * ref to RT 158542
+ */
+ p2s = &window->feature_context->sequence_to_parent;
+
+
if(a && b)
{
- *a = origin - *a;
- *b = origin - *b;
+ double tp; /* temp */
+ *a = p2s->c2 + 1 - *a;
+ *b = p2s->c2 + 1 - *b;
tp = *a;
*a = *b;
*b = tp;
@@ -438,9 +453,7 @@ static void state_mark_restore(ZMapWindow window, ZMapWindowMark mark, ZMapWindo
if(window->revcomped_features != restore.rev_comp_state)
{
- double seq_length;
- seq_length = window->seqLength + 1; /* seqToExtent */
- rev_comp_about_origin(seq_length, &(restore.y1), &(restore.y2));
+ rev_comp_region(window, &(restore.y1), &(restore.y2));
}
if(serialized->item.align_id != 0 && serialized->item.feature_id != 0)
@@ -507,15 +520,13 @@ static void state_position_restore(ZMapWindow window, ZMapWindowPositionStruct *
if(window->revcomped_features != position->rev_comp_state)
{
- int seq_length;
double tmp;
- /* we need to swap positions in the position struct... */
- seq_length = window->seqLength + 1; /* seqToExtent */
if(window_state_debug_G)
print_position(position, "state_position_restore rev-comp status switched! reversing position...");
- rev_comp_about_origin(seq_length, &(new_position.scroll_y1), &(new_position.scroll_y2));
+ rev_comp_region(window, &(new_position.scroll_y1), &(new_position.scroll_y2));
+
#ifdef RDS_DONT_INCLUDE
new_position.scroll_y1 = seq_length - position->scroll_y1;
new_position.scroll_y2 = seq_length - position->scroll_y2;
--
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