Skip to content
Snippets Groups Projects
Commit 4cd79124 authored by mh17's avatar mh17
Browse files

set block sequence to be inner loaded protion not logical seq from 1

parent fa647320
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
src/zmapFeature/zmapFeature3FrameTranslation.c
+ 7
− 5
View file @ 4cd79124
......@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 1 19:01 2009 (rds)
* Created: Wed Apr 8 16:18:11 2009 (rds)
* CVS info: $Id: zmapFeature3FrameTranslation.c,v 1.1 2009-05-08 14:19:54 rds Exp $
* CVS info: $Id: zmapFeature3FrameTranslation.c,v 1.2 2010-02-09 09:28:30 mh17 Exp $
*-------------------------------------------------------------------
*/
......@@ -91,7 +91,7 @@ void zMapFeature3FrameTranslationSetCreateFeatures(ZMapFeatureSet feature_set,
return ;
}
void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, int origin)
void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, RevCompData cb_data)
{
zmapFeature3FrameTranslationPopulate(feature_set, NULL);
......@@ -100,7 +100,7 @@ void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, int orig
* so the numbers don't need rev comping then, so we do it here.
* I figured doing it twice was less hassle than special case
* elsewhere... RDS */
g_hash_table_foreach(feature_set->features, fudge_rev_comp_translation, GINT_TO_POINTER(origin));
g_hash_table_foreach(feature_set->features, fudge_rev_comp_translation, (gpointer) cb_data);
return ;
}
......@@ -202,7 +202,9 @@ static void zmapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_se
static void fudge_rev_comp_translation(gpointer key, gpointer value, gpointer user_data)
{
ZMapFeature feature = (ZMapFeature)value;
zmapFeatureRevComp(Coord, GPOINTER_TO_INT(user_data), feature->x1, feature->x2);
RevCompData cb_data = (RevCompData) user_data;
zmapFeatureRevComp(Coord, cb_data->start, cb_data->end, feature->x1, feature->x2);
return ;
}
......@@ -229,7 +231,7 @@ static void translation_set_populate(ZMapFeatureBlock feature_block,
zMapFeatureSetAddFeature(feature_set, frame_feature);
block_position = feature_block->block_to_sequence.q1;
block_position = feature_block->block_to_sequence.t1; // actual loaded DNA not logical sequence start
for (i = ZMAPFRAME_0; dna && *dna && i <= ZMAPFRAME_2; i++, dna++, block_position++)
{
......
src/zmapWindow/zmapWindowDNA.c
+ 10
− 10
View file @ 4cd79124
......@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 22 11:15 2010 (edgrif)
* Created: Fri Oct 6 16:00:11 2006 (edgrif)
* CVS info: $Id: zmapWindowDNA.c,v 1.23 2010-01-22 13:03:40 edgrif Exp $
* CVS info: $Id: zmapWindowDNA.c,v 1.24 2010-02-09 09:28:30 mh17 Exp $
*-------------------------------------------------------------------
*/
......@@ -160,8 +160,8 @@ void zmapWindowCreateSequenceSearchWindow(ZMapWindow window, FooCanvasItem *feat
search_data->window = window ;
search_data->block = block ;
search_data->sequence_type = sequence_type ;
search_data->search_start = block->block_to_sequence.q1 ;
search_data->search_end = block->block_to_sequence.q2 ;
search_data->search_start = block->block_to_sequence.t1 ;
search_data->search_end = block->block_to_sequence.t2 ;
/* Get block coords in screen coords, saving for min & max of spin buttons */
screen_search_start = zmapWindowCoordToDisplay(search_data->window, search_data->search_start) ;
......@@ -184,7 +184,7 @@ void zmapWindowCreateSequenceSearchWindow(ZMapWindow window, FooCanvasItem *feat
}
/* Clamp to length of sequence, useless to do that but possible.... */
max_errors = max_Ns = block->block_to_sequence.q2 - block->block_to_sequence.q1 + 1 ;
max_errors = max_Ns = block->block_to_sequence.t2 - block->block_to_sequence.t1 + 1 ;
/* set up the top level window */
......@@ -524,8 +524,8 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
/* NEED TO SORT WHOLE COORD JUNK OUT....USER SHOULD SEE BLOCK COORDS WE SHOULD DO RELATIVE COORDS... */
/* Convert to relative coords.... */
start = search_data->search_start - search_data->block->block_to_sequence.q1 ;
end = search_data->search_end - search_data->block->block_to_sequence.q1 ;
start = search_data->search_start - search_data->block->block_to_sequence.t1 ;
end = search_data->search_end - search_data->block->block_to_sequence.t1 ;
dna = search_data->block->sequence.sequence ;
dna_len = strlen(dna) ;
......@@ -567,8 +567,8 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
|| (search_data->max_errors < 0 || search_data->max_errors > dna_len)
|| (search_data->max_Ns < 0 || search_data->max_Ns > dna_len))
err_text = g_strdup_printf("start/end/max errors/max Ns\n must all be within range %d -> %d",
search_data->block->block_to_sequence.q1,
search_data->block->block_to_sequence.q2) ;
search_data->block->block_to_sequence.t1,
search_data->block->block_to_sequence.t2) ;
}
......@@ -762,8 +762,8 @@ static void remapCoords(gpointer data, gpointer user_data)
DNASearchData search_data = (DNASearchData)user_data ;
ZMapFeatureBlock block = (ZMapFeatureBlock)search_data->block ;
match_data->start = match_data->start + block->block_to_sequence.q1 ;
match_data->end = match_data->end + block->block_to_sequence.q1 ;
match_data->start = match_data->start + block->block_to_sequence.t1 ;
match_data->end = match_data->end + block->block_to_sequence.t1 ;
if (search_data->window->display_forward_coords)
{
......
src/zmapWindow/zmapWindowDNAChoose.c
+ 11
− 11
View file @ 4cd79124
......@@ -33,7 +33,7 @@
* HISTORY:
* Last edited: Jun 12 09:26 2009 (rds)
* Created: Fri Nov 10 09:50:48 2006 (edgrif)
* CVS info: $Id: zmapWindowDNAChoose.c,v 1.9 2009-06-19 11:15:29 rds Exp $
* CVS info: $Id: zmapWindowDNAChoose.c,v 1.10 2010-02-09 09:28:30 mh17 Exp $
*-------------------------------------------------------------------
*/
......@@ -139,8 +139,8 @@ char *zmapWindowDNAChoose(ZMapWindow window, FooCanvasItem *feature_item, ZMapWi
return dna ;
}
block_start = block->block_to_sequence.q1 ;
block_end = block->block_to_sequence.q2 ;
block_start = block->block_to_sequence.t1 ;
block_end = block->block_to_sequence.t2 ;
......@@ -237,7 +237,7 @@ char *zmapWindowDNAChoose(ZMapWindow window, FooCanvasItem *feature_item, ZMapWi
dna_data->dna_start, GTK_SIGNAL_FUNC(startSpinCB),
"End: ", dna_data->dna_start, block_end,
dna_data->dna_end, GTK_SIGNAL_FUNC(endSpinCB),
"Flanking bases: ", 0, (block->block_to_sequence.q2 - 1),
"Flanking bases: ", 0, (block->block_to_sequence.t2 - 1),
dna_data->dna_flanking, GTK_SIGNAL_FUNC(flankingSpinCB)) ;
gtk_box_pack_start(GTK_BOX(hbox), start_end, TRUE, TRUE, 0) ;
......@@ -376,8 +376,8 @@ static gboolean checkCoords(DNASearchData dna_data)
start = dna_data->dna_start - dna_data->dna_flanking ;
end = dna_data->dna_end + dna_data->dna_flanking ;
block_start = dna_data->block->block_to_sequence.q1;
block_end = dna_data->block->block_to_sequence.q2;
block_start = dna_data->block->block_to_sequence.t1;
block_end = dna_data->block->block_to_sequence.t2;
if(dna_data->window->display_forward_coords)
{
......@@ -408,7 +408,7 @@ static void getDNA(DNASearchData dna_data)
if (!checkCoords(dna_data))
return ;
block_start = dna_data->block->block_to_sequence.q1;
block_start = dna_data->block->block_to_sequence.t1;
if(dna_data->window->display_forward_coords)
{
......@@ -432,8 +432,8 @@ static void getDNA(DNASearchData dna_data)
|| (end < 0 || end > dna_len)
|| (start - dna_data->dna_flanking < 0 || end + dna_data->dna_flanking > dna_len))
err_text = g_strdup_printf("start/end +/- flanking must be within range %d -> %d",
dna_data->block->block_to_sequence.q1,
dna_data->block->block_to_sequence.q2) ;
dna_data->block->block_to_sequence.t1,
dna_data->block->block_to_sequence.t2) ;
if (err_text)
{
......@@ -628,8 +628,8 @@ static void updateSpinners(DNASearchData dna_data)
end = gtk_spin_button_get_value_as_int(dna_data->end_spin) ;
flanking = gtk_spin_button_get_value_as_int(dna_data->flanking_spin) ;
min_start = dna_data->block->block_to_sequence.q1;
max_end = dna_data->block->block_to_sequence.q2;
min_start = dna_data->block->block_to_sequence.t1;
max_end = dna_data->block->block_to_sequence.t2;
if(dna_data->window->display_forward_coords)
{
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment