From fc542718391478c788ab5a994d5a4aaddcae9adc Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Fri, 8 May 2009 14:19:54 +0000
Subject: [PATCH] DNA and 3 Frame Translation feature code
---
src/zmapFeature/Makefile.am | 27 +-
src/zmapFeature/zmapFeature.c | 35 +--
.../zmapFeature3FrameTranslation.c | 293 ++++++++++++++++++
src/zmapFeature/zmapFeatureContext.c | 33 +-
src/zmapFeature/zmapFeatureDNA.c | 195 ++++++++++++
src/zmapFeature/zmapFeatureUtils.c | 203 +-----------
src/zmapServer/acedb/acedbServer.c | 62 ++--
7 files changed, 542 insertions(+), 306 deletions(-)
create mode 100755 src/zmapFeature/zmapFeature3FrameTranslation.c
create mode 100755 src/zmapFeature/zmapFeatureDNA.c
diff --git a/src/zmapFeature/Makefile.am b/src/zmapFeature/Makefile.am
index cb077f21a..b8277b379 100755
--- a/src/zmapFeature/Makefile.am
+++ b/src/zmapFeature/Makefile.am
@@ -5,19 +5,22 @@ SUBDIRS = . tests
noinst_LTLIBRARIES = libZMapFeature.la
-libZMapFeature_la_SOURCES = zmapFeatureTypes.c \
-zmapStyle_P.h \
+libZMapFeature_la_SOURCES = \
+zmapFeature.c \
+zmapFeature_P.h \
+zmapFeature3FrameTranslation.c \
+zmapFeatureContext.c \
+zmapFeatureContextUtils.c \
+zmapFeatureDNA.c \
+zmapFeatureFormatInput.c \
zmapFeatureOutput.c \
-zmapFeatureFormatInput.c \
-zmapFeature.c \
-zmapFeatureXML.c \
-zmapFeatureUtils.c \
-zmapStyle.c \
-zmapFeature_P.h \
-zmapStyle_I.h \
-zmapFeatureContextUtils.c \
-zmapFeatureContext.c \
-zmapStyleUtils.c \
+zmapFeatureTypes.c \
+zmapFeatureUtils.c \
+zmapFeatureXML.c \
+zmapStyle.c \
+zmapStyle_I.h \
+zmapStyle_P.h \
+zmapStyleUtils.c \
$(NULL)
libZMapFeature_la_CFLAGS = $(INCLUDE_COMMON) -I$(top_srcdir)/zmapUtils
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index db6152ba3..6f9f5a944 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Apr 28 12:44 2009 (edgrif)
+ * Last edited: Apr 29 15:55 2009 (rds)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.110 2009-04-28 14:29:49 edgrif Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.111 2009-05-08 14:19:54 rds Exp $
*-------------------------------------------------------------------
*/
@@ -499,37 +499,6 @@ void zMapFeatureAnyDestroy(ZMapFeatureAny feature_any)
-
-/*!
- * A Blocks DNA
- */
-gboolean zMapFeatureBlockDNA(ZMapFeatureBlock block,
- char **seq_name_out, int *seq_len_out, char **sequence_out)
-{
- gboolean result = FALSE;
- ZMapFeatureContext context = NULL;
-
- zMapAssert( block ) ;
-
- if(block->sequence.sequence &&
- block->sequence.type != ZMAPSEQUENCE_NONE &&
- block->sequence.type == ZMAPSEQUENCE_DNA &&
- (context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
- ZMAPFEATURE_STRUCT_CONTEXT)))
- {
- if(seq_name_out)
- *seq_name_out = (char *)g_quark_to_string(context->sequence_name) ;
- if(seq_len_out)
- *seq_len_out = block->sequence.length ;
- if(sequence_out)
- *sequence_out = block->sequence.sequence ;
- result = TRUE ;
- }
-
- return result;
-}
-
-
/*!
* Returns a single feature correctly intialised to be a "NULL" feature.
*
diff --git a/src/zmapFeature/zmapFeature3FrameTranslation.c b/src/zmapFeature/zmapFeature3FrameTranslation.c
new file mode 100755
index 000000000..78d34d67d
--- /dev/null
+++ b/src/zmapFeature/zmapFeature3FrameTranslation.c
@@ -0,0 +1,293 @@
+/* File: zmapFeature3FrameTranslation.c
+ * Author: Roy Storey (rds@sanger.ac.uk)
+ * Copyright (c) 2009: Genome Research Ltd.
+ *-------------------------------------------------------------------
+ * ZMap is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ *-------------------------------------------------------------------
+ * This file is part of the ZMap genome database package
+ * originally written by:
+ *
+ * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
+ *
+ * Description:
+ *
+ * Exported functions: See XXXXXXXXXXXXX.h
+ * 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 $
+ *-------------------------------------------------------------------
+ */
+
+#include <ZMap/zmapUtils.h>
+#include <ZMap/zmapPeptide.h>
+#include <zmapFeature_P.h>
+
+
+void zmapFeature3FrameTranslationDestroySequenceData(ZMapFeature feature);
+
+
+static void zmapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_set,
+ ZMapFeatureTypeStyle style);
+static void fudge_rev_comp_translation(gpointer key, gpointer value, gpointer user_data);
+static void translation_set_populate(ZMapFeatureBlock feature_block,
+ ZMapFeatureSet feature_set,
+ ZMapFeatureTypeStyle style,
+ char *seq_name,
+ char *seq);
+
+gboolean zMapFeature3FrameTranslationCreateSet(ZMapFeatureBlock block, ZMapFeatureSet *set_out)
+{
+ ZMapFeatureSet feature_set = NULL;
+ GQuark frame_id = 0;
+ gboolean created = FALSE;
+
+ /* No sequence. No Translation _return_ EARLY */
+ if(!(block->sequence.length))
+ return created;
+
+ frame_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
+
+ if(!(feature_set = zMapFeatureBlockGetSetByID(block, frame_id)))
+ {
+ GQuark original_id = 0;
+ GQuark unique_id = frame_id;
+
+ original_id = g_quark_from_string(ZMAP_FIXED_STYLE_3FT_NAME);
+
+ feature_set = zMapFeatureSetIDCreate(original_id, unique_id, NULL, NULL) ;
+
+ zMapFeatureBlockAddFeatureSet(block, feature_set);
+
+ created = TRUE;
+ }
+
+ if(set_out)
+ *set_out = feature_set;
+
+ return created;
+}
+
+void zMapFeature3FrameTranslationSetCreateFeatures(ZMapFeatureSet feature_set,
+ ZMapFeatureTypeStyle style)
+{
+ /* public version of... */
+ zmapFeature3FrameTranslationPopulate(feature_set, style);
+
+ return ;
+}
+
+void zMapFeature3FrameTranslationSetRevComp(ZMapFeatureSet feature_set, int origin)
+{
+ zmapFeature3FrameTranslationPopulate(feature_set, NULL);
+
+ /* We have to do this as the features get rev comped later, but
+ * we're actually recreating the translation in the new orientation
+ * 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));
+
+ return ;
+}
+
+char *zMapFeature3FrameTranslationFeatureName(ZMapFeatureSet feature_set, ZMapFrame frame)
+{
+ char *feature_name = NULL, *frame_str;
+
+ switch (frame)
+ {
+ case ZMAPFRAME_0:
+ frame_str = "0" ;
+ break ;
+ case ZMAPFRAME_1:
+ frame_str = "1" ;
+ break ;
+ case ZMAPFRAME_2:
+ frame_str = "2" ;
+ break ;
+ default:
+ frame_str = "." ;
+ }
+
+ feature_name = g_strdup_printf("%s_frame-%s", g_quark_to_string(feature_set->unique_id), frame_str);
+
+ return feature_name;
+}
+
+void zMapFeature3FrameTranslationAddSequenceData(ZMapFeature feature, char *peptide_str, int sequence_length)
+{
+
+ if(!feature->feature.sequence.sequence &&
+ feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
+ {
+ feature->feature.sequence.sequence = peptide_str;
+ feature->feature.sequence.length = sequence_length;
+ feature->feature.sequence.type = ZMAPSEQUENCE_PEPTIDE;
+ }
+
+ return ;
+}
+
+
+
+void zmapFeature3FrameTranslationDestroySequenceData(ZMapFeature feature)
+{
+ if(feature->feature.sequence.sequence != NULL &&
+ feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
+ {
+ g_free(feature->feature.sequence.sequence);
+ feature->feature.sequence.sequence = NULL;
+ feature->feature.sequence.length = 0;
+ feature->feature.sequence.type = ZMAPSEQUENCE_NONE;
+ }
+
+ return ;
+}
+
+/* INTERNALS */
+
+/* Accepts NULL as style. */
+static void zmapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_set,
+ ZMapFeatureTypeStyle style)
+{
+ ZMapFeatureTypeStyle temp_style = NULL;
+ ZMapFeatureBlock feature_block;
+ char *sequence_name;
+ char *dna_sequence;
+
+ feature_block =
+ (ZMapFeatureBlock)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_set,
+ ZMAPFEATURE_STRUCT_BLOCK);
+
+ zMapAssert(feature_block);
+
+ sequence_name = (char *)g_quark_to_string(feature_block->original_id);
+
+ dna_sequence = feature_block->sequence.sequence;
+
+ if(style == NULL)
+ {
+ temp_style = style = zMapStyleCreate(ZMAP_FIXED_STYLE_3FT_NAME,
+ ZMAP_FIXED_STYLE_3FT_NAME_TEXT);
+ }
+
+ if(dna_sequence)
+ translation_set_populate(feature_block,
+ feature_set,
+ style,
+ sequence_name,
+ dna_sequence);
+
+ if(temp_style)
+ zMapStyleDestroy(temp_style);
+
+ return ;
+}
+
+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);
+ return ;
+}
+
+static void translation_set_populate(ZMapFeatureBlock feature_block,
+ ZMapFeatureSet feature_set,
+ ZMapFeatureTypeStyle style,
+ char *seq_name,
+ char *dna)
+{
+ int i, block_position;
+ ZMapFeature frame_feature;
+ char *feature_name_id = "__delete_me__";
+ char *feature_name = "__delete_me__";
+ char *sequence = "__delete_me__";
+ char *ontology = "sequence";
+
+ frame_feature = zMapFeatureCreateEmpty();
+
+ zMapFeatureAddStandardData(frame_feature, feature_name_id,
+ feature_name, sequence,
+ ontology, ZMAPSTYLE_MODE_PEP_SEQUENCE,
+ style, 1, 10, FALSE, 0.0,
+ ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
+
+ zMapFeatureSetAddFeature(feature_set, frame_feature);
+
+ block_position = feature_block->block_to_sequence.q1;
+
+ for (i = ZMAPFRAME_0; dna && *dna && i <= ZMAPFRAME_2; i++, dna++, block_position++)
+ {
+ ZMapPeptide pep;
+ ZMapFeature translation;
+ char *feature_name = NULL; /* Remember to free this */
+ GQuark feature_id;
+ ZMapFrame curr_frame;
+ char *peptide_str;
+ int peptide_length;
+
+ frame_feature->x1 = block_position;
+
+ curr_frame = zMapFeatureFrame(frame_feature);
+ feature_name = zMapFeature3FrameTranslationFeatureName(feature_set, curr_frame);
+ feature_id = g_quark_from_string(feature_name);
+
+ pep = zMapPeptideCreateSafely(NULL, NULL, dna, NULL, FALSE);
+
+ if((translation = zMapFeatureSetGetFeatureByID(feature_set, feature_id)))
+ {
+ /* clear sequence? */
+ zmapFeature3FrameTranslationDestroySequenceData(translation);
+ }
+ else
+ {
+ int x1, x2;
+
+ x1 = frame_feature->x1;
+ x2 = x1 + zMapPeptideFullSourceCodonLength(pep) - 1;
+
+ translation = zMapFeatureCreateEmpty();
+
+ zMapFeatureAddStandardData(translation, feature_name, feature_name,
+ seq_name, "sequence",
+ ZMAPSTYLE_MODE_PEP_SEQUENCE, style,
+ x1, x2, FALSE, 0.0,
+ ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
+
+ zMapFeatureSetAddFeature(feature_set, translation);
+ }
+
+ peptide_str = zMapPeptideSequence(pep);
+
+ peptide_str = g_strdup(peptide_str);
+
+ peptide_length = zMapPeptideLength(pep);
+
+ zMapFeature3FrameTranslationAddSequenceData(translation, peptide_str, peptide_length);
+
+ zMapPeptideDestroy(pep) ;
+
+ if(feature_name)
+ g_free(feature_name);
+ }
+
+ zMapFeatureSetRemoveFeature(feature_set, frame_feature);
+ zMapFeatureDestroy(frame_feature);
+
+ return ;
+}
diff --git a/src/zmapFeature/zmapFeatureContext.c b/src/zmapFeature/zmapFeatureContext.c
index b2e4eba6b..1f8f08686 100755
--- a/src/zmapFeature/zmapFeatureContext.c
+++ b/src/zmapFeature/zmapFeatureContext.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Feb 4 14:08 2009 (edgrif)
+ * Last edited: May 1 18:45 2009 (rds)
* Created: Tue Jan 17 16:13:12 2006 (edgrif)
- * CVS info: $Id: zmapFeatureContext.c,v 1.42 2009-02-04 16:07:06 edgrif Exp $
+ * CVS info: $Id: zmapFeatureContext.c,v 1.43 2009-05-08 14:19:54 rds Exp $
*-------------------------------------------------------------------
*/
@@ -895,26 +895,13 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
case ZMAPFEATURE_STRUCT_BLOCK:
{
ZMapFeatureBlock feature_block = NULL;
- ZMapFeatureSet translations ;
- GQuark translation_id;
feature_block = (ZMapFeatureBlock)feature_any;
- translation_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
/* Complement the dna. */
if (feature_block->sequence.sequence)
{
revcompDNA(feature_block->sequence.sequence, feature_block->sequence.length) ;
-
- /* Now redo the 3 frame translations from the dna (if they exist). */
- if ((translations = zMapFeatureBlockGetSetByID(feature_block, translation_id)))
- zMapFeature3FrameTranslationRevComp(translations, cb_data->end);
- }
- else
- {
- /* paranoia makes me want to check we haven't got a three frame translation... */
- if ((translations = zMapFeatureBlockGetSetByID(feature_block, translation_id)))
- zMapFeatureSetDestroy(translations, TRUE);
}
zmapFeatureRevComp(Coord, cb_data->end,
@@ -925,8 +912,12 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
case ZMAPFEATURE_STRUCT_FEATURESET:
{
ZMapFeatureSet feature_set = NULL;
+
feature_set = (ZMapFeatureSet)feature_any;
- /* Nothing to swop here, I think..... */
+
+ /* 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);
}
break;
case ZMAPFEATURE_STRUCT_FEATURE:
@@ -937,16 +928,6 @@ static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
revCompFeature(feature_ft, cb_data->end);
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* Shouldn't need to do this, just leave style_id alone..... */
-
- /* If list of styles provided then reset feature style from there. */
- if (cb_data->styles)
- feature_ft->style = zMapFindStyle(cb_data->styles, zMapStyleGetUniqueID(feature_ft->style)) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
break;
}
case ZMAPFEATURE_STRUCT_INVALID:
diff --git a/src/zmapFeature/zmapFeatureDNA.c b/src/zmapFeature/zmapFeatureDNA.c
new file mode 100755
index 000000000..4ce01ce6b
--- /dev/null
+++ b/src/zmapFeature/zmapFeatureDNA.c
@@ -0,0 +1,195 @@
+/* File: zmapFeatureDNA.c
+ * Author: Roy Storey (rds@sanger.ac.uk)
+ * Copyright (c) 2009: Genome Research Ltd.
+ *-------------------------------------------------------------------
+ * ZMap is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ *-------------------------------------------------------------------
+ * This file is part of the ZMap genome database package
+ * originally written by:
+ *
+ * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
+ *
+ * Description:
+ *
+ * Exported functions: See XXXXXXXXXXXXX.h
+ * HISTORY:
+ * Last edited: May 1 18:34 2009 (rds)
+ * Created: Tue Apr 7 10:32:21 2009 (rds)
+ * CVS info: $Id: zmapFeatureDNA.c,v 1.1 2009-05-08 14:19:54 rds Exp $
+ *-------------------------------------------------------------------
+ */
+
+#include <ZMap/zmapUtils.h>
+#include <zmapFeature_P.h>
+
+
+/*!
+ * A Blocks DNA
+ */
+gboolean zMapFeatureBlockDNA(ZMapFeatureBlock block,
+ char **seq_name_out, int *seq_len_out, char **sequence_out)
+{
+ gboolean result = FALSE;
+ ZMapFeatureContext context = NULL;
+
+ zMapAssert( block ) ;
+
+ if(block->sequence.sequence &&
+ block->sequence.type != ZMAPSEQUENCE_NONE &&
+ block->sequence.type == ZMAPSEQUENCE_DNA &&
+ (context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
+ ZMAPFEATURE_STRUCT_CONTEXT)))
+ {
+ if(seq_name_out)
+ *seq_name_out = (char *)g_quark_to_string(context->sequence_name) ;
+ if(seq_len_out)
+ *seq_len_out = block->sequence.length ;
+ if(sequence_out)
+ *sequence_out = block->sequence.sequence ;
+ result = TRUE ;
+ }
+
+ return result;
+}
+
+/* Free return when finished! */
+char *zMapFeatureDNAFeatureName(ZMapFeatureBlock block)
+{
+ char *dna_name = NULL;
+
+ dna_name = g_strdup_printf("%s (%s)", "DNA", g_quark_to_string(block->original_id));
+
+ return dna_name;
+}
+
+
+gboolean zMapFeatureDNACreateFeatureSet(ZMapFeatureBlock block, ZMapFeatureSet *feature_set_out)
+{
+ ZMapFeatureSet dna_feature_set = NULL;
+ gboolean created = FALSE;
+ GQuark dna_set_id = 0;
+
+ dna_set_id = zMapFeatureSetCreateID(ZMAP_FIXED_STYLE_DNA_NAME);
+
+ if(!(dna_feature_set = zMapFeatureBlockGetSetByID(block, dna_set_id)))
+ {
+ GQuark original_id = 0;
+ GQuark unique_id = dna_set_id;
+
+ original_id = g_quark_from_string(ZMAP_FIXED_STYLE_DNA_NAME);
+
+ dna_feature_set = zMapFeatureSetIDCreate(original_id, unique_id, NULL, NULL) ;
+
+ zMapFeatureBlockAddFeatureSet(block, dna_feature_set);
+
+ created = TRUE;
+ }
+
+ if(feature_set_out)
+ *feature_set_out = dna_feature_set;
+
+ return created;
+}
+
+void zMapFeatureDNAAddSequenceData(ZMapFeature dna_feature, char *dna_str, int sequence_length)
+{
+
+ if(!dna_feature->feature.sequence.sequence &&
+ dna_feature->type == ZMAPSTYLE_MODE_RAW_SEQUENCE)
+ {
+ dna_feature->feature.sequence.sequence = dna_str;
+ dna_feature->feature.sequence.length = sequence_length;
+ dna_feature->feature.sequence.type = ZMAPSEQUENCE_DNA;
+ }
+
+ return ;
+}
+
+ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
+ ZMapFeatureTypeStyle style,
+ char *dna_str,
+ int sequence_length)
+{
+ ZMapFeatureSet dna_feature_set = NULL;
+ ZMapFeature dna_feature = NULL;
+ GQuark dna_set_id = 0;
+
+ zMapAssert(block);
+ zMapAssert(dna_str);
+ zMapAssert(sequence_length != 0);
+
+ dna_set_id = zMapFeatureSetCreateID(ZMAP_FIXED_STYLE_DNA_NAME);
+
+ dna_feature_set = zMapFeatureBlockGetSetByID(block, dna_set_id);
+
+ if(dna_feature_set)
+ {
+ char *feature_name, *sequence, *ontology;
+ GQuark dna_id;
+ int block_start, block_end;
+
+ block_start = block->block_to_sequence.q1 ;
+ block_end = block->block_to_sequence.q2 ;
+
+ feature_name = zMapFeatureDNAFeatureName(block);
+
+ dna_id = g_quark_from_string(feature_name);
+
+ if(block->sequence.sequence)
+ {
+ /* hmm, we've already got dna */
+
+ /* We should be able to get the feature from the feature set, */
+ /* but not before issuing a warning */
+ zMapLogWarning("%s", "Block already has DNA");
+
+ dna_feature = zMapFeatureSetGetFeatureByID(dna_feature_set, dna_id);
+ }
+ else
+ {
+ ZMapStrand strand = ZMAPSTRAND_FORWARD; /* DNA is forward */
+
+ /* check dna length == block length? */
+
+ dna_feature = zMapFeatureCreateFromStandardData(feature_name,
+ sequence,
+ ontology,
+ ZMAPSTYLE_MODE_RAW_SEQUENCE,
+ style,
+ block_start,
+ block_end,
+ FALSE, 0.0,
+ strand,
+ ZMAPPHASE_NONE);
+
+ zMapFeatureDNAAddSequenceData(dna_feature, dna_str, sequence_length);
+
+ zMapFeatureSetAddFeature(dna_feature_set, dna_feature);
+
+ block->sequence.sequence = dna_feature->feature.sequence.sequence;
+ block->sequence.type = dna_feature->feature.sequence.type;
+ block->sequence.length = dna_feature->feature.sequence.length;
+
+ }
+
+ if(feature_name)
+ g_free(feature_name);
+ }
+
+
+ return dna_feature;
+}
diff --git a/src/zmapFeature/zmapFeatureUtils.c b/src/zmapFeature/zmapFeatureUtils.c
index 95925546b..29d44f9cb 100755
--- a/src/zmapFeature/zmapFeatureUtils.c
+++ b/src/zmapFeature/zmapFeatureUtils.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Feb 9 15:47 2009 (rds)
+ * Last edited: May 1 19:02 2009 (rds)
* Created: Tue Nov 2 2004 (rnc)
- * CVS info: $Id: zmapFeatureUtils.c,v 1.65 2009-02-09 15:48:13 rds Exp $
+ * CVS info: $Id: zmapFeatureUtils.c,v 1.66 2009-05-08 14:19:54 rds Exp $
*-------------------------------------------------------------------
*/
@@ -54,13 +54,6 @@ static ZMapFrame feature_frame(ZMapFeature feature, int start_coord);
static int feature_block_frame_offset(ZMapFeature feature);
static void get_feature_list_extent(gpointer list_data, gpointer span_data);
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void translation_set_populate(ZMapFeatureSet feature_set, ZMapFeatureTypeStyle style, char *seq_name, char *seq);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
static gint findStyleName(gconstpointer list_data, gconstpointer user_data) ;
static void addTypeQuark(GQuark style_id, gpointer data, gpointer user_data) ;
@@ -570,16 +563,6 @@ GQuark zMapFeatureSetCreateID(char *set_name)
return zMapStyleCreateID(set_name);
}
-/* Free return when finished! */
-char *zMapFeatureMakeDNAFeatureName(ZMapFeatureBlock block)
-{
- char *dna_name = NULL;
-
- dna_name = g_strdup_printf("%s (%s)", "DNA", g_quark_to_string(block->original_id));
-
- return dna_name;
-}
-
void zMapFeatureSortGaps(GArray *gaps)
{
@@ -724,119 +707,6 @@ void zMapFeature2MasterCoords(ZMapFeature feature, double *feature_x1, double *f
return ;
}
-gboolean zMapFeature3FrameTranslationCreateSet(ZMapFeatureBlock block, ZMapFeatureSet *set_out)
-{
- ZMapFeatureContext context = NULL;
- ZMapFeatureSet feature_set = NULL;
- gboolean created = FALSE;
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- style_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
- /* No sequence. No Translation _return_ EARLY */
- if(!(block->sequence.length))
- return created;
-
- if ((context = (ZMapFeatureContext)(zMapFeatureGetParentGroup((ZMapFeatureAny)block, ZMAPFEATURE_STRUCT_CONTEXT))))
- {
- /* DON'T CHECK FOR STYLE, JUST DO IT, IF STYLE IS NOT THERE LATER THEN TOUGH.... */
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- if ((style = zMapFindStyle(context->styles, style_id)) != NULL)
- {
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
- feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_3FT_NAME, NULL);
- //feature_set->style = style;
- created = TRUE;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- }
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
- }
-
- if(set_out && created)
- *set_out = feature_set;
- else
- created = FALSE;
-
- return created;
-}
-
-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);
- return ;
-}
-
-void zMapFeature3FrameTranslationRevComp(ZMapFeatureSet feature_set, int origin)
-{
- zMapFeature3FrameTranslationPopulate(feature_set);
-
- /* We have to do this as the features get rev comped later, but
- * we're actually recreating the translation in the new orientation
- * 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));
-
- return ;
-}
-
-char *zMapFeature3FrameTranslationFeatureName(ZMapFeatureSet feature_set, ZMapFrame frame)
-{
- char *feature_name = NULL, *frame_str;
-
- switch (frame)
- {
- case ZMAPFRAME_0:
- frame_str = "0" ;
- break ;
- case ZMAPFRAME_1:
- frame_str = "1" ;
- break ;
- case ZMAPFRAME_2:
- frame_str = "2" ;
- break ;
- default:
- frame_str = "." ;
- }
-
- feature_name = g_strdup_printf("%s_frame-%s", g_quark_to_string(feature_set->unique_id), frame_str);
-
- return feature_name;
-}
-
-void zMapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_set)
-{
- ZMapFeatureBlock block;
- char *seq = NULL, *seq_name;
-
- block = (ZMapFeatureBlock)(zMapFeatureGetParentGroup((ZMapFeatureAny)feature_set, ZMAPFEATURE_STRUCT_BLOCK));
-
- zMapAssert(block); /* No block! BIG error! */
- zMapAssert(block->sequence.length); /* No sequence. Why we got a 3ft anyway? Error! */
-
- //style = feature_set->style;
- //zMapAssert(style);
-
- seq_name = (char *)g_quark_to_string(block->original_id);
-
- seq = block->sequence.sequence ;
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- translation_set_populate(feature_set, style, seq_name, seq);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
- return ;
-}
-
gboolean zMapFeatureGetFeatureListExtent(GList *feature_list, int *start_out, int *end_out)
{
gboolean done = FALSE;
@@ -1156,75 +1026,6 @@ static int feature_block_frame_offset(ZMapFeature feature)
return offset;
}
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void translation_set_populate(ZMapFeatureSet feature_set, ZMapFeatureTypeStyle style, char *seq_name, char *seq)
-{
- ZMapFeatureBlock block;
- int i, block_position;
- ZMapFeature frame_feature;
-
- frame_feature = zMapFeatureCreateEmpty();
- zMapFeatureAddStandardData(frame_feature, "_delete_me_", "_delete_me_",
- "_delete_me_", "sequence", ZMAPSTYLE_MODE_PEP_SEQUENCE,
- style, 1, 10, FALSE, 0.0, ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
- zMapFeatureSetAddFeature(feature_set, frame_feature);
-
- zMapAssert(feature_set->parent);
- block = (ZMapFeatureBlock)(feature_set->parent);
- block_position = block->block_to_sequence.q1;
-
- for (i = ZMAPFRAME_0; seq && *seq && i <= ZMAPFRAME_2; i++, seq++, block_position++)
- {
- ZMapPeptide pep;
- ZMapFeature translation;
- char *feature_name; /* Remember to free this */
- GQuark feature_id;
- ZMapFrame curr_frame;
-
- frame_feature->x1 = block_position;
-
- curr_frame = zMapFeatureFrame(frame_feature);
- feature_name = zMapFeature3FrameTranslationFeatureName(feature_set, curr_frame);
- feature_id = g_quark_from_string(feature_name);
-
- pep = zMapPeptideCreateSafely(NULL, NULL, seq, NULL, FALSE);
-
- if((translation = zMapFeatureSetGetFeatureByID(feature_set, feature_id)))
- g_free(translation->text);
- else
- {
- int x1, x2;
-
- x1 = frame_feature->x1;
- x2 = x1 + zMapPeptideFullSourceCodonLength(pep) - 1;
-
- translation = zMapFeatureCreateEmpty();
-
- zMapFeatureAddStandardData(translation, feature_name, feature_name,
- seq_name, "sequence",
- ZMAPSTYLE_MODE_PEP_SEQUENCE, style,
- x1, x2, FALSE, 0.0,
- ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
-
- zMapFeatureSetAddFeature(feature_set, translation);
- }
-
- translation->text = g_strdup(zMapPeptideSequence(pep));
-
- zMapPeptideDestroy(pep) ;
-
- g_free(feature_name);
- }
-
- zMapFeatureSetRemoveFeature(feature_set, frame_feature);
- zMapFeatureDestroy(frame_feature);
-
- return ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
static void get_feature_list_extent(gpointer list_data, gpointer span_data)
{
ZMapFeature feature = (ZMapFeature)list_data;
diff --git a/src/zmapServer/acedb/acedbServer.c b/src/zmapServer/acedb/acedbServer.c
index 5509fec35..573811e0c 100755
--- a/src/zmapServer/acedb/acedbServer.c
+++ b/src/zmapServer/acedb/acedbServer.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapServer.h
* HISTORY:
- * Last edited: May 8 09:10 2009 (edgrif)
+ * Last edited: May 8 15:07 2009 (rds)
* Created: Wed Aug 6 15:46:38 2003 (edgrif)
- * CVS info: $Id: acedbServer.c,v 1.132 2009-05-08 08:12:52 edgrif Exp $
+ * CVS info: $Id: acedbServer.c,v 1.133 2009-05-08 14:20:09 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1481,39 +1481,25 @@ static gboolean blockDNARequest(AcedbServer server, GData *styles, ZMapFeatureBl
{
ZMapFeature feature = NULL;
ZMapFeatureSet feature_set = NULL;
- ZMapFeatureTypeStyle style = NULL;
+ ZMapFeatureTypeStyle dna_style = NULL;
- feature_block->sequence.type = ZMAPSEQUENCE_DNA ;
- feature_block->sequence.length = dna_length ;
- feature_block->sequence.sequence = dna_sequence ;
-
- if ((style = zMapFindStyle(styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_DNA_NAME))))
+ if (zMapFeatureDNACreateFeatureSet(feature_block, &feature_set))
{
- feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_DNA_NAME, NULL);
-
- //feature_set->style = style;
- }
-
+ ZMapFeatureTypeStyle temp_style = NULL;
+
+ /* This temp style creation feels wrong, and probably is,
+ * but we don't have the merged in default styles in here,
+ * or so it seems... */
- if (feature_set)
- {
- const char *sequence = g_quark_to_string(feature_block->original_id);
- char *feature_name = NULL;
- feature_name = g_strdup_printf("DNA (%s)", sequence);
- feature =
- zMapFeatureCreateFromStandardData(feature_name,
- (char *)sequence,
- "sequence",
- ZMAPSTYLE_MODE_RAW_SEQUENCE,
- style,
- block_start,
- block_end,
- FALSE, 0.0,
- ZMAPSTRAND_NONE,
- ZMAPPHASE_NONE) ;
- zMapFeatureSetAddFeature(feature_set, feature);
- zMapFeatureBlockAddFeatureSet(feature_block, feature_set);
- g_free(feature_name);
+ if (!(dna_style = zMapFindStyle(styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_DNA_NAME))))
+ temp_style = dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
+
+ feature = zMapFeatureDNACreateFeature(feature_block, dna_style,
+ dna_sequence, dna_length);
+
+ if(temp_style)
+ zMapStyleDestroy(temp_style);
}
/* I'm going to create the three frame translation up front! */
@@ -1521,8 +1507,16 @@ static gboolean blockDNARequest(AcedbServer server, GData *styles, ZMapFeatureBl
{
if ((zMapFeature3FrameTranslationCreateSet(feature_block, &feature_set)))
{
- zMapFeatureBlockAddFeatureSet(feature_block, feature_set);
- zMapFeature3FrameTranslationPopulate(feature_set);
+ ZMapFeatureTypeStyle frame_style = NULL;
+ gboolean style_absolutely_required = FALSE;
+
+ frame_style = zMapFindStyle(styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME));
+
+ if(style_absolutely_required && !frame_style)
+ zMapLogWarning("Cowardly refusing to create features '%s' without style",
+ ZMAP_FIXED_STYLE_3FT_NAME);
+ else
+ zMapFeature3FrameTranslationSetCreateFeatures(feature_set, frame_style);
}
}
--
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