From eaa53c31cf02e3fbfb8e6c70adf82be70ab9cca1 Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Fri, 24 Oct 2008 14:01:12 +0000
Subject: [PATCH] Addition of code to return fasta sequence of isoforms. This
is achieved by dropping the -F flag when there's a '-' in the sequence name.
---
src/libpfetch/libpfetch.c | 27 ++++++++++++++++++++++++---
src/libpfetch/libpfetch_I.h | 6 ++++--
2 files changed, 28 insertions(+), 5 deletions(-)
diff --git a/src/libpfetch/libpfetch.c b/src/libpfetch/libpfetch.c
index 7789b709a..1d1f8bea6 100755
--- a/src/libpfetch/libpfetch.c
+++ b/src/libpfetch/libpfetch.c
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Oct 23 13:29 2008 (rds)
+ * Last edited: Oct 24 14:26 2008 (rds)
* Created: Fri Apr 4 14:21:42 2008 (rds)
- * CVS info: $Id: libpfetch.c,v 1.5 2008-10-23 12:31:41 rds Exp $
+ * CVS info: $Id: libpfetch.c,v 1.6 2008-10-24 14:01:12 rds Exp $
*-------------------------------------------------------------------
*/
@@ -201,6 +201,12 @@ static void pfetch_handle_class_init(PFetchHandleClass pfetch_class)
"Search EMBL and UniProtKB archive, including current data",
FALSE, PFETCH_PARAM_STATIC_RW));
+ g_object_class_install_property(gobject_class,
+ PFETCH_UNIPROT_ISOFORM_SEQ,
+ g_param_spec_boolean("isoform-seq", "isoform-seq",
+ "Return the fasta entry for an isofrom as the -F entries don't exist.",
+ FALSE, PFETCH_PARAM_STATIC_RW));
+
g_object_class_install_property(gobject_class,
PFETCH_DEBUG,
g_param_spec_boolean("debug", "debug",
@@ -304,6 +310,9 @@ static void pfetch_handle_set_property(GObject *gobject, guint param_id, const G
pfetch_handle->location = g_value_dup_string(value);
+ break;
+ case PFETCH_UNIPROT_ISOFORM_SEQ:
+ pfetch_handle->opts.isoform_seq = g_value_get_boolean(value);
break;
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
@@ -335,6 +344,9 @@ static void pfetch_handle_get_property(GObject *gobject, guint param_id, GValue
case PFETCH_LOCATION:
g_value_set_string(value, pfetch_handle->location);
break;
+ case PFETCH_UNIPROT_ISOFORM_SEQ:
+ g_value_set_boolean(value, pfetch_handle->opts.isoform_seq);
+ break;
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
break;
@@ -364,9 +376,18 @@ static void pfetch_handle_finalize (GObject *object)
static void pfetch_get_argv(PFetchHandle handle, char *seq, char **argv)
{
int current = 0;
+ gboolean add_F = FALSE;
argv[current++] = handle->location;
- if(handle->opts.full)
+ add_F = handle->opts.full;
+
+ if(handle->opts.isoform_seq)
+ {
+ if(g_strstr_len(seq, -1, "-"))
+ add_F = FALSE;
+ }
+
+ if(add_F)
argv[current++] = "-F";
if(seq != NULL)
diff --git a/src/libpfetch/libpfetch_I.h b/src/libpfetch/libpfetch_I.h
index 3d1874fa6..77dd82156 100755
--- a/src/libpfetch/libpfetch_I.h
+++ b/src/libpfetch/libpfetch_I.h
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Jun 5 09:41 2008 (rds)
+ * Last edited: Oct 24 14:22 2008 (rds)
* Created: Fri Apr 4 14:20:41 2008 (rds)
- * CVS info: $Id: libpfetch_I.h,v 1.1 2008-06-05 09:49:50 rds Exp $
+ * CVS info: $Id: libpfetch_I.h,v 1.2 2008-10-24 14:01:12 rds Exp $
*-------------------------------------------------------------------
*/
@@ -56,6 +56,7 @@ enum
PFETCH_DEBUG,
PFETCH_LOCATION,
PFETCH_PORT,
+ PFETCH_UNIPROT_ISOFORM_SEQ,
/* http specific stuff */
PFETCH_COOKIE_JAR,
PFETCH_URL, /* same as location */
@@ -159,6 +160,7 @@ typedef struct _pfetchHandleStruct
unsigned int full : 1;
unsigned int archive : 1;
unsigned int debug : 1;
+ unsigned int isoform_seq : 1;
}opts;
} pfetchHandleStruct;
--
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