From 3d0e3daac1f56fab06b89b256b938ea416f7356d Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Thu, 18 Jun 2009 11:26:11 +0000
Subject: [PATCH] fix it up so that blixem can fetch what it wants
---
src/libpfetch/libpfetch.c | 57 +++++++++++++++++++++++++++++++++++--
src/libpfetch/libpfetch_I.h | 17 +++++++----
2 files changed, 66 insertions(+), 8 deletions(-)
diff --git a/src/libpfetch/libpfetch.c b/src/libpfetch/libpfetch.c
index f7e95d11c..cfc1c6f62 100755
--- a/src/libpfetch/libpfetch.c
+++ b/src/libpfetch/libpfetch.c
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Jun 3 10:13 2009 (rds)
+ * Last edited: Jun 18 12:16 2009 (rds)
* Created: Fri Apr 4 14:21:42 2008 (rds)
- * CVS info: $Id: libpfetch.c,v 1.12 2009-06-04 09:15:59 rds Exp $
+ * CVS info: $Id: libpfetch.c,v 1.13 2009-06-18 11:26:11 rds Exp $
*-------------------------------------------------------------------
*/
@@ -213,6 +213,24 @@ static void pfetch_handle_class_init(PFetchHandleClass pfetch_class)
"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_BLIXEM_STYLE,
+ g_param_spec_boolean("blixem-seqs", "fetch like blixem wants",
+ "Return the sequences one per line with lower case dna and upper case AMINOACIDS",
+ FALSE, PFETCH_PARAM_STATIC_RW));
+
+ g_object_class_install_property(gobject_class,
+ PFETCH_ONE_SEQ_PER_LINE,
+ g_param_spec_boolean("one-per-line", "-q option",
+ "Return the sequences one per line.",
+ FALSE, PFETCH_PARAM_STATIC_RW));
+
+ g_object_class_install_property(gobject_class,
+ PFETCH_DNA_LOWER_AA_UPPER,
+ g_param_spec_boolean("case-by-type", "-C option",
+ "Return the fasta entry/sequences with lower case dna and upper case AMINOACIDS",
+ FALSE, PFETCH_PARAM_STATIC_RW));
+
g_object_class_install_property(gobject_class,
PFETCH_DEBUG,
g_param_spec_boolean("debug", "debug",
@@ -320,6 +338,23 @@ static void pfetch_handle_set_property(GObject *gobject, guint param_id, const G
case PFETCH_UNIPROT_ISOFORM_SEQ:
pfetch_handle->opts.isoform_seq = g_value_get_boolean(value);
break;
+ case PFETCH_BLIXEM_STYLE:
+ /* turn full off! */
+ pfetch_handle->opts.full = !(g_value_get_boolean(value));
+ pfetch_handle->opts.one_per_line =
+ pfetch_handle->opts.dna_PROTEIN =
+ g_value_get_boolean(value);
+ break;
+ case PFETCH_ONE_SEQ_PER_LINE:
+ pfetch_handle->opts.one_per_line = g_value_get_boolean(value);
+ if(pfetch_handle->opts.full)
+ pfetch_handle->opts.full = FALSE;
+ break;
+ case PFETCH_DNA_LOWER_AA_UPPER:
+ pfetch_handle->opts.dna_PROTEIN = g_value_get_boolean(value);
+ if(pfetch_handle->opts.full)
+ pfetch_handle->opts.full = FALSE;
+ break;
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
break;
@@ -353,6 +388,15 @@ static void pfetch_handle_get_property(GObject *gobject, guint param_id, GValue
case PFETCH_UNIPROT_ISOFORM_SEQ:
g_value_set_boolean(value, pfetch_handle->opts.isoform_seq);
break;
+ case PFETCH_BLIXEM_STYLE:
+ g_value_set_boolean(value, (pfetch_handle->opts.dna_PROTEIN && pfetch_handle->opts.one_per_line));
+ break;
+ case PFETCH_ONE_SEQ_PER_LINE:
+ g_value_set_boolean(value, pfetch_handle->opts.one_per_line);
+ break;
+ case PFETCH_DNA_LOWER_AA_UPPER:
+ g_value_set_boolean(value, pfetch_handle->opts.dna_PROTEIN);
+ break;
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
break;
@@ -396,6 +440,15 @@ static void pfetch_get_argv(PFetchHandle handle, char *seq, char **argv)
if(add_F)
argv[current++] = "-F";
+ if(handle->opts.one_per_line)
+ argv[current++] = "-q";
+
+ if(handle->opts.dna_PROTEIN)
+ argv[current++] = "-C";
+
+ if(handle->opts.archive)
+ argv[current++] = "-A";
+
if(seq != NULL)
argv[current++] = seq;
diff --git a/src/libpfetch/libpfetch_I.h b/src/libpfetch/libpfetch_I.h
index 4802d682f..b5daa1b04 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: Nov 21 17:22 2008 (rds)
+ * Last edited: Jun 18 11:45 2009 (rds)
* Created: Fri Apr 4 14:20:41 2008 (rds)
- * CVS info: $Id: libpfetch_I.h,v 1.4 2009-04-03 08:04:22 zmap Exp $
+ * CVS info: $Id: libpfetch_I.h,v 1.5 2009-06-18 11:26:11 rds Exp $
*-------------------------------------------------------------------
*/
@@ -57,6 +57,9 @@ enum
PFETCH_LOCATION,
PFETCH_PORT,
PFETCH_UNIPROT_ISOFORM_SEQ,
+ PFETCH_ONE_SEQ_PER_LINE,
+ PFETCH_DNA_LOWER_AA_UPPER,
+ PFETCH_BLIXEM_STYLE,
/* http specific stuff */
PFETCH_COOKIE_JAR,
PFETCH_URL, /* same as location */
@@ -157,10 +160,12 @@ typedef struct _pfetchHandleStruct
struct
{
- unsigned int full : 1;
- unsigned int archive : 1;
- unsigned int debug : 1;
- unsigned int isoform_seq : 1;
+ unsigned int full : 1; /* -F */
+ unsigned int archive : 1; /* -A */
+ unsigned int debug : 1; /* internal debug */
+ unsigned int isoform_seq : 1; /* internal option */
+ unsigned int one_per_line : 1; /* -q */
+ unsigned int dna_PROTEIN : 1; /* -C */
}opts;
} pfetchHandleStruct;
--
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