fix it up so that blixem can fetch what it wants

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;
 

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;