diff --git a/src/include/ZMap/zmapFASTA.h b/src/include/ZMap/zmapFASTA.h
index e1713335da7e0babfe6f158438789c0f273d563e..f416237301ed28e9691e8708bbf5c043a274bbfc 100755
--- a/src/include/ZMap/zmapFASTA.h
+++ b/src/include/ZMap/zmapFASTA.h
@@ -25,9 +25,9 @@
* Description: Interface to FASTA routines.
*
* HISTORY:
- * Last edited: Mar 22 09:24 2006 (edgrif)
+ * Last edited: Mar 5 13:55 2007 (edgrif)
* Created: Fri Mar 17 16:59:08 2006 (edgrif)
- * CVS info: $Id: zmapFASTA.h,v 1.4 2006-11-08 09:23:13 edgrif Exp $
+ * CVS info: $Id: zmapFASTA.h,v 1.5 2007-03-05 14:39:14 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_UTILS_DNA_H
@@ -35,11 +35,13 @@
#include <glib.h>
-gboolean zMapFASTAFile(GIOChannel *file, char *seqname, int seq_len, char *dna,
+typedef enum {ZMAPFASTA_SEQTYPE_INVALID, ZMAPFASTA_SEQTYPE_DNA, ZMAPFASTA_SEQTYPE_AA} ZMapFASTASeqType ;
+
+gboolean zMapFASTAFile(GIOChannel *file, ZMapFASTASeqType seq_type, char *seqname, int seq_len, char *dna,
char *molecule_type, char *gene_name, GError **error_out) ;
-char *zMapFASTAString(char *seq_name, char *molecule_type, char *gene_name,
+char *zMapFASTAString(ZMapFASTASeqType seq_type, char *seq_name, char *molecule_type, char *gene_name,
int sequence_length, char *sequence) ;
-char *zMapFASTATitle(char *seq_name, char *molecule_type, char *gene_name,
+char *zMapFASTATitle(ZMapFASTASeqType seq_type, char *seq_name, char *molecule_type, char *gene_name,
int sequence_length) ;
#endif /* ZMAP_UTILS_DNA_H */
diff --git a/src/zmapUtils/zmapFASTA.c b/src/zmapUtils/zmapFASTA.c
index e295d019730d631d57ed89acd82f0092c9f70b9e..6024b6369c1f84bcd96741e5964b5b73bc5688df 100755
--- a/src/zmapUtils/zmapFASTA.c
+++ b/src/zmapUtils/zmapFASTA.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapFASTA.h
* HISTORY:
- * Last edited: Mar 22 09:48 2006 (edgrif)
+ * Last edited: Mar 5 14:33 2007 (edgrif)
* Created: Fri Mar 17 16:24:30 2006 (edgrif)
- * CVS info: $Id: zmapFASTA.c,v 1.4 2006-11-08 09:24:43 edgrif Exp $
+ * CVS info: $Id: zmapFASTA.c,v 1.5 2007-03-05 14:39:14 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -44,11 +44,15 @@
enum {FASTA_CHARS = 50} ;
+/* NOTE that in all these calls "seq_len" is the length reported in the FASTA header, the code
+ * writes out all of the supplied sequence. */
+
+
/* This code is modified from acedb code (www.acedb.org)
*
* Given a sequence name and its dna sequence, will dump the data in FastA
* format. */
-gboolean zMapFASTAFile(GIOChannel *file, char *seq_name, int seq_len, char *dna,
+gboolean zMapFASTAFile(GIOChannel *file, ZMapFASTASeqType seq_type, char *seq_name, int seq_len, char *dna,
char *molecule_type, char *gene_name, GError **error_out)
{
gboolean result = TRUE ;
@@ -63,7 +67,7 @@ gboolean zMapFASTAFile(GIOChannel *file, char *seq_name, int seq_len, char *dna,
zMapAssert(file && seq_name && seq_len > 0 && dna && error_out) ;
- header = zMapFASTATitle(seq_name, molecule_type, gene_name, seq_len) ;
+ header = zMapFASTATitle(seq_type, seq_name, molecule_type, gene_name, seq_len) ;
if ((status = g_io_channel_write_chars(file, header, -1, &bytes_written, error_out))
!= G_IO_STATUS_NORMAL)
@@ -114,7 +118,7 @@ gboolean zMapFASTAFile(GIOChannel *file, char *seq_name, int seq_len, char *dna,
/* Returns the "title" of a FASTA file, i.e. the text that forms the first line
* of a FASTA file (note that the string _does_ end with a newline).
* Result should be freed using g_free() by caller. */
-char *zMapFASTATitle(char *seq_name, char *molecule_type, char *gene_name,
+char *zMapFASTATitle(ZMapFASTASeqType seq_type, char *seq_name, char *molecule_type, char *gene_name,
int sequence_length)
{
char *title = NULL ;
@@ -122,11 +126,13 @@ char *zMapFASTATitle(char *seq_name, char *molecule_type, char *gene_name,
zMapAssert(seq_name && *seq_name && sequence_length > 0) ;
/* We should add more info. really.... */
- title = g_strdup_printf(">%s %s %s %d bp\n",
+ title = g_strdup_printf(">%s %s %s %d %s\n",
seq_name,
molecule_type ? molecule_type : "",
gene_name ? gene_name : "",
- sequence_length) ;
+ sequence_length,
+ seq_type == ZMAPFASTA_SEQTYPE_DNA ? "bp" : "AA"
+ ) ;
return title ;
}
@@ -138,7 +144,7 @@ char *zMapFASTATitle(char *seq_name, char *molecule_type, char *gene_name,
* supplied sequence and adds to it....so not good for dumping a huge dna
* sequence to file, use zMapFASTAFile() instead.
*/
-char *zMapFASTAString(char *seq_name, char *molecule_type, char *gene_name,
+char *zMapFASTAString(ZMapFASTASeqType seq_type, char *seq_name, char *molecule_type, char *gene_name,
int sequence_length, char *sequence)
{
char *fasta_string = NULL ;
@@ -149,21 +155,23 @@ char *zMapFASTAString(char *seq_name, char *molecule_type, char *gene_name,
int lines = 0, chars_left = 0 ;
char *cp = NULL ;
int i ;
+ int true_sequence_length ;
zMapAssert(seq_name && sequence_length > 0 && sequence) ;
/* We should add more info. really.... */
- title = zMapFASTATitle(seq_name, molecule_type, gene_name, sequence_length) ;
+ title = zMapFASTATitle(seq_type, seq_name, molecule_type, gene_name, sequence_length) ;
header_length = strlen(title) + 1 ; /* + 1 for newline. */
-
- lines = sequence_length / FASTA_CHARS ;
- chars_left = sequence_length % FASTA_CHARS ;
+
+ true_sequence_length = strlen(sequence) ;
+ lines = true_sequence_length / FASTA_CHARS ;
+ chars_left = true_sequence_length % FASTA_CHARS ;
/* Make the string big enough to hold the whole of the FASTA formatted string, the + 10 is
* a fudge factor to avoid reallocation. */
- str = g_string_sized_new(header_length + sequence_length + (lines + 1) + 10) ;
+ str = g_string_sized_new(header_length + true_sequence_length + (lines + 1) + 10) ;
g_string_append_printf(str, "%s", title) ;