diff --git a/blxFetch.c b/blxFetch.c
index 3c158b3c885dc8638f1f9b0e19f1665428ae2131..9333e37ca438521fa494bedf7cf02b8c34c1abe3 100644
--- a/blxFetch.c
+++ b/blxFetch.c
@@ -38,7 +38,7 @@
* HISTORY:
* Last edited: Aug 21 17:34 2009 (edgrif)
* Created: Tue Jun 17 16:20:26 2008 (edgrif)
- * CVS info: $Id: blxFetch.c,v 1.37 2010-09-03 11:15:38 gb10 Exp $
+ * CVS info: $Id: blxFetch.c,v 1.38 2010-09-21 12:50:42 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -574,7 +574,7 @@ static void pfetchEntry(char *seqName, GtkWidget *blxWindow, const gboolean disp
* return anything with the -F option, so if it fails we need to re-try without -F so
* that at least we can display the fasta sequence. */
GString *command = g_string_sized_new(100);
- g_string_append_printf(command, "pfetch --client=acedb_%s_%s -F '%s' &", g_get_host_name(), g_get_user_name(), seqName);
+ g_string_append_printf(command, "pfetch --client=%s_%s_%s -F '%s' &", g_get_prgname(), g_get_host_name(), g_get_user_name(), seqName);
GString *resultText = getExternalCommandOutput(command->str);
@@ -583,7 +583,7 @@ static void pfetchEntry(char *seqName, GtkWidget *blxWindow, const gboolean disp
g_string_truncate(command, 0);
g_string_truncate(resultText, 0);
- g_string_append_printf(command, "pfetch --client=acedb_%s_%s -C '%s' &", g_get_host_name(), g_get_user_name(), seqName);
+ g_string_append_printf(command, "pfetch --client=%s_%s_%s -C '%s' &", g_get_prgname(), g_get_host_name(), g_get_user_name(), seqName);
resultText = getExternalCommandOutput(command->str);
}
diff --git a/blxdotter.c b/blxdotter.c
index 97497f6db57008387caf3e6bd993b8cfddb75326..0e514378124a2333bd245f776417ad4dd172b3c4 100644
--- a/blxdotter.c
+++ b/blxdotter.c
@@ -20,17 +20,19 @@
typedef struct _DotterDialogData
{
- GtkWidget *blxWindow;
+ GtkWidget *blxWindow; /* pointer to the main blixem window */
- GtkWidget *autoButton;
- GtkWidget *manualButton;
+ GtkWidget *autoButton; /* the radio button on the dialog for automatic dotter parameters */
+ GtkWidget *manualButton; /* the radio button on the dialog for manual dotter parameters */
- GtkWidget *startEntry;
- GtkWidget *endEntry;
- GtkWidget *zoomEntry;
+ GtkWidget *startEntry; /* the text entry box on the dialog for the start coord */
+ GtkWidget *endEntry; /* the text entry box on the dialog for the end coord */
+ GtkWidget *zoomEntry; /* the text entry box on the dialog for the zoom value */
- gboolean callOnSelf;
- gboolean hspsOnly;
+ gboolean callOnSelf; /* whether to call dotter on the query seq versus itself */
+ gboolean hspsOnly; /* whether to call dotter on HSPs only */
+
+ char *dotterSSeq; /* the match sequence to call dotter on */
} DotterDialogData;
@@ -44,7 +46,8 @@ typedef enum {
BLX_DOTTER_ERROR_NOT_FOUND, /* failed to find the sequence */
BLX_DOTTER_ERROR_NO_REF_SEQ, /* failed to find the query sequence segment */
BLX_DOTTER_ERROR_INTERNAL_SEQ, /* using internally-stored sequence (because fetch failed) */
- BLX_DOTTER_ERROR_NO_MATCHES /* there are no matches on the requested sequence */
+ BLX_DOTTER_ERROR_NO_MATCHES, /* there are no matches on the requested sequence */
+ BLX_DOTTER_ERROR_NO_SEQ_DATA /* the match sequence has no sequence data (e.g. if could not pfetch it) */
} BlxDotterError;
@@ -54,7 +57,6 @@ static gboolean smartDotterRange(GtkWidget *blxWindow, const char *dotterS
static gboolean smartDotterRangeSelf(GtkWidget *blxWindow, int *dotter_start_out, int *dotter_end_out, GError **error);
static char* fetchSeqRaw(const char *seqname, const char *fetchMode);
static char* fetchSequence(const char *seqname, char *fetch_prog);
-static char* getDotterSSeq(GtkWidget *blxWindow, GError **error);
static gboolean callDotterSelf(GtkWidget *blxWindow, GError **error);
@@ -223,7 +225,7 @@ static void onSelfButtonToggled(GtkWidget *button, gpointer data)
int autoStart = UNSET_INT, autoEnd = UNSET_INT;
const gboolean autoDotter = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(dialogData->autoButton));
- getDotterRange(dialogData->blxWindow, getDotterSSeq(dialogData->blxWindow, NULL), dialogData->callOnSelf, autoDotter, &autoStart, &autoEnd, NULL, NULL);
+ getDotterRange(dialogData->blxWindow, dialogData->dotterSSeq, dialogData->callOnSelf, autoDotter, &autoStart, &autoEnd, NULL, NULL);
if (autoStart == UNSET_INT)
autoStart = bc->displayRev ? bc->refSeqRange.max : bc->refSeqRange.min;
@@ -274,7 +276,7 @@ static void onResponseDotterDialog(GtkDialog *dialog, gint responseId, gpointer
}
else
{
- destroy = callDotter(dialogData->blxWindow, dialogData->hspsOnly, &error);
+ destroy = callDotter(dialogData->blxWindow, dialogData->hspsOnly, dialogData->dotterSSeq, &error);
}
}
else
@@ -325,7 +327,7 @@ static void onRadioButtonToggled(GtkWidget *button, gpointer data)
{
/* Recalculate auto start/end in case user has selected a different sequence */
int autoStart = UNSET_INT, autoEnd = UNSET_INT;
- getDotterRange(dialogData->blxWindow, getDotterSSeq(dialogData->blxWindow, NULL), dialogData->callOnSelf, TRUE, &autoStart, &autoEnd, NULL, NULL);
+ getDotterRange(dialogData->blxWindow, dialogData->dotterSSeq, dialogData->callOnSelf, TRUE, &autoStart, &autoEnd, NULL, NULL);
if (autoStart == UNSET_INT)
autoStart = bc->displayRev ? bc->refSeqRange.max : bc->refSeqRange.min;
@@ -530,6 +532,7 @@ void showDotterDialog(GtkWidget *blxWindow, const gboolean bringToFront)
dialogData->zoomEntry = zoomEntry;
dialogData->callOnSelf = FALSE;
dialogData->hspsOnly = FALSE;
+ dialogData->dotterSSeq = getDotterSSeq(blxWindow, NULL);
/* There is an issue if the user selects a different sequence while the dotter dialog
* is still open: the auto range does not update automatically for the new sequence. To
@@ -648,8 +651,8 @@ static gboolean getDotterRange(GtkWidget *blxWindow,
* This function assumes that if multiple MSPs are selected, that they are all for
* the same match sequence. Returns null if no MSPs are selected, with details of the error
* in 'error'. If the sequence was found but there were warnings, it returns non-null with
- * the warnings in 'error'. */
-static char* getDotterSSeq(GtkWidget *blxWindow, GError **error)
+ * the warnings in 'error'. The return value should be free'd with g_free */
+char* getDotterSSeq(GtkWidget *blxWindow, GError **error)
{
g_return_val_if_fail(!error || *error == NULL, FALSE); /* if error is passed, its contents must be NULL */
@@ -956,8 +959,8 @@ static char *fetchSequence(const char *seqname, char *fetch_prog)
{
/* --client gives logging information to pfetch server,
* -q Sequence only output (one line) */
- fetchstr = hprintf(0, "%s --client=acedb_%s_%s -q '%s' &",
- fetch_prog, getSystemName(), getLogin(TRUE), seqname) ;
+ fetchstr = hprintf(0, "%s --client=%s_%s_%s -q '%s' &",
+ fetch_prog, g_get_prgname(), getSystemName(), getLogin(TRUE), seqname) ;
}
else
{
@@ -1028,7 +1031,7 @@ static char *fetchSequence(const char *seqname, char *fetch_prog)
/* Call dotter. Returns true if dotter was called; false if we quit trying. */
-gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **error)
+gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, char *dotterSSeqIn, GError **error)
{
g_return_val_if_fail(!error || *error == NULL, FALSE); /* if error is passed, its contents must be NULL */
BlxViewContext *bc = blxWindowGetContext(blxWindow);
@@ -1056,18 +1059,22 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
return FALSE;
}
- /* Get the match sequence. */
- GError *tmpError = NULL;
- char *dotterSSeq = getDotterSSeq(blxWindow, &tmpError);
-
- if (!dotterSSeq)
+ /* Make a copy of the match sequence, because dotter takes ownership of this. */
+ char *dotterSSeq = NULL;
+ if (dotterSSeqIn)
{
- g_propagate_error(error, tmpError);
+ dotterSSeq = g_strdup(dotterSSeqIn);
+ }
+ else
+ {
+ g_set_error(error, BLX_DOTTER_ERROR, BLX_DOTTER_ERROR_NO_SEQ_DATA, "No sequence data for this sequence.\n");
return FALSE;
}
/* Get the coords */
int dotterStart = UNSET_INT, dotterEnd = UNSET_INT, dotterZoom = 0;
+ GError *tmpError = NULL;
+
if (!getDotterRange(blxWindow, dotterSSeq, FALSE, bc->autoDotter, &dotterStart, &dotterEnd, &dotterZoom, &tmpError))
{
g_propagate_error(error, tmpError);
diff --git a/blxdotter.h b/blxdotter.h
index 6359e104410a581d704d2c0483e95361e7411509..9e2d81cd3bc53fe96a631fc0862b9a665b49a5bf 100644
--- a/blxdotter.h
+++ b/blxdotter.h
@@ -19,7 +19,8 @@
void showDotterDialog(GtkWidget *blxWindow, const gboolean bringToFront);
-gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **error);
+gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, char *dotterSSeq, GError **error);
+char* getDotterSSeq(GtkWidget *blxWindow, GError **error);
#endif /* _blx_dotter_h_included_ */
diff --git a/blxview.c b/blxview.c
index 5b49c09c09bda854afa141c1ba03ef4af262a87e..28ac5f5a1f1610648ff120d3cb05f82b771da353 100644
--- a/blxview.c
+++ b/blxview.c
@@ -88,7 +88,7 @@
01-10-05 Added getsseqsPfetch to fetch all missing sseqs in one go via socket connection to pfetch [RD]
* Created: Thu Feb 20 10:27:39 1993 (esr)
- * CVS info: $Id: blxview.c,v 1.65 2010-09-03 11:15:38 gb10 Exp $
+ * CVS info: $Id: blxview.c,v 1.66 2010-09-21 12:50:43 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -767,7 +767,13 @@ static void blviewCreate(char *opts,
blxWindowSelectSeq(blixemWindow, options->mspList->sSequence);
GError *error = NULL;
- callDotter(blixemWindow, FALSE, &error);
+ char *dotterSSeq = getDotterSSeq(blixemWindow, &error);
+
+ if (!error)
+ {
+ callDotter(blixemWindow, FALSE, dotterSSeq, &error);
+ }
+
reportAndClearIfError(&error, G_LOG_LEVEL_CRITICAL);
}
diff --git a/blxwindow.c b/blxwindow.c
index c47f15536fcaab7e26e80e0926b7d5cf15b24ee0..7016bb984a20bcb282b937f9ac81e76c30d58e66 100755
--- a/blxwindow.c
+++ b/blxwindow.c
@@ -5376,7 +5376,7 @@ GtkWidget* createBlxWindow(CommandLineOptions *options,
/* Realise the widgets */
- printf("Starting Blixem\n");
+ g_debug("Running %s\n", g_get_prgname());
gtk_widget_show_all(window);
/* If the options don't say to show the reverse strand grid, hide it now. (This must be done
diff --git a/detailview.c b/detailview.c
index edc6ce74634d0b2ed41aedfdb457be7415604f73..cb9b7d4849265ed0d979e7cd7aed21ad0b4853ed 100755
--- a/detailview.c
+++ b/detailview.c
@@ -181,7 +181,7 @@ static const char* findFixedWidthFontFamily(GtkWidget *widget, GList *pref_famil
if (match_family)
{
result = pango_font_family_get_name(match_family);
- printf("Using fixed-width font '%s'\n", result);
+ g_debug("Using fixed-width font '%s'\n", result);
}
else
{