diff --git a/src/belvuApp/belvu.cpp b/src/belvuApp/belvu.cpp
index 7b23a1ae6f55e77eef29cac42deb106aedc9de09..bd5f4f5581b05a0896eb4ef4828499d306f802c1 100644
--- a/src/belvuApp/belvu.cpp
+++ b/src/belvuApp/belvu.cpp
@@ -2501,8 +2501,8 @@ BelvuContext* createBelvuContext()
bc->fileName = NULL;
bc->dirName = NULL;
bc->organismLabel[0] = 'O';
- bc->organismLabel[0] = 'S';
- bc->organismLabel[0] = '\0';
+ bc->organismLabel[1] = 'S';
+ bc->organismLabel[2] = '\0';
bc->conservCount = NULL;
bc->colorMap = NULL;
@@ -4244,9 +4244,21 @@ static void parseMulAnnotationLine(BelvuContext *bc, const char *seqLine)
ALN *aln = createEmptyAln();
aln->organism = valuep; /* Find organism string in permanent stack */
- g_array_append_val(bc->organismArr, aln);
- g_array_sort(bc->organismArr, organism_order);
+
+ /* Add to organisms array, if not already there */
+ int org_idx = 0 ;
+ if (!alnArrayFind(bc->organismArr, aln, &org_idx, organism_order))
+ {
+ g_array_append_val(bc->organismArr, aln);
+ g_array_sort(bc->organismArr, organism_order);
+ /* Set the max organism name length */
+ int organismLen = strlen(aln->organism);
+
+ if (organismLen > bc->maxOrganismLen)
+ bc->maxOrganismLen = organismLen ;
+ }
+
if (strchr(cp, '/') && strchr(cp, '-'))
{
str2aln(bc, namep, aln);
@@ -4416,7 +4428,6 @@ static void readMul(BelvuContext *bc, FILE *pipe)
/* Store all annotation lines in a list. Prepend the items because that
* is more efficient, and then reverse the list at the end */
bc->annotationList = g_slist_prepend(bc->annotationList, g_strdup(line));
- parseMulAnnotationLine(bc, line);
}
else if (!strncmp(line, "#=GC ", 5) ||
!strncmp(line, "#=GR ", 5) ||
@@ -4451,6 +4462,14 @@ static void readMul(BelvuContext *bc, FILE *pipe)
g_slist_free(alnList);
alnList = NULL;
+
+ /* Loop through all the annotation lines and parse them (must be done after adding alignment
+ * lines) */
+ for (GSList *annItem = bc->annotationList; annItem; annItem = annItem->next)
+ {
+ char *line = (char*)(annItem->data) ;
+ parseMulAnnotationLine(bc, line);
+ }
/* For debugging * /
for (i = 0; i < nseq; i++) {
diff --git a/src/belvuApp/belvuMain.cpp b/src/belvuApp/belvuMain.cpp
index ab695a74ec9d3784c2f32fef4dcb45e9fe0993e7..e09d0931fbaf37f05ad1879d336bfb8027c09b81 100644
--- a/src/belvuApp/belvuMain.cpp
+++ b/src/belvuApp/belvuMain.cpp
@@ -355,7 +355,7 @@ static void showCompiledInfo()
/* Convert swissprot name suffixes to organisms */
-static void suffix2organism(GArray *alignArr, GArray *organismArr)
+static void suffix2organism(BelvuContext *bc, GArray *alignArr, GArray *organismArr)
{
int i = 0;
char *cp = NULL;
@@ -384,6 +384,12 @@ static void suffix2organism(GArray *alignArr, GArray *organismArr)
g_array_append_val(organismArr, organism);
g_array_sort(organismArr, organism_order);
+
+ // Calculate the max organism name len
+ const int organismLen = strlen(alnp->organism) ;
+
+ if (organismLen > bc->maxOrganismLen)
+ bc->maxOrganismLen = organismLen ;
}
else
{
@@ -550,6 +556,8 @@ int main(int argc, char **argv)
* There are two handlers: the default one for all non-critical messages, which will just log
* output to the console, and one for critical messages and errors, which will display a
* pop-up message (the idea being that we don't bother the user unless it's something serious).
+ * Note that the latter needs to display a gtk dialog so can't be set up until after gtk_init
+ * has been called.
*
* All errors and warnings will be sent to stderr, as will info messages (g_message_info).
* Program output destined for stdout should use g_message.
@@ -570,8 +578,6 @@ int main(int argc, char **argv)
msgData.statusBar = NULL;
g_log_set_default_handler(defaultMessageHandler, &msgData);
- g_log_set_handler(NULL, (GLogLevelFlags)(G_LOG_LEVEL_ERROR | G_LOG_LEVEL_CRITICAL | G_LOG_FLAG_FATAL | G_LOG_FLAG_RECURSION),
- popupMessageHandler, &msgData);
/* Initialise up the context with default values */
@@ -585,8 +591,6 @@ int main(int argc, char **argv)
setTreeScaleCorr(bc, bc->treeMethod);
- char *OrganismLabel = g_strdup("OS");
-
gboolean verbose = FALSE;
gboolean init_rmPartial = FALSE;
@@ -635,7 +639,7 @@ int main(int argc, char **argv)
case 'L': markupColorCodesFile = g_strdup(optarg); break;
case 'm': readMatchFile = g_strdup(optarg); break;
case 'n': makeNRinit = atof(optarg); break;
- case 'O': strncpy(OrganismLabel, optarg, 2); break;
+ case 'O': strncpy(bc->organismLabel, optarg, 2); break;
case 'o': output_format = g_strdup(optarg); break;
case 'P': init_rmPartial = TRUE; break;
case 'Q': init_rmGappyColumns = atof(optarg); break;
@@ -782,7 +786,7 @@ int main(int argc, char **argv)
}
if (bc->organismArr->len == 0)
- suffix2organism(bc->alignArr, bc->organismArr);
+ suffix2organism(bc, bc->alignArr, bc->organismArr);
setOrganismColors(bc->organismArr);
@@ -965,6 +969,10 @@ int main(int argc, char **argv)
/* We've finished all of the command-line-only options so now initialise the GTK GUI */
gtk_init(&argc, &argv);
+ /* After gtk_init is called, we can start using the popup message handler */
+ g_log_set_handler(NULL, (GLogLevelFlags)(G_LOG_LEVEL_ERROR | G_LOG_LEVEL_CRITICAL | G_LOG_FLAG_FATAL | G_LOG_FLAG_RECURSION),
+ popupMessageHandler, &msgData);
+
/* Update bits of the context that require the display to be initialised */
bc->removeSeqsCursor = gdk_cursor_new(GDK_PIRATE);
bc->busyCursor = gdk_cursor_new(GDK_WATCH);
@@ -1011,7 +1019,5 @@ int main(int argc, char **argv)
gtk_main();
}
- g_free(OrganismLabel) ;
-
return(EXIT_SUCCESS) ;
}
diff --git a/src/belvuApp/belvuWindow.cpp b/src/belvuApp/belvuWindow.cpp
index 6c3b8985b58a2a97185678c0e2f3413907c01e71..d7c8017bc1f07cd03c06f0a188f00efa7371bbba 100644
--- a/src/belvuApp/belvuWindow.cpp
+++ b/src/belvuApp/belvuWindow.cpp
@@ -3463,8 +3463,9 @@ static void drawOrganisms(GtkWidget *widget, GdkDrawable *drawable, BelvuContext
convertColorNumToGdkColor(alnp->color, FALSE, &color);
gdk_gc_set_foreground(gc, &color);
- drawText(widget, drawable, gc, x, y, alnp->organism, NULL, NULL);
-
+ int text_width = 0;
+ drawText(widget, drawable, gc, x, y, alnp->organism, &text_width, NULL);
+
y += charHeight;
}
@@ -3543,9 +3544,17 @@ static void createOrganismWindow(BelvuContext *bc)
/* Set layout size big enough to fit all organisms */
gdouble width = 0, height = 0;
getFontCharSize(drawing, drawing->style->font_desc, &width, &height);
- width *= (bc->maxNameLen + 1);
+ width *= (bc->maxOrganismLen + 1);
height *= (bc->organismArr->len + 1);
- gtk_layout_set_size(GTK_LAYOUT(drawing), width, height);
+
+ /* The size is only approximate (especially the width), so add a sizeable buffer (e.g. double
+ * it). It's important the layout is not too small but doesn't matter if it's too big (because
+ * it will be in a scrollwin) */
+ gtk_layout_set_size(GTK_LAYOUT(drawing), width * 2, height + 10);
+
+ /* Add some padding in the main window for space around the layout etc. It doesn't matter too
+ * much if this is too small because the window is resizable */
+ gtk_window_set_default_size(GTK_WINDOW(bc->orgsWindow), width * 2 + 20, height + 20) ;
/* Set default background color */
GdkColor *bgColor = getGdkColor(BELCOLOR_BACKGROUND, bc->defaultColors, FALSE, FALSE);
diff --git a/src/belvuApp/belvu_.hpp b/src/belvuApp/belvu_.hpp
index 2e9b2b3e481c547882bf96c49328fc4ff74ad253..93e6bd4cfa67374d8b27de1651ff3f162a151135 100644
--- a/src/belvuApp/belvu_.hpp
+++ b/src/belvuApp/belvu_.hpp
@@ -351,6 +351,7 @@ typedef struct BelvuContextStruct
int maxLen; /* number of columns in alignment */
int maxTreeWidth;
int maxNameLen; /* Max string length of any sequence name */
+ int maxOrganismLen; /* Max string length of any organism name */
int maxStartLen; /* Max string length of any sequence start */
int maxEndLen; /* Max string length of any sequence end */
int maxScoreen; /* Max string length of any sequence score */