diff --git a/blxwindow.c b/blxwindow.c
index 6b0c9180db352b5bb4a3286f1deeb2ac2f3a533e..4b4f3e4ac321b984310da355e0fb3b6c98e4496e 100755
--- a/blxwindow.c
+++ b/blxwindow.c
@@ -4968,21 +4968,27 @@ void blxWindowDeselectAllSeqs(GtkWidget *blxWindow)
}
-/* Returns true if the given sequence is selected */
-gboolean blxWindowIsSeqSelected(GtkWidget *blxWindow, const BlxSequence *seq)
+gboolean blxContextIsSeqSelected(BlxViewContext *bc, const BlxSequence *seq)
{
GList *foundItem = NULL;
- BlxViewContext *blxContext = blxWindowGetContext(blxWindow);
-
- if (blxContext)
+
+ if (bc)
{
- foundItem = g_list_find(blxContext->selectedSeqs, seq);
+ foundItem = g_list_find(bc->selectedSeqs, seq);
}
return (foundItem != NULL);
}
+/* Returns true if the given sequence is selected */
+gboolean blxWindowIsSeqSelected(GtkWidget *blxWindow, const BlxSequence *seq)
+{
+ BlxViewContext *blxContext = blxWindowGetContext(blxWindow);
+ return blxContextIsSeqSelected(blxContext, seq);
+}
+
+
/* Set the given sequence as selected or unselected, depending on the given argument */
void blxWindowSetSeqSelected(GtkWidget *blxWindow, BlxSequence *seq, const gboolean selected)
{
diff --git a/blxwindow.h b/blxwindow.h
index 2c037c4d1808a547869ac74c0355e9a9dc33a962..169f268ad20c5a045885d414d54c6513c2b2f52b 100755
--- a/blxwindow.h
+++ b/blxwindow.h
@@ -144,6 +144,8 @@ void blxWindowSetSeqSelected(GtkWidget *blxWindow, BlxSequence *seq, const g
void blxWindowSelectionChanged(GtkWidget *blxWindow);
BlxSequence* blxWindowGetLastSelectedSeq(GtkWidget *blxWindow);
+gboolean blxContextIsSeqSelected(BlxViewContext *bc, const BlxSequence *seq);
+
int sequenceGetGroupOrder(GtkWidget *blxWindow, const BlxSequence *seq);
void copySelectionToClipboard(GtkWidget *blxWindow);
void findSeqsFromClipboard(GtkClipboard *clipboard, const char *clipboardText, gpointer data);
diff --git a/detailview.c b/detailview.c
index ed256376b9e3b107edb5d33b5f3374fcba2a4268..53974886ddf00daaa83eb90b397fb2960a7ffd72 100755
--- a/detailview.c
+++ b/detailview.c
@@ -1715,8 +1715,19 @@ static void getVariationDisplayRange(const MSP *msp,
/* Determine whether the given coord in the given frame/strand is affected by
- * a variation */
-static gboolean coordAffectedByVariation(const int dnaIdx, const BlxStrand strand, const MSP *mspList)
+ * a variation. Sets whether to draw the start/end/top/bottom boundaries for the coord
+ * when outlining it by the extent of the found variation. Also sets drawBackground to true
+ * if the background of the base should be highlighted in the variation color (i.e. if the base
+ * is part of a selected variation). */
+static gboolean coordAffectedByVariation(const int dnaIdx,
+ const BlxStrand strand,
+ const MSP *mspList,
+ BlxViewContext *bc,
+ gboolean *drawStartBoundary,
+ gboolean *drawEndBoundary,
+ gboolean *drawTopBoundary,
+ gboolean *drawBottomBoundary,
+ gboolean *drawBackground)
{
gboolean result = FALSE;
@@ -1728,6 +1739,32 @@ static gboolean coordAffectedByVariation(const int dnaIdx, const BlxStrand stran
if (mspIsVariation(msp) && mspGetRefStrand(msp) == strand && valueWithinRange(dnaIdx, &msp->qRange))
{
result = TRUE;
+
+ /* We draw the start boundary of this base if it's the first base in the variation's range
+ * and the end boundary if it's the last, unless it's a zero-length feature, i.e. an insertion
+ * site; in this case we draw a line to the right of the coord in the direction of the
+ * reference sequence (i.e. to give just a vertical line at the site, not an outline around the bases) */
+ const gboolean isFirst = (dnaIdx == msp->qRange.min);
+ const gboolean isLast = (dnaIdx == msp->qRange.max);
+ const gboolean isZeroLen = mspIsZeroLenVariation(msp);
+
+ *drawStartBoundary = (isZeroLen ? isLast : isFirst);
+ *drawEndBoundary = (isZeroLen ? isFirst : isLast);
+
+ /* Swap left and right if the display is reversed */
+ if (bc->displayRev)
+ {
+ gboolean tmp = *drawStartBoundary;
+ *drawStartBoundary = *drawEndBoundary;
+ *drawEndBoundary = tmp;
+ }
+
+ *drawTopBoundary = !isZeroLen;
+ *drawBottomBoundary = !isZeroLen;
+
+ /* Highlight the background if the variation is selected (unless it's a zero-length variation) */
+ *drawBackground = !isZeroLen && blxContextIsSeqSelected(bc, msp->sSequence);
+
break;
}
}
@@ -1744,7 +1781,11 @@ static void drawRectangle(GdkDrawable *drawable,
const int x,
const int y,
const int width,
- const int height)
+ const int height,
+ const gboolean drawLeft,
+ const gboolean drawRight,
+ const gboolean drawTop,
+ const gboolean drawBottom)
{
const int lineWidth = 1;
@@ -1758,7 +1799,23 @@ static void drawRectangle(GdkDrawable *drawable,
{
gdk_gc_set_foreground(gc, outlineColor);
gdk_gc_set_line_attributes(gc, lineWidth, GDK_LINE_SOLID, GDK_CAP_BUTT, GDK_JOIN_MITER);
- gdk_draw_rectangle(drawable, gc, FALSE, x, y, width - lineWidth, height - lineWidth);
+
+ int w = width - lineWidth;
+ int h = height - lineWidth;
+
+ if (drawLeft)
+ gdk_draw_line(drawable, gc, x, y, x, y + h);
+
+ if (drawRight)
+ gdk_draw_line(drawable, gc, x + w, y, x + w, y + h);
+
+ if (drawTop)
+ gdk_draw_line(drawable, gc, x, y, x + w, y);
+
+ if (drawBottom)
+ gdk_draw_line(drawable, gc, x, y + h, x + w, y + h);
+
+ //gdk_draw_rectangle(drawable, gc, FALSE, x, y, width - lineWidth, height - lineWidth);
}
}
@@ -1837,7 +1894,10 @@ void drawHeaderChar(BlxViewContext *bc,
{
GdkColor *fillColor = NULL;
GdkColor *outlineColor = NULL;
-
+
+ /* If drawing an outline, these can be set to false to omit certain parts of the outline */
+ gboolean drawLeft = TRUE, drawRight = TRUE, drawTop = TRUE, drawBottom = TRUE;
+
/* Shade the background if the base is selected XOR if the base is within the range of a
* selected sequence. (If both conditions are true we don't shade, to give the effect of an
* inverted selection color.) */
@@ -1870,18 +1930,23 @@ void drawHeaderChar(BlxViewContext *bc,
}
}
- if (showSnps && coordAffectedByVariation(dnaIdx, strand, bc->mspList))
+ if (showSnps)
{
- /* The coord is affected by a SNP. Outline it in the "selected" SNP color
- * (which is darker than the normal color) */
- outlineColor = getGdkColor(BLXCOLOR_SNP, bc->defaultColors, TRUE, bc->usePrintColors);
-
- /* If the SNP is selected, also fill it with the SNP color (using the
- * "unselected" SNP color, which is lighter than the outline). */
- if (dnaIdxSelected)
- {
- fillColor = getGdkColor(BLXCOLOR_SNP, bc->defaultColors, FALSE, bc->usePrintColors);
- }
+ gboolean drawBackground = TRUE;
+
+ if (coordAffectedByVariation(dnaIdx, strand, bc->mspList, bc, &drawLeft, &drawRight, &drawTop, &drawBottom, &drawBackground))
+ {
+ /* The coord is affected by a SNP. Outline it in the "selected" SNP color
+ * (which is darker than the normal color) */
+ outlineColor = getGdkColor(BLXCOLOR_SNP, bc->defaultColors, TRUE, bc->usePrintColors);
+
+ /* If the SNP is selected, also fill it with the SNP color (using the
+ * "unselected" SNP color, which is lighter than the outline). */
+ if (drawBackground)
+ {
+ fillColor = getGdkColor(BLXCOLOR_SNP, bc->defaultColors, shadeBackground, bc->usePrintColors);
+ }
+ }
}
if (!fillColor)
@@ -1904,7 +1969,7 @@ void drawHeaderChar(BlxViewContext *bc,
}
- drawRectangle(drawable, gc, fillColor, outlineColor, x, y, properties->charWidth, properties->charHeight);
+ drawRectangle(drawable, gc, fillColor, outlineColor, x, y, properties->charWidth, properties->charHeight, drawLeft, drawRight, drawTop, drawBottom);
}
@@ -1963,7 +2028,7 @@ static void drawSnpTrack(GtkWidget *snpTrack, GtkWidget *detailView)
GdkColor *fillColor = isSelected ? getGdkColor(BLXCOLOR_SNP, bc->defaultColors, FALSE, bc->usePrintColors) : NULL;
/* Draw the background rectangle for the char */
- drawRectangle(drawable, gc, fillColor, outlineColor, x, y, width, properties->charHeight);
+ drawRectangle(drawable, gc, fillColor, outlineColor, x, y, width, properties->charHeight, TRUE, TRUE, TRUE, TRUE);
/* Draw the text */
PangoLayout *layout = gtk_widget_create_pango_layout(detailView, mspGetMatchSeq(msp));