diff --git a/blxGff3Parser.c b/blxGff3Parser.c
index d89bd5b7c4446d36a29cb7257c95f549be6695bc..b7645e7064237149da5c0de4b6e4eb22cacf26b9 100644
--- a/blxGff3Parser.c
+++ b/blxGff3Parser.c
@@ -532,6 +532,31 @@ static void parseAttributes(char *attributes,
}
+/* Utility to remove any GFF3 escape characters from the given string and replace them with
+ * the real characters they represent. Takes into account special chars for generic attributes,
+ * and also the Target-name and ID attributes if requested */
+static void replaceGff3EscapeChars(char **text, const gboolean targetNameAtt, const gboolean idAtt)
+{
+ GString *gstr = g_string_new(*text);
+
+ seqtools_g_string_replace(gstr, "%3b", ";");
+ seqtools_g_string_replace(gstr, "%3d", "=");
+ seqtools_g_string_replace(gstr, "%09", "\t");
+
+ /* Target-name and ID attributes additionally have whitespace escaped */
+ if (targetNameAtt || idAtt)
+ seqtools_g_string_replace(gstr, "%20", " ");
+
+ /* ID attribute additional has ">" escaped */
+ if (idAtt)
+ seqtools_g_string_replace(gstr, "%e3", ">");
+
+ g_free(*text);
+ *text = gstr->str;
+ g_string_free(gstr, FALSE);
+}
+
+
/* Parse a tag/data pair of the format "tag=data" */
static void parseTagDataPair(char *text,
const int lineNum,
@@ -577,6 +602,7 @@ static void parseTagDataPair(char *text,
else if (!strcmp(tokens[0], "url"))
{
gffData->url = g_strdup(tokens[1]);
+ replaceGff3EscapeChars(&gffData->url, FALSE, FALSE);
}
else
{
diff --git a/detailview.c b/detailview.c
index dd0593db3627e64ccda4d2f0c6be3f6b7830f7e0..74347e4fa7ca42bf7b5b7458a2754ea101d467d7 100755
--- a/detailview.c
+++ b/detailview.c
@@ -1732,15 +1732,16 @@ static void getVariationDisplayRange(const MSP *msp,
* 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 coordAffectedByVariation(const int dnaIdx,
+ const BlxStrand strand,
+ const MSP *mspList,
+ BlxViewContext *bc,
+ const MSP **mspOut, /* the variation we found */
+ gboolean *drawStartBoundary,
+ gboolean *drawEndBoundary,
+ gboolean *drawTopBoundary,
+ gboolean *drawBottomBoundary,
+ gboolean *drawBackground)
{
gboolean result = FALSE;
@@ -1753,6 +1754,9 @@ static gboolean coordAffectedByVariation(const int dnaIdx,
{
result = TRUE;
+ if (mspOut)
+ *mspOut = msp;
+
/* 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
@@ -1760,23 +1764,22 @@ static gboolean coordAffectedByVariation(const int dnaIdx,
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;
- }
+ if (drawStartBoundary)
+ *drawStartBoundary = (isZeroLen != bc->displayRev ? isLast : isFirst);
+
+ if (drawEndBoundary)
+ *drawEndBoundary = (isZeroLen != bc->displayRev ? isFirst : isLast);
- *drawTopBoundary = !isZeroLen;
- *drawBottomBoundary = !isZeroLen;
+ if (drawTopBoundary)
+ *drawTopBoundary = !isZeroLen;
+
+ if (drawBottomBoundary)
+ *drawBottomBoundary = !isZeroLen;
/* Highlight the background if the variation is selected (unless it's a zero-length variation) */
- *drawBackground = !isZeroLen && blxContextIsSeqSelected(bc, msp->sSequence);
+ if (drawBackground)
+ *drawBackground = !isZeroLen && blxContextIsSeqSelected(bc, msp->sSequence);
break;
}
@@ -1947,7 +1950,7 @@ void drawHeaderChar(BlxViewContext *bc,
{
gboolean drawBackground = TRUE;
- if (coordAffectedByVariation(dnaIdx, strand, bc->mspList, bc, &drawLeft, &drawRight, &drawTop, &drawBottom, &drawBackground))
+ if (coordAffectedByVariation(dnaIdx, strand, bc->mspList, bc, NULL, &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) */
@@ -2914,19 +2917,53 @@ static gboolean onButtonPressSnpTrack(GtkWidget *snpTrack, GdkEventButton *event
{
case 1:
{
- /* Select the SNP that was clicked on. */
GtkWidget *detailView = GTK_WIDGET(data);
- blxWindowDeselectAllSeqs(detailViewGetBlxWindow(detailView));
+ GtkWidget *blxWindow = detailViewGetBlxWindow(detailView);
+
+ if (event->type == GDK_BUTTON_PRESS) /* first click */
+ {
+ /* Select the variation that was clicked on. */
+ blxWindowDeselectAllSeqs(blxWindow);
- /* The SNP track is not the same width as the sequence column, so pass the
- * sequence column header so that we can convert to the correct coords */
- DetailViewColumnInfo *seqColInfo = detailViewGetColumnInfo(detailView, BLXCOL_SEQUENCE);
+ /* The SNP track is not the same width as the sequence column, so pass the
+ * sequence column header so that we can convert to the correct coords */
+ DetailViewColumnInfo *seqColInfo = detailViewGetColumnInfo(detailView, BLXCOL_SEQUENCE);
+
+ selectClickedSnp(snpTrack, seqColInfo->headerWidget, detailView, event->x, event->y, FALSE, TRUE, UNSET_INT); /* SNPs are always expanded in the SNP track */
+
+ refreshDetailViewHeaders(detailView);
+ callFuncOnAllDetailViewTrees(detailView, refreshTreeHeaders, NULL);
+ }
+ else if (event->type == GDK_2BUTTON_PRESS) /* double-click */
+ {
+ /* If a variation was double-clicked, open its URL in a browser. If multiple are selected,
+ * use the last-selected one. */
+ GList *seqItem = g_list_last(blxWindowGetSelectedSeqs(blxWindow));
+
+ if (seqItem)
+ {
+ BlxSequence *seq = (BlxSequence*)(seqItem->data);
+
+ /* (The url lives in the MSP, and there is only one MSP in a BlxSequence for a variation,
+ * so perhaps the url should be moved to the BlxSequence...) */
+ if (seq->type == BLXSEQUENCE_VARIATION && g_list_length(seq->mspList) > 0)
+ {
+ const MSP const *msp = (const MSP const *)(seq->mspList->data);
+
+ if (msp->url)
+ {
+ GError *error = NULL;
+ seqtoolsLaunchWebBrowser(msp->url, &error);
+ reportAndClearIfError(&error, G_LOG_LEVEL_CRITICAL);
+ }
+ else
+ {
+ g_warning("Variation '%s' does not have a URL.\n", mspGetSName(msp));
+ }
+ }
+ }
+ }
- selectClickedSnp(snpTrack, seqColInfo->headerWidget, detailView, event->x, event->y, FALSE, TRUE, UNSET_INT); /* SNPs are always expanded in the SNP track */
-
- refreshDetailViewHeaders(detailView);
- callFuncOnAllDetailViewTrees(detailView, refreshTreeHeaders, NULL);
-
handled = TRUE;
break;
}
diff --git a/detailview.h b/detailview.h
index 4c0b7698f990f0235c8a39615ad25e339ac1d533..ed3d841ed3bb215f8e0d708a674a2f92a3bf74e3 100644
--- a/detailview.h
+++ b/detailview.h
@@ -181,6 +181,17 @@ GHashTable* getRefSeqBasesToHighlight(GtkWidget *detailView, const I
void drawColumnSeparatorLine(GtkWidget *widget, GdkDrawable *drawable, GdkGC *gc, const BlxViewContext *bc);
gboolean onExposeGenericHeader(GtkWidget *headerWidget, GdkEventExpose *event, gpointer data);
+gboolean coordAffectedByVariation(const int dnaIdx,
+ const BlxStrand strand,
+ const MSP *mspList,
+ BlxViewContext *bc,
+ const MSP **msp,
+ gboolean *drawStartBoundary,
+ gboolean *drawEndBoundary,
+ gboolean *drawTopBoundary,
+ gboolean *drawBottomBoundary,
+ gboolean *drawBackground);
+
void drawHeaderChar(BlxViewContext *bc,
DetailViewProperties *properties,
const int dnaIdx,
diff --git a/detailviewtree.c b/detailviewtree.c
index d8f58e3cc9b6e2c4f0ca2567067ca90eb6ea367f..1e7086fc93cf1e20ecbd5b8f3b470d15845b3877 100755
--- a/detailviewtree.c
+++ b/detailviewtree.c
@@ -1401,6 +1401,7 @@ static gboolean onMouseMoveTree(GtkWidget *tree, GdkEventMotion *event, gpointer
!(event->state & GDK_BUTTON4_MASK) &&
!(event->state & GDK_BUTTON5_MASK))
{
+ /* Feed back details about the currently-hovered over row in the detail-view statusbar area */
GtkStatusbar *statusBar = treeGetStatusBar(tree);
/* Remove any previous message */
@@ -1450,21 +1451,86 @@ static gboolean onMouseMoveTree(GtkWidget *tree, GdkEventMotion *event, gpointer
}
}
-
-static gboolean onMouseMoveTreeHeader(GtkWidget *header, GdkEventMotion *event, gpointer data)
+
+/* Get the display index at the given position in the tree header */
+static int treeHeaderGetCoordAtPos(GtkWidget *header, GtkWidget *tree, const int x, const int y)
{
- GtkWidget *tree = GTK_WIDGET(data);
+ int baseIdx = UNSET_INT;
- /* The start of the header widget is at the start of the sequence column, so offset the
- * coords before propagating to the detail view */
GtkWidget *detailView = treeGetDetailView(tree);
- IntRange xRange;
- detailViewGetColumnXCoords(detailView, BLXCOL_SEQUENCE, &xRange);
- event->x += xRange.min;
+ GtkAdjustment *adjustment = detailViewGetAdjustment(detailView);
- propagateEventMotion(tree, treeGetDetailView(tree), event);
+ if (x >= 0 && x <= header->allocation.width)
+ {
+ /* Get the 0-based char index at x */
+ gint charWidth = detailViewGetCharWidth(detailView);
+ int charIdx = (int)((double)x / (double)charWidth);
+
+ /* Add the start of the scroll range to convert this to the display index */
+ baseIdx = charIdx + adjustment->value;
+ }
+ else if (x < 0)
+ {
+ baseIdx = adjustment->value;
+ }
+ else if (x > header->allocation.width)
+ {
+ baseIdx = adjustment->value = adjustment->page_size;
+ }
- return FALSE;
+ return baseIdx;
+}
+
+
+static gboolean onMouseMoveTreeHeader(GtkWidget *header, GdkEventMotion *event, gpointer data)
+{
+ gboolean handled = FALSE;
+ GtkWidget *tree = GTK_WIDGET(data);
+
+ if (event->state & GDK_BUTTON2_MASK)
+ {
+ /* Propagate the event to the detail view. The start of the header widget is at
+ * the start of the sequence column, so offset the coords before propagating. */
+ GtkWidget *detailView = treeGetDetailView(tree);
+ IntRange xRange;
+ detailViewGetColumnXCoords(detailView, BLXCOL_SEQUENCE, &xRange);
+ event->x += xRange.min;
+
+ propagateEventMotion(tree, treeGetDetailView(tree), event);
+ handled = FALSE;
+ }
+ else
+ {
+ /* If we're hovering over a base that's affected by a variation, then feed back info
+ * about the variation to the user. */
+
+ /* First remove any previous message from the feedback area */
+ GtkStatusbar *statusBar = treeGetStatusBar(tree);
+ guint contextId = gtk_statusbar_get_context_id(GTK_STATUSBAR(statusBar), DETAIL_VIEW_STATUSBAR_CONTEXT);
+ gtk_statusbar_pop(GTK_STATUSBAR(statusBar), contextId);
+
+ /* Get the index we're hovering over */
+ const int displayIdx = treeHeaderGetCoordAtPos(header, tree, event->x, event->y);
+ GtkWidget *detailView = treeGetDetailView(tree);
+ BlxViewContext *bc = treeGetContext(tree);
+
+ const int dnaIdx = convertDisplayIdxToDnaIdx(displayIdx, bc->seqType, detailViewGetActiveFrame(detailView), treeGetFrame(tree), bc->numFrames, bc->displayRev, &bc->refSeqRange);
+
+ /* See if there's a variation here */
+ const MSP *msp = NULL;
+
+ if (coordAffectedByVariation(dnaIdx, treeGetStrand(tree), bc->mspList, bc, &msp, NULL, NULL, NULL, NULL, NULL))
+ {
+ if (msp && mspGetSName(msp))
+ {
+ char *displayText = mspGetSSeq(msp) ? blxprintf("%s : %s", mspGetSName(msp), mspGetSSeq(msp)) : blxprintf("%s", mspGetSName(msp));
+ gtk_statusbar_push(GTK_STATUSBAR(statusBar), contextId, displayText);
+ g_free(displayText);
+ }
+ }
+ }
+
+ return handled;
}
@@ -1491,18 +1557,36 @@ static gboolean onEnterTree(GtkWidget *tree, GdkEventCrossing *event, gpointer d
}
-static gboolean onLeaveTree(GtkWidget *tree, GdkEventCrossing *event, gpointer data)
+/* Clear the detail-view feedback area */
+static void clearStatusbar(GtkWidget *tree)
{
- /* Remove any message that was added by mousing over the tree rows */
GtkStatusbar *statusBar = treeGetStatusBar(tree);
guint contextId = gtk_statusbar_get_context_id(GTK_STATUSBAR(statusBar), DETAIL_VIEW_STATUSBAR_CONTEXT);
-
gtk_statusbar_pop(GTK_STATUSBAR(statusBar), contextId);
+}
+
+static gboolean onLeaveTree(GtkWidget *tree, GdkEventCrossing *event, gpointer data)
+{
+ /* Remove any statusbar message that was added by mousing over the tree rows */
+ clearStatusbar(tree);
+
/* Return true to stop the default handler re-drawing when the focus changes */
return TRUE;
}
+static gboolean onLeaveTreeHeader(GtkWidget *header, GdkEventCrossing *event, gpointer data)
+{
+ /* Remove any statusbar message that was added by mousing over the tree header */
+ GtkWidget *tree = GTK_WIDGET(data);
+ GtkStatusbar *statusBar = treeGetStatusBar(tree);
+ guint contextId = gtk_statusbar_get_context_id(GTK_STATUSBAR(statusBar), DETAIL_VIEW_STATUSBAR_CONTEXT);
+
+ gtk_statusbar_pop(GTK_STATUSBAR(statusBar), contextId);
+
+ /* Return true to stop the default handler re-drawing when the focus changes */
+ return TRUE;
+}
/* Add a row to the given tree containing the given MSP */
void addMspToTree(GtkWidget *tree, MSP *msp)
@@ -2157,14 +2241,16 @@ static TreeColumnHeaderInfo* createTreeColHeader(GList **columnHeaders,
gtk_widget_add_events(columnHeader, GDK_BUTTON_PRESS_MASK);
gtk_widget_add_events(columnHeader, GDK_BUTTON_RELEASE_MASK);
- gtk_widget_add_events(columnHeader, GDK_BUTTON2_MOTION_MASK);
+ gtk_widget_add_events(columnHeader, GDK_POINTER_MOTION_MASK);
+ gtk_widget_add_events(columnHeader, GDK_LEAVE_NOTIFY);
g_signal_connect(G_OBJECT(columnHeader), "button-press-event", G_CALLBACK(onButtonPressTreeHeader), tree);
g_signal_connect(G_OBJECT(columnHeader), "button-release-event", G_CALLBACK(onButtonReleaseTreeHeader), tree);
g_signal_connect(G_OBJECT(columnHeader), "motion-notify-event", G_CALLBACK(onMouseMoveTreeHeader), tree);
-
+ g_signal_connect(G_OBJECT(columnHeader), "leave-notify-event", G_CALLBACK(onLeaveTreeHeader), tree);
+
break;
}
-
+
case BLXCOL_START:
{
/* The start column header displays the start index of the current display range */
@@ -2653,7 +2739,7 @@ GtkWidget* createDetailViewTree(GtkWidget *grid,
g_signal_connect(G_OBJECT(tree), "drag-end", G_CALLBACK(onDragEndTree), NULL);
g_signal_connect(G_OBJECT(tree), "drag-motion", G_CALLBACK(onDragMotionTree), NULL);
g_signal_connect(G_OBJECT(tree), "expose-event", G_CALLBACK(onExposeDetailViewTree), NULL);
-
+
GtkTreeSelection *selection = gtk_tree_view_get_selection(GTK_TREE_VIEW(tree));
g_signal_connect(G_OBJECT(selection), "changed", G_CALLBACK(onSelectionChangedTree), tree);
diff --git a/seqtoolsWebBrowser.c b/seqtoolsWebBrowser.c
index 3f8d16789b77196ee4acc1b15c96c399308a74f9..8b0034a99c83fa063db1ee15fc7021c732917570 100644
--- a/seqtoolsWebBrowser.c
+++ b/seqtoolsWebBrowser.c
@@ -49,7 +49,7 @@ typedef struct
static char *findBrowser(BrowserConfig browsers, BrowserConfig *browser_out, GError **error) ;
static void makeBrowserCmd(GString *cmd, BrowserConfig best_browser, char *url) ;
-static char *translateURLChars(char *orig_link) ;
+static char *translateURLChars(const char *orig_link) ;
gboolean seqtools_g_string_replace(GString *string, char *target, char *source);
@@ -119,7 +119,7 @@ static GQuark err_domain_G = 0 ;
* @param error pointer to NULL GError pointer for return of errors.
* @return gboolean TRUE if launch of browser successful.
*/
-gboolean seqtoolsLaunchWebBrowser(char *link, GError **error)
+gboolean seqtoolsLaunchWebBrowser(const char *link, GError **error)
{
gboolean result = FALSE ;
BrowserConfig best_browser = NULL ;
@@ -294,7 +294,7 @@ static void makeBrowserCmd(GString *cmd, BrowserConfig best_browser, char *url)
*
* mh17: second thoughts: don't use, these rely on quoting: thrid thoughts: no amount of escaped quoting seems to work
*/
-static char *translateURLChars(char *orig_link)
+static char *translateURLChars(const char *orig_link)
{
char *url = NULL ;
diff --git a/utilities.c b/utilities.c
index ddc575ea6f36647a38a1f1faba81f830a7366cf9..9e6acaedda03937b79a9aee1769e4c7141b99b00 100644
--- a/utilities.c
+++ b/utilities.c
@@ -1074,6 +1074,11 @@ int mspGetSEnd(const MSP const *msp)
return (mspGetMatchStrand(msp) == mspGetRefStrand(msp) ? msp->sRange.max : msp->sRange.min);
}
+char* mspGetSSeq(const MSP const *msp)
+{
+ return (msp && msp->sSequence && msp->sSequence->sequence ? msp->sSequence->sequence->str : NULL);
+}
+
/* Return the match sequence name. (Gets it from the BlxSequence if the MSP itself doesn't have
* a name) */
const char *mspGetSName(const MSP const *msp)
diff --git a/utilities.h b/utilities.h
index 46605ab809d905142a8428122e4c71a19c12f329..712634b1f42939e11b7b2d91f3ac1421bb8d03c9 100644
--- a/utilities.h
+++ b/utilities.h
@@ -230,6 +230,7 @@ int mspGetQStart(const MSP const *msp);
int mspGetQEnd(const MSP const *msp);
int mspGetSStart(const MSP const *msp);
int mspGetSEnd(const MSP const *msp);
+char* mspGetSSeq(const MSP const *msp);
int mspGetQRangeLen(const MSP const *msp);
int mspGetSRangeLen(const MSP const *msp);
int mspGetMatchSeqLen(const MSP const *msp);
@@ -394,7 +395,8 @@ void gtk_text_buffer_set_markup (GtkTextBuffer *buffer,
/* seqtoolsWebBrowser.c */
-gboolean seqtoolsLaunchWebBrowser(char *link, GError **error);
+gboolean seqtoolsLaunchWebBrowser(const char *link, GError **error);
+gboolean seqtools_g_string_replace(GString *string, char *target, char *source);
#endif /* _utilities_h_included_ */