From c256bd4c149afd375c243b066e5dafefbe1ae67a Mon Sep 17 00:00:00 2001
From: gb10 <gb10>
Date: Mon, 27 Sep 2010 17:16:11 +0000
Subject: [PATCH] Can now view polyA tails
---
blxGff3Parser.c | 14 ++--
blxview.c | 9 ++-
blxwindow.c | 165 +++++++++++++++++++++++------------------
blxwindow.h | 24 +-----
detailview.c | 22 ++----
detailview.h | 1 -
detailviewtree.c | 11 ++-
sequencecellrenderer.c | 13 ++--
utilities.c | 86 +++++++++++++++++----
utilities.h | 50 +++++++++++--
10 files changed, 244 insertions(+), 151 deletions(-)
diff --git a/blxGff3Parser.c b/blxGff3Parser.c
index 228baa1a..db38d4a2 100644
--- a/blxGff3Parser.c
+++ b/blxGff3Parser.c
@@ -232,9 +232,15 @@ static void createBlixemObject(BlxGffData *gffData,
GError *tmpError = NULL;
- if (typeIsExon(gffData->mspType) || gffData->mspType == BLXMSP_MATCH)
+ if (gffData->mspType == BLXMSP_TRANSCRIPT)
{
- if (!gffData->sName && !gffData->parentIdTag)
+ /* For transcript types, don't create an MSP, but do create a sequence */
+ addBlxSequence(gffData->sName, gffData->idTag, gffData->qStrand, seqList, gffData->sequence, NULL, &tmpError);
+ }
+ else
+ {
+ /* For all other types, create an MSP */
+ if (!gffData->sName && !gffData->parentIdTag && (typeIsExon(gffData->mspType) || typeIsMatch(gffData->mspType)))
{
g_set_error(error, BLX_ERROR, 1, "Target/name/parent-ID must be specified for exons and alignments.\n");
return;
@@ -286,10 +292,6 @@ static void createBlixemObject(BlxGffData *gffData,
parseGapString(gffData->gapString, opts, msp, &tmpError);
}
}
- else if (gffData->mspType == BLXMSP_TRANSCRIPT)
- {
- addBlxSequence(gffData->sName, gffData->idTag, gffData->qStrand, seqList, gffData->sequence, NULL, &tmpError);
- }
if (tmpError)
{
diff --git a/blxview.c b/blxview.c
index faeff3a7..72f6bff5 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 1.68 2010-09-27 11:55:15 gb10 Exp $
+ * CVS info: $Id: blxview.c,v 1.69 2010-09-27 17:16:11 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -1415,8 +1415,11 @@ MSP* createNewMsp(MSP **lastMsp,
sprintf(msp->qframe, "(%c%d)", getStrandAsChar(qStrand), qFrame);
sprintf(msp->sframe, "(%c%d)", getStrandAsChar(sStrand), 1);
- /* Add/create a BlxSequence for this MSP's sequence name */
- addBlxSequence(msp->sname, idTag, sStrand, seqList, sequence, msp, error);
+ /* For matches, exons and introns, add (or add to if already exists) a BlxSequence */
+ if (typeIsExon(mspType) || typeIsIntron(mspType) || typeIsMatch(mspType))
+ {
+ addBlxSequence(msp->sname, idTag, sStrand, seqList, sequence, msp, error);
+ }
if (error && *error)
{
diff --git a/blxwindow.c b/blxwindow.c
index 7016bb98..6dcc1601 100755
--- a/blxwindow.c
+++ b/blxwindow.c
@@ -1664,7 +1664,7 @@ void showInfoDialog(GtkWidget *blxWindow)
/* Compile the message text from the selected sequence(s) */
GString *resultStr = g_string_new("");
- const gboolean dataLoaded = blxContextGetFlag(bc, BLXFLAG_EMBL_DATA_LOADED);
+ const gboolean dataLoaded = bc->flags[BLXFLAG_EMBL_DATA_LOADED];
GList *seqItem = bc->selectedSeqs;
for ( ; seqItem; seqItem = seqItem->next)
@@ -2724,30 +2724,6 @@ static GtkWidget* dialogChildGetBlxWindow(GtkWidget *child)
}
-/* Set the given flag to the given value */
-void blxContextSetFlag(BlxViewContext *bc, const BlxFlag flag, const gboolean newValue)
-{
- gboolean *value = &g_array_index(bc->blxFlags, gboolean, flag);
- *value = newValue;
-}
-
-
-/* Get the value of the given flag */
-gboolean blxContextGetFlag(const BlxViewContext *bc, const BlxFlag flag)
-{
- gboolean result = g_array_index(bc->blxFlags, gboolean, flag);
-
- /* Special case for the show-unaligned-sequnece option: only allow this to be true if
- * squash matches is off, because they don't work well together */
- if (result && flag == BLXFLAG_SHOW_UNALIGNED_SEQ && blxContextGetFlag(bc, BLXFLAG_SQUASH_MATCHES))
- {
- result = FALSE;
- }
-
- return result;
-}
-
-
/* Updates the given flag from the given button. The passed in widget is the toggle button and
* the data is an enum indicating which flag was toggled. Returns the new value that was set.
* Returns the new value that was set. */
@@ -2759,7 +2735,7 @@ static gboolean setFlagFromButton(GtkWidget *button, gpointer data)
BlxFlag flag = GPOINTER_TO_INT(data);
const gboolean newValue = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(button));
- blxContextSetFlag(bc, flag, newValue);
+ bc->flags[flag] = newValue;
return newValue;
}
@@ -2888,7 +2864,7 @@ static void onButtonClickedLoadEmblData(GtkWidget *button, gpointer data)
if (success)
{
/* Set the flag to say that the data has now been loaded */
- blxContextSetFlag(bc, BLXFLAG_EMBL_DATA_LOADED, TRUE);
+ bc->flags[BLXFLAG_EMBL_DATA_LOADED] = TRUE;
/* Disable the button so user can't try to load data again. */
gtk_widget_set_sensitive(button, FALSE);
@@ -2922,7 +2898,7 @@ static GtkWidget* createColumnLoadDataButton(GtkBox *box, GtkWidget *detailView)
gtk_box_pack_start(GTK_BOX(box), hbox, FALSE, FALSE, 12);
BlxViewContext *bc = blxWindowGetContext(detailViewGetBlxWindow(detailView));
- const gboolean dataLoaded = blxContextGetFlag(bc, BLXFLAG_EMBL_DATA_LOADED);
+ const gboolean dataLoaded = bc->flags[BLXFLAG_EMBL_DATA_LOADED];
GtkWidget *button = gtk_button_new_with_label(LOAD_DATA_TEXT);
gtk_widget_set_sensitive(button, !dataLoaded); /* only enable if data not yet loaded */
@@ -3213,25 +3189,39 @@ static void onTogglePrintColors(GtkWidget *button, gpointer data)
}
-/* Callback function called when the 'Show unaligned sequence' button is toggled */
+/* Callback function called when the 'Show unaligned sequence' button is toggled. Could be consolidated
+ * with onShowPolyAToggled (we'd just need to pass both the sub-container and the flag in the user
+ * data) */
static void onShowUnalignedSeqToggled(GtkWidget *button, gpointer data)
{
/* Get the new value */
- const gboolean showUnalignedSeq = setFlagFromButton(button, GINT_TO_POINTER(BLXFLAG_SHOW_UNALIGNED_SEQ));
+ const gboolean active = setFlagFromButton(button, GINT_TO_POINTER(BLXFLAG_SHOW_UNALIGNED));
/* Enable/disable the sub-options. Their widgets are all in the container passed as the data. */
GtkWidget *subComponents = GTK_WIDGET(data);
- gtk_widget_set_sensitive(subComponents, showUnalignedSeq);
+ gtk_widget_set_sensitive(subComponents, active);
- /* Get the detail view from the main window */
GtkWidget *blxWindow = dialogChildGetBlxWindow(button);
- GtkWidget *detailView = blxWindowGetDetailView(blxWindow);
-
- /* Update the value */
- detailViewUpdateShowUnalignedSeq(detailView, showUnalignedSeq);
+ blxWindowRedrawAll(blxWindow);
}
+/* Callback function called when the 'Show polyA tails' button is toggled. Could be consolidated
+ * with onShowUnalignedSeqToggled (we'd just need to pass both the sub-container and the flag in the user
+ * data) */
+static void onShowPolyAToggled(GtkWidget *button, gpointer data)
+{
+ /* Get the new value */
+ const gboolean active = setFlagFromButton(button, GINT_TO_POINTER(BLXFLAG_SHOW_POLYA));
+
+ /* Enable/disable the sub-options. Their widgets are all in the container passed as the data. */
+ GtkWidget *subComponents = GTK_WIDGET(data);
+ gtk_widget_set_sensitive(subComponents, active);
+
+ GtkWidget *blxWindow = dialogChildGetBlxWindow(button);
+ blxWindowRedrawAll(blxWindow);
+}
+
/* Callback function called when the 'Limit unaligned bases' button is toggled */
static void onLimitUnalignedBasesToggled(GtkWidget *button, gpointer data)
{
@@ -3265,27 +3255,20 @@ static gboolean onSetNumUnalignedBases(GtkWidget *entry, const gint responseId,
}
-/* Create option buttons for enabling/disabling display of unaligned sequence */
-static void createUnalignedSeqButtons(GtkWidget *parent, GtkWidget *detailView, BlxViewContext *bc)
+/* Create the check button for the 'limit number of unaligned bases' option on the settings dialog
+ * and pack it into the given container. */
+static void createLimitUnalignedBasesButton(GtkContainer *parent, GtkWidget *detailView, BlxViewContext *bc)
{
- const gboolean showUnalignedSeq = blxContextGetFlag(bc, BLXFLAG_SHOW_UNALIGNED_SEQ);
-
- GtkWidget *vbox = gtk_vbox_new(FALSE, 0);
- gtk_box_pack_start(GTK_BOX(parent), vbox, FALSE, FALSE, 0);
-
- /* Create an hbox for the sub-components. Create it now so we can pass it to the main toggle
- * button callback, but don't pack it in the container till we've added the other. */
+ /* Create an hbox for the "limit to so-many bases" option, which has a check button, text
+ * entry and some labels. Pack the hbox into the given parent. */
GtkWidget *hbox = gtk_hbox_new(FALSE, 0);
- gtk_widget_set_sensitive(hbox, showUnalignedSeq);
-
- /* Main check button to enable/disable the option */
- createCheckButton(GTK_BOX(vbox), "Show _unaligned sequence (only works if Squash Matches is off)", showUnalignedSeq, G_CALLBACK(onShowUnalignedSeqToggled), hbox);
-
- /* Text entry box to specify the limit */
+ gtk_container_add(parent, hbox);
+
+ /* Create a text entry box so the user can enter the number of bases */
GtkWidget *entry = gtk_entry_new();
gtk_entry_set_activates_default(GTK_ENTRY(entry), TRUE);
widgetSetCallbackData(entry, onSetNumUnalignedBases, detailView);
-
+
DetailViewProperties *properties = detailViewGetProperties(detailView);
char *numStr = convertIntToString(properties->numUnalignedBases);
@@ -3294,19 +3277,52 @@ static void createUnalignedSeqButtons(GtkWidget *parent, GtkWidget *detailView,
g_free(numStr);
/* Check button to enable/disable setting the limit */
- GtkWidget *button = gtk_check_button_new_with_mnemonic("_Limit to ");
- gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(button), blxContextGetFlag(bc, BLXFLAG_LIMIT_UNALIGNED_BASES));
+ GtkWidget *button = gtk_check_button_new_with_mnemonic("Li_mit to ");
+ gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(button), bc->flags[BLXFLAG_LIMIT_UNALIGNED_BASES]);
g_signal_connect(G_OBJECT(button), "toggled", G_CALLBACK(onLimitUnalignedBasesToggled), entry);
-
+
/* Pack it all in the hbox */
- gtk_box_pack_start(GTK_BOX(vbox), hbox, FALSE, FALSE, 0);
- gtk_box_pack_start(GTK_BOX(hbox), gtk_label_new(" "), FALSE, FALSE, 0);
gtk_box_pack_start(GTK_BOX(hbox), button, FALSE, FALSE, 0);
gtk_box_pack_start(GTK_BOX(hbox), entry, FALSE, FALSE, 0);
gtk_box_pack_start(GTK_BOX(hbox), gtk_label_new(" additional bases"), FALSE, FALSE, 0);
}
+/* Create a "parent" option button that has a vbox container for "sub-components", i.e. more
+ * option buttons (or other dialog widgets) that will be enabled only when the parent option is
+ * active. Returns the container for the sub-options, which should be packed with the sub-option widgets. */
+static GtkContainer* createParentCheckButton(GtkWidget *parent,
+ GtkWidget *detailView,
+ BlxViewContext *bc,
+ const char *label,
+ const gboolean active,
+ GCallback callbackFunc)
+{
+ /* We'll the main button and any sub-components into a vbox */
+ GtkWidget *vbox = gtk_vbox_new(FALSE, 0);
+ gtk_box_pack_start(GTK_BOX(parent), vbox, FALSE, FALSE, 0);
+
+ /* Create a vbox for the sub-components. Create the vbox now so we can pass it to the main toggle
+ * button callback, but don't pack it in the container till we've added the main check button. The sub
+ * components are only active if the main check button is active. */
+ GtkWidget *subContainer = gtk_vbox_new(FALSE, 0);
+ gtk_widget_set_sensitive(subContainer, active);
+
+ /* Main check button to enable/disable the option. This call puts it in the vbox. */
+ createCheckButton(GTK_BOX(vbox), label, active, callbackFunc, subContainer);
+
+ /* Now add the subcomponent container to the vbox. Bit of a hack - put it inside an hbox with
+ * a blank label preceeding it, so that the sub-components appear offset to the right slightly
+ * from the main button. */
+ GtkWidget *hbox = gtk_hbox_new(FALSE, 0);
+ gtk_box_pack_start(GTK_BOX(hbox), gtk_label_new(" "), FALSE, FALSE, 0);
+ gtk_box_pack_start(GTK_BOX(hbox), subContainer, FALSE, FALSE, 0);
+ gtk_box_pack_start(GTK_BOX(vbox), hbox, FALSE, FALSE, 0);
+
+ return GTK_CONTAINER(subContainer);
+}
+
+
/* Refresh the given dialog, if it is open */
void refreshDialog(const BlxDialogId dialogId, GtkWidget *blxWindow)
{
@@ -3410,12 +3426,21 @@ void showSettingsDialog(GtkWidget *blxWindow, const gboolean bringToFront)
/* Display options */
GtkWidget *vbox1 = createVBoxWithBorder(mainVBox, borderWidth, TRUE, "Display options");
- createCheckButton(GTK_BOX(vbox1), "_Squash matches", blxContextGetFlag(bc, BLXFLAG_SQUASH_MATCHES), G_CALLBACK(onSquashMatches), GINT_TO_POINTER(BLXFLAG_SQUASH_MATCHES));
- createUnalignedSeqButtons(vbox1, detailView, bc);
- createCheckButton(GTK_BOX(vbox1), "_Invert sort order", blxContextGetFlag(bc, BLXFLAG_INVERT_SORT), G_CALLBACK(onSortOrderToggled), GINT_TO_POINTER(BLXFLAG_INVERT_SORT));
- createCheckButton(GTK_BOX(vbox1), "_Highlight differences", blxContextGetFlag(bc, BLXFLAG_HIGHLIGHT_DIFFS), G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_HIGHLIGHT_DIFFS));
- createCheckButton(GTK_BOX(vbox1), "Show SN_P track", blxContextGetFlag(bc, BLXFLAG_SHOW_SNP_TRACK), G_CALLBACK(onShowSnpTrackToggled), GINT_TO_POINTER(BLXFLAG_SHOW_SNP_TRACK));
- createCheckButton(GTK_BOX(vbox1), "Show Sp_lice Sites for selected seqs", blxContextGetFlag(bc, BLXFLAG_SHOW_SPLICE_SITES), G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_SHOW_SPLICE_SITES));
+ createCheckButton(GTK_BOX(vbox1), "_Squash matches", bc->flags[BLXFLAG_SQUASH_MATCHES], G_CALLBACK(onSquashMatches), GINT_TO_POINTER(BLXFLAG_SQUASH_MATCHES));
+
+ /* show-polyA-tails option and its sub-options */
+ GtkContainer *polyAContainer = createParentCheckButton(vbox1, detailView, bc, "Show polyA _tails", bc->flags[BLXFLAG_SHOW_POLYA], G_CALLBACK(onShowPolyAToggled));
+ createCheckButton(GTK_BOX(polyAContainer), "Selected sequences only", bc->flags[BLXFLAG_SHOW_POLYA_SELECTED], G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_SHOW_POLYA_SELECTED));
+
+ /* show-unaligned-sequence option and its sub-options */
+ GtkContainer *unalignContainer = createParentCheckButton(vbox1, detailView, bc, "Show _unaligned sequence (only works if Squash Matches is off)", bc->flags[BLXFLAG_SHOW_UNALIGNED], G_CALLBACK(onShowUnalignedSeqToggled));
+ createLimitUnalignedBasesButton(unalignContainer, detailView, bc);
+ createCheckButton(GTK_BOX(unalignContainer), "Selected sequences only", bc->flags[BLXFLAG_SHOW_UNALIGNED_SELECTED], G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_SHOW_UNALIGNED_SELECTED));
+
+ createCheckButton(GTK_BOX(vbox1), "_Invert sort order", bc->flags[BLXFLAG_INVERT_SORT], G_CALLBACK(onSortOrderToggled), GINT_TO_POINTER(BLXFLAG_INVERT_SORT));
+ createCheckButton(GTK_BOX(vbox1), "_Highlight differences", bc->flags[BLXFLAG_HIGHLIGHT_DIFFS], G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_HIGHLIGHT_DIFFS));
+ createCheckButton(GTK_BOX(vbox1), "Show SN_P track", bc->flags[BLXFLAG_SHOW_SNP_TRACK], G_CALLBACK(onShowSnpTrackToggled), GINT_TO_POINTER(BLXFLAG_SHOW_SNP_TRACK));
+ createCheckButton(GTK_BOX(vbox1), "Show Sp_lice Sites for selected seqs", bc->flags[BLXFLAG_SHOW_SPLICE_SITES], G_CALLBACK(onToggleFlag), GINT_TO_POINTER(BLXFLAG_SHOW_SPLICE_SITES));
GtkWidget *pfetchBox = createVBoxWithBorder(mainVBox, borderWidth, TRUE, "Fetch mode");
createPfetchDropDownBox(GTK_BOX(pfetchBox), blxWindow);
@@ -4211,11 +4236,6 @@ static void destroyBlxContext(BlxViewContext **bc)
(*bc)->defaultColors = NULL;
}
- if ((*bc)->blxFlags)
- {
- g_array_free((*bc)->blxFlags, FALSE);
- }
-
destroyMspList(&((*bc)->mspList));
destroyBlxSequenceList(&((*bc)->matchSeqs));
blxDestroyGffTypeList(&((*bc)->supportedTypes));
@@ -4498,18 +4518,17 @@ static BlxViewContext* blxWindowCreateContext(CommandLineOptions *options,
createBlxColors(blxContext, widget);
- blxContext->blxFlags = g_array_sized_new(FALSE, TRUE, sizeof(gboolean), BLXFLAG_NUM_FLAGS);
-
/* Initialise all the flags to false */
int flag = BLXFLAG_MIN + 1;
for ( ; flag < BLXFLAG_NUM_FLAGS; ++flag)
{
- blxContextSetFlag(blxContext, flag, FALSE);
+ blxContext->flags[flag] = FALSE;
}
/* Set any specific flags that we want initialised to TRUE */
- blxContextSetFlag(blxContext, BLXFLAG_LIMIT_UNALIGNED_BASES, TRUE);
- blxContextSetFlag(blxContext, BLXFLAG_EMBL_DATA_LOADED, options->parseFullEmblInfo);
+ blxContext->flags[BLXFLAG_LIMIT_UNALIGNED_BASES] = TRUE;
+ blxContext->flags[BLXFLAG_SHOW_POLYA_SELECTED] = TRUE;
+ blxContext->flags[BLXFLAG_EMBL_DATA_LOADED] = options->parseFullEmblInfo;
/* Null out all the entries in the dialogs list */
int dialogId = 0;
diff --git a/blxwindow.h b/blxwindow.h
index 87510b4e..2c037c4d 100755
--- a/blxwindow.h
+++ b/blxwindow.h
@@ -42,25 +42,6 @@ typedef struct _CommandLineOptions
} CommandLineOptions;
-/* This enum contains a list of all the boolean options that the user can toggle on/off */
-typedef enum
- {
- BLXFLAG_MIN, /* Start index for looping through flags */
-
- BLXFLAG_SQUASH_MATCHES, /* Puts all MSPs from the same sequence on the same row in the detail view */
- BLXFLAG_INVERT_SORT, /* Inverts the default sort order */
- BLXFLAG_HIGHLIGHT_DIFFS, /* Hides matching bases and highlights mis-matching ones */
- BLXFLAG_SHOW_SNP_TRACK, /* Shows the SNP track */
- BLXFLAG_SHOW_UNALIGNED_SEQ, /* Shows additional bits of the match sequence that are not part of the aligned section */
- BLXFLAG_LIMIT_UNALIGNED_BASES, /* If the above option is on, limits how many bases from the unaligned sequence are shown */
- BLXFLAG_SHOW_SPLICE_SITES, /* Highlights splice sites in the reference sequence for the currently-selected MSPs */
- BLXFLAG_EMBL_DATA_LOADED, /* Gets set to true if the full EMBL data is parsed and populated in the MSPs */
- BLXFLAG_SHOW_CDS, /* True if CDS/UTR regions should be shown; false if plain exons should be shown */
-
- BLXFLAG_NUM_FLAGS /* Number of flags, for looping through flags or creating an array */
- } BlxFlag;
-
-
/* This enum contains IDs for all the persistent dialogs in the application, and should be used
* to access a stored dialog in the dialogList array in the BlxViewContext. Note that the dialogList
* array will contain null entries until the dialogs are created for the first time */
@@ -120,7 +101,7 @@ typedef struct _BlxViewContext
GArray *defaultColors; /* Default colors used by Blixem */
gboolean usePrintColors; /* Whether to use print colors (i.e. black and white) */
- GArray *blxFlags; /* Array of all the flags the user can toggle. Indexed by the BlxFlags enum. */
+ gboolean flags[BLXFLAG_NUM_FLAGS]; /* Array of all the flags the user can toggle. Indexed by the BlxFlags enum. */
GtkWidget *dialogList[BLXDIALOG_NUM_DIALOGS]; /* Array of all the persistent dialogs in the application */
} BlxViewContext;
@@ -153,9 +134,6 @@ const char* blxWindowGetPaddingSeq(GtkWidget *blxWindow);
int blxWindowGetOffset(GtkWidget *blxWindow);
BlxStrand blxWindowGetActiveStrand(GtkWidget *blxWindow);
-void blxContextSetFlag(BlxViewContext *bc, const BlxFlag flag, const gboolean newValue);
-gboolean blxContextGetFlag(const BlxViewContext *bc, const BlxFlag flag);
-
GList* blxWindowGetSelectedSeqs(GtkWidget *blxWindow);
void blxWindowSelectSeq(GtkWidget *blxWindow, BlxSequence *seq);
void blxWindowSetSelectedSeqList(GtkWidget *blxWindow, GList *seqList);
diff --git a/detailview.c b/detailview.c
index 5b2a522c..aac152b1 100755
--- a/detailview.c
+++ b/detailview.c
@@ -620,7 +620,7 @@ void refreshTextHeader(GtkWidget *header, gpointer data)
/* SNP track */
BlxViewContext *bc = detailViewGetContext(detailView);
- if (!blxContextGetFlag(bc, BLXFLAG_SHOW_SNP_TRACK))
+ if (!bc->flags[BLXFLAG_SHOW_SNP_TRACK])
{
/* SNP track is hidden, so set the height to 0 */
gtk_layout_set_size(GTK_LAYOUT(header), header->allocation.width, 0);
@@ -806,13 +806,13 @@ static char* getFeedbackText(GtkWidget *detailView, const BlxSequence *seq, cons
if (qIdx != UNSET_INT)
{
GList *mspListItem = seq->mspList;
+ const int numUnalignedBases = detailViewGetNumUnalignedBases(detailView);
for ( ; mspListItem; mspListItem = mspListItem->next)
{
MSP *msp = (MSP*)(mspListItem->data);
- sIdx = gapCoord(msp, qIdx, bc->numFrames, mspGetRefFrame(msp, bc->seqType), bc->displayRev,
- FALSE, FALSE, UNSET_INT);/* don't show unaligned base coords */
+ sIdx = gapCoord(msp, qIdx, bc->numFrames, mspGetRefFrame(msp, bc->seqType), bc->displayRev, TRUE, numUnalignedBases, bc->flags, bc->mspList);
if (sIdx != UNSET_INT)
{
@@ -959,14 +959,6 @@ void detailViewUpdateShowSnpTrack(GtkWidget *detailView, const gboolean showSnpT
}
-/* Set the value of the 'Show Unaligned Sequence' flag */
-void detailViewUpdateShowUnalignedSeq(GtkWidget *detailView, const gboolean showUnalignedSeq)
-{
- /* Just re-draw */
- gtk_widget_queue_draw(detailView);
-}
-
-
/* Set the value of the 'Limit Unaligned Bases' flag */
void detailViewUpdateLimitUnalignedBases(GtkWidget *detailView, const gboolean limitUnalignedBases)
{
@@ -1456,7 +1448,7 @@ GHashTable* getIntronBasesToHighlight(GtkWidget *detailView,
/* We only highlight nucleotides, so there is nothing to do if we're showing a peptide sequence,
* or if the show-splice-sites option is disabled. */
- if (seqType == BLXSEQ_PEPTIDE || !blxContextGetFlag(bc, BLXFLAG_SHOW_SPLICE_SITES))
+ if (seqType == BLXSEQ_PEPTIDE || !bc->flags[BLXFLAG_SHOW_SPLICE_SITES])
{
return result;
}
@@ -1862,7 +1854,7 @@ static void drawSnpTrack(GtkWidget *snpTrack, GtkWidget *detailView)
GtkWidget *blxWindow = detailViewGetBlxWindow(detailView);
BlxViewContext *bc = blxWindowGetContext(blxWindow);
- if (!blxContextGetFlag(bc, BLXFLAG_SHOW_SNP_TRACK))
+ if (!bc->flags[BLXFLAG_SHOW_SNP_TRACK])
{
return;
}
@@ -2936,9 +2928,9 @@ static gboolean onButtonPressSeqColHeader(GtkWidget *header, GdkEventButton *eve
{
/* Double-click: toggle SNP track visibility */
BlxViewContext *bc = detailViewGetContext(detailView);
- gboolean showSnpTrack = !blxContextGetFlag(bc, BLXFLAG_SHOW_SNP_TRACK);
+ gboolean showSnpTrack = !bc->flags[BLXFLAG_SHOW_SNP_TRACK];
- blxContextSetFlag(bc, BLXFLAG_SHOW_SNP_TRACK, showSnpTrack);
+ bc->flags[BLXFLAG_SHOW_SNP_TRACK] = showSnpTrack;
detailViewUpdateShowSnpTrack(detailView, showSnpTrack);
}
diff --git a/detailview.h b/detailview.h
index a99fab43..acf59c23 100644
--- a/detailview.h
+++ b/detailview.h
@@ -163,7 +163,6 @@ void detailViewRedrawAll(GtkWidget *detailView);
void detailViewUpdateSquashMatches(GtkWidget *detailView, const gboolean squash);
void detailViewUpdateSortInverted(GtkWidget *detailView, const gboolean invert);
void detailViewUpdateShowSnpTrack(GtkWidget *detailView, const gboolean showSnpTrack);
-void detailViewUpdateShowUnalignedSeq(GtkWidget *detailView, const gboolean showUnalignedSeq);
void detailViewUpdateLimitUnalignedBases(GtkWidget *detailView, const gboolean limitUnalignedBases);
void detailViewSetNumUnalignedBases(GtkWidget *detailView, const int numBases);
diff --git a/detailviewtree.c b/detailviewtree.c
index dea62783..4e9d2ab7 100755
--- a/detailviewtree.c
+++ b/detailviewtree.c
@@ -638,7 +638,7 @@ static GtkSortType treeGetColumnSortOrder(GtkWidget *tree, const BlxColumnId col
break;
};
- if (blxContextGetFlag(bc, BLXFLAG_INVERT_SORT))
+ if (bc->flags[BLXFLAG_INVERT_SORT])
{
result = (result == GTK_SORT_ASCENDING) ? GTK_SORT_DESCENDING : GTK_SORT_ASCENDING;
}
@@ -687,11 +687,10 @@ static gboolean isMspVisible(const MSP const *msp,
{
/* Check the MSP in the current display range. Get the full MSP display range including
* any portions outside the actual alignment. */
- const gboolean showUnalignedSeq = blxContextGetFlag(bc, BLXFLAG_SHOW_UNALIGNED_SEQ);
- const gboolean limitUnalignedBases = blxContextGetFlag(bc, BLXFLAG_LIMIT_UNALIGNED_BASES);
+ const gboolean seqSelected = blxWindowIsSeqSelected(blxWindow, msp->sSequence);
IntRange mspDisplayRange;
- mspGetFullQRange(msp, showUnalignedSeq, limitUnalignedBases, numUnalignedBases, bc->numFrames, &mspDisplayRange);
+ mspGetFullQRange(msp, seqSelected, bc->flags, numUnalignedBases, bc->mspList, bc->numFrames, &mspDisplayRange);
/* Convert q coords to display coords */
const int idx1 = convertDnaIdxToDisplayIdx(mspDisplayRange.min, bc->seqType, frame, bc->numFrames, bc->displayRev, &bc->refSeqRange, NULL);
@@ -1212,9 +1211,9 @@ static gboolean onButtonPressTreeHeader(GtkWidget *header, GdkEventButton *event
else if (event->type == GDK_2BUTTON_PRESS)
{
BlxViewContext *bc = treeGetContext(tree);
- gboolean showSnpTrack = !blxContextGetFlag(bc, BLXFLAG_SHOW_SNP_TRACK);
+ gboolean showSnpTrack = !bc->flags[BLXFLAG_SHOW_SNP_TRACK];
- blxContextSetFlag(bc, BLXFLAG_SHOW_SNP_TRACK, showSnpTrack);
+ bc->flags[BLXFLAG_SHOW_SNP_TRACK] = showSnpTrack;
detailViewUpdateShowSnpTrack(detailView, showSnpTrack);
}
diff --git a/sequencecellrenderer.c b/sequencecellrenderer.c
index 99701860..7ec3d355 100755
--- a/sequencecellrenderer.c
+++ b/sequencecellrenderer.c
@@ -64,6 +64,7 @@ typedef struct _RenderData
GdkLineStyle exonBoundaryStyleStart;
GdkLineStyle exonBoundaryStyleEnd;
gboolean showUnalignedSeq;
+ gboolean showUnalignedSelected;
gboolean limitUnalignedBases;
int numUnalignedBases;
} RenderData;
@@ -576,8 +577,7 @@ static void drawBase(MSP *msp,
const int displayIdx = segmentRange->min + segmentIdx;
*qIdx = convertDisplayIdxToDnaIdx(displayIdx, data->bc->seqType, data->qFrame, 1, data->bc->numFrames, data->bc->displayRev, &data->bc->refSeqRange);
- *sIdx = gapCoord(msp, *qIdx, data->bc->numFrames, data->qStrand, data->bc->displayRev,
- data->showUnalignedSeq, data->limitUnalignedBases, data->numUnalignedBases);
+ *sIdx = gapCoord(msp, *qIdx, data->bc->numFrames, data->qStrand, data->bc->displayRev, data->seqSelected, data->numUnalignedBases, data->bc->flags, data->bc->mspList);
/* Highlight the base if its base index is selected, or if its sequence is selected.
* (If it is selected in both, show it in the normal color) */
@@ -814,7 +814,7 @@ static IntRange getVisibleMspRange(MSP *msp, RenderData *data)
{
/* Find the full display range of the MSP including any portions of unaligned sequence etc. */
IntRange result;
- mspGetFullQRange(msp, data->showUnalignedSeq, data->limitUnalignedBases, data->numUnalignedBases, data->bc->numFrames, &result);
+ mspGetFullQRange(msp, data->seqSelected, data->bc->flags, data->numUnalignedBases, data->bc->mspList, data->bc->numFrames, &result);
/* Convert to display coords */
const int idx1 = convertDnaIdxToDisplayIdx(result.min, data->bc->seqType, data->qFrame, data->bc->numFrames, data->bc->displayRev, &data->bc->refSeqRange, NULL);
@@ -978,7 +978,7 @@ static void drawMsps(SequenceCellRenderer *renderer,
DetailViewProperties *detailViewProperties = detailViewGetProperties(treeProperties->detailView);
BlxViewContext *bc = blxWindowGetContext(detailViewProperties->blxWindow);
- const gboolean highlightDiffs = blxContextGetFlag(bc, BLXFLAG_HIGHLIGHT_DIFFS); /* swap match/mismatch colors if this is true */
+ const gboolean highlightDiffs = bc->flags[BLXFLAG_HIGHLIGHT_DIFFS]; /* swap match/mismatch colors if this is true */
const MSP *firstMsp = (const MSP*)(renderer->mspGList->data);
const BlxSequence *seq = firstMsp ? firstMsp->sSequence : NULL;
@@ -1029,8 +1029,9 @@ static void drawMsps(SequenceCellRenderer *renderer,
detailViewProperties->exonBoundaryLineWidth,
detailViewProperties->exonBoundaryLineStyleStart,
detailViewProperties->exonBoundaryLineStyleEnd,
- blxContextGetFlag(bc, BLXFLAG_SHOW_UNALIGNED_SEQ),
- blxContextGetFlag(bc, BLXFLAG_LIMIT_UNALIGNED_BASES),
+ bc->flags[BLXFLAG_SHOW_UNALIGNED],
+ bc->flags[BLXFLAG_SHOW_UNALIGNED_SELECTED],
+ bc->flags[BLXFLAG_LIMIT_UNALIGNED_BASES],
detailViewProperties->numUnalignedBases
};
diff --git a/utilities.c b/utilities.c
index 81b36bae..bd9342d6 100644
--- a/utilities.c
+++ b/utilities.c
@@ -489,6 +489,16 @@ gboolean typeIsExon(const BlxMspType mspType)
return (mspType == BLXMSP_CDS || mspType == BLXMSP_UTR || mspType == BLXMSP_EXON);
}
+gboolean typeIsIntron(const BlxMspType mspType)
+{
+ return (mspType == BLXMSP_INTRON);
+}
+
+gboolean typeIsMatch(const BlxMspType mspType)
+{
+ return (mspType == BLXMSP_MATCH);
+}
+
gboolean mspIsExon(const MSP const *msp)
{
@@ -872,9 +882,10 @@ int gapCoord(const MSP *msp,
const int numFrames,
const BlxStrand strand,
const gboolean displayRev,
- const gboolean showUnalignedSeq,
- const gboolean limitUnalignedBases,
- const int numUnalignedBases)
+ const gboolean seqSelected,
+ const int numUnalignedBases,
+ gboolean *flags,
+ const MSP const *mspList)
{
int result = UNSET_INT;
@@ -940,7 +951,7 @@ int gapCoord(const MSP *msp,
/* Get the full display range of the match sequence. If the result is still out of range
* then there's nothing to show for this qIdx. */
IntRange fullSRange;
- mspGetFullSRange(msp, showUnalignedSeq, limitUnalignedBases, numUnalignedBases, &fullSRange);
+ mspGetFullSRange(msp, seqSelected, flags, numUnalignedBases, mspList, &fullSRange);
if (!valueWithinRange(result, &fullSRange))
{
@@ -1049,27 +1060,58 @@ const char *mspGetSName(const MSP const *msp)
}
+/* Returns true if there is a polyA site at the 3' end of this MSP's alignment range. */
+static gboolean mspHasPolyATail(const MSP const *msp, const MSP const *mspList)
+{
+ /* For now, loop through all poly A sites and see if the site coord matches the 3' end coord of
+ * the alignment. If speed proves to be an issue we could do some pre-processing to link MSPs
+ * to relevant polyA signals/sites so that we don't have to loop each time we want to check. */
+ const MSP *curMsp = mspList;
+ gboolean found = FALSE;
+
+ for ( ; !found && curMsp; curMsp = curMsp->next)
+ {
+ if (mspIsPolyASite(curMsp))
+ {
+ const int qEnd = mspGetQEnd(msp);
+
+ if (mspGetRefStrand(msp) == BLXSTRAND_FORWARD)
+ {
+ found = (qEnd == curMsp->qRange.min);
+ }
+ else
+ {
+ found = (qEnd == curMsp->qRange.min + 1);
+ }
+ }
+ }
+
+ return found;
+}
+
+
/* Get the full range of the given MSP that we want to display, in s coords. This will generally
* be the coords of the alignment but could extend outside this range we are displaying unaligned
* portions of the match sequence or polyA tails etc. */
void mspGetFullSRange(const MSP const *msp,
- const gboolean showUnalignedSeq,
- const gboolean limitUnalignedBases,
+ const gboolean seqSelected,
+ const gboolean *flags,
const int numUnalignedBases,
+ const MSP const *mspList,
IntRange *result)
{
/* Normally we just display the part of the sequence in the alignment */
result->min = msp->sRange.min;
result->max = msp->sRange.max;
- if (showUnalignedSeq && mspGetMatchSeq(msp)) /* must have the sequence data to be able to do this... */
+ if (flags[BLXFLAG_SHOW_UNALIGNED] && mspGetMatchSeq(msp) && (!flags[BLXFLAG_SHOW_UNALIGNED_SELECTED] || seqSelected))
{
/* We're displaying additional unaligned sequence outside the alignment range. Get
* the full range of the match sequence */
result->min = 1;
result->max = mspGetMatchSeqLen(msp);
- if (limitUnalignedBases)
+ if (flags[BLXFLAG_LIMIT_UNALIGNED_BASES])
{
/* Only include up to 'numUnalignedBases' each side of the MSP range (still limited
* to the range we found above, though). */
@@ -1077,6 +1119,23 @@ void mspGetFullSRange(const MSP const *msp,
result->max = min(result->max, msp->sRange.max + numUnalignedBases);
}
}
+
+ if (flags[BLXFLAG_SHOW_POLYA] && mspHasPolyATail(msp, mspList) && (!flags[BLXFLAG_SHOW_POLYA_SELECTED] || seqSelected))
+ {
+ /* We're displaying polyA tails, so override the 3' end coord with the full extent of
+ * the s sequence if there is a polyA site here. The 3' end is the min q coord if the
+ * match is on forward ref seq strand or the max coord if on the reverse. */
+ const gboolean sameDirection = (mspGetRefStrand(msp) == mspGetMatchStrand(msp));
+
+ if (sameDirection)
+ {
+ result->max = mspGetMatchSeqLen(msp);
+ }
+ else
+ {
+ result->min = 1;
+ }
+ }
}
@@ -1084,9 +1143,10 @@ void mspGetFullSRange(const MSP const *msp,
* be the coords of the alignment but could extend outside this range we are displaying unaligned
* portions of the match sequence or polyA tails etc. */
void mspGetFullQRange(const MSP const *msp,
- const gboolean showUnalignedSeq,
- const gboolean limitUnalignedBases,
+ const gboolean seqSelected,
+ const gboolean *flags,
const int numUnalignedBases,
+ const MSP const *mspList,
const int numFrames,
IntRange *result)
{
@@ -1094,11 +1154,11 @@ void mspGetFullQRange(const MSP const *msp,
result->min = msp->qRange.min;
result->max = msp->qRange.max;
- if (showUnalignedSeq)
+ if (flags[BLXFLAG_SHOW_UNALIGNED] || flags[BLXFLAG_SHOW_POLYA])
{
-
+ /* Get the full display range of the MSP including any unaligned portions of the match sequence. */
IntRange fullSRange;
- mspGetFullSRange(msp, showUnalignedSeq, limitUnalignedBases, numUnalignedBases, &fullSRange);
+ mspGetFullSRange(msp, seqSelected, flags, numUnalignedBases, mspList, &fullSRange);
/* Find the offset of the start and end of the full range compared to the alignment range and
* offset the ref seq range by the same amount. We need to multiply by the number of reading
diff --git a/utilities.h b/utilities.h
index 88f0c96b..e9d0bbde 100644
--- a/utilities.h
+++ b/utilities.h
@@ -87,6 +87,30 @@
#define BLX_BURLYWOOD "#deb887"
#define BLX_TAN "#d2b48c"
+
+/* This enum contains a list of all the boolean options that the user can toggle on/off */
+typedef enum
+ {
+ BLXFLAG_MIN, /* Start index for looping through flags */
+
+ BLXFLAG_SQUASH_MATCHES, /* Puts all MSPs from the same sequence on the same row in the detail view */
+ BLXFLAG_INVERT_SORT, /* Inverts the default sort order */
+ BLXFLAG_HIGHLIGHT_DIFFS, /* Hides matching bases and highlights mis-matching ones */
+ BLXFLAG_SHOW_SNP_TRACK, /* Shows the SNP track */
+ BLXFLAG_SHOW_UNALIGNED, /* Shows additional bits of the match sequence that are not part of the aligned section */
+ BLXFLAG_SHOW_UNALIGNED_SELECTED,/* Only show unaligned bits of sequence for the currently-selected sequence(s) */
+ BLXFLAG_LIMIT_UNALIGNED_BASES, /* If the show-unaligned-sequence option is on, limits how many bases from the unaligned sequence are shown */
+ BLXFLAG_SHOW_POLYA, /* Show polyA tails */
+ BLXFLAG_SHOW_POLYA_SELECTED, /* Only show polyA tails for the currently-selected sequence(s) */
+ BLXFLAG_SHOW_SPLICE_SITES, /* Highlights splice sites in the reference sequence for the currently-selected MSPs */
+ BLXFLAG_EMBL_DATA_LOADED, /* Gets set to true if the full EMBL data is parsed and populated in the MSPs */
+ BLXFLAG_SHOW_CDS, /* True if CDS/UTR regions should be shown; false if plain exons should be shown */
+
+ BLXFLAG_NUM_FLAGS /* Number of flags, for looping through flags or creating an array */
+ } BlxFlag;
+
+
+
/* Function pointer for callback functions used by widgets on dialog boxes. */
typedef gboolean (*BlxResponseCallback)(GtkWidget *widget, const gint responseId, gpointer data);
@@ -138,6 +162,8 @@ void adjustColorBrightness(GdkColor *origColor, const double factor, GdkC
gboolean mspLayerIsVisible(const MSP const *msp);
gboolean typeIsExon(const BlxMspType mspType);
+gboolean typeIsIntron(const BlxMspType mspType);
+gboolean typeIsMatch(const BlxMspType mspType);
gboolean mspIsExon(const MSP const *msp);
gboolean mspIsIntron(const MSP const *msp);
gboolean mspIsSnp(const MSP const *msp);
@@ -198,8 +224,21 @@ char* mspGetGeneName(const MSP const *msp);
char* mspGetTissueType(const MSP const *msp);
char* mspGetStrain(const MSP const *msp);
char* mspGetCoordsAsString(const MSP const *msp);
-void mspGetFullSRange(const MSP const *msp, const gboolean showUnalignedSeq, const gboolean limitUnalignedBases, const int numUnalignedBases, IntRange *sSeqRange);
-void mspGetFullQRange(const MSP const *msp, const gboolean showUnalignedSeq, const gboolean limitUnalignedBases, const int numUnalignedBases, const int numFrames, IntRange *sSeqRange);
+
+void mspGetFullSRange(const MSP const *msp,
+ const gboolean seqSelected,
+ const gboolean *flags,
+ const int numUnalignedBases,
+ const MSP const *mspList,
+ IntRange *sSeqRange);
+
+void mspGetFullQRange(const MSP const *msp,
+ const gboolean seqSelected,
+ const gboolean *flags,
+ const int numUnalignedBases,
+ const MSP const *mspList,
+ const int numFrames,
+ IntRange *sSeqRange);
char getStrandAsChar(const BlxStrand strand);
@@ -234,9 +273,10 @@ int gapCoord(const MSP *msp,
const int numFrames,
const BlxStrand strand,
const gboolean displayRev,
- const gboolean showUnalignedSeq,
- const gboolean limitUnalignedBases,
- const gboolean numUnalignedBases);
+ const gboolean seqSelected,
+ const int numUnalignedBases,
+ gboolean *flags,
+ const MSP const *mspList);
int wildcardSearch(const char *textToSearch, const char *searchStr);
--
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