Skip to content
Snippets Groups Projects
Commit e1b1cb73 authored by gb10's avatar gb10
Browse files

Added dotter vs self and hsps-only options

parent 9f434f2c
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 206 additions and 89 deletions
blxdotter.c
+ 206
− 89
View file @ e1b1cb73
......@@ -9,9 +9,13 @@
#include <SeqTools/blxdotter.h>
#include <SeqTools/blxwindow.h>
#include <SeqTools/bigpicture.h>
#include <SeqTools/detailview.h>
#include <SeqTools/utilities.h>
#include <SeqTools/dotter.h>
#define DEFAULT_DOTTER_RANGE_SELF 2000
typedef struct _DotterDialogData
{
GtkWidget *blxWindow;
......@@ -22,6 +26,9 @@ typedef struct _DotterDialogData
GtkWidget *startEntry;
GtkWidget *endEntry;
GtkWidget *zoomEntry;
gboolean callOnSelf;
gboolean hspsOnly;
} DotterDialogData;
......@@ -40,10 +47,13 @@ typedef enum {
/* Local function declarations */
static gboolean getDotterRange(GtkWidget *blxWindow, const char *dotterSSeq, const gboolean callOnSelf, int *dotterStart, int *dotterEnd, int *dotterZoom, GError **error);
static gboolean smartDotterRange(GtkWidget *blxWindow, const char *dotterSSeq, int *dotter_start_out, int *dotter_end_out, GError **error);
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);
/*******************************************************************
......@@ -165,6 +175,47 @@ static void onBpRangeButtonClicked(GtkWidget *button, gpointer data)
}
/* Called when the "call on self" button is toggled on the dotter dialog */
static void onSelfButtonToggled(GtkWidget *button, gpointer data)
{
DotterDialogData *dialogData = (DotterDialogData*)data;
BlxViewContext *bc = blxWindowGetContext(dialogData->blxWindow);
dialogData->callOnSelf = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(button));
/* Recalculate auto start/end */
int autoStart = UNSET_INT, autoEnd = UNSET_INT;
getDotterRange(dialogData->blxWindow, getDotterSSeq(dialogData->blxWindow, NULL), dialogData->callOnSelf, &autoStart, &autoEnd, NULL, NULL);
if (autoStart == UNSET_INT)
autoStart = bc->displayRev ? bc->refSeqRange.max : bc->refSeqRange.min;
if (autoEnd == UNSET_INT)
autoEnd = bc->displayRev ? bc->refSeqRange.min : bc->refSeqRange.max;
char *startString = convertIntToString(autoStart);
char *endString = convertIntToString(autoEnd);
char *zoomString = convertIntToString(bc->dotterZoom);
/* Display the new values */
gtk_entry_set_text(GTK_ENTRY(dialogData->startEntry), startString);
gtk_entry_set_text(GTK_ENTRY(dialogData->endEntry), endString);
gtk_entry_set_text(GTK_ENTRY(dialogData->zoomEntry), zoomString);
g_free(startString);
g_free(endString);
g_free(zoomString);
}
/* Called when the "call on self" button is toggled on the dotter dialog */
static void onHspsButtonToggled(GtkWidget *button, gpointer data)
{
DotterDialogData *dialogData = (DotterDialogData*)data;
dialogData->hspsOnly = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(button));
}
/* Called when the user has hit a response button on the dotter settings dialog */
static void onResponseDotterDialog(GtkDialog *dialog, gint responseId, gpointer data)
{
......@@ -177,7 +228,7 @@ static void onResponseDotterDialog(GtkDialog *dialog, gint responseId, gpointer
{
case GTK_RESPONSE_ACCEPT:
widgetCallAllCallbacks(GTK_WIDGET(dialog), NULL);
destroy = callDotter(dialogData->blxWindow, FALSE, &error); /* only destroy dialog if dotter launched successfully */
destroy = dialogData->callOnSelf ? callDotterSelf(dialogData->blxWindow, &error) : callDotter(dialogData->blxWindow, dialogData->hspsOnly, &error);
break;
case GTK_RESPONSE_APPLY:
......@@ -215,7 +266,7 @@ 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;
smartDotterRange(dialogData->blxWindow, getDotterSSeq(dialogData->blxWindow, NULL), &autoStart, &autoEnd, NULL);
getDotterRange(dialogData->blxWindow, getDotterSSeq(dialogData->blxWindow, NULL), dialogData->callOnSelf, &autoStart, &autoEnd, NULL, NULL);
if (autoStart == UNSET_INT)
autoStart = bc->displayRev ? bc->refSeqRange.max : bc->refSeqRange.min;
......@@ -308,24 +359,24 @@ void showDotterDialog(GtkWidget *blxWindow)
gtk_container_add(contentArea, GTK_WIDGET(hbox));
/* Radio buttons for auto/manual params */
GtkBox *vbox3 = GTK_BOX(gtk_vbox_new(FALSE, 0));
gtk_box_pack_start(hbox, GTK_WIDGET(vbox3), FALSE, FALSE, spacing);
GtkBox *vbox1 = GTK_BOX(gtk_vbox_new(FALSE, 0));
gtk_box_pack_start(hbox, GTK_WIDGET(vbox1), FALSE, FALSE, spacing);
GtkWidget *autoButton = gtk_radio_button_new_with_mnemonic(NULL, "_Auto");
gtk_box_pack_start(vbox3, autoButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox1, autoButton, FALSE, FALSE, spacing);
widgetSetCallbackData(autoButton, onSaveDotterMode, blxWindow);
GtkWidget *manualButton = gtk_radio_button_new_with_mnemonic_from_widget(GTK_RADIO_BUTTON(autoButton), "_Manual");
gtk_box_pack_start(vbox3, manualButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox1, manualButton, FALSE, FALSE, spacing);
/* Buttons that the user can click to populate the parameter boxes with certain values */
GtkWidget *lastSavedButton = gtk_button_new_with_mnemonic("_Last saved ->");
GtkWidget *fullRangeButton = gtk_button_new_with_mnemonic("_Full range ->");
GtkWidget *bpRangeButton = gtk_button_new_with_mnemonic("_Big picture range ->");
gtk_box_pack_start(vbox3, lastSavedButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox3, fullRangeButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox3, bpRangeButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox1, lastSavedButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox1, fullRangeButton, FALSE, FALSE, spacing);
gtk_box_pack_start(vbox1, bpRangeButton, FALSE, FALSE, spacing);
/* Disable last-saved button if no saved values exist */
if (bc->dotterStart == UNSET_INT)
......@@ -342,6 +393,15 @@ void showDotterDialog(GtkWidget *blxWindow)
GtkWidget *endEntry = createTextEntry(table, 1, 2, xpad, ypad, "<i>End:</i>", onSaveDotterEnd, blxWindow, bc->dotterEnd);
GtkWidget *zoomEntry = createTextEntry(table, 1, 3, xpad, ypad, "<i>Zoom:</i>", onSaveDotterZoom, blxWindow, bc->dotterZoom);
/* Create check buttons for the various options */
GtkBox *vbox3 = GTK_BOX(gtk_vbox_new(FALSE, 0));
gtk_box_pack_start(hbox, GTK_WIDGET(vbox3), FALSE, FALSE, spacing);
GtkWidget *selfButton = gtk_check_button_new_with_mnemonic("Call on _self");
gtk_box_pack_start(vbox3, selfButton, FALSE, FALSE, 0);
GtkWidget *hspsButton = gtk_check_button_new_with_mnemonic("_HSPs only");
gtk_box_pack_start(vbox3, hspsButton, FALSE, FALSE, 0);
/* Create the data struct we need to pass to the toggled callback, and connect signals */
DotterDialogData *dialogData = g_malloc(sizeof(DotterDialogData));
dialogData->blxWindow = blxWindow;
......@@ -350,6 +410,8 @@ void showDotterDialog(GtkWidget *blxWindow)
dialogData->startEntry = startEntry;
dialogData->endEntry = endEntry;
dialogData->zoomEntry = zoomEntry;
dialogData->callOnSelf = FALSE;
dialogData->hspsOnly = FALSE;
/* 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
......@@ -364,6 +426,9 @@ void showDotterDialog(GtkWidget *blxWindow)
g_signal_connect(G_OBJECT(fullRangeButton), "clicked", G_CALLBACK(onFullRangeButtonClicked), dialogData);
g_signal_connect(G_OBJECT(bpRangeButton), "clicked", G_CALLBACK(onBpRangeButtonClicked), dialogData);
g_signal_connect(G_OBJECT(selfButton), "toggled", G_CALLBACK(onSelfButtonToggled), dialogData);
g_signal_connect(G_OBJECT(hspsButton), "toggled", G_CALLBACK(onHspsButtonToggled), dialogData);
g_signal_connect(dialog, "response", G_CALLBACK(onResponseDotterDialog), dialogData);
/* Set the initial state of the toggle buttons and entry widgets */
......@@ -410,7 +475,13 @@ char getDotterMode(const BlxBlastMode blastMode)
/* Get the start/end coords. If the autoDotter flag is set, calculate coords
* automatically - otherwise use the stored manual coords */
static gboolean getDotterRange(GtkWidget *blxWindow, const char *dotterSSeq, int *dotterStart, int *dotterEnd, int *dotterZoom, GError **error)
static gboolean getDotterRange(GtkWidget *blxWindow,
const char *dotterSSeq,
const gboolean callOnSelf,
int *dotterStart,
int *dotterEnd,
int *dotterZoom,
GError **error)
{
g_return_val_if_fail(!error || *error == NULL, FALSE); /* if error is passed, its contents must be NULL */
......@@ -420,23 +491,28 @@ static gboolean getDotterRange(GtkWidget *blxWindow, const char *dotterSSeq, int
if (!bc->autoDotter)
{
/* Use manual coords */
*dotterStart = bc->dotterStart;
*dotterEnd = bc->dotterEnd;
*dotterZoom = bc->dotterZoom;
if (dotterStart) *dotterStart = bc->dotterStart;
if (dotterEnd) *dotterEnd = bc->dotterEnd;
if (dotterZoom) *dotterZoom = bc->dotterZoom;
if (*dotterStart == UNSET_INT || *dotterEnd == UNSET_INT)
if ((dotterStart && *dotterStart == UNSET_INT) || (dotterEnd && *dotterEnd == UNSET_INT))
{
g_debug("Manual dotter parameters were requested but one or more coord is not set (start=%d, end=%d). Calculating automatic parameters instead.\n",
*dotterStart, *dotterEnd);
}
}
if (*dotterStart == UNSET_INT || *dotterEnd == UNSET_INT)
if ((dotterStart && *dotterStart == UNSET_INT) || (dotterEnd && *dotterEnd == UNSET_INT))
{
GError *tmpError = NULL;
if (!smartDotterRange(blxWindow, dotterSSeq, dotterStart, dotterEnd, &tmpError))
if (callOnSelf)
success = smartDotterRangeSelf(blxWindow, dotterStart, dotterEnd, &tmpError);
else
success = smartDotterRange(blxWindow, dotterSSeq, dotterStart, dotterEnd, &tmpError);
if (!success)
{
success = FALSE;
g_propagate_prefixed_error(error, tmpError, "Failed to calculate dotter coordinates. ");
}
}
......@@ -550,24 +626,29 @@ static char* getDotterSSeq(GtkWidget *blxWindow, GError **error)
}
//static int smartDotterRangeSelf(void)
//{
// int len, mid;
//
// len = 2000;
// mid = dispstart + plusmin*displen/2;
//
// dotterStart = mid - plusmin*len/2;
// dotterEnd = mid + plusmin*len/2;
//
// /* Keep it within bounds */
// if (dotterStart < 1) dotterStart = 1;
// if (dotterStart > qlen) dotterStart = qlen;
// if (dotterEnd > qlen) dotterEnd = qlen;
// if (dotterEnd < 1) dotterEnd = 1;
/* Attempts to set the range of dotter in a sensible way, when calling dotter on the reference
* sequence versus itself. */
static gboolean smartDotterRangeSelf(GtkWidget *blxWindow,
int *dotter_start_out,
int *dotter_end_out,
GError **error)
{
/* We'll just use a large-ish range centred on the current display range */
GtkWidget *detailView = blxWindowGetDetailView(blxWindow);
const IntRange const *displayRange = detailViewGetDisplayRange(detailView);
const int mid = getRangeCentre(displayRange);
const int offset = DEFAULT_DOTTER_RANGE_SELF / 2;
*dotter_start_out = mid - offset;
*dotter_end_out = *dotter_start_out + DEFAULT_DOTTER_RANGE_SELF;
// return 1;
//}
const BlxViewContext *bc = blxWindowGetContext(blxWindow);
boundsLimitValue(dotter_start_out, &bc->refSeqRange);
boundsLimitValue(dotter_end_out, &bc->refSeqRange);
return TRUE;
}
/* Attempts to set the range of dotter in some sort of sensible way. The problem is that
......@@ -879,15 +960,12 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
/* Get the coords */
int dotterStart = UNSET_INT, dotterEnd = UNSET_INT, dotterZoom = 0;
if (!getDotterRange(blxWindow, dotterSSeq, &dotterStart, &dotterEnd, &dotterZoom, &tmpError))
if (!getDotterRange(blxWindow, dotterSSeq, FALSE, &dotterStart, &dotterEnd, &dotterZoom, &tmpError))
{
g_propagate_error(error, tmpError);
return FALSE;
}
/* Get the reference sequence name */
const char *dotterQName = bc->refSeqName;
/* Get the section of reference sequence that we're interested in */
const BlxStrand strand = bc->seqType == BLXSEQ_DNA ? mspGetRefStrand(firstMsp) : blxWindowGetActiveStrand(blxWindow);
const int frame = mspGetRefFrame(firstMsp, bc->seqType);
......@@ -911,13 +989,11 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
return FALSE;
}
/* Again, dotter will free this with messfree, so we need to pass a string allocated with messalloc */
char *querySeqSegment = messalloc(strlen(querySeqSegmentTemp) + 1);
strcpy(querySeqSegment, querySeqSegmentTemp);
g_free(querySeqSegmentTemp);
/* Get the match sequence name (chopping off the letters before the colon, if there is one). */
char *dotterSName = strchr(firstMsp->sname, ':');
if (dotterSName)
......@@ -944,59 +1020,100 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
printf("Calling dotter with query sequence region: %d - %d\n", dotterStart, dotterEnd);
printf(" query sequence: name - %s, offset - %d\n"
"subject sequence: name - %s, offset - %d\n", dotterQName, offset, dotterSName, 0);
"subject sequence: name - %s, offset - %d\n", bc->refSeqName, offset, dotterSName, 0);
dotter(type, opts, dotterQName, querySeqSegment, offset, dotterSName, dotterSSeq, 0,
dotter(type, opts, bc->refSeqName, querySeqSegment, offset, dotterSName, dotterSSeq, 0,
0, 0, NULL, NULL, NULL, 0.0, dotterZoom, bc->mspList, 0, 0, 0);
return TRUE;
}
//static void callDotterSelf(const MSP const *msplist)
//{//
// static char opts[] = " ";
// char type, *queryseq;
// int offset;
//
// type = ' ';
// if (blastp || tblastn || tblastx)
// type = 'P';
// else if (blastx || blastn)
// type = 'N';
//
// if (smartDotter)
// if (!smartDotterRangeSelf())
// return;
//
// if (!*dotterqname)
// {
// if (!*qname_G)
// strcpy(dotterqname, "Blixem-seq");
// else
// strncpy(dotterqname, qname_G, LONG_NAMESIZE);
// dotterqname[LONG_NAMESIZE] = 0;
// }
//
// /* Get query sequence */
// /* Can't do reversed strand since Dotter can't reverse vertical scale */
// /* Avoid translating queryseq by pretending to be blastn - very sneaky and dangerous */
// if (blastx || tblastx)
// blastn = 1;
//
// if (!(queryseq = getqseq(min(dotterStart, dotterEnd), max(dotterStart, dotterEnd), q)))
// return;
//
// if (blastx || tblastx)
// blastn = 0;
//
// dottersseq = g_malloc(strlen(queryseq)+1);
// strcpy(dottersseq, queryseq);
//
// offset = min(dotterStart, dotterEnd)-1 + qoffset;
//
// printf("Calling dotter with query sequence region: %d - %d\n", dotterStart, dotterEnd);
//
// dotter(type, opts, dotterqname, queryseq, offset, dotterqname, dottersseq, offset,
// 0, 0, NULL, NULL, NULL, 0.0, dotterZoom, msplist, qoffset, 0, 0);
//}
/* Call dotter on the reference sequence versus itself.
*
* The follow notes on this are from http://sonnhammer.sbc.su.se/Dotter.html:
*
* When looking for overlaps between many sequences, for instance when assembling contigs, it can
* be uselful to make a dotplot of all sequences vs. each other. This way any overlap will show up
* as a diagonal in the corner of a subsequence dotplot. Dotter has a built-in mechanism for this.
* To run Dotter on many sequences at once, concatenate the sequence files (in fasta format). Then
* run dotter on the concatenated sequence file against itself, and green partitioning lines will
* appear between the sequences. At each partitioning line, the name of the following sequence is
* printed. These lines can be turned on and off with the button "Draw lines a segment ends" in
* the "Feature series selection tool", which is launched from the main menu.
*/
static gboolean callDotterSelf(GtkWidget *blxWindow, GError **error)
{
BlxViewContext *bc = blxWindowGetContext(blxWindow);
/* Get the auto range, if requested */
int dotterStart = UNSET_INT;
int dotterEnd = UNSET_INT;
int dotterZoom = 0;
GError *tmpError = NULL;
if (!getDotterRange(blxWindow, NULL, TRUE, &dotterStart, &dotterEnd, &dotterZoom, &tmpError))
{
g_propagate_error(error, tmpError);
return FALSE;
}
/* Set the options string (no options are required) */
static char opts[] = " ";
/* Set the type */
char type = ' ';
if (bc->blastMode == BLXMODE_BLASTP || bc->blastMode == BLXMODE_TBLASTN || bc->blastMode == BLXMODE_TBLASTX)
{
type = 'P';
}
else if (bc->blastMode == BLXMODE_BLASTX || bc->blastMode == BLXMODE_BLASTN)
{
type = 'N';
}
/* Get the section of reference sequence that we're interested in */
const BlxStrand strand = blxWindowGetActiveStrand(blxWindow);
const int frame = 1;
char *querySeqSegmentTemp = getSequenceSegment(bc,
bc->refSeq,
dotterStart,
dotterEnd,
strand,
BLXSEQ_DNA, /* calculated dotter coords are always in terms of DNA seq */
frame,
FALSE, /* input coords are always left-to-right, even if display reversed */
bc->displayRev, /* whether to reverse */
bc->displayRev, /* whether to allow rev strands to be complemented */
FALSE, /* don't allow translation to a peptide seq */
&tmpError);
if (!querySeqSegmentTemp)
{
g_propagate_error(error, tmpError);
return FALSE;
}
/* dotter will free this memory with messfree, so we need to pass a string allocated with messalloc */
char *querySeqSegment = messalloc(strlen(querySeqSegmentTemp) + 1);
strcpy(querySeqSegment, querySeqSegmentTemp);
g_free(querySeqSegmentTemp);
/* Make a copy of the reference sequence segment to pass as the match sequence */
char *dotterSSeq = messalloc(strlen(querySeqSegment) + 1);
strcpy(dotterSSeq, querySeqSegment);
int offset = min(dotterStart, dotterEnd) - 1;
printf("Calling dotter with query sequence region: %d - %d\n", dotterStart, dotterEnd);
dotter(type, opts, bc->refSeqName, querySeqSegment, offset, bc->refSeqName, dotterSSeq, offset,
0, 0, NULL, NULL, NULL, 0.0, dotterZoom, bc->mspList, 0, 0, 0);
return TRUE;
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment