static void showBedMergeOptions()
/* Show subtrack merge operation options for tables that are distilled
* to BED (not wiggle/bedGraph). */
{
char *op = cartUsualString(cart, hgtaNextSubtrackMergeOp, "any");
char *setting = NULL;
hPrintf("These combinations will maintain the gene/alignment structure "
"(if any) of %s: <P>\n", curTable);
makeOpButton("any", op);
printf("All %s records that have any overlap with any other selected subtrack<BR>\n",
curTable);
makeOpButton("none", op);
printf("All %s records that have no overlap with any other selected subtrack<BR>\n",
curTable);
makeOpButton("more", op);
printf("All %s records that have at least ",
curTable);
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMoreThreshold, "80");
cgiMakeTextVar(hgtaNextSubtrackMergeMoreThreshold, setting, 3);
printf(" %% overlap with any other selected subtrack<BR>\n");
makeOpButton("less", op);
printf("All %s records that have at most ",
curTable);
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeLessThreshold, "80");
cgiMakeTextVar(hgtaNextSubtrackMergeLessThreshold, setting, 3);
printf(" %% overlap with any other selected subtrack<BR>\n");
makeOpButton("cat", op);
printf("All %s records, as well as all records from all other selected subtracks<P>\n",
curTable);
printf("These combinations will discard the gene/alignment structure (if any) "
"of %s and produce a simple list of position ranges.<P>\n",
curTable);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and other selected subtracks<BR>\n",
curTable);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and other selected subtracks<P>\n",
curTable);
}
void doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
htmlClose();
}
