void genomicFormatPage(struct sqlConnection *conn)
/* Put up page asking for what sort of genomic sequence. */
{
struct hTableInfo *hti = getHti(database, curTable, conn);
htmlOpen("%s Genomic Sequence", curTableLabel());
if (doGalaxy())
startGalaxyForm();
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hgSeqOptionsHtiCart(hti, cart);
hPrintf("<BR>\n");
if (doGalaxy())
{
/* pass parameter to get sequence to Galaxy */
cgiMakeHiddenVar(hgtaDoGenomicDna, "get sequence");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGenomicDna, "get sequence");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
}
cgiDown(0.9);
htmlClose();
}
void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
void doGenePredSequence(struct sqlConnection *conn)
/* Output genePred sequence. */
{
char *type = cartString(cart, hgtaGeneSeqType);
if (sameWord(type, "protein"))
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
else
doGenePredNongenomic(conn, 1);
}
else if (sameWord(type, "mRNA"))
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
else
doGenePredNongenomic(conn, 2);
}
else
genomicFormatPage(conn);
}
static void showOutDropDown(struct outputType *otList, struct outputType *otDefault)
/* Display output drop-down. */
{
struct outputType *ot;
char *outputType = cartUsualString(cart, hgtaOutputType, otList->name);
if (otDefault != NULL && otDefault != otList)
{
boolean otInOtList = FALSE;
for (ot = otList; ot != NULL; ot = ot->next)
if (sameString(ot->name, outputType))
{
otInOtList = TRUE;
break;
}
if (! otInOtList)
outputType = otDefault->name;
}
hPrintf("<SELECT NAME=\"%s\">", hgtaOutputType);
for (ot = otList; ot != NULL; ot = ot->next)
{
hPrintf(" <OPTION VALUE=%s", ot->name);
if (sameString(ot->name, outputType))
hPrintf(" SELECTED");
if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed))
hPrintf(" id=\"outBed\"");
hPrintf(">%s\n", ot->label);
}
hPrintf("</SELECT>\n");
hPrintf(" ");
hPrintf(" Send output to ");
cgiMakeCheckBoxIdAndJS("sendToGalaxy", doGalaxy(),
"checkboxGalaxy",
"onclick=\"document.getElementById('checkboxGreat').checked=false; return true;\"");
hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n");
nbSpaces(2);
cgiMakeCheckBoxIdAndJS("sendToGreat", doGreat(),
"checkboxGreat",
"onclick=\"return onSelectGreat();\"");
hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>");
hPrintf("</TD></TR>\n");
}
static void showTableButtons(char *db, char *table, boolean withGetButton)
/* Put up the last buttons in a showTable section. */
{
hPrintf("<BR>\n");
if (withGetButton)
{
if (doGalaxy()) /* need form fields here and Galaxy so add step to Galaxy */
cgiMakeButton(hgtaDoGalaxySelectedFields, "done with selections");
else
cgiMakeButton(hgtaDoPrintSelectedFields, "get output");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf(" ");
}
jsInit();
cgiMakeOnClickSubmitButton(jsSetVerticalPosition("mainForm"),
setClearAllVar(hgtaDoSetAllFieldPrefix,db,table),
"check all");
hPrintf(" ");
cgiMakeOnClickSubmitButton(jsSetVerticalPosition("mainForm"),
setClearAllVar(hgtaDoClearAllFieldPrefix,db,table),
"clear all");
cgiDown(0.7); // Extra spacing below the buttons
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
