void doMiddle(struct cart *cart)
/* Print out middle parts. */
{
char *old;
printf("<FORM ACTION=\"../cgi-bin/testCart\" METHOD=GET>\n");
cartSaveSession(cart, "testCart");
printf("<H3>Just a Test</H3>\n");
printf("<B>Filter:</B> ");
old = cartUsualString(cart, "filter", "red");
cgiMakeRadioButton("filter", "red", sameString(old, "red"));
printf("red ");
cgiMakeRadioButton("filter", "green", sameString(old, "green"));
printf("green ");
cgiMakeRadioButton("filter", "blue", sameString(old, "blue"));
printf("blue ");
cgiMakeButton("submit", "Submit");
printf("<BR>\n");
printf("<B>Font Attributes:</B> ");
cgiMakeCheckBox("fBold", cartUsualBoolean(cart, "fBold", FALSE, "testCart"));
printf("bold ");
cgiMakeCheckBox("fItalic", cartUsualBoolean(cart, "fItalic", FALSE, "testCart"));
printf("italic ");
cgiMakeCheckBox("fUnderline", cartUsualBoolean(cart, "fUnderline", FALSE, "testCart"));
printf("underline ");
printf("<BR>\n");
printf("</FORM>");
printf("<TT><PRE>");
cartDump(cart);
}
static void howRadioButton(char *how)
/* Put up a getSeqHow radio button. */
{
char *howName = getSeqHowVarName;
char *oldVal = cartUsualString(cart, howName, "protein");
cgiMakeRadioButton(howName, how, sameString(how, oldVal));
}
void makeForm(struct slName *dbs)
/* If the button wasn't pressed already, show it. */
{
struct slName *cur;
cgiParagraph("Pressing the button below will trigger an update to the MGC RTDB database:");
/* HTML form */
puts("<FORM ACTION=\"../cgi-bin/rtdbWebUpdate\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
for (cur = dbs; cur != NULL; cur = cur->next)
{
cgiMakeRadioButton("db", cur->name, FALSE);
printf(" %s\n<BR>\n", cur->name);
}
puts("<BR>\n");
cgiMakeButton("RTDBSubmit","Update RTDB");
cartSaveSession(cart);
puts("</FORM>");
}
static void hgSeqDisplayOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons, boolean offerRevComp)
/* Print out HTML FORM entries for sequence display options. */
{
char *casing, *repMasking;
puts("\n<H3> Sequence Formatting Options: </H3>\n");
casing = cartCgiUsualString(cart, "hgSeq.casing", "exon");
if (canDoIntrons)
{
cgiMakeRadioButton("hgSeq.casing", "exon", sameString(casing, "exon"));
if (canDoUTR)
puts("Exons in upper case, everything else in lower case. <BR>");
else
puts("Blocks in upper case, everything else in lower case. <BR>");
}
if (canDoUTR)
{
if (sameString(casing, "exon") && !canDoIntrons)
casing = "cds";
cgiMakeRadioButton("hgSeq.casing", "cds", sameString(casing, "cds"));
puts("CDS in upper case, UTR in lower case. <BR>");
}
if ((sameString(casing, "exon") && !canDoIntrons) ||
(sameString(casing, "cds") && !canDoUTR))
casing = "upper";
cgiMakeRadioButton("hgSeq.casing", "upper", sameString(casing, "upper"));
puts("All upper case. <BR>");
cgiMakeRadioButton("hgSeq.casing", "lower", sameString(casing, "lower"));
puts("All lower case. <BR>");
cgiMakeCheckBox("hgSeq.maskRepeats",
cartCgiUsualBoolean(cart, "hgSeq.maskRepeats", FALSE));
puts("Mask repeats: ");
repMasking = cartCgiUsualString(cart, "hgSeq.repMasking", "lower");
cgiMakeRadioButton("hgSeq.repMasking", "lower",
sameString(repMasking, "lower"));
puts(" to lower case ");
cgiMakeRadioButton("hgSeq.repMasking", "N", sameString(repMasking, "N"));
puts(" to N <BR>");
if (offerRevComp)
{
cgiMakeCheckBox("hgSeq.revComp",
cartCgiUsualBoolean(cart, "hgSeq.revComp", FALSE));
puts("Reverse complement (get \'-\' strand sequence)");
}
}
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();
}
void configMultiRegionPage()
/* Do multi-region config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
int vis = -2;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<BR>\n");
hTableStart();
virtModeType = cartUsualString(cart, "virtModeType", virtModeType);
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Exit multi-region mode");
hPrintf("</TD></TR>\n");
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database)) // no db conn for assembly hubs
conn = hAllocConn(database);
// Do we have a gene table for exonMostly?
findBestEMGeneTable(trackList);
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show exons using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
/* obsolete
if (conn && sqlTableExists(conn,"knownCanonical"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show gene regions genome-wide.");
hPrintf("</TD></TR>\n");
}
*/
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Enter Custom regions as BED, or a URL to them:<br>");
multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl);
struct dyString *dyMultiRegionsBedInput = dyStringNew(256);
if (strstr(multiRegionsBedUrl,"://"))
{
dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl);
}
else
{
if (fileExists(multiRegionsBedUrl))
{
struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE);
char *line;
int lineSize;
while (lineFileNext(lf, &line, &lineSize))
{
dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line);
}
lineFileClose(&lf);
}
}
hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>",
dyMultiRegionsBedInput->string);
hPrintf("</TD></TR>\n");
/* The AllChroms option will be released in future
if (emGeneTable && sqlTableExists(conn, emGeneTable))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel);
char *trans = cartUsualString(cart, "singleTransId", singleTransId);
char sql[1024];
sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans);
char *result = sqlQuickString(conn, sql);
if (!result)
{
sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable);
trans = sqlQuickString(conn, sql);
}
hTextVar("singleTransId", trans, 20);
hPrintf("</TD></TR>\n");
}
*/
if (conn)
{
boolean altLocExists = sqlTableExists(conn, "altLocations");
boolean fixLocExists = sqlTableExists(conn, "fixLocations");
if (altLocExists || fixLocExists)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleAltHaplo",
sameWord("singleAltHaplo", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show one alternate haplotype");
if (fixLocExists)
hPrintf(" or fix patch");
hPrintf(", placed on its chromosome, using ID: ");
char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId);
char *foundHaplo = NULL;
char sql[1024];
if (altLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo && fixLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo)
{
if (altLocExists)
sqlSafef(sql, sizeof sql, "select name from altLocations limit 1");
else
sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1");
haplo = sqlQuickString(conn, sql);
chopSuffixAt(haplo, ':');
}
hTextVar("singleAltHaploId", haplo, 60);
hPrintf("</TD></TR>\n");
}
}
/* disable demo for now
if (sameString(database,"hg19") || sameString(database, "hg38"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo2 multiple ");
hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3);
hPrintf(" windows on one chrom chr21 def posn, window size ");
hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3);
hPrintf(" and step size ");
hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3);
hPrintf(" exon-like");
hPrintf("</TD></TR>\n");
*/
/* The AllChroms option will be released in future
if (conn) // requires chromInfo from database.
{ // TODO allow it to use assembly hubs via trackHubAllChromInfo() ?
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType));
hPrintf("</TD><TD>");
hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks.");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2.");
hPrintf("</TD></TR>\n");
*/
hTableEnd();
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>");
hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE));
hPrintf("</TD><TD>");
hPrintf("Highlight alternating regions in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px;width:650px \">\n");
hPrintf("<TR><TD>");
cgiMakeButton("topSubmit", "submit");
hPrintf("</TD><TD align=right>");
hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hFreeConn(&conn);
cgiDown(0.9);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
static void makeWigOpButton(char *val, char *selVal)
/* Make merge-wiggle-op radio button. */
{
cgiMakeRadioButton(hgtaNextSubtrackMergeWigOp, val, sameString(val, selVal));
}
static void genePredTypeButton(char *val, char *selVal)
/* Make region radio button including a little Javascript
* to save selection state. */
{
cgiMakeRadioButton(hgtaGeneSeqType, val, sameString(val, selVal));
}
void showMainControlTable(struct sqlConnection *conn)
/* Put up table with main controls for main page. */
{
struct grp *selGroup;
boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;
hPrintf("<TABLE BORDER=0>\n");
/* Print clade, genome and assembly line. */
{
if (gotClade)
{
hPrintf("<TR><TD><B>clade:</B>\n");
printCladeListHtml(hGenome(database), onChangeClade());
nbSpaces(3);
hPrintf("<B>genome:</B>\n");
printGenomeListForCladeHtml(database, onChangeOrg());
}
else
{
hPrintf("<TR><TD><B>genome:</B>\n");
printGenomeListHtml(database, onChangeOrg());
}
nbSpaces(3);
hPrintf("<B>assembly:</B>\n");
printAssemblyListHtml(database, onChangeDb());
hPrintf("</TD></TR>\n");
}
/* Print group and track line. */
{
hPrintf("<TR><TD>");
selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
nbSpaces(3);
curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
nbSpaces(3);
boolean hasCustomTracks = FALSE;
struct trackDb *t;
for (t = fullTrackList; t != NULL; t = t->next)
{
if (isCustomTrack(t->table))
{
hasCustomTracks = TRUE;
break;
}
}
hOnClickButton("document.customTrackForm.submit();return false;",
hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
hPrintf(" ");
if (hubConnectTableExists())
hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
hPrintf("</TD></TR>\n");
}
/* Print table line. */
{
hPrintf("<TR><TD>");
curTable = showTableField(curTrack, hgtaTable, TRUE);
if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL)) /* In same database */
{
hti = getHti(database, curTable, conn);
isPositional = htiIsPositional(hti);
}
isLongTabix = isLongTabixTable( curTable);
isBam = isBamTable( curTable);
isVcf = isVcfTable(curTable, NULL);
isWig = isWiggle(database, curTable);
if (isBigWigTable(curTable))
{
isPositional = TRUE;
isWig = TRUE;
}
isHalSnake = isHalTable( curTable);
isMaf = isMafTable(database, curTrack, curTable);
isBedGr = isBedGraph(curTable);
isArray = isMicroarray(curTrack, curTable);
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
isPal = isPalCompatible(conn, tdb, curTable);
nbSpaces(1);
if (isCustomTrack(curTable))
{
isChromGraphCt = isChromGraph(tdb);
}
cgiMakeButton(hgtaDoSchema, "describe table schema");
hPrintf("</TD></TR>\n");
}
if (curTrack == NULL)
{
struct trackDb *tdb = hTrackDbForTrack(database, curTable);
struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
if (cTdb)
curTrack = cTdb;
else
curTrack = tdb;
isMaf = isMafTable(database, curTrack, curTable);
}
/* Region line */
{
char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
{
boolean doEncode = FALSE;
if (!trackHubDatabase(database))
doEncode = sqlTableExists(conn, "encodeRegions");
hPrintf("<TR><TD><B>region:</B>\n");
/* If regionType not allowed force it to "genome". */
if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
userRegionsFileName() == NULL) ||
(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
regionType = hgtaRegionTypeGenome;
// Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
(curTable && cartTrackDbIsNoGenome(database, curTable)));
// If "genome" is selected but not allowed, force it to "range":
if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
regionType = hgtaRegionTypeRange;
jsTrackingVar("regionType", regionType);
if (disableGenome)
{
makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
hPrintf(" <span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
" ");
}
else
{
makeRegionButton(hgtaRegionTypeGenome, regionType);
hPrintf(" genome ");
}
if (doEncode)
{
makeRegionButton(hgtaRegionTypeEncode, regionType);
hPrintf(" ENCODE Pilot regions ");
}
makeRegionButton(hgtaRegionTypeRange, regionType);
hPrintf(" position ");
hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
cgiMakeButton(hgtaDoLookupPosition, "lookup");
hPrintf(" ");
if (userRegionsFileName() != NULL)
{
makeRegionButton(hgtaRegionTypeUserRegions, regionType);
hPrintf(" defined regions ");
cgiMakeButton(hgtaDoSetUserRegions, "change");
hPrintf(" ");
cgiMakeButton(hgtaDoClearUserRegions, "clear");
}
else
cgiMakeButton(hgtaDoSetUserRegions, "define regions");
hPrintf("</TD></TR>\n");
}
else
{
/* Need to put at least stubs of cgi variables in for JavaScript to work. */
jsTrackingVar("regionType", regionType);
cgiMakeHiddenVar(hgtaRange, range);
cgiMakeHiddenVar(hgtaRegionType, regionType);
}
/* Select identifiers line (if applicable). */
if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
{
hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
hPrintf(" ");
cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
if (identifierFileName() != NULL)
{
hPrintf(" ");
cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
}
hPrintf("</TD></TR>\n");
}
}
/* microarray options */
/* button for option page here (median/log-ratio, etc) */
/* Filter line. */
{
hPrintf("<TR><TD><B>filter:</B>\n");
if (anyFilter())
{
cgiMakeButton(hgtaDoFilterPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearFilter, "clear");
if (isWig || isBedGr)
wigShowFilter(conn);
}
else
{
cgiMakeButton(hgtaDoFilterPage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix);
if (canSubtrackMerge)
{
hPrintf("<TR><TD><B>subtrack merge:</B>\n");
if (anySubtrackMerge(database, curTable))
{
cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
}
else
{
cgiMakeButton(hgtaDoSubtrackMergePage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Intersection line. */
if (isPositional)
{
if (anyIntersection())
{
hPrintf("<TR><TD><B>intersection with %s:</B>\n",
cartString(cart, hgtaIntersectTable));
cgiMakeButton(hgtaDoIntersectPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearIntersect, "clear");
hPrintf("</TD></TR>\n");
}
else if (canIntersect(database, curTable))
{
hPrintf("<TR><TD><B>intersection:</B>\n");
cgiMakeButton(hgtaDoIntersectPage, "create");
hPrintf("</TD></TR>\n");
}
}
/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
{
char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
hPrintf("<TR><TD><B>correlation:</B>\n");
if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2))
{
struct grp *groupList = fullGroupList;
struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
if (tdbIsComposite(tdb2))
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
if (sameString(table2, subTdb->table))
{
tdb2 = subTdb;
break;
}
}
slFreeList(&tdbRefList);
}
cgiMakeButton(hgtaDoCorrelatePage, "calculate");
cgiMakeButton(hgtaDoClearCorrelate, "clear");
if (tdb2 && tdb2->shortLabel)
hPrintf(" (with: %s)", tdb2->shortLabel);
#ifdef NOT_YET
/* debugging dbg vvvvv */
if (curTrack && curTrack->type) /* dbg */
{
hPrintf("<BR> (debug: '%s', '%s(%s)')",
curTrack->type, tdb2->type, table2);
}
/* debugging debug ^^^^^ */
#endif
}
else
cgiMakeButton(hgtaDoCorrelatePage, "create");
hPrintf("</TD></TR>\n");
}
/* Print output type line. */
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
/* Print output destination line. */
{
char *compressType =
cartUsualString(cart, hgtaCompressType, textOutCompressNone);
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
hPrintf("<TR><TD>\n");
hPrintf("<B>output file:</B> ");
cgiMakeTextVar(hgtaOutFileName, fileName, 29);
hPrintf(" (leave blank to keep output in browser)</TD></TR>\n");
hPrintf("<TR><TD>\n");
hPrintf("<B>file type returned: </B>");
cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
sameWord(textOutCompressNone, compressType));
hPrintf(" plain text  ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
sameWord(textOutCompressGzip, compressType));
hPrintf(" gzip compressed");
hPrintf("</TD></TR>\n");
}
hPrintf("</TABLE>\n");
/* Submit buttons. */
{
hPrintf("<BR>\n");
if (isWig || isBam || isVcf || isLongTabix)
{
char *name;
extern char *maxOutMenu[];
char *maxOutput = maxOutMenu[0];
if (isCustomTrack(curTable))
name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
else
name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);
maxOutput = cartUsualString(cart, name, maxOutMenu[0]);
if (isWig)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). The entire data set may be available for download as"
" a very large file that contains the original data values (not"
" compressed into the wiggle format) -- see the Downloads page."
"</I><BR>", maxOutput);
else if (isBam || isVcf || isLongTabix)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). Please consider downloading the entire data from our Download pages."
"</I><BR>", maxOutput);
}
else if (anySubtrackMerge(database, curTable) || anyIntersection())
{
hPrintf("<I>Note: The all fields and selected fields output formats "
"are not available when a%s has been specified.</I><BR>",
canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
}
cgiMakeButton(hgtaDoTopSubmit, "get output");
hPrintf(" ");
if (isPositional || isWig)
{
cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
hPrintf(" ");
}
#ifdef SOMETIMES
hPrintf(" ");
cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
}
hPrintf("<P>"
"To reset <B>all</B> user cart settings (including custom tracks), \n"
"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
getScriptName());
}
static void hgSeqFeatureRegionOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons)
/* Print out HTML FORM entries for feature region options. */
{
char *exonStr = canDoIntrons ? " Exons" : "";
char *setting;
puts("\n<H3> Sequence Retrieval Region Options: </H3>\n");
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.promoter",
cartCgiUsualBoolean(cart, "hgSeq.promoter", FALSE));
puts("Promoter/Upstream by ");
setting = cartCgiUsualString(cart, "hgSeq.promoterSize", "1000");
cgiMakeTextVar("hgSeq.promoterSize", setting, 5);
puts("bases <BR>");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon5",
cartCgiUsualBoolean(cart, "hgSeq.utrExon5", TRUE));
printf("5' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
if (canDoUTR)
printf("CDS Exons <BR>\n");
else
printf("Blocks <BR>\n");
}
else if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
printf("CDS <BR>\n");
}
else
{
cgiMakeHiddenVar("hgSeq.cdsExon", "1");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon3",
cartCgiUsualBoolean(cart, "hgSeq.utrExon3", TRUE));
printf("3' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.intron",
cartCgiUsualBoolean(cart, "hgSeq.intron", TRUE));
if (canDoUTR)
puts("Introns <BR>");
else
puts("Regions between blocks <BR>");
}
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.downstream",
cartCgiUsualBoolean(cart, "hgSeq.downstream", FALSE));
puts("Downstream by ");
setting = cartCgiUsualString(cart, "hgSeq.downstreamSize", "1000");
cgiMakeTextVar("hgSeq.downstreamSize", setting, 5);
puts("bases <BR>");
}
if (canDoIntrons || canDoUTR)
{
setting = cartCgiUsualString(cart, "hgSeq.granularity", "gene");
cgiMakeRadioButton("hgSeq.granularity", "gene",
sameString(setting, "gene"));
if (canDoUTR)
puts("One FASTA record per gene. <BR>");
else
puts("One FASTA record per item. <BR>");
cgiMakeRadioButton("hgSeq.granularity", "feature",
sameString(setting, "feature"));
if (canDoUTR)
puts("One FASTA record per region (exon, intron, etc.) with ");
else
puts("One FASTA record per region (block/between blocks) with ");
}
else
{
puts("Add ");
}
setting = cartCgiUsualString(cart, "hgSeq.padding5", "0");
cgiMakeTextVar("hgSeq.padding5", setting, 5);
puts("extra bases upstream (5') and ");
setting = cartCgiUsualString(cart, "hgSeq.padding3", "0");
cgiMakeTextVar("hgSeq.padding3", setting, 5);
puts("extra downstream (3') <BR>");
if (canDoIntrons && canDoUTR)
{
puts(" ");
cgiMakeCheckBox("hgSeq.splitCDSUTR",
cartCgiUsualBoolean(cart, "hgSeq.splitCDSUTR", FALSE));
puts("Split UTR and CDS parts of an exon into separate FASTA records");
}
puts("<BR>\n");
puts("Note: if a feature is close to the beginning or end of a chromosome \n"
"and upstream/downstream bases are added, they may be truncated \n"
"in order to avoid extending past the edge of the chromosome. <P>");
}
